Virtual screening of bacteriocins from lactic acid bacteria against Monkeypox DNA Polymerase: Sakacin-P is a potent DNA polymerase inhibitor

Virtual screening of bacteriocins from lactic acid bacteria against Monkeypox DNA Polymerase: Sakacin-P is a potent DNA polymerase inhibitor | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Research Article Virtual screening of bacteriocins from lactic acid bacteria against Monkeypox DNA Polymerase: Sakacin-P is a potent DNA polymerase inhibitor Melisa Z. Karaman, Fernando Berton Zanchi, Aykut Ozdarendeli, and 2 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-6529067/v1 This work is licensed under a CC BY 4.0 License Status: Posted Version 1 posted You are reading this latest preprint version Abstract Monkeypox virus (MPXV) has emerged as a significant global health concern, necessitating the development of novel antiviral strategies. In this study, we employed an in silico approaches to investigate the potential of bacteriocins as inhibitors of the MPXV DNA polymerase (MPDP). Initially, protein structure modeling was performed using SWISS-MODEL, and the quality of the generated models was evaluated based on LGscore. The physicochemical properties of selected bacteriocins, including Sakacin-P and Mundticin-KS, were assessed to determine their stability and suitability for molecular docking. Protein-peptide docking simulations using the HADDOCK platform revealed that Sakacin-P exhibited a higher binding affinity for the MPXV DNA polymerase. The docking analysis indicated the presence of strong hydrogen bonds, ionic interactions, and π-π stacking interactions, which contributed to the stability of the protein-ligand complex. Molecular dynamics (MD) simulations further validated the stability of the docked complex by analyzing root mean square deviation (RMSD), root mean square fluctuation (RMSF), radius of gyration (Rg), H-bond and Van der Waals interactions, and solvent-accessible surface area (SASA). Our findings suggest that bacteriocins, particularly Sakacin-P, have promising antiviral properties against MPXV by targeting its DNA replication complex. This study provides a foundation for further experimental validation and the potential development of bacteriocin-based therapeutics against MPXV. Monkeypox virus Bacteriocins Sakacin-P Molecular docking Molecular dynamics simulation Figures Figure 1 Figure 2 Figure 3 Figure 4 Figure 5 Figure 6 Figure 7 Figure 8 Figure 9 Introduction Monkeypox virus (MPXV) was first discovered in 1958 when an unidentified disease appeared in monkeys in Africa [ 1 ]. An unknown virus was identified in the infected monkeys' bodies and since the monkeys developed blisters on their skin that were similar to those caused by smallpox, the disease was therefore named "monkeypox" [ 1 , 2 ]. The WHO declared the current MPXV outbreak a "Public Health Emergency of International Concern" (PHEIC) on 14 August 2024, marking the second MPXV-related PHEIC in two years. The Africa Centres for Disease Control and Prevention (Africa CDC) also declared a regional emergency on 13 August 2024, following the report of 35,341 MPXV cases and 840 deaths across 13 African countries between January 1 and September 23, 2024 [ 3 ]. MPXV is an enveloped double-stranded DNA (dsDNA) virus, which belongs to the genus Orthopoxvirus of the family Poxvirus [ 1 , 4 ]. Orthopox also consists of cowpox, variola (smallpox), and vaccinia viruses [ 5 ]. The clinical signs of this viral disease are similar to those of smallpox but the severity might mostly change from one patient to another or among conditions [ 6 ]. Since MPXV is a zoonotic disease, it can be transmitted from animals to humans, and among humans, and it possesses a 1–8% lethality rate [ 2 ]. Human-to-human transmission of the MPXV can be reasoned by close contact with infected individuals and the virus can be transmitted to the body through respiratory droplets, sexual contact, or contact with infectious skin lesions or bodily fluids [ 2 , 7 – 9 ]. The incubation stage of MPXV infection is generally 3 to 21 days after exposure, and since it initially appears as a non-distinct prodromal phase, the virus might be transmitted before it is noticed [ 5 , 6 ]. This is followed by signature rash symptoms which are the main symptoms of MPXV and take nearly 2 to 5 weeks [ 1 , 5 ]. Patients with MPXV might have headaches, fever, sore throat, swollen lymph nodes, chills nausea, breathlessness, fatigue, lethargy, genital necrosis, weakened digestive tracts, and muscle pains [ 1 , 2 , 6 ]. In addition, MPXV infection might result in serious complications like organ damage leading to skin lesions, eye damage resulting from corneal infection, bronchopneumonia, encephalitis, and sepsis [ 1 , 5 , 6 ]. Notwithstanding, there is no exact therapy or vaccine for MPXV infection. Patients might gain protection through cross-immunity with smallpox vaccination. During the past decade, the MPXV level has increased substantially, which might be associated with a decrease in herd immunity to smallpox because smallpox vaccination was no longer routinely available due to the global eradication of smallpox. Since smallpox vaccination was 85% effective in MPXV prevention, post-exposure immunization can provide to decrease or stop the illness severity [ 4 ]. Moreover, several antiviral drugs such as tecovirimat, cidofovir, and brincindofovir can be employed in the treatment of MPXV infections, but their effectiveness has not been fully affirmed [ 2 , 4 ]. Lactic acid bacteria (LAB) can produce different chemicals that can inhibit the growth of microorganisms [ 10 ]. For example, these are lactic acid, acetic acid, and propanoic acid, which make the environment more acidic and thus decrease the pathogenic microbial population [ 10 , 11 ]. LAB also produces low molecular weight substances such as hydrogen peroxide, carbon dioxide, diacetyl, organic acids, ethanol and bacteriocins, and they can inhibit the growth of several pathogenic bacteria [ 11 , 12 ]. Bacteriocins are extracellular, ribosomally produced small peptides or proteins synthesized by bacteria that are capable of killing or inhibiting other closely related bacteria because the producer strain of bacteriocin is inherently resilient to its fatal effects since it has immunity proteins [ 12 , 13 ]. Bacteriocins possess a variety of biotechnological applications, including in the food and dairy industries as food preservatives, and clinical applications as an alternative to some antibiotics, and they have medical activities as anticancer, antiviral, and antiprotozoal agents [ 12 ]. Several varieties of bacteriocins exist and they have been categorized according to their genetic and physicochemical characteristics [ 10 , 13 ]. In 1993, Klaenhammer proposed classifying Lab bacteriocins into four major classes based on the size of the peptide, post-translational modification, and other characteristics. Class I includes post-translationally modified bacteriocins such as nisin and the rest of the peptides (smaller than 10 kDa) are found in class II [ 12 , 14 ]. Class I possesses lanthionine-containing bacteriocins (lantibiotics), which contain the lanthipeptides, linear azol(in)e-containing peptides, glycocins, cyclized peptides, satibiotics, and lasso peptides. Class II which are bacteriocins without lanthionine includes pediocin-like bacteriocins, non-pediocin-like single peptides, leaderless peptides, and two-peptide bacteriocins. They are capable of remaining stable at high temperatures. Examples of class II bacteriocins are Pediocin PA-1, Enterocin-P, Enterocin-A, Pentocin-31, and Sakacin-G [ 10 ]. While class III includes heat-labile large bacteriocins (bigger than 30 kDa) such as non-lytic peptides and bacteriolysins, class IV includes complex peptides carrying lipid or carbohydrate moieties [ 12 , 14 ]. For instance, lysostaphin (27 kDa peptide) which is accepted as the original bacteriolysin can degrade the cell walls of several Staphylococcus species. Lactocin 27 and leuconocin S are examples of class IV and they can cause damage to bacterial cell walls. Class V bacteriocins have a circular nature in their structures and are thus characterized by greater resilience to the effects of a broad range of stresses. Examples of class V are pumilarin, enterocin AS-48, plantaricyclin A and lactocyclicin Q [ 10 ]. The antiviral effects of bacteriocins against several viruses have been reported [ 15 ]. Enterocin CRL35 produced by Enterococcus faecium CRL35 was the first bacteriocin known to have antiviral activity. Enterocin CRL35 demonstrated activities against both Herpes simplex virus types 1 and 2 (HSV-1 and HSV-2) that cause serious problems such as corneal blindness, genital ulcerations, and encephalitis [ 12 ]. Similarly, enterocin AAR-71 showed high activity against coliphage HSA virus and completely prevented viral progeny [ 15 ]. Furthermore, staphylococcin 188 produced by Staphylococcus aureus AB188 which is a non-LAB-originated bacteriocin shows antiviral activities against the influenza virus, Newcastle disease virus, and coliphage HSA virus [ 15 , 16 ]. Another example is labyrinthopeptin A produced by Actinomadura namibiensis DSM 6313 which shows antiviral activities against HSV-1, and human immunodeficiency virus type 1 (HIV-1) [ 15 ]. Moreover, Lactobacillus delbrueckii subsp. bulgaricus 1043 produces a non-cytotoxic bacteriocin that can be virucidal on the influenza virus [ 16 ]. Additionally, when the duramycin binds to phosphatidylethanolamine in the Zika virus envelope, the TIM1 receptor is hindered and the infection decreases in placental cells and explants. Similarly, micrococcin P1 can hinders the Hepatitis C virus entry without affecting the secretion of viral particles [ 17 ]. To our knowledge, the investigation of the potential bacteriocins in the drug development process for the MPXV has not been reported so far. Thus, this study focused on the in silico evaluation of bacteriocins from lactic acid bacteria against DNA polymerase of MPXV (MPDP). We conducted a virtual screening of 21 bacteriocins against DNA polymerase via protein-protein docking as well as molecular dynamics simulation. Our docking analysis revealed that sakacin-P is the most promising bacteriocin candidate with strong binding affinity and potent physiochemical characteristics as a DNA polymerase inhibitor for MPXV. Materials and Methods In silico Preparation and confirmation of Bacteriocins and Receptors 21 bacteriocin structures were retrieved from Uniprot ( https://www.uniprot.org/ ) and the RCBS Protein Data Bank ( https://www.rcsb.org/ ) in PDB file format. 3D structures of bacteriocin from Uniprot were predicted using Alphafold ( https://alphafold.ebi.ac.uk/ ) and those with an average per-residue model confidence score (pLDDT) above 50 were chosen [ 18 ]. Pure 3D structures generated through X-ray diffraction or solution NMR were selected from the RCSB Protein Data Bank. Cryo-EM structure of monkeypox virus DNA replication holoenzyme (F8, A22 and E4 complex) without DNA at 2.76 angstrom (PDB ID: 8HOY) was also downloaded from the Protein Data Bank [ 19 ]. The monkeypox virus DNA polymerase enzyme chain was extracted from the complex using PyMol v3.1.0 ( https://github.com/schrodinger/pymol-open-source (Schrodinger LLC, New York, NY)). The extracted chain belonging to the monkeypox DNA polymerase enzyme was evaluated using SWISS-MODEL based on GMQE (Global Model Quality Estimate) and QMEANDisCo global scores [ 20 , 21 ]. All solvent molecules found in the PDB files were removed using BIOVIA Discovery Studio 2024 Client (Dassault Systèmes, Vélizy-Villacoublay, France). Afterwards, these protein structures were confirmed using the PROCHECK tool via the SAVES 6.1 structure validation server ( https://saves.mbi.ucla.edu/ ). Moreover, the PROCHECK tool generated Ramachandran scores, which represent the percentage of amino acids found in the most favored regions. Additionally, the quality of the structures was assessed, and authentication was carried out using the ProQ server ( https://proq.bioinfo.se/cgi-bin/ProQ/ProQ.cgi ). Protein–Protein Docking and Physicochemical Features HADDOCK v2.4 was employed in protein–protein docking simulations [ 22 ]. Active residues from the positively charged groove of the F8 thumb domain of MPXV DNA polymerase (MPDP), responsible for DNA binding, were acquired from the literature. Reported active residues comprised ARG302, LYS308, LYS340, LYS525, ARG674, LYS803, LYS804, LYS805, ARG832, ARG833, LYS973, ARG974, and ARG1000, located within the F8 thumb domain of the MPDP [ 19 ]. The server utilized the default protocol along with default parameter sets for docking and refinement. Passive residues were defined automatically in proximity to the active residues. The top-ranking complexes from HADDOCK were downloaded and submitted to the PROtein binDIng enerGY prediction (PRODIGY) server [ 23 ] to calculate binding energies at a temperature of 310K (36,85°C). Subsequently, protein-protein residue interactions were determined through the Residue Interaction Network Generator (RING, v4) web server, using the PDB dataset acquired via PRODIGY. Closest nodes, strict threshold, add hydrogens, and include water parameters were chosen for residue interaction analysis in the RING. All figures were generated by PyMol v2.1 ( https://github.com/schrodinger/pymol-open-source (Schrodinger LLC, New York, NY)). In the manuscript, we defined the MPDP as chain A and the bacteriocins as chain B. For example, A805-B23 denotes the interaction between the 805th amino acid of the MPDPs and the 23rd amino acid of the bacteriocins. The physicochemical characteristics of bacteriocins, including amino acid sequence and length, molecular weight, isoelectric point (pI), instability index, aliphatic index, grand average of hydropathicity (GRAVY) score, and estimated in vitro half-life in mammalian reticulocytes, were predicted using Expasy’s ProtParam tool ( https://web.expasy.org/protparam/ ) to confirm their stability. Molecular dynamics simulation In order to verify the stability and behavior of the complexed MPDP in the presence of the Sakacin-P, two systems were simulated in the APO form and another presence in the Sakacin-P. Molecular dynamics (MD) simulations were performed using Gromacs 2024.2 [ 24 ] with interface Visual Dynamics [ 25 ] for generate scripts. AMBER99 force field [ 26 ]. Electrostatic interactions were treated using the particle mesh Ewald (PME) algorithm with a cut-off of 12 Å. Each system was simulated under periodic boundary conditions in a cubic box, whose dimensions were automatically defined, considering 1 nm from the outermost protein atoms in all Cartesian directions. The simulation box was filled with TIP3P water molecules [ 27 ]. Subsequently, a two-step energy minimization procedure was performed (2000 steps of steepest descent and 2000 steps of conjugate-gradient or until the system reaches a resistance force lower than 1000 kJ.mol-1.nm-1. Next, initial atomic velocities were assigned using the Maxwell-Boltzmann distribution corresponding to a temperature of 300 K. All systems were subsequently equilibrated during two successive NVT and NPT equilibration simulations with 200 ps for each. After this period, all the systems were simulated with no restraints at 300 K in the Gibbs ensemble with a 1 atm pressure using isotropic coupling. All chemical bonds containing hydrogen atoms were restricted using the SHAKE algorithm [ 28 ] and the time step was set to 2 fs. Finally, we simulated three independent MD runs of 500 ns for the complex and Apo form. Simulation trajectories were analyzed with GROMACS package tools [ 24 ]. Root-mean-square deviation (RMSD), root-mean-square fluctuation (RMSF) were calculated separately for each system fitting their heavy atoms, taking the initial structure of the production dynamics as a reference. Hydrogen bonds (H-bond) were calculated intramolecularly for protein and between protein and ligand complexes. We considered a hit when the distance between two polar heavy atoms, with at least one hydrogen atom attached, was less than 3.5 Å and using an H-donor angle higher than 120°). Radius of Gyration (RG) and Solvent-Accessible Surface Areas (SASA) were also calculated. Furthermore, interaction analysis of ligands with the respective receptor molecule was performed using MMPBSA [ 29 ] of the both docked structure for the period of 100ns. Results Prediction and verification of bacteriocins and Monkeypox DNA polymerase Determining the 3D structures of MPXV DNA polymerase (receptor) and bacteriocins (ligands) from their amino acid sequences was an essential step in assessing receptor-ligand binding affinities. The selection of a protein modeling method based on amino acid sequences relies on the resemblance to established templates in the database. Homology modeling is favored when the similarity exceeds 30%. The interpretation of computationally generated data is straightforward and dependable, effectively bridging the gap between the template and the unknown protein structure [ 21 ]. The structure of MPDP was derived from human monkeypox viral replication complexes (8HOY) in the PDB database. Structure validation of MPDP (Fig. 1 .) was conducted utilizing the PROCHECK tool through the SAVES v6.1 structure validation server, similar to other bacteriocin structures. For the MPDP, Ramachandran plot statistics revealed that 83.1% of residues lie in the most favored regions, 15.8% in additional allowed regions, 0.4% in generously allowed regions, and 0.6% in disallowed regions. This indicates a high-quality model, as over 90% of residues in the favored regions are typically expected for a good-quality structure. The Ramachandran plot serves as a universal criterion for validating predicted protein structures by estimating their stability [ 30 ]. The secondary structure elements (helix, beta strand, random coil) and estimated accessibility (buried, accessible) were annotated. This provided a visual representation of the protein’s fold and surface properties shown in Figs. 1 and 2 . Additionally, Fig. 1 illustrates the relationships between specific amino acids in the polypeptide chain and their respective ramachandran regions: most favored, allowed, generous, and disallowed. Additionally, models were constructed utilizing SWISS-MODEL with the protein FASTA sequence of the MPDP. Subsequently, Qualitative Model Energy Analysis (QMEAN) was employed to assess the quality of the projected structures by global and local estimations [ 31 ]. QMEANDisCo predicts interatomic distances by utilizing information gathered from experimentally validated homologous protein structures, which serve as templates to verify the modeled structure [ 20 ]. The QMEANDisCo and GMQE (Global Model Quality Estimate) values, ranging from 0 to 1, were deemed adequate for verifying a modeled structure, with both scores recorded at 0.86 for MPDP. Bacteriocins were modeled using the AlphaFold Server, which can predict complexes containing almost all molecular types found in the Protein Data Bank (PDB) with high accuracy. AlphaFold can directly predict raw atom coordinates with a diffusion module due to its capacity to work on amino acid-specific frames and side chain torsion angles [ 18 ]. Over 90% of the amino acid residues in the bacteriocin models were located inside the favorable region of the Ramachandran plot, which was essential for further analysis. Moreover, the quality of these structures was evaluated using the ProQ server for determining the Levitt-Gerstein (LG) score. The LG score measures similarity to a known structure by superimposing two structures and was utilized to assess the quality of these structures. Protein/peptide models exhibiting an LGscore greater than 4 were deemed of high quality [ 32 ]. Except for the two bacteriocin models used in this study, all other models had LG scores between 6,605 and 11,927. The LG score values for Lacticin Q and Enterocin HF were found to be negative. ProQ scores (LG scores) and Ramachandran values for all bacteriocins are presented in Table 1 . Table 1 Structure confirmation parameters and binding energies of bacteriocins versus monkeypox DNA polymerase. Organism Bacteriocin LG score* Ramachandran score (%) ** Binding Energy (Kcal/mol) Kd (M) at 36.85℃ Enterococcus mundtii Mundticin_KS 7.838 98.8 -17 9.6e-13 Latilactobacillus sakei Sakacin-A 11.168 100 -13 6.7e-10 Latilactobacillus sakei Sakacin-P 9.050 100 -16.7 1.6e-12 Lactiplantibacillus plantarum Plantaricin_W_beta 9.456 98.2 -16.2 4.00e-12 Lactiplantibacillus plantarum Plantaricin_W_alpha 11.292 100 -12.3 2.3e-09 Pediococcus acidilactici Pediocin_PA1 11.071 98 -12.1 2.8e-09 Lactococcus lactis subsp. lactis Nisin 11.553 100 -12.2 2.3e-09 Leuconostoc mesenteroides LeucocinC_TA33a 10.580 100 -13.5 3.2e-10 Leuconostoc mesenteroides LeucocinB_TA33a 10.533 95.4 -11.1 1.5e-08 Leuconostoc mesenteroides LeucocinB_TA11A 10.445 96 -13.7 2.1e-10 Lactococcus lactis subsp. lactis Lactococcin_G_beta 11.090 100 -10.2 6.1e-08 Lactococcus lactis subsp. lactis Lactococcin_G_Alpha 10.781 100 -12.7 1.1e-09 Lactococcus lactis subsp. lactis Lactococcin_Mmfii 11.062 96.8 -9.7 1.4e-07 Lactococcus lactis Lacticin_Q -0.835 100 -12.7 1.1e-09 Lactococcus lactis subsp. lactis Lacticin_481 11.927 97.8 -11.3 1.1e-08 Enterococcus faecium Enterocin CRL_35 6.605 100 -13.7 2.1e-10 Enterococcus faecium Enterocin_HF -0.835 96.9 -12.5 1.6e-09 Enterococcus faecalis Enterocin_EJ97 11.448 100 -13.5 3.2e-10 Enterococcus faecalis Enterocin_A 11.154 100 -11.5 7.8e-09 Carnobacterium maltaromaticum Carnobacteriocin 11.102 100 -14.8 3.5e-11 Lactobacillus acidophilus AcidocinJ_1132beta 11.031 100 -10.8 2.5e-08 *According to ProQ interpretation; LGscore > 1.5 fairly good model, LGscore > 2.5 very good model, LGscore > 4 extremly good model. **The percentage represents the residues in the most favored [A, B, L] and allowed [a, b, l, p] regions. Molecular Docking and Physicochemical Properties Predictions Indicate Sakacin-P as the Most Effective Binder The interactions between computer-assisted MPDP and bacteriocins were analyzed to elucidate their binding affinities through molecular docking techniques. The molecular docking, or binding pose, is determined by a number of three-dimensional interactions, such as hydrogen bonding, hydrophobic interactions, and other non-covalent interactions that happen in the catalytic sites of MPDP with the bacteriocins [ 33 ]. This approach allows the virtual screening of inhibitory molecules for target proteins, whereas effective docking tools can evaluate and rank them according to a scoring system reflecting their respective interactions [ 30 ]. For this purpose, this study employed HADDOCK and PRODIGY to estimate binding energies, while the RING web server was utilized to identify residue interactions. The docking results of MPDP with all bacteriocins analyzed in this study, including their binding energies, are presented in Table 1 . Protein-protein docking simulations revealed Sakacin-P from Latilactobacillus sakei as the most efficient bacteriocin for binding to MPDP. The docking results indicated a binding energy of -16.7 kcal/mol, suggesting a high-affinity interaction between the two protein structures. The physicochemical properties of Sakacin-P and all studied bacteriocins were evaluated using ExPASy’s ProtParam tool (Table 2 ). Sakacin-P has a molecular weight of 6385.13 Da and an isoelectric point (pI) of 7.81, indicating a balanced charge distribution suitable for physiological conditions. Its instability index of 21.43 and aliphatic index of 64.10 suggested that it is a stable and moderately hydrophobic molecule, making it well-suited for interactions in aqueous environments. The Grand Average of Hydropathicity (GRAVY) score of -0.307 further supported its balanced hydrophilic and hydrophobic characteristics, which are critical for effective binding in biological systems. In comparison, Mundticin_KS from Enterococcus mundtii exhibited a higher instability index (42.57) and binding energy (-17 kcal/mol), yet it possessed a larger molecular weight (13265.16 Da), potentially restricting its bioavailability and cellular uptake. Plantaricin_W_beta from Lactiplantibacillus plantarum demonstrated a strong binding energy of -16.2 kcal/mol, alongside a higher aliphatic index of 47.23 and a less favorable GRAVY score of -0.499, suggesting a suboptimal balance of hydrophilic and hydrophobic characteristics. Moreover, Mundticin_KS and Plantaricin_W_beta exhibited slightly lower Ramachandran plot scores of 98.8% and 98.2%, respectively, compared to Sakacin-P, suggesting possible compromises in structural stability. Therefore, Sakacin-P is selected as the most effective binding bacteriocin structure. Moreover, the surface illustration of the catalytic site of MPDP and an insertion view of Sakacin-P into the catalytic site of MPDP were also shown in Fig. 4 A. Table 2 Physicochemical features of bacteriocins evaluated against monkeypox virus DNA polymerase which predicted via Expasy’s ProtParam tool. Nr. Bacteriocin Sequence AA Length Molecular Weight pI Instability Index Aliphatic index GRAVY Score* Estimated half-life** 1 AcidocinJ_1132beta GNPKVAHCASQIGRSTAWGAVSGA 24 2325.59 9.51 12.71 61.25 -0.058 30 hours 2 Carnobacteriocin B2 MNSVKELNVKEMKQLHGGVNYGNGVSCSKTKCSVN WGQAFQERYTAGINSFVSGVASGAGSIGRRP 66 6993.88 9.70 19.32 60.45 -0.417 30 hours 3 Enterocin_A TVDWAKATTCIAGMSIGGFLGGAFPGK 27 2657.10 7.87 24.76 68.89 0.559 7.2 hours 4 Enterocin_EJ97 MLAKIKAMIKKFPNPYTLAAKLTTYEINWYKQQYGRYPWERPVA 44 5322.32 9.92 19.46 71.14 -0.589 30 hours 5 Enterocin_HF KYYGNGVSCNKKGCSVDWGKAIGIIGNNAAANLTTGGKAGWKG 43 4330.91 9.63 4.29 61.40 -0.374 1.3 hours 6 EnterocinCRL_35 MSNLKWFSGGDDRRKKAEVIITELLDDLEIDLGNESLRKVLGSYL EKLKNEGTSVPLVLSRMNIEISNAIKKDGVSLNENQSKKLKELISISNIRYGY 98 11084.74 7.91 41.34 108.37 -0.448 30 hours 7 Lacticin_481 MKEQNSFNLLQEVTESELDLILGAKGGSGVIHTISHECNMNSWQFVFTCCS 51 5677.41 4.68 44.36 80.20 -0.049 30 hours 8 Lacticin_Q MAGFLKVVQLLAKYGSKAVQWAWANK GKILDWLNAGQAIDWVVSKIKQILGIK 53 5898.10 10.10 7.38 121.51 0.300 30 hours 9 Lactococcin_G_Alpha GTWDDIGQGIGRVAYWVGKAMGNMSDVNQASRINRKKKH 39 4345.93 10.16 4.44 60.00 -0.841 30 hours 10 Lactococcin_Mmfii TSYGNGVHCNKSKCWIDVSELETYKAGTVSNPKDILW 37 4144.64 6.43 27.62 68.38 -0.535 7.2 hours 11 Lactococcin_G_beta KKWGWLAWVDPAYEFIKGFGKGAIKEGNKDKWKNI 35 4109.79 9.70 10.35 61.43 -0.806 1.3 hours 12 LeucocinB_TA11A MNNMKSADNYQQLDNNALEQVVGGKYYGNGVH CTKSGCSVNWGEAFSAGVHRLANGGNGFW 61 6568.18 6.69 5.95 51.15 -0.597 30 hours 13 LeucocinB_TA33a KGKGFWSWASKATSWLTGPQQPGSPLLKKHR 31 3466.01 11.39 27.93 44.19 -0.971 1.3 hours 14 LeucocinC_TA33a KNYGNGVHCTKKGCSVDWGYAWTNIANNSVMNGLTGGNAGWHN 43 4598.04 8.79 18.09 45.35 -0.665 1.3 hours 15 Mundticin_KS MGSSHHHHHHSSGLVPRGSHMSNLKWFSGGDDRRKKAEVII TELLDDLEIDLGNESLRKVLGSYLKKLKNEGTSVPLVLSRMN IEISNAIKKDGVSLNENQSKKLKELMSISNIRYGY 118 13265.16 9.40 42.57 92.46 -0.599 30 hours 16 Nisin MSTKDFNLDLVSVSKKDSGASPRITSISLC TPGCKTGALMGCNMKTATCHCSIHVSK 57 5962.98 8.99 35.11 68.42 -0.005 30 hours 17 Pediocin_PA1 MKKIEKLTEKEMANIIGGKYYGNGVTCGKHSCS VDWGKATTCIINNGAMAWATGGHQGNHKC 62 6643.64 9.02 19.72 55.16 -0.482 30 hours 18 Plantaricin_W_alpha MKISKIEAQARKDFFKKIDTNSNLLNVNGAKCK WWNISCDLGNNGHVCTLSHECQVSCN 59 6656.62 8.71 30.34 72.71 -0.473 30 hours 19 Plantaricin_W_beta MTKTSRRKNAIANYLEPVDEKSINESFGAGDPEAR SGIPCTIGAAVAASIAVCPTTKCSKRCGKRKK 67 7085.18 9.64 47.23 61.34 -0.499 30 hours 20 Sakacin-A MNNVKELSMTELQTITGGARSYGNGVYCNNKKCW VNRGEATQSIIGGMISGWASGLAGM 59 6257.13 8.77 29.28 67.80 -0.214 30 hours 21 Sakacin-P MEKFIELSLKEVTAITGGKYYGNGVHCGKHSCTVD WGTAIGNIGNNAAANWATGGNAGWNK 61 6385.13 7.81 21.43 64.10 -0.307 30 hours *GRAVY: Grand average of hydropathicity, **mammalian reticulocytes, in vitro The RING 4.0 tool was used to carry out a comprehensive residue interaction analysis, which revealed a strong network of non-covalent contacts between Sakacin-P and MPDP. The stability and specificity of the complex were influenced by these interactions, which consisted of hydrogen bonds, π-π stacking, π-cation interactions, and van der Waals forces. The interactions associated with the docking pose of Sakacin-P are summarized in Table 3 . The hydrogen bonds identified for Sakacin-P include A305-B2, A310-B33, A311-B29, A315-B2, A316-B1, A340-B30, B525-B8, A525-B11, A529-B16, A894-B35, A991-B60, A994-B50, A994-B55, and A1000-B47 (Fig. 4 B). The hydrogen bonds among the active residues of MPDP and Sakacin-P at A340-B30, B525-B8, A525-B11, and A1000-B47 were readily observable, contributing receptor-ligand binding stability. Hydrogen bonding is known to be the weak electrostatic attraction that occurs between a hydrogen atom, which is covalently bonded to a highly electronegative atom (such as oxygen, nitrogen, or fluorine), and another electronegative atom in a separate molecule or within a different region of the same molecule [ 34 ]. The docking pose of Sakacin-P revealed the presence of an ionic bond between A525-B11, a π-cation bond between A973-B59, and π-π stacking interactions between A930-B36 and A932-B36 in conjunction with MPDP and Sakacin-P (Fig. 4 C). Apart from hydrogen bonds, these were other non-covalent interactions that contribute to receptor-ligand interaction. Ionic bonds arise from the transfer of electrons between atoms, resulting in the creation of cations and anions. Opposite charges attract, leading to a strong electrostatic bond that defines the ionic bond. Ionic bonds can form between the positively charged amino group (-NH3 + ) and the negatively charged carboxyl group (-COO - ) within amino acids [ 33 ]. The π-π stacking is a non-covalent interaction that transpires between the aromatic rings containing aminoacids in molecules. It is associated with the alignment and interaction of the electron-dense π orbitals of one aromatic system with those of another. This interaction enhanced structural stabilization by generating attractive forces among electron clouds [ 35 ]. The π-cation interaction can be described as a non-covalent interaction involving a positively charged cation and the electron rich π orbitals of an aromatic groups. The π-cation interactions contributed to the stability of protein structures by providing essential structural support and modifying their conformational states. Interactions involving basic and aromatic amino acids are crucial in membrane proteins, as they contribute to the stabilization of the overall structure [ 36 ]. Table 3 List of interchain interactions exist between monkeypox virus DNA polymerase (8HOY) and Sakacin-P. Hidrogen bonds Ionic bonds Van der Waals forces Chain-A (8HOY) Chain-B (Sakacin-P) Chain-A (8HOY) Chain-B (Sakacin-P) Chain-A (8HOY) Chain-B (Sakacin-P) 305-Ser 2-Glu 525-Lys* 11-Glu 305-Ser 2-Glu 310-Val 33-Thr π -cation 305-Ser 3-Lys 311-Cys 29-Lys 973-Lys* 59-Trp 308-Lys* 15-Ile 315-Asn 2-Glu π-π stack 309-Gly 15-Ile 316-Thr 1-Met 930-Phe 36-Trp 310-Val 18-Gly 340-Lys* 30-Hıs 932-Tyr 36-Trp 313-Met 4-Phe 525-Lys* 8-Ser 314-Ala 2-Glu 525-Lys* 11-Glu 525-Lys* 10-Lys 529-Glu 16-Thr 525-Lys* 11-Glu 894-Arg 35-Asp 527-Pro 14-Ala 991-Ser 60-Asn 529-Glu 16-Thr 994-Gln 50-Asn 803-Lys* 19-Lys 994-Gln 55-Gly 832-Arg* 25-Val 1000-Arg* 47-Ala 834-Asp 34-Val 894-Arg 36-Trp 930-Phe 36-Trp 970-Val 43-Ile 1000-Arg* 51-Trp * The amino acids highlighted in bold represent the active residues of MPDP. Sakacin-P may form bonds with 53.84% of active residues from the MPDP. On the other hand, the observed Wan der waals forces in Sakacin-P docking pose were as follows: A305-B2, A305-B3, A308-B15, A309-B15, A310-B18, A313-B4, A314-B2, A525-B10, A525-B11, A527-B14, A529-B16, A803-B19, A832-B25, A834-B34, A894-B36, A930-B36, A970-B43, and A1000-B51. Particularly, van der waals forces between MPDP active residues and Sakacin-P (A308-B15, A525-B10, A525-B11, A803-B19, A832-B25, and A1000-B51) contributed significantly to the inhibitory effect of Sakacin-P (Fig. 4 D). Additionally, van der Waals forces facilitated a snug fit between the two molecules by optimizing atomic packing, particularly around the hydrophobic core of the bacteriocin. These detailed interactions underlined the synergistic effects of multiple non-covalent forces in achieving high-affinity binding [ 37 – 39 ]. When comparing Sakacin-P's docking pose to that of Munditicin_KS, Sakacin-P was found to bind to 53.84% of the active residues of MPDP, whereas Munditicin_KS bound to only 46.15%. Overall, the superior binding affinity and balanced physicochemical characteristics of Sakacin-P highlighted its potential as a lead compound for targeting MPDP. These findings provided a strong foundation for further experimental validation and optimization of Sakacin-P as a potential therapeutic agent against Monkeypox DNA Polymerase. Future studies should focus on in vitro and in vivo validation, as well as chemical modifications to enhance Sakacin-P's selectivity and bioavailability. Molecular Dynamics Simulations Sakacin-P complexed with MPDP was further analyzed via molecular dynamics simulations to validate docking results. MD simulations were conducted with GROMACS for 500 ns. Firstly, Fig. 5 shows the comparisons of root mean square deviations (RMSD) for two states of a protein: Protein complexed (blue) and Protein free (red). Both states started with low RMSD values (~ 0.4–0.5 nm), indicating minimal deviation from their respective initial structures. Then, a sharp increase was observed at the beginning, likely representing the system moving out of the energy-minimized starting configuration to explore conformational space. After that, RMSD stabilized relatively quickly (~ 100 ps) around ~ 0.5–0.6 nm for free protein, suggesting it was equilibrated. For the complexed protein, RMSD stabilized later (~ 200–300 ps) and at a higher average (~ 0.6–0.7 nm). This may reflect greater conformational changes or flexibility due to interactions with the binding partner. In addition, the complexed protein showed higher fluctuations compared to the free protein throughout the simulation. This may indicate the dynamic behavior induced by binding interactions and a larger conformational search space due to the influence of the sakacin-P. Overall, both states of protein exhibited stable RMSD after initial equilibration, implying no significant structural destabilization during the simulated time. Furthermore, Root Mean Square Fluctuation (RMSF) analysis for both states of the protein-complexed and free- were conducted (Fig. 6 ). RMSF is a measure of the flexibility of each residue over the simulation time, with higher values indicating more flexibility. Both the complexed and free protein exhibited distinct regions of higher and lower RMSF, suggesting that some residues are inherently more flexible than others, regardless of the state. The RMSF values were generally higher for the free protein, indicating that it is more flexible overall compared to the complexed protein. The sakacin-P likely stabilized the protein structure, reducing the fluctuations, especially in regions directly or indirectly interacting with the ligand. The peaks of fluctuation were observed in loop regions or termini, which are typically less structured and more flexible. Higher RMSF peaks in the free state suggested that ligand binding reduced flexibility in some regions, possibly locking them into more rigid conformations. Near the end of the graph (e.g., residue index 1000), both states showed increased fluctuations, potentially representing disordered or terminal regions. Overall, the complexed protein indicated reduced flexibility due to stabilization from interactions with the ligand. This is typical for ligand-binding proteins, where binding induces a conformational change or rigidity in certain regions. Figure 7 shows the Solvent Accessible Surface Area (SASA) of a protein in two states: complexed and free. Both states exhibited relatively stable SASA values over time, indicating minimal structural fluctuations. However, the complexed protein had consistently higher SASA values than the free protein, suggesting that binding to sakacin-P may expose more surface area to the solvent. After the equilibration, SASA stabilized around 535–540 Ų for the complexed protein and 505–510 Ų for the free protein, suggesting the system reached equilibrium. The binding event in the complexed protein may increase conformational flexibility, leading to a more solvent-exposed structure. It is also indicative to the stabilization of the structure, which could prevent compaction, maintaining a higher SASA. Figure 8 represents the radius of gyration (Rg) over time for two different states of a protein. Both the protein-free and protein-complexed states started with a relatively high Rg value (~ 3.45–3.50 nm). A sharp drop in Rg occured within the first ~ 50 ns, which indicates an initial compaction of both structures. The drop was more significant in the protein-complexed state, suggesting the complexation induces a tighter conformation. After ~ 100 ns, both structures stabilized. The protein-complexed form had a lower Rg, indicating that the bound state maintained a more compact structure. Beyond 300 ns, the Rg values for both states appeared to fluctuate within a stable range. The protein-complexed state remained consistently lower (~ 3.20–3.25 nm), while the free protein fluctuated around 3.25–3.30 nm. This supported the idea that the binding of sakacin-P stabilized the protein structure, reducing overall flexibility. The number of hydrogen bonds (H-bonds) and Van der Waals (vdW) interactions formed between MPDP and sakacin-P anthroughout a 500 ns molecular dynamics (MD) simulation were demonstrated in Fig. 9 . The H-bond count quickly fluctuated and stabilized around 6–12 bonds. This suggested that the complex quickly established consistent intermolecular interactions after the simulation begins. Then, the H-bond count remained relatively consistent, fluctuating between 6 and 12, with occasional peaks reaching up to 15. This indicated a stable binding interface, implying that the protein-ligand complex was well-formed and hold together by persistent H-bond interactions. Overall, the H-bonding profile reflected a dynamic but generally stable interaction between the protein and ligand for the majority of the simulation. Throughout most of the simulation, vdW interactions fluctuated between 10 and 20 contacts, indicating a persistent and strong non-covalent interaction between the protein and ligand. The frequency and density of these interactions suggested that the ligand remained closely associated with the protein, contributing to the stability of the complex. Despite the short-lived drops, the system consistently re-established strong vdW interactions, indicating robust binding and favorable surface complementarity between the interacting partners. No long-term loss of interactions was observed, supporting the structural and energetic stability of the complex. The dominance of vdW interactions, together with hydrogen bonding data, supported the stable and possibly functionally relevant association of sakacin-P within the binding site of MPDP. Collectively, these findings suggested that the binding of sakacin-P to MPDP was stable in MD simulations over 500 ns, validating the molecular docking analysis for sakacin-P as an MPDP inhibitor. Discussion In this study, bacteriocins from various sources were virtually screened against the MPDP using the HADDOCK platform. Among the tested bacteriocins, mundticin KS, sakacin-P, and plantaricin W_beta exhibited the strongest affinities for the MPDP with ΔG values of -17.0, -16.7, and − 16.2 kcal/mol, respectively. Physicochemical analysis showed that mundticin KS and plantaricin W_beta had higher instability index scores than the threshold value of 42, while sakacin-P demonstrated good stability with a low instability index score. Based on these findings, sakacin-P was selected for molecular dynamics (MD) simulation to assess its stability and behavior within the DNA replication complex. The MD simulations, conducted over 500 ns, confirmed the stability of sakacin-P when bound to MPDP, highlighting its potential as a candidate for further investigation. Plantaricin W is a class IIb bacteriocin produced by Lactobacillus plantarum , consisting of two complementary peptides that work synergistically to exert antimicrobial activity against a large number of Gram-positive bacteria, including several foodborne pathogens. Plantaricin W showed a remarkable anti-Listeria activity [ 40 – 42 ]. Plantaricin W also demonstrated heat stability and retains activity across a broad pH spectrum, making it valuable for use in food preservation. The antifungal activity of plantaricin has been demonstrated against various fungal species, including Penicillium roqueforti, Mucor plumbeus, Penicillium expansum, Cladosporium sp., Fusarium sp., and Debaromyces hansenii [ 43 ]. In an in silico study, plantaricin W exhibited potential as an antiviral agent against COVID-19, showing strong binding affinity to key druggable targets of SARS-CoV-2, including RNA-dependent RNA polymerase, the receptor-binding domain (RBD) of the spike protein, and the human ACE2 receptor [ 44 ]. Similarly, plantaricin NC8 αβ was reported to rapidly and efficiently inhibit flaviviruses and SARS-CoV-2 by disrupting their viral envelopes [ 45 ]. Mundticin KS is a class IIa bacteriocin produced by Enterococcus mundtii , known for its potent antimicrobial activity against closely related lactic acid bacteria and the food-borne pathogen Listeria monocytogenes . This small cationic peptide exhibited strong heat stability, retaining significant antimicrobial activity at temperatures up to 100°C, and remained stable across a wide pH range, but is sensitive to trypsin and proteinase K while resistant to lipase and RNase A [ 46 ]. Mundticin KS, produced by E. mundtii Tw56, was also reported to exhibit a broad spectrum of activity, effectively targeting Pseudomonas aeruginosa and Shewanella putrefaciens [ 47 ]. While a bacteriocin produced by E. mundtii ST4V demonstrated broad antiviral activity against herpes simplex viruses HSV-1 and HSV-2, polio virus, and measles virus [ 48 ], no antiviral activity has been reported for mundticin KS. Sakacin-P is a class IIa bacteriocin produced by Lactobacillus sakei , commonly found in fermented foods [ 49 , 50 ]. It is a small, cationic peptide with antimicrobial properties, characterized by a narrow spectrum of activity. While it exhibits minimal antibacterial efficacy against Gram-negative bacteria, it demonstrates potent activity against Listeria monocytogenes [ 51 ]. Additionally, both sakacin-P and L. sakei demonstrated potential for use in controlling L. monocytogenes in chicken cold cuts [ 52 ]. Furthermore, sakacin-P producing L. sakei was reported in both in vitro and in vivo studies to exhibit significant preventive effects against carbapenem-resistant Klebsiella pneumonia (CRKP) infection. Treatment with lyophilized probiotics notably reduced body weight loss, mortality, and illness severity in CRKP-infected mice, highlighting the potential of L. sakei in combating CRKP infections [ 53 ]. Similarly, a recent study showed that L. sakei HEM 224, isolated from traditional Korean kimchi, can alleviate inflammatory conditions in the gastrointestinal and respiratory tracts by the reinforcement of the epithelial barrier and immunomodulation [ 54 ]. L. sakei also demonstrated anti-inflammatory effects in a rheumatoid arthritis (RA) animal model by regulating Th17 and regulatory B cell differentiation and suppressing osteoclastogenesis [ 55 ]. In another study, L. sakei Pro-Bio65 was shown to reduce TNF-α expression while upregulating glutathione levels and enhancing antioxidant enzymatic activities in human conjunctival cells [ 56 ]. The extract of the same L. sakei Pro-Bio65 strain demonstrated significant in vitro therapeutic efficacy by inhibiting viral replication and reducing pathogenicity of the SARS-CoV-2 [ 57 ]. Notably, sakacin-P was reported to exhibit strong binding affinity to the human ACE2 receptor in an in silico study, suggesting its potential antiviral activity against SARS-CoV-2 [ 58 ]. These studies clearly demonstrated that L. sakei and its bacteriocin, sakacin-P, holds significant therapeutic potential for the treatment of various diseases. While there are studies exploring the antiviral activity of sakacin-P against SARS-CoV-2, to our knowledge, no research has been reported on its potential antiviral activities against other viruses, including the MPXV. Therefore, our findings on sakacin-P pave the way for the development of antiviral agent against MPXV. However, this study requires further validation through in vitro and in vivo studies. Conclusion This study demonstrates the potential of bacteriocins as inhibitors of the MPDP using computational approaches. Structural modeling, molecular docking, and MD simulations collectively indicated that Sakacin-P exhibited superior binding affinity and stability in complex with MPDP compared to Mundticin-KS. Key interactions, including hydrogen bonding, ionic interactions, and π-π stacking, were identified as crucial contributors to ligand binding stability. MD simulations confirmed the conformational stability of the protein-ligand complex, highlighting reduced solvent accessibility and enhanced structural compactness upon binding. These findings provide an essential step toward the rational design of bacteriocin-based antiviral agents against MPXV. Future studies should focus on experimental validation of these interactions to explore the therapeutic potential of bacteriocins in combating MPXV infections. Declarations Conflict of Interest The authors declare no competing interests. Author Contribution All authors contributed to the study’s conception and design. Material preparation, data collection, and analyses wereconducted by Melisa Z. Karaman, Fernando Berton Zanchi, Özkan Fidan, and Ahmet E. Yetiman.The first draft of the manuscript was written by Melisa Z. Karaman, Özkan Fidan, and Ahmet E. Yetiman and was proofread by Aykut Özdarendeli and Fernando Berton Zanchi. All authors read and approved the final manuscript. Acknowledgement The authors gratefully acknowledge the Scientific and Technological Research Council of Türkiye (TÜBİTAK) for awarding a 2210/A National MSc/MA Scholarship to M.Z.K. Data Availability The data used to support the findings of this study will be made available on reasonable request. References Luo YH, Zhang T, Cao JL et al (2024) Monkeypox: An outbreak of a rare viral disease. J Microbiol Immunol Infect 57:1–10. https://doi.org/10.1016/J.JMII.2023.12.006 Sun Y, Nie W, Tian D, Ye Q (2024) Human monkeypox virus: Epidemiologic review and research progress in diagnosis and treatment. J Clin Virol 171:105662. https://doi.org/10.1016/J.JCV.2024.105662 Zumla A, Rosenthal PJ, Sam-Agudu NA et al (2024) The 2024 Public Health Emergency of International Concern: A Global Failure to Control Mpox. 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Sci Rep 13:1–12. https://doi.org/10.1038/s41598-023-45043-0 Jhun J, Min HK, Ryu J et al (2020) Lactobacillus sakei suppresses collagen-induced arthritis and modulates the differentiation of T helper 17 cells and regulatory B cells. J Transl Med 18:1–11. https://doi.org/10.1186/S12967-020-02477-8/FIGURES/5 Iorio R, Petricca S, Luzi C et al (2021) Lactobacillus sakei Pro-Bio65 Reduces TNF-α Expression and Upregulates GSH Content and Antioxidant Enzymatic Activities in Human Conjunctival Cells. Transl Vis Sci Technol 10:8–8. https://doi.org/10.1167/TVST.10.6.8 Rather IA, Lew LC, Kamli MR et al (2022) The Inhibition of SARS-CoV-2 and the Modulation of Inflammatory Responses by the Extract of Lactobacillus sakei Probio65. Vaccines 10:2106. https://doi.org/10.3390/VACCINES10122106 Manna S, Chowdhury T, Chakraborty R, Mandal SM (2020) Probiotics-Derived Peptides and Their Immunomodulatory Molecules Can Play a Preventive Role Against Viral Diseases Including COVID-19. Probiotics Antimicrob Proteins 1–13 Additional Declarations No competing interests reported. Cite Share Download PDF Status: Posted Version 1 posted You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. We do this by developing innovative software and high quality services for the global research community. Our growing team is made up of researchers and industry professionals working together to solve the most critical problems facing scientific publishing. Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-6529067","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":452563394,"identity":"3f8b6122-9730-4d77-b358-5ae5c2476784","order_by":0,"name":"Melisa Z. Karaman","email":"","orcid":"","institution":"Abdullah Gül University","correspondingAuthor":false,"prefix":"","firstName":"Melisa","middleName":"Z.","lastName":"Karaman","suffix":""},{"id":452563396,"identity":"c7ba7fa0-7492-4c45-98e0-42b32d63b024","order_by":1,"name":"Fernando Berton Zanchi","email":"","orcid":"","institution":"Oswaldo Cruz Foundation","correspondingAuthor":false,"prefix":"","firstName":"Fernando","middleName":"Berton","lastName":"Zanchi","suffix":""},{"id":452563398,"identity":"dc60e406-5934-41f4-83eb-6dad4d1127f6","order_by":2,"name":"Aykut Ozdarendeli","email":"","orcid":"","institution":"Erciyes University","correspondingAuthor":false,"prefix":"","firstName":"Aykut","middleName":"","lastName":"Ozdarendeli","suffix":""},{"id":452563400,"identity":"daa765bd-d2ef-42fb-861a-97d6988b5d63","order_by":3,"name":"Ozkan Fidan","email":"","orcid":"","institution":"Abdullah Gül University","correspondingAuthor":false,"prefix":"","firstName":"Ozkan","middleName":"","lastName":"Fidan","suffix":""},{"id":452563404,"identity":"cb1fc6d2-9a15-4dbc-91b0-95bee1d2da3e","order_by":4,"name":"Ahmet E. Yetiman","email":"data:image/png;base64,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","orcid":"","institution":"Erciyes University","correspondingAuthor":true,"prefix":"","firstName":"Ahmet","middleName":"E.","lastName":"Yetiman","suffix":""}],"badges":[],"createdAt":"2025-04-25 12:53:14","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-6529067/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-6529067/v1","draftVersion":[],"editorialEvents":[],"editorialNote":"","failedWorkflow":false,"files":[{"id":82171055,"identity":"bd3449a2-5fa5-4001-b1d8-fa1a8d83a5ba","added_by":"auto","created_at":"2025-05-07 10:05:53","extension":"png","order_by":1,"title":"Figure 1","display":"","copyAsset":false,"role":"figure","size":8191540,"visible":true,"origin":"","legend":"\u003cp\u003eStructure confirmation of the monkeypox DNA polymerase enzyme. (A) Confirmation of the 3D structure predicted via the Ramachandran plot. (B) Cartoon illustration of 3D structure of The Monkeypox DNA polymerase enzyme. (C) The secondary structure of the monkeypox DNA polymerase comprises α-helices, β-sheets, and random-coiled polypeptide configurations. (D) The peptide sequence and Ramachandran fields are depicted.\u003c/p\u003e","description":"","filename":"floatimage1.png","url":"https://assets-eu.researchsquare.com/files/rs-6529067/v1/adbab71b82056900ad059c5a.png"},{"id":82170774,"identity":"38c98997-d795-4d33-8b95-096914074399","added_by":"auto","created_at":"2025-05-07 09:57:52","extension":"png","order_by":2,"title":"Figure 2","display":"","copyAsset":false,"role":"figure","size":523575,"visible":true,"origin":"","legend":"\u003cp\u003eThree-dimensional structure of Sakacin-P (P35618) from \u003cem\u003eLatilactobacillus sakei\u003c/em\u003e and its confirmation via Ramachandran plot.\u003cstrong\u003e \u003c/strong\u003e(A) Cartoon illustration of 3D structure of Sakacin-P bacteriocin. (B) Verification of the 3D structure predicted via the Ramachandran plot. For Sakacin-P, 85.4% of residues (black dots) have been determined in the favored areas. (C) Description of the secondary structure of Sakacin-P, which is composed of α-helices, β-sheets, and random-coiled polypeptide structures. (D) The peptide sequence and Ramachandran regions are illustrated.\u003c/p\u003e","description":"","filename":"floatimage2.png","url":"https://assets-eu.researchsquare.com/files/rs-6529067/v1/4ca7717721da5ca9b787e424.png"},{"id":82171054,"identity":"bb793925-2cd5-4a5c-b856-bfeb91acc1f9","added_by":"auto","created_at":"2025-05-07 10:05:53","extension":"png","order_by":3,"title":"Figure 3","display":"","copyAsset":false,"role":"figure","size":4513937,"visible":true,"origin":"","legend":"\u003cp\u003eThree-dimensional structure of Mundticin KS (2ZRR) from \u003cem\u003eEnterococcus mundtii\u003c/em\u003e and its confirmation via Ramachandran plot. (A) Cartoon illustration of 3D structure of Mundticin KS. (B) Verification of the 3D structure predicted via the Ramachandran plot. For Mundticin KS, 93.4% of residues (black dots) have been determined in the favored areas. (C) Description of the secondary structure of Mundticin KS, which is composed of α-helices and random-coiled polypeptide structures. (D) The peptide sequence and Ramachandran regions are illustrated.\u003c/p\u003e","description":"","filename":"floatimage3.png","url":"https://assets-eu.researchsquare.com/files/rs-6529067/v1/e1d4420fe6b01d0d58a3a4e4.png"},{"id":82170793,"identity":"0c386109-fb14-471e-8ad2-4098e8bd39fc","added_by":"auto","created_at":"2025-05-07 09:57:54","extension":"jpeg","order_by":4,"title":"Figure 4","display":"","copyAsset":false,"role":"figure","size":342115,"visible":true,"origin":"","legend":"\u003cp\u003e(A) The surface view of the catalytic site of MPDP (lemon green) and the snapping into slot view of Sakacin-P (dark blue cartoon) into the catalytic site of MPDP are shown. (B) The figure illustrates the hydrogen bonds that exist between Sakacin-P and MPDP. The hydrogen bond-forming residues in MPDP were colored in light light-orange while hydrogen bond-forming residues in Sakacin-P have been colored in lemon green. (C) The ionic bond amongst LYS-525 (Chain-A) and GLU-11 (Chain-B), the pi-cation interaction between LYS-973 (Chain-A) and TRP-59 (Chain-B), and the pi-pi stack interactions between PHE-930 (Chain-A), TYR-932 (Chain-A), and TRP-36 (Chain-B) were depicted based on RING 4.0 web webserver results. The bond-forming residues from MPDP were represented in purple, whereas the interacting residues from Sakacin-P were shown in blue. (D) The van der Waals interactions between detected catalytic residues of MPDP (green) and bond-forming residues from Sakacin-P (turquoise) were demonstrated.\u003c/p\u003e","description":"","filename":"floatimage4.jpeg","url":"https://assets-eu.researchsquare.com/files/rs-6529067/v1/23037ec606e805e270c03ca4.jpeg"},{"id":82170775,"identity":"c5b18074-5b7e-40ea-9262-2299b958b5e3","added_by":"auto","created_at":"2025-05-07 09:57:52","extension":"jpeg","order_by":5,"title":"Figure 5","display":"","copyAsset":false,"role":"figure","size":115464,"visible":true,"origin":"","legend":"\u003cp\u003eRMSD graph for free MPDP and complexed MPDP with sakacin-P.\u003c/p\u003e","description":"","filename":"floatimage5.jpeg","url":"https://assets-eu.researchsquare.com/files/rs-6529067/v1/a60282e473bd16b4ff72bfe9.jpeg"},{"id":82170777,"identity":"40618671-605a-499b-b0a4-58b4b6f2a15e","added_by":"auto","created_at":"2025-05-07 09:57:53","extension":"jpeg","order_by":6,"title":"Figure 6","display":"","copyAsset":false,"role":"figure","size":121004,"visible":true,"origin":"","legend":"\u003cp\u003eRMSF graph for free MPDP and complexed MPDP with sakacin-P.\u003c/p\u003e","description":"","filename":"floatimage6.jpeg","url":"https://assets-eu.researchsquare.com/files/rs-6529067/v1/7e1de1374bee2f3bb1349685.jpeg"},{"id":82171053,"identity":"edea4bc5-905d-4881-ab2b-cc872de3cde3","added_by":"auto","created_at":"2025-05-07 10:05:53","extension":"jpeg","order_by":7,"title":"Figure 7","display":"","copyAsset":false,"role":"figure","size":130841,"visible":true,"origin":"","legend":"\u003cp\u003eSolvent accessible surface area graph for free MPDP and complexed MPDP with sakacin-P.\u003c/p\u003e","description":"","filename":"floatimage7.jpeg","url":"https://assets-eu.researchsquare.com/files/rs-6529067/v1/335df252b66706b2a74c17d3.jpeg"},{"id":82170778,"identity":"e482026b-5f12-4de1-b780-0dfb35e0ca36","added_by":"auto","created_at":"2025-05-07 09:57:53","extension":"jpeg","order_by":8,"title":"Figure 8","display":"","copyAsset":false,"role":"figure","size":124657,"visible":true,"origin":"","legend":"\u003cp\u003eRadius of gyration graph for free MPDP and complexed MPDP with sakacin-P.\u003c/p\u003e","description":"","filename":"floatimage8.jpeg","url":"https://assets-eu.researchsquare.com/files/rs-6529067/v1/986a60aa782923e3f0bf9cdb.jpeg"},{"id":82170787,"identity":"4c894e05-c023-4e8d-9e74-39784f2e4e64","added_by":"auto","created_at":"2025-05-07 09:57:53","extension":"png","order_by":9,"title":"Figure 9","display":"","copyAsset":false,"role":"figure","size":1416451,"visible":true,"origin":"","legend":"\u003cp\u003eHydrogen bond (A) and Van der Waals interactions (B) for complexed MPDP with sakacin-P.\u003c/p\u003e","description":"","filename":"floatimage9.png","url":"https://assets-eu.researchsquare.com/files/rs-6529067/v1/a693a610dacbeacef91fd781.png"},{"id":85556501,"identity":"6b7edfe2-86f7-41ad-9e31-dc10832ad90d","added_by":"auto","created_at":"2025-06-27 11:17:01","extension":"pdf","order_by":0,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":17400660,"visible":true,"origin":"","legend":"","description":"","filename":"manuscript.pdf","url":"https://assets-eu.researchsquare.com/files/rs-6529067/v1/9484a401-b980-4576-813c-79bdb22d85f6.pdf"}],"financialInterests":"No competing interests reported.","formattedTitle":"Virtual screening of bacteriocins from lactic acid bacteria against Monkeypox DNA Polymerase: Sakacin-P is a potent DNA polymerase inhibitor","fulltext":[{"header":"Introduction","content":"\u003cp\u003eMonkeypox virus (MPXV) was first discovered in 1958 when an unidentified disease appeared in monkeys in Africa [\u003cspan citationid=\"CR1\" class=\"CitationRef\"\u003e1\u003c/span\u003e]. An unknown virus was identified in the infected monkeys' bodies and since the monkeys developed blisters on their skin that were similar to those caused by smallpox, the disease was therefore named \"monkeypox\" [\u003cspan citationid=\"CR1\" class=\"CitationRef\"\u003e1\u003c/span\u003e, \u003cspan citationid=\"CR2\" class=\"CitationRef\"\u003e2\u003c/span\u003e]. The WHO declared the current MPXV outbreak a \"Public Health Emergency of International Concern\" (PHEIC) on 14 August 2024, marking the second MPXV-related PHEIC in two years. The Africa Centres for Disease Control and Prevention (Africa CDC) also declared a regional emergency on 13 August 2024, following the report of 35,341 MPXV cases and 840 deaths across 13 African countries between January 1 and September 23, 2024 [\u003cspan citationid=\"CR3\" class=\"CitationRef\"\u003e3\u003c/span\u003e].\u003c/p\u003e \u003cp\u003eMPXV is an enveloped double-stranded DNA (dsDNA) virus, which belongs to the genus Orthopoxvirus of the family Poxvirus [\u003cspan citationid=\"CR1\" class=\"CitationRef\"\u003e1\u003c/span\u003e, \u003cspan citationid=\"CR4\" class=\"CitationRef\"\u003e4\u003c/span\u003e]. Orthopox also consists of cowpox, variola (smallpox), and vaccinia viruses [\u003cspan citationid=\"CR5\" class=\"CitationRef\"\u003e5\u003c/span\u003e]. The clinical signs of this viral disease are similar to those of smallpox but the severity might mostly change from one patient to another or among conditions [\u003cspan citationid=\"CR6\" class=\"CitationRef\"\u003e6\u003c/span\u003e]. Since MPXV is a zoonotic disease, it can be transmitted from animals to humans, and among humans, and it possesses a 1\u0026ndash;8% lethality rate [\u003cspan citationid=\"CR2\" class=\"CitationRef\"\u003e2\u003c/span\u003e]. Human-to-human transmission of the MPXV can be reasoned by close contact with infected individuals and the virus can be transmitted to the body through respiratory droplets, sexual contact, or contact with infectious skin lesions or bodily fluids [\u003cspan citationid=\"CR2\" class=\"CitationRef\"\u003e2\u003c/span\u003e, \u003cspan additionalcitationids=\"CR8\" citationid=\"CR7\" class=\"CitationRef\"\u003e7\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR9\" class=\"CitationRef\"\u003e9\u003c/span\u003e].\u003c/p\u003e \u003cp\u003eThe incubation stage of MPXV infection is generally 3 to 21 days after exposure, and since it initially appears as a non-distinct prodromal phase, the virus might be transmitted before it is noticed [\u003cspan citationid=\"CR5\" class=\"CitationRef\"\u003e5\u003c/span\u003e, \u003cspan citationid=\"CR6\" class=\"CitationRef\"\u003e6\u003c/span\u003e]. This is followed by signature rash symptoms which are the main symptoms of MPXV and take nearly 2 to 5 weeks [\u003cspan citationid=\"CR1\" class=\"CitationRef\"\u003e1\u003c/span\u003e, \u003cspan citationid=\"CR5\" class=\"CitationRef\"\u003e5\u003c/span\u003e]. Patients with MPXV might have headaches, fever, sore throat, swollen lymph nodes, chills nausea, breathlessness, fatigue, lethargy, genital necrosis, weakened digestive tracts, and muscle pains [\u003cspan citationid=\"CR1\" class=\"CitationRef\"\u003e1\u003c/span\u003e, \u003cspan citationid=\"CR2\" class=\"CitationRef\"\u003e2\u003c/span\u003e, \u003cspan citationid=\"CR6\" class=\"CitationRef\"\u003e6\u003c/span\u003e]. In addition, MPXV infection might result in serious complications like organ damage leading to skin lesions, eye damage resulting from corneal infection, bronchopneumonia, encephalitis, and sepsis [\u003cspan citationid=\"CR1\" class=\"CitationRef\"\u003e1\u003c/span\u003e, \u003cspan citationid=\"CR5\" class=\"CitationRef\"\u003e5\u003c/span\u003e, \u003cspan citationid=\"CR6\" class=\"CitationRef\"\u003e6\u003c/span\u003e]. Notwithstanding, there is no exact therapy or vaccine for MPXV infection. Patients might gain protection through cross-immunity with smallpox vaccination. During the past decade, the MPXV level has increased substantially, which might be associated with a decrease in herd immunity to smallpox because smallpox vaccination was no longer routinely available due to the global eradication of smallpox. Since smallpox vaccination was 85% effective in MPXV prevention, post-exposure immunization can provide to decrease or stop the illness severity [\u003cspan citationid=\"CR4\" class=\"CitationRef\"\u003e4\u003c/span\u003e]. Moreover, several antiviral drugs such as tecovirimat, cidofovir, and brincindofovir can be employed in the treatment of MPXV infections, but their effectiveness has not been fully affirmed [\u003cspan citationid=\"CR2\" class=\"CitationRef\"\u003e2\u003c/span\u003e, \u003cspan citationid=\"CR4\" class=\"CitationRef\"\u003e4\u003c/span\u003e].\u003c/p\u003e \u003cp\u003eLactic acid bacteria (LAB) can produce different chemicals that can inhibit the growth of microorganisms [\u003cspan citationid=\"CR10\" class=\"CitationRef\"\u003e10\u003c/span\u003e]. For example, these are lactic acid, acetic acid, and propanoic acid, which make the environment more acidic and thus decrease the pathogenic microbial population [\u003cspan citationid=\"CR10\" class=\"CitationRef\"\u003e10\u003c/span\u003e, \u003cspan citationid=\"CR11\" class=\"CitationRef\"\u003e11\u003c/span\u003e]. LAB also produces low molecular weight substances such as hydrogen peroxide, carbon dioxide, diacetyl, organic acids, ethanol and bacteriocins, and they can inhibit the growth of several pathogenic bacteria [\u003cspan citationid=\"CR11\" class=\"CitationRef\"\u003e11\u003c/span\u003e, \u003cspan citationid=\"CR12\" class=\"CitationRef\"\u003e12\u003c/span\u003e]. Bacteriocins are extracellular, ribosomally produced small peptides or proteins synthesized by bacteria that are capable of killing or inhibiting other closely related bacteria because the producer strain of bacteriocin is inherently resilient to its fatal effects since it has immunity proteins [\u003cspan citationid=\"CR12\" class=\"CitationRef\"\u003e12\u003c/span\u003e, \u003cspan citationid=\"CR13\" class=\"CitationRef\"\u003e13\u003c/span\u003e]. Bacteriocins possess a variety of biotechnological applications, including in the food and dairy industries as food preservatives, and clinical applications as an alternative to some antibiotics, and they have medical activities as anticancer, antiviral, and antiprotozoal agents [\u003cspan citationid=\"CR12\" class=\"CitationRef\"\u003e12\u003c/span\u003e].\u003c/p\u003e \u003cp\u003eSeveral varieties of bacteriocins exist and they have been categorized according to their genetic and physicochemical characteristics [\u003cspan citationid=\"CR10\" class=\"CitationRef\"\u003e10\u003c/span\u003e, \u003cspan citationid=\"CR13\" class=\"CitationRef\"\u003e13\u003c/span\u003e]. In 1993, Klaenhammer proposed classifying Lab bacteriocins into four major classes based on the size of the peptide, post-translational modification, and other characteristics. Class I includes post-translationally modified bacteriocins such as nisin and the rest of the peptides (smaller than 10 kDa) are found in class II [\u003cspan citationid=\"CR12\" class=\"CitationRef\"\u003e12\u003c/span\u003e, \u003cspan citationid=\"CR14\" class=\"CitationRef\"\u003e14\u003c/span\u003e]. Class I possesses lanthionine-containing bacteriocins (lantibiotics), which contain the lanthipeptides, linear azol(in)e-containing peptides, glycocins, cyclized peptides, satibiotics, and lasso peptides. Class II which are bacteriocins without lanthionine includes pediocin-like bacteriocins, non-pediocin-like single peptides, leaderless peptides, and two-peptide bacteriocins. They are capable of remaining stable at high temperatures. Examples of class II bacteriocins are Pediocin PA-1, Enterocin-P, Enterocin-A, Pentocin-31, and Sakacin-G [\u003cspan citationid=\"CR10\" class=\"CitationRef\"\u003e10\u003c/span\u003e]. While class III includes heat-labile large bacteriocins (bigger than 30 kDa) such as non-lytic peptides and bacteriolysins, class IV includes complex peptides carrying lipid or carbohydrate moieties [\u003cspan citationid=\"CR12\" class=\"CitationRef\"\u003e12\u003c/span\u003e, \u003cspan citationid=\"CR14\" class=\"CitationRef\"\u003e14\u003c/span\u003e]. For instance, lysostaphin (27 kDa peptide) which is accepted as the original bacteriolysin can degrade the cell walls of several \u003cem\u003eStaphylococcus\u003c/em\u003e species. Lactocin 27 and leuconocin S are examples of class IV and they can cause damage to bacterial cell walls. Class V bacteriocins have a circular nature in their structures and are thus characterized by greater resilience to the effects of a broad range of stresses. Examples of class V are pumilarin, enterocin AS-48, plantaricyclin A and lactocyclicin Q [\u003cspan citationid=\"CR10\" class=\"CitationRef\"\u003e10\u003c/span\u003e].\u003c/p\u003e \u003cp\u003eThe antiviral effects of bacteriocins against several viruses have been reported [\u003cspan citationid=\"CR15\" class=\"CitationRef\"\u003e15\u003c/span\u003e]. Enterocin CRL35 produced by \u003cem\u003eEnterococcus faecium\u003c/em\u003e CRL35 was the first bacteriocin known to have antiviral activity. Enterocin CRL35 demonstrated activities against both Herpes simplex virus types 1 and 2 (HSV-1 and HSV-2) that cause serious problems such as corneal blindness, genital ulcerations, and encephalitis [\u003cspan citationid=\"CR12\" class=\"CitationRef\"\u003e12\u003c/span\u003e]. Similarly, enterocin AAR-71 showed high activity against coliphage HSA virus and completely prevented viral progeny [\u003cspan citationid=\"CR15\" class=\"CitationRef\"\u003e15\u003c/span\u003e]. Furthermore, staphylococcin 188 produced by \u003cem\u003eStaphylococcus aureus\u003c/em\u003e AB188 which is a non-LAB-originated bacteriocin shows antiviral activities against the influenza virus, Newcastle disease virus, and coliphage HSA virus [\u003cspan citationid=\"CR15\" class=\"CitationRef\"\u003e15\u003c/span\u003e, \u003cspan citationid=\"CR16\" class=\"CitationRef\"\u003e16\u003c/span\u003e]. Another example is labyrinthopeptin A produced by \u003cem\u003eActinomadura namibiensis\u003c/em\u003e DSM 6313 which shows antiviral activities against HSV-1, and human immunodeficiency virus type 1 (HIV-1) [\u003cspan citationid=\"CR15\" class=\"CitationRef\"\u003e15\u003c/span\u003e]. Moreover, \u003cem\u003eLactobacillus delbrueckii subsp. bulgaricus\u003c/em\u003e 1043 produces a non-cytotoxic bacteriocin that can be virucidal on the influenza virus [\u003cspan citationid=\"CR16\" class=\"CitationRef\"\u003e16\u003c/span\u003e]. Additionally, when the duramycin binds to phosphatidylethanolamine in the Zika virus envelope, the TIM1 receptor is hindered and the infection decreases in placental cells and explants. Similarly, micrococcin P1 can hinders the Hepatitis C virus entry without affecting the secretion of viral particles [\u003cspan citationid=\"CR17\" class=\"CitationRef\"\u003e17\u003c/span\u003e].\u003c/p\u003e \u003cp\u003eTo our knowledge, the investigation of the potential bacteriocins in the drug development process for the MPXV has not been reported so far. Thus, this study focused on the \u003cem\u003ein silico\u003c/em\u003e evaluation of bacteriocins from lactic acid bacteria against DNA polymerase of MPXV (MPDP). We conducted a virtual screening of 21 bacteriocins against DNA polymerase via protein-protein docking as well as molecular dynamics simulation. Our docking analysis revealed that sakacin-P is the most promising bacteriocin candidate with strong binding affinity and potent physiochemical characteristics as a DNA polymerase inhibitor for MPXV.\u003c/p\u003e"},{"header":"Materials and Methods","content":"\u003cp\u003e \u003cb\u003eIn silico\u003c/b\u003e \u003cb\u003ePreparation and confirmation of Bacteriocins and Receptors\u003c/b\u003e\u003c/p\u003e \u003cp\u003e21 bacteriocin structures were retrieved from Uniprot (\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://www.uniprot.org/\u003c/span\u003e\u003cspan address=\"https://www.uniprot.org/\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e) and the RCBS Protein Data Bank (\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://www.rcsb.org/\u003c/span\u003e\u003cspan address=\"https://www.rcsb.org/\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e) in PDB file format. 3D structures of bacteriocin from Uniprot were predicted using Alphafold (\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://alphafold.ebi.ac.uk/\u003c/span\u003e\u003cspan address=\"https://alphafold.ebi.ac.uk/\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e) and those with an average per-residue model confidence score (pLDDT) above 50 were chosen [\u003cspan citationid=\"CR18\" class=\"CitationRef\"\u003e18\u003c/span\u003e]. Pure 3D structures generated through X-ray diffraction or solution NMR were selected from the RCSB Protein Data Bank. Cryo-EM structure of monkeypox virus DNA replication holoenzyme (F8, A22 and E4 complex) without DNA at 2.76 angstrom (PDB ID: 8HOY) was also downloaded from the Protein Data Bank [\u003cspan citationid=\"CR19\" class=\"CitationRef\"\u003e19\u003c/span\u003e]. The monkeypox virus DNA polymerase enzyme chain was extracted from the complex using PyMol v3.1.0 (\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://github.com/schrodinger/pymol-open-source\u003c/span\u003e\u003cspan address=\"https://github.com/schrodinger/pymol-open-source\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e (Schrodinger LLC, New York, NY)). The extracted chain belonging to the monkeypox DNA polymerase enzyme was evaluated using SWISS-MODEL based on GMQE (Global Model Quality Estimate) and QMEANDisCo global scores [\u003cspan citationid=\"CR20\" class=\"CitationRef\"\u003e20\u003c/span\u003e, \u003cspan citationid=\"CR21\" class=\"CitationRef\"\u003e21\u003c/span\u003e]. All solvent molecules found in the PDB files were removed using BIOVIA Discovery Studio 2024 Client (Dassault Syst\u0026egrave;mes, V\u0026eacute;lizy-Villacoublay, France). Afterwards, these protein structures were confirmed using the PROCHECK tool via the SAVES 6.1 structure validation server (\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://saves.mbi.ucla.edu/\u003c/span\u003e\u003cspan address=\"https://saves.mbi.ucla.edu/\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e). Moreover, the PROCHECK tool generated Ramachandran scores, which represent the percentage of amino acids found in the most favored regions. Additionally, the quality of the structures was assessed, and authentication was carried out using the ProQ server (\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://proq.bioinfo.se/cgi-bin/ProQ/ProQ.cgi\u003c/span\u003e\u003cspan address=\"https://proq.bioinfo.se/cgi-bin/ProQ/ProQ.cgi\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e).\u003c/p\u003e \u003cdiv id=\"Sec3\" class=\"Section2\"\u003e \u003ch2\u003eProtein\u0026ndash;Protein Docking and Physicochemical Features\u003c/h2\u003e \u003cp\u003eHADDOCK v2.4 was employed in protein\u0026ndash;protein docking simulations [\u003cspan citationid=\"CR22\" class=\"CitationRef\"\u003e22\u003c/span\u003e]. Active residues from the positively charged groove of the F8 thumb domain of MPXV DNA polymerase (MPDP), responsible for DNA binding, were acquired from the literature. Reported active residues comprised ARG302, LYS308, LYS340, LYS525, ARG674, LYS803, LYS804, LYS805, ARG832, ARG833, LYS973, ARG974, and ARG1000, located within the F8 thumb domain of the MPDP [\u003cspan citationid=\"CR19\" class=\"CitationRef\"\u003e19\u003c/span\u003e]. The server utilized the default protocol along with default parameter sets for docking and refinement. Passive residues were defined automatically in proximity to the active residues. The top-ranking complexes from HADDOCK were downloaded and submitted to the PROtein binDIng enerGY prediction (PRODIGY) server [\u003cspan citationid=\"CR23\" class=\"CitationRef\"\u003e23\u003c/span\u003e] to calculate binding energies at a temperature of 310K (36,85\u0026deg;C). Subsequently, protein-protein residue interactions were determined through the Residue Interaction Network Generator (RING, v4) web server, using the PDB dataset acquired via PRODIGY. Closest nodes, strict threshold, add hydrogens, and include water parameters were chosen for residue interaction analysis in the RING. All figures were generated by PyMol v2.1 (\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://github.com/schrodinger/pymol-open-source\u003c/span\u003e\u003cspan address=\"https://github.com/schrodinger/pymol-open-source\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e (Schrodinger LLC, New York, NY)). In the manuscript, we defined the MPDP as chain A and the bacteriocins as chain B. For example, A805-B23 denotes the interaction between the 805th amino acid of the MPDPs and the 23rd amino acid of the bacteriocins. The physicochemical characteristics of bacteriocins, including amino acid sequence and length, molecular weight, isoelectric point (pI), instability index, aliphatic index, grand average of hydropathicity (GRAVY) score, and estimated \u003cem\u003ein vitro\u003c/em\u003e half-life in mammalian reticulocytes, were predicted using Expasy\u0026rsquo;s ProtParam tool (\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://web.expasy.org/protparam/\u003c/span\u003e\u003cspan address=\"https://web.expasy.org/protparam/\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e) to confirm their stability.\u003c/p\u003e \u003c/div\u003e\n\u003ch3\u003eMolecular dynamics simulation\u003c/h3\u003e\n\u003cp\u003eIn order to verify the stability and behavior of the complexed MPDP in the presence of the Sakacin-P, two systems were simulated in the APO form and another presence in the Sakacin-P. Molecular dynamics (MD) simulations were performed using Gromacs 2024.2 [\u003cspan citationid=\"CR24\" class=\"CitationRef\"\u003e24\u003c/span\u003e] with interface Visual Dynamics [\u003cspan citationid=\"CR25\" class=\"CitationRef\"\u003e25\u003c/span\u003e] for generate scripts. AMBER99 force field [\u003cspan citationid=\"CR26\" class=\"CitationRef\"\u003e26\u003c/span\u003e]. Electrostatic interactions were treated using the particle mesh Ewald (PME) algorithm with a cut-off of 12 \u0026Aring;. Each system was simulated under periodic boundary conditions in a cubic box, whose dimensions were automatically defined, considering 1 nm from the outermost protein atoms in all Cartesian directions. The simulation box was filled with TIP3P water molecules [\u003cspan citationid=\"CR27\" class=\"CitationRef\"\u003e27\u003c/span\u003e]. Subsequently, a two-step energy minimization procedure was performed (2000 steps of steepest descent and 2000 steps of conjugate-gradient or until the system reaches a resistance force lower than 1000 kJ.mol-1.nm-1. Next, initial atomic velocities were assigned using the Maxwell-Boltzmann distribution corresponding to a temperature of 300 K. All systems were subsequently equilibrated during two successive NVT and NPT equilibration simulations with 200 ps for each. After this period, all the systems were simulated with no restraints at 300 K in the Gibbs ensemble with a 1 atm pressure using isotropic coupling. All chemical bonds containing hydrogen atoms were restricted using the SHAKE algorithm [\u003cspan citationid=\"CR28\" class=\"CitationRef\"\u003e28\u003c/span\u003e] and the time step was set to 2 fs. Finally, we simulated three independent MD runs of 500 ns for the complex and Apo form.\u003c/p\u003e \u003cp\u003eSimulation trajectories were analyzed with GROMACS package tools [\u003cspan citationid=\"CR24\" class=\"CitationRef\"\u003e24\u003c/span\u003e]. Root-mean-square deviation (RMSD), root-mean-square fluctuation (RMSF) were calculated separately for each system fitting their heavy atoms, taking the initial structure of the production dynamics as a reference. Hydrogen bonds (H-bond) were calculated intramolecularly for protein and between protein and ligand complexes. We considered a hit when the distance between two polar heavy atoms, with at least one hydrogen atom attached, was less than 3.5 \u0026Aring; and using an H-donor angle higher than 120\u0026deg;). Radius of Gyration (RG) and Solvent-Accessible Surface Areas (SASA) were also calculated. Furthermore, interaction analysis of ligands with the respective receptor molecule was performed using MMPBSA [\u003cspan citationid=\"CR29\" class=\"CitationRef\"\u003e29\u003c/span\u003e] of the both docked structure for the period of 100ns.\u003c/p\u003e"},{"header":"Results","content":"\u003cdiv id=\"Sec6\" class=\"Section2\"\u003e \u003ch2\u003ePrediction and verification of bacteriocins and Monkeypox DNA polymerase\u003c/h2\u003e \u003cp\u003eDetermining the 3D structures of MPXV DNA polymerase (receptor) and bacteriocins (ligands) from their amino acid sequences was an essential step in assessing receptor-ligand binding affinities. The selection of a protein modeling method based on amino acid sequences relies on the resemblance to established templates in the database. Homology modeling is favored when the similarity exceeds 30%. The interpretation of computationally generated data is straightforward and dependable, effectively bridging the gap between the template and the unknown protein structure [\u003cspan citationid=\"CR21\" class=\"CitationRef\"\u003e21\u003c/span\u003e]. The structure of MPDP was derived from human monkeypox viral replication complexes (8HOY) in the PDB database. Structure validation of MPDP (Fig.\u0026nbsp;\u003cspan refid=\"Fig2\" class=\"InternalRef\"\u003e1\u003c/span\u003e.) was conducted utilizing the PROCHECK tool through the SAVES v6.1 structure validation server, similar to other bacteriocin structures. For the MPDP, Ramachandran plot statistics revealed that 83.1% of residues lie in the most favored regions, 15.8% in additional allowed regions, 0.4% in generously allowed regions, and 0.6% in disallowed regions. This indicates a high-quality model, as over 90% of residues in the favored regions are typically expected for a good-quality structure. The Ramachandran plot serves as a universal criterion for validating predicted protein structures by estimating their stability [\u003cspan citationid=\"CR30\" class=\"CitationRef\"\u003e30\u003c/span\u003e]. The secondary structure elements (helix, beta strand, random coil) and estimated accessibility (buried, accessible) were annotated. This provided a visual representation of the protein\u0026rsquo;s fold and surface properties shown in Figs.\u0026nbsp;\u003cspan refid=\"Fig2\" class=\"InternalRef\"\u003e1\u003c/span\u003e and \u003cspan refid=\"Fig3\" class=\"InternalRef\"\u003e2\u003c/span\u003e. Additionally, Fig.\u0026nbsp;\u003cspan refid=\"Fig2\" class=\"InternalRef\"\u003e1\u003c/span\u003e illustrates the relationships between specific amino acids in the polypeptide chain and their respective ramachandran regions: most favored, allowed, generous, and disallowed. Additionally, models were constructed utilizing SWISS-MODEL with the protein FASTA sequence of the MPDP. Subsequently, Qualitative Model Energy Analysis (QMEAN) was employed to assess the quality of the projected structures by global and local estimations [\u003cspan citationid=\"CR31\" class=\"CitationRef\"\u003e31\u003c/span\u003e]. QMEANDisCo predicts interatomic distances by utilizing information gathered from experimentally validated homologous protein structures, which serve as templates to verify the modeled structure [\u003cspan citationid=\"CR20\" class=\"CitationRef\"\u003e20\u003c/span\u003e]. The QMEANDisCo and GMQE (Global Model Quality Estimate) values, ranging from 0 to 1, were deemed adequate for verifying a modeled structure, with both scores recorded at 0.86 for MPDP.\u003c/p\u003e \u003cp\u003eBacteriocins were modeled using the AlphaFold Server, which can predict complexes containing almost all molecular types found in the Protein Data Bank (PDB) with high accuracy. AlphaFold can directly predict raw atom coordinates with a diffusion module due to its capacity to work on amino acid-specific frames and side chain torsion angles [\u003cspan citationid=\"CR18\" class=\"CitationRef\"\u003e18\u003c/span\u003e]. Over 90% of the amino acid residues in the bacteriocin models were located inside the favorable region of the Ramachandran plot, which was essential for further analysis. Moreover, the quality of these structures was evaluated using the ProQ server for determining the Levitt-Gerstein (LG) score. The LG score measures similarity to a known structure by superimposing two structures and was utilized to assess the quality of these structures. Protein/peptide models exhibiting an LGscore greater than 4 were deemed of high quality [\u003cspan citationid=\"CR32\" class=\"CitationRef\"\u003e32\u003c/span\u003e]. Except for the two bacteriocin models used in this study, all other models had LG scores between 6,605 and 11,927. The LG score values for Lacticin Q and Enterocin HF were found to be negative. ProQ scores (LG scores) and Ramachandran values for all bacteriocins are presented in Table\u0026nbsp;\u003cspan refid=\"Tab1\" class=\"InternalRef\"\u003e1\u003c/span\u003e.\u003c/p\u003e \u003cp\u003e \u003cdiv class=\"gridtable\"\u003e\u003ctable float=\"Yes\" id=\"Tab1\" border=\"1\"\u003e \u003ccaption language=\"En\"\u003e \u003cdiv class=\"CaptionNumber\"\u003eTable 1\u003c/div\u003e \u003cdiv class=\"CaptionContent\"\u003e \u003cp\u003eStructure confirmation parameters and binding energies of bacteriocins versus monkeypox DNA polymerase.\u003c/p\u003e \u003c/div\u003e \u003c/caption\u003e \u003ccolgroup cols=\"6\"\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c1\" colnum=\"1\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c2\" colnum=\"2\"\u003e\u003c/div\u003e \u003cdiv align=\"char\" char=\".\" class=\"colspec\" colname=\"c3\" colnum=\"3\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c4\" colnum=\"4\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c5\" colnum=\"5\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c6\" colnum=\"6\"\u003e\u003c/div\u003e \u003cthead\u003e \u003ctr\u003e \u003cth align=\"left\" colname=\"c1\"\u003e \u003cp\u003eOrganism\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c2\"\u003e \u003cp\u003eBacteriocin\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c3\"\u003e \u003cp\u003eLG score*\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c4\"\u003e \u003cp\u003eRamachandran score (%) **\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c5\"\u003e \u003cp\u003eBinding Energy (Kcal/mol)\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c6\"\u003e \u003cp\u003eKd\u0026nbsp;(M) at 36.85℃\u003c/p\u003e \u003c/th\u003e \u003c/tr\u003e \u003c/thead\u003e \u003ctbody\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eEnterococcus mundtii\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eMundticin_KS\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e7.838\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e98.8\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e-17\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e9.6e-13\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eLatilactobacillus sakei\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eSakacin-A\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e11.168\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e-13\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e6.7e-10\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eLatilactobacillus sakei\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eSakacin-P\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e9.050\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e-16.7\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e1.6e-12\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eLactiplantibacillus plantarum\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003ePlantaricin_W_beta\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e9.456\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e98.2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e-16.2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e4.00e-12\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eLactiplantibacillus plantarum\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003ePlantaricin_W_alpha\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e11.292\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e-12.3\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e2.3e-09\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003ePediococcus acidilactici\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003ePediocin_PA1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e11.071\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e98\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e-12.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e2.8e-09\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eLactococcus lactis\u003c/em\u003e subsp. \u003cem\u003elactis\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eNisin\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e11.553\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e-12.2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e2.3e-09\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eLeuconostoc mesenteroides\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eLeucocinC_TA33a\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e10.580\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e-13.5\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e3.2e-10\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eLeuconostoc mesenteroides\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eLeucocinB_TA33a\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e10.533\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e95.4\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e-11.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e1.5e-08\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eLeuconostoc mesenteroides\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eLeucocinB_TA11A\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e10.445\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e96\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e-13.7\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e2.1e-10\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eLactococcus lactis\u003c/em\u003e subsp. \u003cem\u003elactis\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eLactococcin_G_beta\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e11.090\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e-10.2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e6.1e-08\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eLactococcus lactis\u003c/em\u003e subsp. \u003cem\u003elactis\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eLactococcin_G_Alpha\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e10.781\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e-12.7\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e1.1e-09\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eLactococcus lactis\u003c/em\u003e subsp. \u003cem\u003elactis\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eLactococcin_Mmfii\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e11.062\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e96.8\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e-9.7\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e1.4e-07\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eLactococcus lactis\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eLacticin_Q\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e-0.835\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e-12.7\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e1.1e-09\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eLactococcus lactis\u003c/em\u003e subsp. \u003cem\u003elactis\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eLacticin_481\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e11.927\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e97.8\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e-11.3\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e1.1e-08\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eEnterococcus faecium\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eEnterocin CRL_35\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e6.605\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e-13.7\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e2.1e-10\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eEnterococcus faecium\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eEnterocin_HF\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e-0.835\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e96.9\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e-12.5\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e1.6e-09\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eEnterococcus faecalis\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eEnterocin_EJ97\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e11.448\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e-13.5\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e3.2e-10\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eEnterococcus faecalis\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eEnterocin_A\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e11.154\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e-11.5\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e7.8e-09\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eCarnobacterium maltaromaticum\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eCarnobacteriocin\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e11.102\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e-14.8\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e3.5e-11\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eLactobacillus acidophilus\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eAcidocinJ_1132beta\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e11.031\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e-10.8\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e2.5e-08\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003c/tbody\u003e \u003c/colgroup\u003e \u003ctfoot\u003e \u003ctr\u003e\u003ctd colspan=\"6\"\u003e*According to ProQ interpretation; LGscore\u0026thinsp;\u0026gt;\u0026thinsp;1.5 fairly good model, LGscore\u0026thinsp;\u0026gt;\u0026thinsp;2.5 very good model, LGscore\u0026thinsp;\u0026gt;\u0026thinsp;4 extremly good model.\u003c/td\u003e\u003c/tr\u003e \u003ctr\u003e\u003ctd colspan=\"6\"\u003e**The percentage represents the residues in the most favored [A, B, L] and allowed [a, b, l, p] regions.\u003c/td\u003e\u003c/tr\u003e \u003c/tfoot\u003e \u003c/table\u003e\u003c/div\u003e \u003c/p\u003e \u003c/div\u003e\n\u003ch3\u003eMolecular Docking and Physicochemical Properties Predictions Indicate Sakacin-P as the Most Effective Binder\u003c/h3\u003e\n\u003cp\u003eThe interactions between computer-assisted MPDP and bacteriocins were analyzed to elucidate their binding affinities through molecular docking techniques. The molecular docking, or binding pose, is determined by a number of three-dimensional interactions, such as hydrogen bonding, hydrophobic interactions, and other non-covalent interactions that happen in the catalytic sites of MPDP with the bacteriocins [\u003cspan citationid=\"CR33\" class=\"CitationRef\"\u003e33\u003c/span\u003e]. This approach allows the virtual screening of inhibitory molecules for target proteins, whereas effective docking tools can evaluate and rank them according to a scoring system reflecting their respective interactions [\u003cspan citationid=\"CR30\" class=\"CitationRef\"\u003e30\u003c/span\u003e]. For this purpose, this study employed HADDOCK and PRODIGY to estimate binding energies, while the RING web server was utilized to identify residue interactions.\u003c/p\u003e \u003cp\u003eThe docking results of MPDP with all bacteriocins analyzed in this study, including their binding energies, are presented in Table\u0026nbsp;\u003cspan refid=\"Tab1\" class=\"InternalRef\"\u003e1\u003c/span\u003e. Protein-protein docking simulations revealed Sakacin-P from \u003cem\u003eLatilactobacillus sakei\u003c/em\u003e as the most efficient bacteriocin for binding to MPDP. The docking results indicated a binding energy of -16.7 kcal/mol, suggesting a high-affinity interaction between the two protein structures. The physicochemical properties of Sakacin-P and all studied bacteriocins were evaluated using ExPASy\u0026rsquo;s ProtParam tool (Table\u0026nbsp;\u003cspan refid=\"Tab2\" class=\"InternalRef\"\u003e2\u003c/span\u003e). Sakacin-P has a molecular weight of 6385.13 Da and an isoelectric point (pI) of 7.81, indicating a balanced charge distribution suitable for physiological conditions. Its instability index of 21.43 and aliphatic index of 64.10 suggested that it is a stable and moderately hydrophobic molecule, making it well-suited for interactions in aqueous environments. The Grand Average of Hydropathicity (GRAVY) score of -0.307 further supported its balanced hydrophilic and hydrophobic characteristics, which are critical for effective binding in biological systems. In comparison, Mundticin_KS from \u003cem\u003eEnterococcus mundtii\u003c/em\u003e exhibited a higher instability index (42.57) and binding energy (-17 kcal/mol), yet it possessed a larger molecular weight (13265.16 Da), potentially restricting its bioavailability and cellular uptake. Plantaricin_W_beta from \u003cem\u003eLactiplantibacillus plantarum\u003c/em\u003e demonstrated a strong binding energy of -16.2 kcal/mol, alongside a higher aliphatic index of 47.23 and a less favorable GRAVY score of -0.499, suggesting a suboptimal balance of hydrophilic and hydrophobic characteristics. Moreover, Mundticin_KS and Plantaricin_W_beta exhibited slightly lower Ramachandran plot scores of 98.8% and 98.2%, respectively, compared to Sakacin-P, suggesting possible compromises in structural stability. Therefore, Sakacin-P is selected as the most effective binding bacteriocin structure. Moreover, the surface illustration of the catalytic site of MPDP and an insertion view of Sakacin-P into the catalytic site of MPDP were also shown in Fig.\u0026nbsp;\u003cspan refid=\"Fig5\" class=\"InternalRef\"\u003e4\u003c/span\u003eA.\u003c/p\u003e \u003cp\u003e \u003cdiv class=\"gridtable\"\u003e\u003ctable float=\"Yes\" id=\"Tab2\" border=\"1\"\u003e \u003ccaption language=\"En\"\u003e \u003cdiv class=\"CaptionNumber\"\u003eTable 2\u003c/div\u003e \u003cdiv class=\"CaptionContent\"\u003e \u003cp\u003ePhysicochemical features of bacteriocins evaluated against monkeypox virus DNA polymerase which predicted via Expasy\u0026rsquo;s ProtParam tool.\u003c/p\u003e \u003c/div\u003e \u003c/caption\u003e \u003ccolgroup cols=\"10\"\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c1\" colnum=\"1\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c2\" colnum=\"2\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c3\" colnum=\"3\"\u003e\u003c/div\u003e \u003cdiv align=\"char\" char=\".\" class=\"colspec\" colname=\"c4\" colnum=\"4\"\u003e\u003c/div\u003e \u003cdiv align=\"char\" char=\".\" class=\"colspec\" colname=\"c5\" colnum=\"5\"\u003e\u003c/div\u003e \u003cdiv align=\"char\" char=\".\" class=\"colspec\" colname=\"c6\" colnum=\"6\"\u003e\u003c/div\u003e \u003cdiv align=\"char\" char=\".\" class=\"colspec\" colname=\"c7\" colnum=\"7\"\u003e\u003c/div\u003e \u003cdiv align=\"char\" char=\".\" class=\"colspec\" colname=\"c8\" colnum=\"8\"\u003e\u003c/div\u003e \u003cdiv align=\"char\" char=\".\" class=\"colspec\" colname=\"c9\" colnum=\"9\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c10\" colnum=\"10\"\u003e\u003c/div\u003e \u003cthead\u003e \u003ctr\u003e \u003cth align=\"left\" colname=\"c1\"\u003e \u003cp\u003eNr.\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c2\"\u003e \u003cp\u003eBacteriocin\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c3\"\u003e \u003cp\u003eSequence\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c4\"\u003e \u003cp\u003eAA Length\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c5\"\u003e \u003cp\u003eMolecular Weight\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c6\"\u003e \u003cp\u003epI\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c7\"\u003e \u003cp\u003eInstability Index\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c8\"\u003e \u003cp\u003eAliphatic index\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c9\"\u003e \u003cp\u003eGRAVY\u003c/p\u003e \u003cp\u003eScore*\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c10\"\u003e \u003cp\u003eEstimated half-life**\u003c/p\u003e \u003c/th\u003e \u003c/tr\u003e \u003c/thead\u003e \u003ctbody\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eAcidocinJ_1132beta\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGNPKVAHCASQIGRSTAWGAVSGA\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e24\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e2325.59\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e9.51\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e12.71\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c8\"\u003e \u003cp\u003e61.25\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c9\"\u003e \u003cp\u003e-0.058\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c10\"\u003e \u003cp\u003e30 hours\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eCarnobacteriocin B2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eMNSVKELNVKEMKQLHGGVNYGNGVSCSKTKCSVN\u003c/p\u003e \u003cp\u003eWGQAFQERYTAGINSFVSGVASGAGSIGRRP\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e66\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e6993.88\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e9.70\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e19.32\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c8\"\u003e \u003cp\u003e60.45\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c9\"\u003e \u003cp\u003e-0.417\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c10\"\u003e \u003cp\u003e30 hours\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e3\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eEnterocin_A\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eTVDWAKATTCIAGMSIGGFLGGAFPGK\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e27\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e2657.10\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e7.87\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e24.76\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c8\"\u003e \u003cp\u003e68.89\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c9\"\u003e \u003cp\u003e0.559\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c10\"\u003e \u003cp\u003e7.2 hours\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e4\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eEnterocin_EJ97\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eMLAKIKAMIKKFPNPYTLAAKLTTYEINWYKQQYGRYPWERPVA\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e44\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e5322.32\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e9.92\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e19.46\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c8\"\u003e \u003cp\u003e71.14\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c9\"\u003e \u003cp\u003e-0.589\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c10\"\u003e \u003cp\u003e30 hours\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e5\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eEnterocin_HF\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eKYYGNGVSCNKKGCSVDWGKAIGIIGNNAAANLTTGGKAGWKG\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e43\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e4330.91\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e9.63\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e4.29\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c8\"\u003e \u003cp\u003e61.40\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c9\"\u003e \u003cp\u003e-0.374\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c10\"\u003e \u003cp\u003e1.3 hours\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e6\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eEnterocinCRL_35\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eMSNLKWFSGGDDRRKKAEVIITELLDDLEIDLGNESLRKVLGSYL\u003c/p\u003e \u003cp\u003eEKLKNEGTSVPLVLSRMNIEISNAIKKDGVSLNENQSKKLKELISISNIRYGY\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e98\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e11084.74\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e7.91\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e41.34\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c8\"\u003e \u003cp\u003e108.37\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c9\"\u003e \u003cp\u003e-0.448\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c10\"\u003e \u003cp\u003e30 hours\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e7\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eLacticin_481\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eMKEQNSFNLLQEVTESELDLILGAKGGSGVIHTISHECNMNSWQFVFTCCS\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e51\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e5677.41\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e4.68\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e44.36\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c8\"\u003e \u003cp\u003e80.20\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c9\"\u003e \u003cp\u003e-0.049\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c10\"\u003e \u003cp\u003e30 hours\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e8\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eLacticin_Q\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eMAGFLKVVQLLAKYGSKAVQWAWANK\u003c/p\u003e \u003cp\u003eGKILDWLNAGQAIDWVVSKIKQILGIK\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e53\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e5898.10\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e10.10\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e7.38\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c8\"\u003e \u003cp\u003e121.51\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c9\"\u003e \u003cp\u003e0.300\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c10\"\u003e \u003cp\u003e30 hours\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e9\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eLactococcin_G_Alpha\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGTWDDIGQGIGRVAYWVGKAMGNMSDVNQASRINRKKKH\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e39\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e4345.93\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e10.16\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e4.44\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c8\"\u003e \u003cp\u003e60.00\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c9\"\u003e \u003cp\u003e-0.841\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c10\"\u003e \u003cp\u003e30 hours\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e10\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eLactococcin_Mmfii\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eTSYGNGVHCNKSKCWIDVSELETYKAGTVSNPKDILW\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e37\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e4144.64\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e6.43\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e27.62\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c8\"\u003e \u003cp\u003e68.38\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c9\"\u003e \u003cp\u003e-0.535\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c10\"\u003e \u003cp\u003e7.2 hours\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e11\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eLactococcin_G_beta\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eKKWGWLAWVDPAYEFIKGFGKGAIKEGNKDKWKNI\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e35\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e4109.79\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e9.70\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e10.35\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c8\"\u003e \u003cp\u003e61.43\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c9\"\u003e \u003cp\u003e-0.806\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c10\"\u003e \u003cp\u003e1.3 hours\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e12\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eLeucocinB_TA11A\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eMNNMKSADNYQQLDNNALEQVVGGKYYGNGVH\u003c/p\u003e \u003cp\u003eCTKSGCSVNWGEAFSAGVHRLANGGNGFW\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e61\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e6568.18\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e6.69\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e5.95\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c8\"\u003e \u003cp\u003e51.15\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c9\"\u003e \u003cp\u003e-0.597\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c10\"\u003e \u003cp\u003e30 hours\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e13\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eLeucocinB_TA33a\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eKGKGFWSWASKATSWLTGPQQPGSPLLKKHR\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e31\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e3466.01\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e11.39\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e27.93\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c8\"\u003e \u003cp\u003e44.19\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c9\"\u003e \u003cp\u003e-0.971\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c10\"\u003e \u003cp\u003e1.3 hours\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e14\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eLeucocinC_TA33a\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eKNYGNGVHCTKKGCSVDWGYAWTNIANNSVMNGLTGGNAGWHN\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e43\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e4598.04\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e8.79\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e18.09\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c8\"\u003e \u003cp\u003e45.35\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c9\"\u003e \u003cp\u003e-0.665\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c10\"\u003e \u003cp\u003e1.3 hours\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e15\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eMundticin_KS\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eMGSSHHHHHHSSGLVPRGSHMSNLKWFSGGDDRRKKAEVII\u003c/p\u003e \u003cp\u003eTELLDDLEIDLGNESLRKVLGSYLKKLKNEGTSVPLVLSRMN\u003c/p\u003e \u003cp\u003eIEISNAIKKDGVSLNENQSKKLKELMSISNIRYGY\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e118\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e13265.16\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e9.40\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e42.57\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c8\"\u003e \u003cp\u003e92.46\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c9\"\u003e \u003cp\u003e-0.599\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c10\"\u003e \u003cp\u003e30 hours\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e16\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eNisin\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eMSTKDFNLDLVSVSKKDSGASPRITSISLC\u003c/p\u003e \u003cp\u003eTPGCKTGALMGCNMKTATCHCSIHVSK\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e57\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e5962.98\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e8.99\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e35.11\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c8\"\u003e \u003cp\u003e68.42\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c9\"\u003e \u003cp\u003e-0.005\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c10\"\u003e \u003cp\u003e30 hours\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e17\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003ePediocin_PA1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eMKKIEKLTEKEMANIIGGKYYGNGVTCGKHSCS\u003c/p\u003e \u003cp\u003eVDWGKATTCIINNGAMAWATGGHQGNHKC\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e62\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e6643.64\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e9.02\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e19.72\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c8\"\u003e \u003cp\u003e55.16\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c9\"\u003e \u003cp\u003e-0.482\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c10\"\u003e \u003cp\u003e30 hours\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e18\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003ePlantaricin_W_alpha\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eMKISKIEAQARKDFFKKIDTNSNLLNVNGAKCK\u003c/p\u003e \u003cp\u003eWWNISCDLGNNGHVCTLSHECQVSCN\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e59\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e6656.62\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e8.71\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e30.34\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c8\"\u003e \u003cp\u003e72.71\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c9\"\u003e \u003cp\u003e-0.473\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c10\"\u003e \u003cp\u003e30 hours\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e19\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003ePlantaricin_W_beta\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eMTKTSRRKNAIANYLEPVDEKSINESFGAGDPEAR\u003c/p\u003e \u003cp\u003eSGIPCTIGAAVAASIAVCPTTKCSKRCGKRKK\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e67\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e7085.18\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e9.64\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e47.23\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c8\"\u003e \u003cp\u003e61.34\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c9\"\u003e \u003cp\u003e-0.499\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c10\"\u003e \u003cp\u003e30 hours\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e20\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eSakacin-A\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eMNNVKELSMTELQTITGGARSYGNGVYCNNKKCW\u003c/p\u003e \u003cp\u003eVNRGEATQSIIGGMISGWASGLAGM\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e59\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e6257.13\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e8.77\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e29.28\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c8\"\u003e \u003cp\u003e67.80\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c9\"\u003e \u003cp\u003e-0.214\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c10\"\u003e \u003cp\u003e30 hours\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e21\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eSakacin-P\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eMEKFIELSLKEVTAITGGKYYGNGVHCGKHSCTVD\u003c/p\u003e \u003cp\u003eWGTAIGNIGNNAAANWATGGNAGWNK\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e61\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e6385.13\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e7.81\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e21.43\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c8\"\u003e \u003cp\u003e64.10\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c9\"\u003e \u003cp\u003e-0.307\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c10\"\u003e \u003cp\u003e30 hours\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003c/tbody\u003e \u003c/colgroup\u003e \u003ctfoot\u003e \u003ctr\u003e\u003ctd colspan=\"10\"\u003e*GRAVY: Grand average of hydropathicity, **mammalian reticulocytes, \u003cem\u003ein vitro\u003c/em\u003e\u003c/td\u003e\u003c/tr\u003e \u003c/tfoot\u003e \u003c/table\u003e\u003c/div\u003e \u003c/p\u003e \u003cp\u003eThe RING 4.0 tool was used to carry out a comprehensive residue interaction analysis, which revealed a strong network of non-covalent contacts between Sakacin-P and MPDP. The stability and specificity of the complex were influenced by these interactions, which consisted of hydrogen bonds, π-π stacking, π-cation interactions, and van der Waals forces. The interactions associated with the docking pose of Sakacin-P are summarized in Table\u0026nbsp;\u003cspan refid=\"Tab3\" class=\"InternalRef\"\u003e3\u003c/span\u003e. The hydrogen bonds identified for Sakacin-P include A305-B2, A310-B33, A311-B29, A315-B2, A316-B1, A340-B30, B525-B8, A525-B11, A529-B16, A894-B35, A991-B60, A994-B50, A994-B55, and A1000-B47 (Fig.\u0026nbsp;\u003cspan refid=\"Fig5\" class=\"InternalRef\"\u003e4\u003c/span\u003eB). The hydrogen bonds among the active residues of MPDP and Sakacin-P at A340-B30, B525-B8, A525-B11, and A1000-B47 were readily observable, contributing receptor-ligand binding stability. Hydrogen bonding is known to be the weak electrostatic attraction that occurs between a hydrogen atom, which is covalently bonded to a highly electronegative atom (such as oxygen, nitrogen, or fluorine), and another electronegative atom in a separate molecule or within a different region of the same molecule [\u003cspan citationid=\"CR34\" class=\"CitationRef\"\u003e34\u003c/span\u003e]. The docking pose of Sakacin-P revealed the presence of an ionic bond between A525-B11, a π-cation bond between A973-B59, and π-π stacking interactions between A930-B36 and A932-B36 in conjunction with MPDP and Sakacin-P (Fig.\u0026nbsp;\u003cspan refid=\"Fig5\" class=\"InternalRef\"\u003e4\u003c/span\u003eC). Apart from hydrogen bonds, these were other non-covalent interactions that contribute to receptor-ligand interaction. Ionic bonds arise from the transfer of electrons between atoms, resulting in the creation of cations and anions. Opposite charges attract, leading to a strong electrostatic bond that defines the ionic bond. Ionic bonds can form between the positively charged amino group (-NH3\u003csup\u003e+\u003c/sup\u003e) and the negatively charged carboxyl group (-COO\u003csup\u003e-\u003c/sup\u003e) within amino acids [\u003cspan citationid=\"CR33\" class=\"CitationRef\"\u003e33\u003c/span\u003e]. The π-π stacking is a non-covalent interaction that transpires between the aromatic rings containing aminoacids in molecules. It is associated with the alignment and interaction of the electron-dense π orbitals of one aromatic system with those of another. This interaction enhanced structural stabilization by generating attractive forces among electron clouds [\u003cspan citationid=\"CR35\" class=\"CitationRef\"\u003e35\u003c/span\u003e]. The π-cation interaction can be described as a non-covalent interaction involving a positively charged cation and the electron rich π orbitals of an aromatic groups. The π-cation interactions contributed to the stability of protein structures by providing essential structural support and modifying their conformational states. Interactions involving basic and aromatic amino acids are crucial in membrane proteins, as they contribute to the stabilization of the overall structure [\u003cspan citationid=\"CR36\" class=\"CitationRef\"\u003e36\u003c/span\u003e].\u003c/p\u003e \u003cp\u003e \u003cdiv class=\"gridtable\"\u003e\u003ctable float=\"Yes\" id=\"Tab3\" border=\"1\"\u003e \u003ccaption language=\"En\"\u003e \u003cdiv class=\"CaptionNumber\"\u003eTable 3\u003c/div\u003e \u003cdiv class=\"CaptionContent\"\u003e \u003cp\u003eList of interchain interactions exist between monkeypox virus DNA polymerase (8HOY) and Sakacin-P.\u003c/p\u003e \u003c/div\u003e \u003c/caption\u003e \u003ccolgroup cols=\"6\"\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c1\" colnum=\"1\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c2\" colnum=\"2\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c3\" colnum=\"3\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c4\" colnum=\"4\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c5\" colnum=\"5\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c6\" colnum=\"6\"\u003e\u003c/div\u003e \u003cthead\u003e \u003ctr\u003e \u003cth align=\"left\" colspan=\"2\" nameend=\"c2\" namest=\"c1\"\u003e \u003cp\u003eHidrogen bonds\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colspan=\"2\" nameend=\"c4\" namest=\"c3\"\u003e \u003cp\u003eIonic bonds\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colspan=\"2\" nameend=\"c6\" namest=\"c5\"\u003e \u003cp\u003eVan der Waals forces\u003c/p\u003e \u003c/th\u003e \u003c/tr\u003e \u003ctr\u003e \u003cth align=\"left\" colname=\"c1\"\u003e \u003cp\u003eChain-A (8HOY)\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c2\"\u003e \u003cp\u003eChain-B (Sakacin-P)\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c3\"\u003e \u003cp\u003eChain-A (8HOY)\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c4\"\u003e \u003cp\u003eChain-B (Sakacin-P)\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c5\"\u003e \u003cp\u003eChain-A (8HOY)\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c6\"\u003e \u003cp\u003eChain-B (Sakacin-P)\u003c/p\u003e \u003c/th\u003e \u003c/tr\u003e \u003c/thead\u003e \u003ctbody\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e305-Ser\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e2-Glu\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e\u003cb\u003e525-Lys*\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e11-Glu\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e305-Ser\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e2-Glu\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e310-Val\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e33-Thr\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colspan=\"2\" nameend=\"c4\" namest=\"c3\"\u003e \u003cp\u003e\u003cb\u003eπ -cation\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e305-Ser\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e3-Lys\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e311-Cys\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e29-Lys\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e\u003cb\u003e973-Lys*\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e59-Trp\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e\u003cb\u003e308-Lys*\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e15-Ile\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e315-Asn\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e2-Glu\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colspan=\"2\" nameend=\"c4\" namest=\"c3\"\u003e \u003cp\u003e\u003cb\u003eπ-π stack\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e309-Gly\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e15-Ile\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e316-Thr\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e1-Met\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e930-Phe\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e36-Trp\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e310-Val\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e18-Gly\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cb\u003e340-Lys*\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e30-Hıs\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e932-Tyr\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e36-Trp\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e313-Met\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e4-Phe\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cb\u003e525-Lys*\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e8-Ser\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e314-Ala\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e2-Glu\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cb\u003e525-Lys*\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e11-Glu\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e\u003cb\u003e525-Lys*\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e10-Lys\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e529-Glu\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e16-Thr\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e\u003cb\u003e525-Lys*\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e11-Glu\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e894-Arg\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e35-Asp\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e527-Pro\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e14-Ala\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e991-Ser\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e60-Asn\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e529-Glu\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e16-Thr\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e994-Gln\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e50-Asn\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e\u003cb\u003e803-Lys*\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e19-Lys\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e994-Gln\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e55-Gly\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e\u003cb\u003e832-Arg*\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e25-Val\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cb\u003e1000-Arg*\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e47-Ala\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e834-Asp\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e34-Val\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e894-Arg\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e36-Trp\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e930-Phe\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e36-Trp\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e970-Val\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e43-Ile\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e\u003cb\u003e1000-Arg*\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e51-Trp\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003c/tbody\u003e \u003c/colgroup\u003e \u003ctfoot\u003e \u003ctr\u003e\u003ctd colspan=\"6\"\u003e* The amino acids highlighted in bold represent the active residues of MPDP. Sakacin-P may form bonds with 53.84% of active residues from the MPDP.\u003c/td\u003e\u003c/tr\u003e \u003c/tfoot\u003e \u003c/table\u003e\u003c/div\u003e \u003c/p\u003e \u003cp\u003eOn the other hand, the observed Wan der waals forces in Sakacin-P docking pose were as follows: A305-B2, A305-B3, A308-B15, A309-B15, A310-B18, A313-B4, A314-B2, A525-B10, A525-B11, A527-B14, A529-B16, A803-B19, A832-B25, A834-B34, A894-B36, A930-B36, A970-B43, and A1000-B51. Particularly, van der waals forces between MPDP active residues and Sakacin-P (A308-B15, A525-B10, A525-B11, A803-B19, A832-B25, and A1000-B51) contributed significantly to the inhibitory effect of Sakacin-P (Fig.\u0026nbsp;\u003cspan refid=\"Fig5\" class=\"InternalRef\"\u003e4\u003c/span\u003eD). Additionally, van der Waals forces facilitated a snug fit between the two molecules by optimizing atomic packing, particularly around the hydrophobic core of the bacteriocin. These detailed interactions underlined the synergistic effects of multiple non-covalent forces in achieving high-affinity binding [\u003cspan additionalcitationids=\"CR38\" citationid=\"CR37\" class=\"CitationRef\"\u003e37\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR39\" class=\"CitationRef\"\u003e39\u003c/span\u003e]. When comparing Sakacin-P's docking pose to that of Munditicin_KS, Sakacin-P was found to bind to 53.84% of the active residues of MPDP, whereas Munditicin_KS bound to only 46.15%. Overall, the superior binding affinity and balanced physicochemical characteristics of Sakacin-P highlighted its potential as a lead compound for targeting MPDP. These findings provided a strong foundation for further experimental validation and optimization of Sakacin-P as a potential therapeutic agent against Monkeypox DNA Polymerase. Future studies should focus on \u003cem\u003ein vitro\u003c/em\u003e and \u003cem\u003ein vivo\u003c/em\u003e validation, as well as chemical modifications to enhance Sakacin-P's selectivity and bioavailability.\u003c/p\u003e \u003cdiv id=\"Sec8\" class=\"Section2\"\u003e \u003ch2\u003eMolecular Dynamics Simulations\u003c/h2\u003e \u003cp\u003eSakacin-P complexed with MPDP was further analyzed via molecular dynamics simulations to validate docking results. MD simulations were conducted with GROMACS for 500 ns. Firstly, Fig.\u0026nbsp;\u003cspan refid=\"Fig6\" class=\"InternalRef\"\u003e5\u003c/span\u003e shows the comparisons of root mean square deviations (RMSD) for two states of a protein: Protein complexed (blue) and Protein free (red). Both states started with low RMSD values (~\u0026thinsp;0.4\u0026ndash;0.5 nm), indicating minimal deviation from their respective initial structures. Then, a sharp increase was observed at the beginning, likely representing the system moving out of the energy-minimized starting configuration to explore conformational space. After that, RMSD stabilized relatively quickly (~\u0026thinsp;100 ps) around ~\u0026thinsp;0.5\u0026ndash;0.6 nm for free protein, suggesting it was equilibrated. For the complexed protein, RMSD stabilized later (~\u0026thinsp;200\u0026ndash;300 ps) and at a higher average (~\u0026thinsp;0.6\u0026ndash;0.7 nm). This may reflect greater conformational changes or flexibility due to interactions with the binding partner. In addition, the complexed protein showed higher fluctuations compared to the free protein throughout the simulation. This may indicate the dynamic behavior induced by binding interactions and a larger conformational search space due to the influence of the sakacin-P. Overall, both states of protein exhibited stable RMSD after initial equilibration, implying no significant structural destabilization during the simulated time.\u003c/p\u003e \u003cp\u003eFurthermore, Root Mean Square Fluctuation (RMSF) analysis for both states of the protein-complexed and free- were conducted (Fig.\u0026nbsp;\u003cspan refid=\"Fig7\" class=\"InternalRef\"\u003e6\u003c/span\u003e). RMSF is a measure of the flexibility of each residue over the simulation time, with higher values indicating more flexibility. Both the complexed and free protein exhibited distinct regions of higher and lower RMSF, suggesting that some residues are inherently more flexible than others, regardless of the state. The RMSF values were generally higher for the free protein, indicating that it is more flexible overall compared to the complexed protein. The sakacin-P likely stabilized the protein structure, reducing the fluctuations, especially in regions directly or indirectly interacting with the ligand. The peaks of fluctuation were observed in loop regions or termini, which are typically less structured and more flexible. Higher RMSF peaks in the free state suggested that ligand binding reduced flexibility in some regions, possibly locking them into more rigid conformations. Near the end of the graph (e.g., residue index 1000), both states showed increased fluctuations, potentially representing disordered or terminal regions. Overall, the complexed protein indicated reduced flexibility due to stabilization from interactions with the ligand. This is typical for ligand-binding proteins, where binding induces a conformational change or rigidity in certain regions.\u003c/p\u003e \u003cp\u003eFigure\u0026nbsp;\u003cspan refid=\"Fig8\" class=\"InternalRef\"\u003e7\u003c/span\u003e shows the Solvent Accessible Surface Area (SASA) of a protein in two states: complexed and free. Both states exhibited relatively stable SASA values over time, indicating minimal structural fluctuations. However, the complexed protein had consistently higher SASA values than the free protein, suggesting that binding to sakacin-P may expose more surface area to the solvent. After the equilibration, SASA stabilized around 535\u0026ndash;540 \u0026Aring;\u0026sup2; for the complexed protein and 505\u0026ndash;510 \u0026Aring;\u0026sup2; for the free protein, suggesting the system reached equilibrium. The binding event in the complexed protein may increase conformational flexibility, leading to a more solvent-exposed structure. It is also indicative to the stabilization of the structure, which could prevent compaction, maintaining a higher SASA. Figure\u0026nbsp;\u003cspan refid=\"Fig9\" class=\"InternalRef\"\u003e8\u003c/span\u003e represents the radius of gyration (Rg) over time for two different states of a protein. Both the protein-free and protein-complexed states started with a relatively high Rg value (~\u0026thinsp;3.45\u0026ndash;3.50 nm). A sharp drop in Rg occured within the first\u0026thinsp;~\u0026thinsp;50 ns, which indicates an initial compaction of both structures. The drop was more significant in the protein-complexed state, suggesting the complexation induces a tighter conformation. After ~\u0026thinsp;100 ns, both structures stabilized. The protein-complexed form had a lower Rg, indicating that the bound state maintained a more compact structure. Beyond 300 ns, the Rg values for both states appeared to fluctuate within a stable range. The protein-complexed state remained consistently lower (~\u0026thinsp;3.20\u0026ndash;3.25 nm), while the free protein fluctuated around 3.25\u0026ndash;3.30 nm. This supported the idea that the binding of sakacin-P stabilized the protein structure, reducing overall flexibility.\u003c/p\u003e \u003cp\u003eThe number of hydrogen bonds (H-bonds) and Van der Waals (vdW) interactions formed between MPDP and sakacin-P anthroughout a 500 ns molecular dynamics (MD) simulation were demonstrated in Fig.\u0026nbsp;\u003cspan refid=\"Fig10\" class=\"InternalRef\"\u003e9\u003c/span\u003e. The H-bond count quickly fluctuated and stabilized around 6\u0026ndash;12 bonds. This suggested that the complex quickly established consistent intermolecular interactions after the simulation begins. Then, the H-bond count remained relatively consistent, fluctuating between 6 and 12, with occasional peaks reaching up to 15. This indicated a stable binding interface, implying that the protein-ligand complex was well-formed and hold together by persistent H-bond interactions. Overall, the H-bonding profile reflected a dynamic but generally stable interaction between the protein and ligand for the majority of the simulation. Throughout most of the simulation, vdW interactions fluctuated between 10 and 20 contacts, indicating a persistent and strong non-covalent interaction between the protein and ligand. The frequency and density of these interactions suggested that the ligand remained closely associated with the protein, contributing to the stability of the complex. Despite the short-lived drops, the system consistently re-established strong vdW interactions, indicating robust binding and favorable surface complementarity between the interacting partners. No long-term loss of interactions was observed, supporting the structural and energetic stability of the complex. The dominance of vdW interactions, together with hydrogen bonding data, supported the stable and possibly functionally relevant association of sakacin-P within the binding site of MPDP. Collectively, these findings suggested that the binding of sakacin-P to MPDP was stable in MD simulations over 500 ns, validating the molecular docking analysis for sakacin-P as an MPDP inhibitor.\u003c/p\u003e \u003c/div\u003e"},{"header":"Discussion","content":"\u003cp\u003eIn this study, bacteriocins from various sources were virtually screened against the MPDP using the HADDOCK platform. Among the tested bacteriocins, mundticin KS, sakacin-P, and plantaricin W_beta exhibited the strongest affinities for the MPDP with ΔG values of -17.0, -16.7, and \u0026minus;\u0026thinsp;16.2 kcal/mol, respectively. Physicochemical analysis showed that mundticin KS and plantaricin W_beta had higher instability index scores than the threshold value of 42, while sakacin-P demonstrated good stability with a low instability index score. Based on these findings, sakacin-P was selected for molecular dynamics (MD) simulation to assess its stability and behavior within the DNA replication complex. The MD simulations, conducted over 500 ns, confirmed the stability of sakacin-P when bound to MPDP, highlighting its potential as a candidate for further investigation.\u003c/p\u003e \u003cp\u003ePlantaricin W is a class IIb bacteriocin produced by \u003cem\u003eLactobacillus plantarum\u003c/em\u003e, consisting of two complementary peptides that work synergistically to exert antimicrobial activity against a large number of Gram-positive bacteria, including several foodborne pathogens. Plantaricin W showed a remarkable anti-Listeria activity [\u003cspan additionalcitationids=\"CR41\" citationid=\"CR40\" class=\"CitationRef\"\u003e40\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR42\" class=\"CitationRef\"\u003e42\u003c/span\u003e]. Plantaricin W also demonstrated heat stability and retains activity across a broad pH spectrum, making it valuable for use in food preservation. The antifungal activity of plantaricin has been demonstrated against various fungal species, including \u003cem\u003ePenicillium roqueforti, Mucor plumbeus, Penicillium expansum, Cladosporium\u003c/em\u003e sp., \u003cem\u003eFusarium\u003c/em\u003e sp., and \u003cem\u003eDebaromyces hansenii\u003c/em\u003e [\u003cspan citationid=\"CR43\" class=\"CitationRef\"\u003e43\u003c/span\u003e]. In an \u003cem\u003ein silico\u003c/em\u003e study, plantaricin W exhibited potential as an antiviral agent against COVID-19, showing strong binding affinity to key druggable targets of SARS-CoV-2, including RNA-dependent RNA polymerase, the receptor-binding domain (RBD) of the spike protein, and the human ACE2 receptor [\u003cspan citationid=\"CR44\" class=\"CitationRef\"\u003e44\u003c/span\u003e]. Similarly, plantaricin NC8 αβ was reported to rapidly and efficiently inhibit flaviviruses and SARS-CoV-2 by disrupting their viral envelopes [\u003cspan citationid=\"CR45\" class=\"CitationRef\"\u003e45\u003c/span\u003e].\u003c/p\u003e \u003cp\u003eMundticin KS is a class IIa bacteriocin produced by \u003cem\u003eEnterococcus mundtii\u003c/em\u003e, known for its potent antimicrobial activity against closely related lactic acid bacteria and the food-borne pathogen \u003cem\u003eListeria monocytogenes\u003c/em\u003e. This small cationic peptide exhibited strong heat stability, retaining significant antimicrobial activity at temperatures up to 100\u0026deg;C, and remained stable across a wide pH range, but is sensitive to trypsin and proteinase K while resistant to lipase and RNase A [\u003cspan citationid=\"CR46\" class=\"CitationRef\"\u003e46\u003c/span\u003e]. Mundticin KS, produced by \u003cem\u003eE. mundtii\u003c/em\u003e Tw56, was also reported to exhibit a broad spectrum of activity, effectively targeting \u003cem\u003ePseudomonas aeruginosa\u003c/em\u003e and \u003cem\u003eShewanella putrefaciens\u003c/em\u003e [\u003cspan citationid=\"CR47\" class=\"CitationRef\"\u003e47\u003c/span\u003e]. While a bacteriocin produced by \u003cem\u003eE. mundtii\u003c/em\u003e ST4V demonstrated broad antiviral activity against herpes simplex viruses HSV-1 and HSV-2, polio virus, and measles virus [\u003cspan citationid=\"CR48\" class=\"CitationRef\"\u003e48\u003c/span\u003e], no antiviral activity has been reported for mundticin KS.\u003c/p\u003e \u003cp\u003eSakacin-P is a class IIa bacteriocin produced by \u003cem\u003eLactobacillus sakei\u003c/em\u003e, commonly found in fermented foods [\u003cspan citationid=\"CR49\" class=\"CitationRef\"\u003e49\u003c/span\u003e, \u003cspan citationid=\"CR50\" class=\"CitationRef\"\u003e50\u003c/span\u003e]. It is a small, cationic peptide with antimicrobial properties, characterized by a narrow spectrum of activity. While it exhibits minimal antibacterial efficacy against Gram-negative bacteria, it demonstrates potent activity against \u003cem\u003eListeria monocytogenes\u003c/em\u003e [\u003cspan citationid=\"CR51\" class=\"CitationRef\"\u003e51\u003c/span\u003e]. Additionally, both sakacin-P and \u003cem\u003eL. sakei\u003c/em\u003e demonstrated potential for use in controlling \u003cem\u003eL. monocytogenes\u003c/em\u003e in chicken cold cuts [\u003cspan citationid=\"CR52\" class=\"CitationRef\"\u003e52\u003c/span\u003e]. Furthermore, sakacin-P producing \u003cem\u003eL. sakei\u003c/em\u003e was reported in both \u003cem\u003ein vitro\u003c/em\u003e and \u003cem\u003ein vivo\u003c/em\u003e studies to exhibit significant preventive effects against carbapenem-resistant \u003cem\u003eKlebsiella pneumonia\u003c/em\u003e (CRKP) infection. Treatment with lyophilized probiotics notably reduced body weight loss, mortality, and illness severity in CRKP-infected mice, highlighting the potential of \u003cem\u003eL. sakei\u003c/em\u003e in combating CRKP infections [\u003cspan citationid=\"CR53\" class=\"CitationRef\"\u003e53\u003c/span\u003e]. Similarly, a recent study showed that \u003cem\u003eL. sakei\u003c/em\u003e HEM 224, isolated from traditional Korean kimchi, can alleviate inflammatory conditions in the gastrointestinal and respiratory tracts by the reinforcement of the epithelial barrier and immunomodulation [\u003cspan citationid=\"CR54\" class=\"CitationRef\"\u003e54\u003c/span\u003e]. \u003cem\u003eL. sakei\u003c/em\u003e also demonstrated anti-inflammatory effects in a rheumatoid arthritis (RA) animal model by regulating Th17 and regulatory B cell differentiation and suppressing osteoclastogenesis [\u003cspan citationid=\"CR55\" class=\"CitationRef\"\u003e55\u003c/span\u003e]. In another study, \u003cem\u003eL. sakei\u003c/em\u003e Pro-Bio65 was shown to reduce TNF-α expression while upregulating glutathione levels and enhancing antioxidant enzymatic activities in human conjunctival cells [\u003cspan citationid=\"CR56\" class=\"CitationRef\"\u003e56\u003c/span\u003e]. The extract of the same \u003cem\u003eL. sakei\u003c/em\u003e Pro-Bio65 strain demonstrated significant \u003cem\u003ein vitro\u003c/em\u003e therapeutic efficacy by inhibiting viral replication and reducing pathogenicity of the SARS-CoV-2 [\u003cspan citationid=\"CR57\" class=\"CitationRef\"\u003e57\u003c/span\u003e]. Notably, sakacin-P was reported to exhibit strong binding affinity to the human ACE2 receptor in an in silico study, suggesting its potential antiviral activity against SARS-CoV-2 [\u003cspan citationid=\"CR58\" class=\"CitationRef\"\u003e58\u003c/span\u003e]. These studies clearly demonstrated that \u003cem\u003eL. sakei\u003c/em\u003e and its bacteriocin, sakacin-P, holds significant therapeutic potential for the treatment of various diseases. While there are studies exploring the antiviral activity of sakacin-P against SARS-CoV-2, to our knowledge, no research has been reported on its potential antiviral activities against other viruses, including the MPXV. Therefore, our findings on sakacin-P pave the way for the development of antiviral agent against MPXV. However, this study requires further validation through \u003cem\u003ein vitro\u003c/em\u003e and \u003cem\u003ein vivo\u003c/em\u003e studies.\u003c/p\u003e"},{"header":"Conclusion","content":"\u003cp\u003eThis study demonstrates the potential of bacteriocins as inhibitors of the MPDP using computational approaches. Structural modeling, molecular docking, and MD simulations collectively indicated that Sakacin-P exhibited superior binding affinity and stability in complex with MPDP compared to Mundticin-KS. Key interactions, including hydrogen bonding, ionic interactions, and π-π stacking, were identified as crucial contributors to ligand binding stability. MD simulations confirmed the conformational stability of the protein-ligand complex, highlighting reduced solvent accessibility and enhanced structural compactness upon binding. These findings provide an essential step toward the rational design of bacteriocin-based antiviral agents against MPXV. Future studies should focus on experimental validation of these interactions to explore the therapeutic potential of bacteriocins in combating MPXV infections.\u003c/p\u003e"},{"header":"Declarations","content":"\u003ch2\u003eConflict of Interest\u003c/strong\u003e \u003cp\u003eThe authors declare no competing interests.\u003c/p\u003e \u003ch2\u003eAuthor Contribution\u003c/h2\u003e\u003cp\u003eAll authors contributed to the study\u0026rsquo;s conception and design. Material preparation, data collection, and analyses wereconducted by Melisa Z. Karaman, Fernando Berton Zanchi, \u0026Ouml;zkan Fidan, and Ahmet E. Yetiman.The first draft of the manuscript was written by Melisa Z. Karaman, \u0026Ouml;zkan Fidan, and Ahmet E. Yetiman and was proofread by Aykut \u0026Ouml;zdarendeli and Fernando Berton Zanchi. All authors read and approved the final manuscript.\u003c/p\u003e\u003ch2\u003eAcknowledgement\u003c/h2\u003e\u003cp\u003eThe authors gratefully acknowledge the Scientific and Technological Research Council of T\u0026uuml;rkiye (T\u0026Uuml;BİTAK) for awarding a 2210/A National MSc/MA Scholarship to M.Z.K.\u003c/p\u003e\u003ch2\u003eData Availability\u003c/h2\u003e \u003cp\u003eThe data used to support the findings of this study will be made available on reasonable request.\u003c/p\u003e"},{"header":"References","content":"\u003col\u003e\u003cli\u003e\u003cspan\u003eLuo YH, Zhang T, Cao JL et al (2024) Monkeypox: An outbreak of a rare viral disease. 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Probiotics Antimicrob Proteins 1\u0026ndash;13\u003c/span\u003e\u003c/li\u003e\u003c/ol\u003e"}],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":true,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"hideJournal":true,"highlight":"","institution":"","isAcceptedByJournal":false,"isAuthorSuppliedPdf":false,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":false,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true},"keywords":"Monkeypox virus, Bacteriocins, Sakacin-P, Molecular docking, Molecular dynamics simulation","lastPublishedDoi":"10.21203/rs.3.rs-6529067/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-6529067/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003eMonkeypox virus (MPXV) has emerged as a significant global health concern, necessitating the development of novel antiviral strategies. In this study, we employed an \u003cem\u003ein silico\u003c/em\u003e approaches to investigate the potential of bacteriocins as inhibitors of the MPXV DNA polymerase (MPDP). Initially, protein structure modeling was performed using SWISS-MODEL, and the quality of the generated models was evaluated based on LGscore. The physicochemical properties of selected bacteriocins, including Sakacin-P and Mundticin-KS, were assessed to determine their stability and suitability for molecular docking. Protein-peptide docking simulations using the HADDOCK platform revealed that Sakacin-P exhibited a higher binding affinity for the MPXV DNA polymerase. The docking analysis indicated the presence of strong hydrogen bonds, ionic interactions, and π-π stacking interactions, which contributed to the stability of the protein-ligand complex. Molecular dynamics (MD) simulations further validated the stability of the docked complex by analyzing root mean square deviation (RMSD), root mean square fluctuation (RMSF), radius of gyration (Rg), H-bond and Van der Waals interactions, and solvent-accessible surface area (SASA). Our findings suggest that bacteriocins, particularly Sakacin-P, have promising antiviral properties against MPXV by targeting its DNA replication complex. This study provides a foundation for further experimental validation and the potential development of bacteriocin-based therapeutics against MPXV.\u003c/p\u003e","manuscriptTitle":"Virtual screening of bacteriocins from lactic acid bacteria against Monkeypox DNA Polymerase: Sakacin-P is a potent DNA polymerase inhibitor","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2025-05-07 09:57:47","doi":"10.21203/rs.3.rs-6529067/v1","editorialEvents":[{"type":"communityComments","content":0}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true}}],"origin":"","ownerIdentity":"423437a1-01a1-475e-99c8-62bd97edb25e","owner":[],"postedDate":"May 7th, 2025","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"posted","subjectAreas":[],"tags":[],"updatedAt":"2025-06-27T11:08:33+00:00","versionOfRecord":[],"versionCreatedAt":"2025-05-07 09:57:47","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-6529067","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-6529067","identity":"rs-6529067","version":["v1"]},"buildId":"8U1c8b4HqxoKbykW_rLl7","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}