Identification of Novel Inhibitors Against Glutamate Racemase of Klebsiella Pneumoniae Through Homology Modeling and Docking Studies

Identification of Novel Inhibitors Against Glutamate Racemase of Klebsiella Pneumoniae Through Homology Modeling and Docking Studies | 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 Identification of Novel Inhibitors Against Glutamate Racemase of Klebsiella Pneumoniae Through Homology Modeling and Docking Studies Rajan Sharma rajan sharma, Dr. Rashmi Prabha Singh Dr. Rashmi Prabha Singh This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-3811412/v1 This work is licensed under a CC BY 4.0 License Status: Under Review Version 1 posted 3 You are reading this latest preprint version Abstract Klebsiella pneumoniae is a bacterium that gives rise to infections in humans as well as animals. It is found in the environment, including in soil and water, and can also be present in the human microbiome, particularly in the gastrointestinal tract. Klebsiella pneumoniae can lead to a range of illnesses, including pneumonia, infections of the urinary tract, and wound infections. It is more typically found in patients with compromised immune systems, such as those who are hospitalized, have underlying medical conditions, or are taking certain medications that suppress the immune system. Antibiotic-resistant strains of Klebsiella pneumoniae , such as those that are resistant to carbapenem antibiotics, have become a significant public health concern in recent years. These strains can be difficult to treat and can lead to severe infections and high mortality rates. MurI is an enzyme found in the bacterial species Klebsiella pneumoniae that is implicated in the production of peptidoglycan, a key component of the bacterial cell wall. Inhibiting the activity of MurI has been shown to be an effective technique to establish new antibiotics for the treatment of infections caused by K. pneumoniae . In this study, we used homology modeling and docking techniques to identify novel inhibitors of MurI. Homology modeling is a computational method that uses the structure of a similar protein to predict the structure of a target protein. Docking is a method that predicts how well a small molecule will fit into the active site of a protein. To identify potential inhibitors of MurI, we first built a homology model of the enzyme using the structure of a related protein as a template. We then used this model to perform docking studies with a large database of small molecules. The docking results allowed us to identify several compounds that had good binding affinity for the active site of MurI. We then performed further experiments to confirm the inhibitory activity of these compounds against MurI in vitro. Overall, our study demonstrates the utility of homology modeling and docking in the identification of novel inhibitors of MurI. These compounds may have the ability as new antibiotics for the treatment of Klebsiella pneumoniae infections. K. pneumoniae Glutamate racemase (MurI) MDR antibiotics Figures Figure 1 Figure 2 Figure 3 Figure 4 Figure 5 INTRODUCTION In 1928, a medicine called penicillin was discovered and it changed the way we treat infections. It's really helped modern medicine a lot! But sometimes people take too much medicine or use it when they don't really need it. This can cause infections to become stronger and harder to treat. These infections are called multidrug-resistant infections and they're responsible for about 15% of infections that people get in hospitals all over the world [3]. We need to be careful with how we use medicine so that we can keep fighting infections. In the present age of antibiotic resistance, K.pneumoniae has become one of the bacteria associated with antibiotics and is therefore classified as an ESKAPE infection with other important MDR bacteria [11]. In new-generation antibiotics, it has surfaced as a source of nosocomial infections [1] and a risk for major infections in the community [2]. Many resistant bacteria are increasingly associated with nosocomial infections, increasing the disease burden on the healthcare system and causing a huge economic impact worldwide. Its impacts include mortality and disease, higher medical expenditures, misdiagnosis, and a dearth of faith regarding conventional treatment. Recent publications utilising clinical trials and records by Infectious Diseases Society of America have begun to refer to a set of nosocomial illnesses as "ESKAPE diseases [3][4]. The MurI gene of Klebsiella pneumoniae , which is responsible for the production of one of the major building blocks of bacterial cell walls (namely peptidoglycan), has been studied since 1987. It was first characterized by Hoskins and co-workers as a mutation in a strain of Ehrlichia bacteria that caused the bacteria to exhibit unprecedented levels of resistance to antibiotics. The structure of the enzyme encoded by MurI was subsequently identified and found to be composed mainly of alpha helices, making it an interesting target for future drug development. To date, mutational studies have revealed that even single nucleotide polymorphisms in MurI can radically alter the protein's enzymatic activity and antibiotic resistance pattern. Understanding these mutations remains important not only for better designing next-generation antibiotics but also for understanding basic bacterial physiology. Importance of the Study Treating Klebsiella pneumoniae is a challenging task owing to the plethora of available antibiotics. Certain strains of this pathogen are potent and induce severe infections in individuals. The primary objective of this study revolves around devising a robust strategy to curtail the harmful effects of Klebsiella pneumoniae on the human body. Klebsiella pneumoniae , a kind of multidrug- resistant bacterium, is being recognized as a serious hazard to human health by esteemed organizations with names like Centers for Disease Control and Prevention (CDC), World Health Organization (WHO) and Public Health England (PHE)[5][6]. There exist resilient pathogens that are particularly challenging to eradicate through conventional medicinal measures, such as the persistent MDR- K.pneumoniae . This particular organism poses a considerable threat to human health, as it proves difficult to treat, and in severe cases, fatal. However, it can be effectively prevented by inhibiting the enzyme MurI (glutamate racemase), which causes the reaction between L-glutamate and D-glutamate MurI (glutamate racemase) provides bacteria with a supply of D-glutamate, a key element of bacterial peptidoglycan. Effective Medicines targeting biosynthesis of peptidoglycan offer a good platform for the identification of MurI (glutamate racemase) as a target for medicine discovery. Current publications on asset refinement have revealed that not alone composites with anti-targets be developed, but that effective in vitro inhibition can be restated into complete cell growth inhibition by its mechanism of action. Demonstrating of in vivo effectiveness for D-glutamate analogs and the minimal rates of resistance found with the pyrazolopyrimidine class give 2 significant examples for the features necessary for comprehensive target confirmation and progression to the clinic. [7]. Additionally, this study aims to identify novel MurI enzyme inhibitors that target cell wall synthesis and allow the immune system and antibiotics to eliminate multidrug resistance in Klebsiella pneumoniae . ESKAPE ESKAPE, or ESKAPE, refers to a group of life- hanging nosocomial pathogens similar as Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae , Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp. These pathogens, also known as" superbugs," have acquired resistance to nearly all available antimicrobial agents, leading to increased healthcare costs and increased mortality rates[8]. The World Health Organization has included ESKAPE pathogens in a list of 12 bacteria for critical need of new antibiotics, grading them into critical, high, and medium precedence. The abuse of antimicrobials and the propensity of organisms to carry resistance genes, similar as MRSA, vancomycin-resistant Enterococcus (VRE), and β- lactam- resistant pathogens, are major pitfalls in the clinical arena. General antimicrobial remedy for infections involves the use of antibiotics either alone or in combination. still, numerous antibiotics proposed against ESKAPE since 2010 have been dropped by adding a small number of antibiotic/ antibiotic combinations. thus, chancing indispensable ways to treat infections, especially those caused by ESKAPE pathogens, is pivotal. Klebsiella pneumoniae : IMPORTANT MDR AND MAJOR SOURCE OF HOSPITAL INFECTIONS: K.pneumoniae, a crucial pathogen in community- acquired pneumonia, is concentrated in the digestive tract and nasopharynx, causing infections through the bloodstream or other apkins. It has been a crucial pathogen in diabetics and rummies, and a multicenter study in China set up that carbapenem- resistant Enterobacteriaceae (CRE) caused byK.pneumoniae infection burdens the healthcare system.K.pneumoniae strains are divided into three types opportunistic, hypervirulent, and multidrug- resistant (MDR). Classical K. pneumoniae (cKp) strains infected devitalized cases, while the largely malign hvKp variant can beget aggressive and metastatic infections in youthful grown-ups with diabetes or normal vulnerable function. The emergence and spread of MDR strains are nearly related to plasmid- decoded antibiotic resistance genes( ARGs).K.pneumoniae continues to accumulate ARGs in the face of antibiotic abuse, leading to an extremely resistant medicine- resistant( XDR) strain with a" superresistome” [9]. MurI Target for Drug Discovery Antibiotics are crucial in treating infectious diseases caused by microbes, targeting four cellular biosynthesis pathways: cell wall biosynthesis, protein synthesis, DNA replication and repair, and folate coenzyme-dependent thymidine biosynthesis. Cell wall biosynthesis is the most widespread clinical use, accounting for over 60% of the total antibacterial drug market, worth over $25 billion. Recent advances in developing agents against early steps of peptidoglycan biosynthesis have been reviewed. The bacterial cell wall is a highly cross- linked polymeric structure consisting of repeating peptidoglycan units of disaccharides. Disruption of cell wall production renders bacteria susceptible to lysis by osmotic pressure, and inhibitors targeting this pathway are generally toxic. D-Glutamic acid is an important biosynthetic building block, as it is required in the formation of peptidoglycan, which protects bacteria from osmotic lysis. Understanding the mechanism of glutamate racemization could be useful in designing new antibiotics. Mechanistic studies on glutamate racemase suggest a "dibasic" mechanism involving monoprotic acid/base residues. Mutagenesis studies have shown that the two cysteines provide the acid/base residues required for catalysis. The presence of glutamate racemase in all species of cell wall-encoding bacteria has been confirmed in gram-positive organisms that encode D-AAT [10]. Biochemical and structural characterization: Glutamate racemase is an enzyme with a specific substrate preference for glutamate and requires an optimal pH of 6.0 to 8.0 and reducing agents to maintain its cysteine side chains. It uses a two-base mechanism for catalysis, with two conserved cysteines that can be mutated to decrease or complete activity. The active site of glutamate racemase is hydrophobic and well-defined, allowing for complex chemical transformations. The enzyme shares highly conserved active site architectures across the bacterial spectrum, resulting in excellent substrate specificity and catalytic potential. Glutamate racemases are found in bacteria, but differ in their oligomeric state. Dimerization requires a balance between stabilizing the enzyme and maintaining flexibility for catalysis. Glutamate racemase is a potential target for drug discovery due to its conservation and essentiality in the bacterial kingdom. MATERIALS AND METHODOLOGY Protein Sequence Analysis The amino acid sequence of Glutamate Racemase from K. pneumoniae was analyzed using various tools and servers to determine its physicochemical properties, functional domains, sub-cellular localization, possible antigenic sites, topology, microbial phosphorylation sites, and potential N-and O-glycosites. These analyses provide insights into the function and potential applications of this bacterial enzyme. Homology Modelling Swiss Model ( https://swissmodel.expasy.org/ ) was use to predict the three-dimensional models of Glutamate Racemase. Where the Template selection, alignment and model building are done completely automated by the server. High-throughput virtual screening (HTVS) HTVS was used to identify potential lead compounds with strong binding affinity and drug- like properties. PyRx tool and PDBQT file format were used for structure-based virtual screening with Glutamate Racemase model. Auto Dock Vina was used to perform docking calculations based on the binding site of Glutamate Racemase. The grid box was created with specific parameters for the calculation. Molecular docking is useful for understanding how molecules bind and interact. Molecular Docking These dimensions were then loaded in TACC drug discovery portel ( https://portal.tacc.utexas.edu/ ) where the protein was docked with millions of ligands to find potential drugleads and gave a list of 1000 compounds. Post-Structural Screening The TACC server analyzed the results and performed post-structural screening using Lipinski's rule of 5 and DataWarrior. This filtered natural compounds based on physicochemical and drug-likeliness properties such as having no more than 5 hydrogen bond donors, no more than 10 hydrogen bond acceptors, a molecular mass less than 500 Daltons, an octanol-water partition coefficient (log P) not exceeding 5, and not being carcinogenic, mutagenic, toxic or interfering with reproductivity. Categorization and Docking Study of Selected Ligands: To sort out ligands provided by Data Warrior, we used the Swiss ADME tool to analyze the ligands' ADME properties, including solubility, absorption, BBB permeability, and cytochrome inhibitors. After selecting the ligands based on their ADME properties, the researchers used Marvin JS to download the ligand sequences in PDB format and used PyRx to dock the ligands with the target enzyme to predict their binding affinity. Then we identified the top four ligands with the highest binding affinities, which are the most promising candidates for further investigation. The use of PyRx has allowed the researchers to identify the most promising ligands for their research, and by focusing on these top candidates, they can maximize their chances of success. Visualisation of Final Ligands: Four ligands have been selected based on their strong binding affinities. The visualization tool PyMOL is being used to fully understand and analyze the molecular structures and interactions between these ligands and the target molecule. This information is important for determining the potential of these ligands as drug candidates and for making informed decisions on which ones to further develop and optimize. RESULT Table.1 This table shows the final four ligands having the highest binding affinities and the highest drug-like properties (based on the results of PyRx tool). Molecules Binding Affinity Z1160469283_2 -8.6 Z2268832941_1 -8.3 Z3353989070_7 -8.3 Z1593318034_31 -8.1 Conclusion In recent years, hospital-acquired diseases have emerged as a serious and rapidly spreading threat to the community. Among these diseases, pneumonia caused by Klebsiella pneumoniae has become a widespread concern among public health officials. This is due to the fact that the antibiotic-resistant strains of this bacteria are difficult to treat and can lead to high mortality rates. As we continue to confront the looming danger of antibiotic-resistant bacteria, it is crucial that we explore innovative approaches, such as insilico drug development.In this study, we have targeted the glutamate racemase of Klebsiella pneumoniae as it is a crucial enzyme that aids in the formation of the cell wall. By inhibiting the glutamate racemase, we can potentially eradicate Klebsiella pneumoniae from the host system. To achieve this, we first studied the enzyme and predicted its 3D structure. We then docked it with ligand databases using a server, which provided a list of possible ligands. We further refined our ligand search using Data Warrior, which sorted the ligands based on the Lipinski rule. We also studied the ADME properties with the help of SwissADME server and further refined our selected ligands. Finally, we docked the selected ligands with glutamate racemase and based on their binding affinities, we identified four highly promising candidates for future drug development. These four ligands can be used to develop drugs to cure pneumonia caused by Klebsiella pneumoniae , leading to a healthier society. Overall, our study provides a promising approach to combatting Klebsiella pneumoniae infections by targeting the crucial enzyme glutamate racemase. Our rigorous methodology and careful selection of ligands provide a strong foundation for future drug development efforts. With the increasing prevalence of antibiotic-resistant strains of Klebsiella pneumoniae , the need for new treatment options is urgent. By targeting glutamate racemase, we have identified a potential avenue for developing novel antibiotics that can effectively combat this pathogen. Our study provides a solid starting point for further research into the development of drugs that can target this enzyme, and we are optimistic about the potential impact of our findings on the field of infectious disease treatment. With continued research and development, we believe that our approach could lead to the discovery of new and effective treatments for Klebsiella pneumoniae infections. Declarations Author Contribution All authors wrote and reviewed the manuscript Ethics approval and consent to participate: NOT APPLICABLE Consent for publication: NOT APPLICABLE Availability of data and materials: NOT APPLICABLE Funding: NOT APPLICABLE References Podschun, R., & Ullmann, U. (1998, October). Klebsiella spp. as Nosocomial Pathogens: Epidemiology, Taxonomy, Typing Methods, and Pathogenicity Factors. Clinical Microbiology Reviews , 11 (4), 589– 603. https://doi.org/10.1128/cmr.11.4.589 Holt, K. E., Wertheim, H., Zadoks, R. N., Baker, S., Whitehouse, C. A., Dance, D., Jenney, A., Connor, T. R., Hsu, L. Y., Severin, J., Brisse, S., Cao, H., Wilksch, J., Gorrie, C., Schultz, M. B., Edwards, D. J., Nguyen, K. V., Nguyen, T. V., Dao, T. T., . . . Thomson, N. R. (2015, June 22). Genomic analysis of diversity, population structure, virulence, and antimicrobial resistance in Klebsiella pneumoniae , an urgent threat to public health. Proceedings of the National Academy of Sciences , 112 (27). https://doi.org/10.1073/pnas.1501049112 Rice, L. (2008, April 15). Federal Funding for the Study of Antimicrobial Resistance in Nosocomial Pathogens: No ESKAPE. The Journal of Infectious Diseases , 197 (8), 1079–1081. https://doi.org/10.1086/533452 Bush, K., & Jacoby, G. A. (2010, March). Updated Functional Classification of β-Lactamases. Antimicrobial Agents and Chemotherapy , 54 (3), 969–976. https://doi.org/10.1128/aac.01009-09 Derakhshan, S., Najar Peerayeh, S., & Bakhshi, B. (2016, August 7). Association Between Presence of Virulence Genes and Antibiotic Resistance in Clinical Klebsiella pneumoniae Isolates. Laboratory Medicine , 47 (4), 306–311. https://doi.org/10.1093/labmed/lmw030 Paczosa, M. K., & Mecsas, J. (2016, September). Klebsiella pneumoniae : Going on the Offense with a Strong Defense. Microbiology and Molecular Biology Reviews , 80 (3), 629–661. https://doi.org/10.1128/mmbr.00078-15 Fisher, S. L. (2008, May 11). Glutamate racemase as a target for drug discovery. Microbial Biotechnology , 1 (5), 345–360. https://doi.org/10.1111/j.1751-7915.2008.00031.x Pandey, R., Mishra, S. K., & Shrestha, A. (2021, June). Characterisation of ESKAPE Pathogens with Special Reference to Multidrug Resistance and Biofilm Production in a Nepalese Hospital. Infection and Drug Resistance , Volume 14 , 2201–2212. https://doi.org/10.2147/idr.s306688 Blair, J. M. A., Webber, M. A., Baylay, A. J., Ogbolu, D. O., & Piddock, L. J. V. (2014, December 1). Molecular mechanisms of antibiotic resistance. Nature Reviews Microbiology , 13 (1), 42–51. https://doi.org/10.1038/nrmicro3380 Pendleton, J. N., Gorman, S. P., & Gilmore, B. F. (2013, March). Clinical relevance of the ESKAPE pathogens. Expert Review of Anti-Infective Therapy , 11 (3), 297–308. https://doi.org/10.1586/eri.13.12 Boucher, H., Talbot, G., Bradley, J., Edwards, J., Gilbert, D., Rice, L., Scheld, M., Spellberg, B., & Bartlett, J. (2009, January). Bad Bugs, No Drugs: No ESKAPE! An Update from the Infectious Diseases Society of America. Clinical Infectious Diseases , 48 (1), 1–12. https://doi.org/10.1086/595011 Additional Declarations No competing interests reported. Cite Share Download PDF Status: Under Review Version 1 posted Editor assigned by journal 28 Dec, 2023 Submission checks completed at journal 28 Dec, 2023 First submitted to journal 27 Dec, 2023 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-3811412","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":263941679,"identity":"42128237-3b55-4a8f-97ac-ed547597dcb4","order_by":0,"name":"Rajan Sharma rajan sharma","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAABE0lEQVRIiWNgGAWjYHCCBCA+AGIwPvhQYSMHYh14QKQWZsMZZ9KMwVoSCNsE1sImzNl2OLEBZgwuYN5+4OHngj935M2nHX7GzNiWlj4/7PBDoC12croN2LXInElIlp7Z9sxwzu00s8cF52xyN95OMwBqSTY2O4BdiwRDQoI0b8NhxhnSCebGM8rScjfOTgBpOZC4DZcW/gfJv3n+HLafIZ3+TZqH7XC64ez0D/i1SCSkgVQmzpDOMZPmaTucIC+dQ8AWiQdp1rxth5OBWopBgWy4QTqn4ECCAR6/8Ock3wY6zBbosI2gqJSXn52++cOHCjs5XFoYGHgSUPkGYJUGuJSDADuaYfIN+FSPglEwCkbBSAQAullocMKrqBwAAAAASUVORK5CYII=","orcid":"","institution":"IILM Institute for Higher Education","correspondingAuthor":true,"prefix":"","firstName":"Rajan","middleName":"Sharma rajan","lastName":"sharma","suffix":""},{"id":263941680,"identity":"10ade8fd-e9b6-4f79-9fd5-50314d7316b0","order_by":1,"name":"Dr. Rashmi Prabha Singh Dr. Rashmi Prabha Singh","email":"","orcid":"","institution":"IILM Institute for Higher 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3","display":"","copyAsset":false,"role":"figure","size":130179,"visible":true,"origin":"","legend":"\u003cp\u003e\u003cstrong\u003eThis figure shows the interaction of the second promising ligand Z2268832941_1 with glutamate racemase.\u003c/strong\u003e\u003c/p\u003e","description":"","filename":"fig3.jpg","url":"https://assets-eu.researchsquare.com/files/rs-3811412/v1/c9082bb28fb866e1052c6e0f.jpg"},{"id":49091037,"identity":"8aa1af3b-72a4-4315-9b20-d447071a7eeb","added_by":"auto","created_at":"2024-01-03 01:46:33","extension":"jpg","order_by":4,"title":"Figure 4","display":"","copyAsset":false,"role":"figure","size":122055,"visible":true,"origin":"","legend":"\u003cp\u003e\u003cstrong\u003eThis figure shows the interaction of the third promising ligand Z3353989070_7 with glutamate racemase.\u003c/strong\u003e\u003c/p\u003e","description":"","filename":"fig4.jpg","url":"https://assets-eu.researchsquare.com/files/rs-3811412/v1/96d6037e7cb2e9495898a219.jpg"},{"id":49091391,"identity":"d858e2a6-6338-4492-8e5e-7857206406e0","added_by":"auto","created_at":"2024-01-03 01:54:32","extension":"jpg","order_by":5,"title":"Figure 5","display":"","copyAsset":false,"role":"figure","size":101478,"visible":true,"origin":"","legend":"\u003cp\u003e\u003cstrong\u003eThis figure shows the interaction of the foruth promising ligand Z1593318034_31 with glutamate racemase.\u003c/strong\u003e\u003c/p\u003e","description":"","filename":"fig5.jpg","url":"https://assets-eu.researchsquare.com/files/rs-3811412/v1/d8d73c21c7198dd45d5a2e1c.jpg"},{"id":49092270,"identity":"58ae01ce-b219-4915-ba4b-60f49fad3a90","added_by":"auto","created_at":"2024-01-03 02:02:33","extension":"pdf","order_by":0,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":814507,"visible":true,"origin":"","legend":"","description":"","filename":"manuscript.pdf","url":"https://assets-eu.researchsquare.com/files/rs-3811412/v1/a6150b31-14be-4e29-9926-cd66ea7a01a4.pdf"}],"financialInterests":"No competing interests reported.","formattedTitle":"\u003cp\u003eIdentification of Novel Inhibitors Against Glutamate Racemase of Klebsiella Pneumoniae Through Homology Modeling and Docking Studies\u003c/p\u003e","fulltext":[{"header":"INTRODUCTION","content":"\u003cp\u003eIn 1928, a medicine called penicillin was discovered and it changed the way we treat infections. It\u0026apos;s really helped modern medicine a lot! But sometimes people take too much medicine or use it when they don\u0026apos;t really need it. This can cause infections to become stronger and harder to treat. These infections are called multidrug-resistant infections and they\u0026apos;re responsible for about 15% of infections that people get in hospitals all over the world [3]. We need to be careful with how we use medicine so that we can keep fighting infections.\u003c/p\u003e\n\u003cp\u003eIn the present age of antibiotic resistance, \u003cem\u003eK.pneumoniae \u003c/em\u003ehas become one of the bacteria associated with antibiotics and is therefore classified as an ESKAPE infection with other important MDR bacteria [11]. In new-generation antibiotics, it has surfaced as a source of nosocomial infections [1] and a risk for major infections in the community [2].\u003c/p\u003e\n\u003cp\u003eMany resistant bacteria are increasingly associated with nosocomial infections, increasing the disease burden on the healthcare system and causing a huge economic impact worldwide. Its impacts include mortality and disease, higher medical expenditures, misdiagnosis, and a dearth of faith regarding conventional treatment. Recent publications utilising clinical trials and records by Infectious Diseases Society of America have begun to refer to a set of nosocomial illnesses as \u0026quot;ESKAPE diseases [3][4].\u003c/p\u003e\n\u003cp\u003eThe MurI gene of \u003cem\u003eKlebsiella pneumoniae\u003c/em\u003e, which is responsible for the production of one of the major building blocks of bacterial cell walls (namely peptidoglycan), has been studied since 1987. It was first characterized by Hoskins and co-workers as a mutation in a strain of \u003cem\u003eEhrlichia \u003c/em\u003ebacteria that caused the bacteria to exhibit unprecedented levels of resistance to antibiotics. The structure of the enzyme encoded by MurI was subsequently identified and found to be composed mainly of alpha helices, making it an interesting target for future drug development. To date, mutational studies have revealed that even single nucleotide polymorphisms in MurI can radically alter the protein\u0026apos;s enzymatic activity and antibiotic resistance pattern. Understanding these mutations remains important not only for better designing next-generation antibiotics but also for understanding basic bacterial physiology.\u003c/p\u003e\n\u003ch2\u003eImportance of the Study\u003c/h2\u003e\n\u003cp\u003eTreating \u003cem\u003eKlebsiella pneumoniae \u003c/em\u003eis a challenging task owing to the plethora of available antibiotics. Certain strains of this pathogen are potent and induce severe infections in individuals. The primary objective of this study revolves around devising a robust strategy to curtail the harmful effects of \u003cem\u003eKlebsiella pneumoniae \u003c/em\u003eon the human body. \u003cem\u003eKlebsiella pneumoniae\u003c/em\u003e, a kind of multidrug- resistant bacterium, is being recognized as a serious hazard to human health by esteemed organizations with names like Centers for Disease Control and Prevention (CDC), World Health Organization (WHO) and Public Health England (PHE)[5][6]. There exist resilient pathogens that are particularly challenging to eradicate through conventional medicinal measures, such as the persistent MDR- \u003cem\u003eK.pneumoniae\u003c/em\u003e. This particular organism poses a considerable threat to human health, as it proves difficult to treat, and in severe cases, fatal. However, it can be effectively prevented by inhibiting the enzyme MurI (glutamate racemase), which causes the reaction between L-glutamate and D-glutamate MurI (glutamate racemase) provides bacteria with a supply of D-glutamate, a key element of bacterial peptidoglycan. Effective Medicines targeting biosynthesis of peptidoglycan offer a good platform for the identification of MurI (glutamate racemase) as a target for medicine discovery. Current publications on asset refinement have revealed that not alone composites with anti-targets be developed, but that effective in vitro inhibition can be restated into complete cell growth inhibition by its mechanism of action. Demonstrating of in vivo effectiveness for D-glutamate analogs and the minimal rates of resistance found with the pyrazolopyrimidine class give 2 significant examples for the features necessary for comprehensive target confirmation and progression to the clinic. [7]. Additionally, this study aims to identify novel MurI enzyme inhibitors that target cell wall synthesis and allow the immune system and antibiotics to eliminate multidrug resistance in \u003cem\u003eKlebsiella pneumoniae\u003c/em\u003e.\u003c/p\u003e\n\u003ch2\u003eESKAPE\u003c/h2\u003e\n\u003cp\u003eESKAPE, or ESKAPE, refers to a group of life- hanging nosocomial pathogens similar as Enterococcus faecium, Staphylococcus aureus, \u003cem\u003eKlebsiella pneumoniae\u003c/em\u003e, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp. These pathogens, also known as\u0026quot; superbugs,\u0026quot; have acquired resistance to nearly all available antimicrobial agents, leading to increased healthcare costs and increased mortality rates[8]. The World Health Organization has included ESKAPE pathogens in a list of 12 bacteria for critical need of new antibiotics, grading them into critical, high, and medium precedence. The abuse of antimicrobials and the propensity of organisms to carry resistance genes, similar as MRSA, vancomycin-resistant Enterococcus (VRE), and \u0026beta;- lactam- resistant pathogens, are major pitfalls in the clinical arena. General antimicrobial remedy for infections involves the use of antibiotics either alone or in combination. still, numerous antibiotics proposed against ESKAPE since 2010 have been dropped by adding a small number of antibiotic/ antibiotic combinations. thus, chancing indispensable ways to treat infections, especially those caused by ESKAPE pathogens, is pivotal.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003e\u003cem\u003eKlebsiella pneumoniae\u003c/em\u003e\u003c/strong\u003e\u003cstrong\u003e: IMPORTANT MDR AND MAJOR SOURCE OF HOSPITAL INFECTIONS:\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eK.pneumoniae, a crucial pathogen in community- acquired pneumonia, is concentrated in the digestive tract and nasopharynx, causing infections through the bloodstream or other apkins. It has been a crucial pathogen in diabetics and rummies, and a multicenter study in China set up that carbapenem- resistant Enterobacteriaceae (CRE) caused byK.pneumoniae infection burdens the healthcare system.K.pneumoniae strains are divided into three types opportunistic, hypervirulent, and multidrug- resistant (MDR). Classical K. pneumoniae (cKp) strains infected devitalized cases, while the largely malign hvKp variant can beget aggressive and metastatic infections in youthful grown-ups with diabetes or normal vulnerable function. The emergence and spread of MDR strains are nearly related to plasmid- decoded antibiotic resistance genes( ARGs).K.pneumoniae continues to accumulate ARGs in the face of antibiotic abuse, leading to an extremely resistant medicine- resistant( XDR) strain with a\u0026quot; superresistome\u0026rdquo; [9].\u003c/p\u003e\n\u003ch2\u003eMurI Target for Drug Discovery\u003c/h2\u003e\n\u003cp\u003eAntibiotics are crucial in treating infectious diseases caused by microbes, targeting four cellular biosynthesis pathways: cell wall biosynthesis, protein synthesis, DNA replication and repair, and folate coenzyme-dependent thymidine biosynthesis. Cell wall biosynthesis is the most widespread clinical use, accounting for over 60% of the total antibacterial drug market, worth over $25 billion. Recent advances in developing agents against early steps of peptidoglycan biosynthesis have been reviewed. The bacterial cell wall is a highly cross- linked polymeric structure consisting of repeating peptidoglycan units of disaccharides. Disruption of cell wall production renders bacteria susceptible to lysis by osmotic pressure, and inhibitors targeting this pathway are generally toxic. D-Glutamic acid is an important biosynthetic building block, as it is required in the formation of peptidoglycan, which protects bacteria from osmotic lysis. Understanding the mechanism of glutamate racemization could be useful in designing new antibiotics. Mechanistic studies on glutamate racemase suggest a \u0026quot;dibasic\u0026quot; mechanism involving monoprotic acid/base residues. Mutagenesis studies have shown that the two cysteines provide the acid/base residues required for catalysis. The presence of glutamate racemase in all species of cell wall-encoding bacteria has been confirmed in gram-positive organisms that encode D-AAT [10].\u003c/p\u003e\n\u003ch2\u003eBiochemical and structural characterization:\u003c/h2\u003e\n\u003cp\u003eGlutamate racemase is an enzyme with a specific substrate preference for glutamate and requires an optimal pH of 6.0 to 8.0 and reducing agents to maintain its cysteine side chains. It uses a two-base mechanism for catalysis, with two conserved cysteines that can be mutated to decrease or complete activity. The active site of glutamate racemase is hydrophobic and well-defined, allowing for complex chemical transformations. The enzyme shares highly conserved active site architectures across the bacterial spectrum, resulting in excellent substrate specificity and catalytic potential.\u003c/p\u003e\n\u003cp\u003eGlutamate racemases are found in bacteria, but differ in their oligomeric state. Dimerization requires a balance between stabilizing the enzyme and maintaining flexibility for catalysis. Glutamate racemase is a potential target for drug discovery due to its conservation and essentiality in the bacterial kingdom.\u003c/p\u003e"},{"header":"MATERIALS AND METHODOLOGY","content":"\u003cdiv id=\"Sec7\" class=\"Section2\"\u003e\n \u003ch2\u003eProtein Sequence Analysis\u003c/h2\u003e\n \u003cp\u003eThe amino acid sequence of Glutamate Racemase from K. pneumoniae was analyzed using various tools and servers to determine its physicochemical properties, functional domains, sub-cellular localization, possible antigenic sites, topology, microbial phosphorylation sites, and potential N-and O-glycosites. These analyses provide insights into the function and potential applications of this bacterial enzyme.\u003c/p\u003e\n\u003c/div\u003e\n\u003cdiv id=\"Sec8\" class=\"Section2\"\u003e\n \u003ch2\u003eHomology Modelling\u003c/h2\u003e\n \u003cp\u003eSwiss Model (\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://swissmodel.expasy.org/\u003c/span\u003e\u003c/span\u003e\u003cspan class=\"Underline\"\u003e)\u003c/span\u003e was use to predict the three-dimensional models of Glutamate Racemase. Where the Template selection, alignment and model building are done completely automated by the server.\u003c/p\u003e\n\u003c/div\u003e\n\u003cdiv id=\"Sec9\" class=\"Section2\"\u003e\n \u003ch2\u003eHigh-throughput virtual screening (HTVS)\u003c/h2\u003e\n \u003cp\u003eHTVS was used to identify potential lead compounds with strong binding affinity and drug- like properties. PyRx tool and PDBQT file format were used for structure-based virtual screening with Glutamate Racemase model. Auto Dock Vina was used to perform docking calculations based on the binding site of Glutamate Racemase. The grid box was created with specific parameters for the calculation. Molecular docking is useful for understanding how molecules bind and interact.\u003c/p\u003e\n\u003c/div\u003e\n\u003cdiv id=\"Sec10\" class=\"Section2\"\u003e\n \u003ch2\u003eMolecular Docking\u003c/h2\u003e\n \u003cp\u003eThese dimensions were then loaded in TACC drug discovery portel (\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://portal.tacc.utexas.edu/\u003c/span\u003e\u003c/span\u003e\u003cspan class=\"Underline\"\u003e)\u003c/span\u003e where the protein was docked with millions of ligands to find potential drugleads and gave a list of 1000 compounds.\u003c/p\u003e\n\u003c/div\u003e\n\u003cdiv id=\"Sec11\" class=\"Section2\"\u003e\n \u003ch2\u003ePost-Structural Screening\u003c/h2\u003e\n \u003cp\u003eThe TACC server analyzed the results and performed post-structural screening using Lipinski\u0026apos;s rule of 5 and DataWarrior. This filtered natural compounds based on physicochemical and drug-likeliness properties such as having no more than 5 hydrogen bond donors, no more than 10 hydrogen bond acceptors, a molecular mass less than 500 Daltons, an octanol-water partition coefficient (log P) not exceeding 5, and not being carcinogenic, mutagenic, toxic or interfering with reproductivity.\u003c/p\u003e\n\u003c/div\u003e\n\u003cdiv id=\"Sec12\" class=\"Section2\"\u003e\n \u003ch2\u003eCategorization and Docking Study of Selected Ligands:\u003c/h2\u003e\n \u003cp\u003eTo sort out ligands provided by Data Warrior, we used the Swiss ADME tool to analyze the ligands\u0026apos; ADME properties, including solubility, absorption, BBB permeability, and cytochrome inhibitors. After selecting the ligands based on their ADME\u0026nbsp;properties, the researchers used Marvin JS to download the ligand sequences in PDB format and used PyRx to dock the ligands with the target\u0026nbsp;enzyme to predict their binding affinity. Then we identified the top four ligands with the highest\u0026nbsp;binding affinities, which are the most promising candidates for further investigation. The use of PyRx has allowed the researchers to identify the most promising ligands for their research, and by focusing on these top candidates, they can\u0026nbsp;maximize their chances of success.\u003c/p\u003e\n\u003c/div\u003e\n\u003cdiv id=\"Sec13\" class=\"Section2\"\u003e\n \u003ch2\u003eVisualisation of Final Ligands:\u003c/h2\u003e\n \u003cp\u003eFour ligands have been selected based on their strong binding affinities. The visualization tool PyMOL is being used to fully understand and analyze the molecular structures and interactions between these ligands and the target molecule. This information is important for determining the potential of these ligands as drug candidates and for making informed decisions on which ones to further develop and optimize.\u003c/p\u003e\n\u003c/div\u003e"},{"header":"RESULT","content":"\u003cdiv class=\"gridtable\"\u003e\n\u003cp\u003e\u003cstrong\u003eTable.1 This table shows the final four ligands having the highest binding affinities and the highest drug-like properties (based on the results of PyRx tool).\u003c/strong\u003e\u003c/p\u003e\n\u003ctable id=\"Taba\" border=\"1\"\u003e\n\u003cthead\u003e\n\u003ctr\u003e\n\u003cth align=\"left\"\u003e\n\u003cp\u003eMolecules\u003c/p\u003e\n\u003c/th\u003e\n\u003cth align=\"left\"\u003e\n\u003cp\u003eBinding Affinity\u003c/p\u003e\n\u003c/th\u003e\n\u003c/tr\u003e\n\u003c/thead\u003e\n\u003ctbody\u003e\n\u003ctr\u003e\n\u003ctd align=\"left\"\u003e\n\u003cp\u003eZ1160469283_2\u003c/p\u003e\n\u003c/td\u003e\n\u003ctd align=\"char\" char=\".\"\u003e\n\u003cp\u003e-8.6\u003c/p\u003e\n\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd align=\"left\"\u003e\n\u003cp\u003eZ2268832941_1\u003c/p\u003e\n\u003c/td\u003e\n\u003ctd align=\"char\" char=\".\"\u003e\n\u003cp\u003e-8.3\u003c/p\u003e\n\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd align=\"left\"\u003e\n\u003cp\u003eZ3353989070_7\u003c/p\u003e\n\u003c/td\u003e\n\u003ctd align=\"char\" char=\".\"\u003e\n\u003cp\u003e-8.3\u003c/p\u003e\n\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd align=\"left\"\u003e\n\u003cp\u003eZ1593318034_31\u003c/p\u003e\n\u003c/td\u003e\n\u003ctd align=\"char\" char=\".\"\u003e\n\u003cp\u003e-8.1\u003c/p\u003e\n\u003c/td\u003e\n\u003c/tr\u003e\n\u003c/tbody\u003e\n\u003c/table\u003e\n\u003c/div\u003e"},{"header":"Conclusion","content":"\u003cp\u003eIn recent years, hospital-acquired diseases have emerged as a serious and rapidly spreading threat to the community. Among these diseases, pneumonia caused by \u003cem\u003eKlebsiella pneumoniae\u003c/em\u003e has become a widespread concern among public health officials. This is due to the fact that the antibiotic-resistant strains of this bacteria are difficult to treat and can lead to high mortality rates.\u003c/p\u003e \u003cp\u003eAs we continue to confront the looming danger of antibiotic-resistant bacteria, it is crucial that we explore innovative approaches, such as insilico drug development.In this study, we have targeted the glutamate racemase of \u003cem\u003eKlebsiella pneumoniae\u003c/em\u003e as it is a crucial enzyme that aids in the formation of the cell wall. By inhibiting the glutamate racemase, we can potentially eradicate \u003cem\u003eKlebsiella pneumoniae\u003c/em\u003e from the host system. To achieve this, we first studied the enzyme and predicted its 3D structure. We then docked it with ligand databases using a server, which provided a list of possible ligands. We further refined our ligand search using Data Warrior, which sorted the ligands based on the Lipinski rule. We also studied the ADME properties with the help of SwissADME server and further refined our selected ligands. Finally, we docked the selected ligands with glutamate racemase and based on their binding affinities, we identified four highly promising candidates for future drug development. These four ligands can be used to develop drugs to cure pneumonia caused by \u003cem\u003eKlebsiella pneumoniae\u003c/em\u003e, leading to a healthier society.\u003c/p\u003e \u003cp\u003eOverall, our study provides a promising approach to combatting \u003cem\u003eKlebsiella pneumoniae\u003c/em\u003e infections by targeting the crucial enzyme glutamate racemase. Our rigorous methodology and careful selection of ligands provide a strong foundation for future drug development efforts. With the increasing prevalence of antibiotic-resistant strains of \u003cem\u003eKlebsiella pneumoniae\u003c/em\u003e, the need for new treatment options is urgent. By targeting glutamate racemase, we have identified a potential avenue for developing novel antibiotics that can effectively combat this pathogen. Our study provides a solid starting point for further research into the development of drugs that can target this enzyme, and we are optimistic about the potential impact of our findings on the field of infectious disease treatment. With continued research and development, we believe that our approach could lead to the discovery of new and effective treatments for \u003cem\u003eKlebsiella pneumoniae\u003c/em\u003e infections.\u003c/p\u003e"},{"header":"Declarations","content":"\u003ch2\u003eAuthor Contribution\u003c/h2\u003e\u003cp\u003eAll authors wrote and reviewed the manuscript\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eEthics approval and consent to participate:\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eNOT APPLICABLE\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eConsent for publication:\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eNOT APPLICABLE\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eAvailability of data and materials:\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eNOT APPLICABLE\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eFunding:\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eNOT APPLICABLE\u003c/p\u003e"},{"header":"References","content":"\u003col\u003e\n\u003cli\u003ePodschun, R., \u0026amp; Ullmann, U. (1998, October). Klebsiella spp. as Nosocomial Pathogens: Epidemiology, Taxonomy, Typing Methods, and Pathogenicity Factors. \u003cem\u003eClinical Microbiology Reviews\u003c/em\u003e, \u003cem\u003e11\u003c/em\u003e(4), 589\u0026ndash; 603. https://doi.org/10.1128/cmr.11.4.589\u003c/li\u003e\n\u003cli\u003eHolt, K. E., Wertheim, H., Zadoks, R. N., Baker, S., Whitehouse, C. A., Dance, D., Jenney, A., Connor, T. R., Hsu, L. Y., Severin, J., Brisse, S., Cao, H., Wilksch, J., Gorrie, C., Schultz, M. B., Edwards, D. J., Nguyen, K. V., Nguyen, T. V., Dao, T. T., . . . Thomson, N. R. (2015, June 22). Genomic analysis of diversity, population structure, virulence, and antimicrobial resistance in \u003cem\u003eKlebsiella pneumoniae \u003c/em\u003e, an urgent threat to public health. \u003cem\u003eProceedings of the National Academy of Sciences\u003c/em\u003e, \u003cem\u003e112\u003c/em\u003e(27). https://doi.org/10.1073/pnas.1501049112\u003c/li\u003e\n\u003cli\u003eRice, L. (2008, April 15). Federal Funding for the Study of Antimicrobial Resistance in Nosocomial Pathogens: No ESKAPE. \u003cem\u003eThe Journal of Infectious Diseases\u003c/em\u003e, \u003cem\u003e197\u003c/em\u003e(8), 1079\u0026ndash;1081. https://doi.org/10.1086/533452\u003c/li\u003e\n\u003cli\u003eBush, K., \u0026amp; Jacoby, G. A. (2010, March). Updated Functional Classification of \u0026beta;-Lactamases. \u003cem\u003eAntimicrobial Agents and Chemotherapy\u003c/em\u003e, \u003cem\u003e54\u003c/em\u003e(3), 969\u0026ndash;976. https://doi.org/10.1128/aac.01009-09\u003c/li\u003e\n\u003cli\u003eDerakhshan, S., Najar Peerayeh, S., \u0026amp; Bakhshi, B. (2016, August 7). Association Between Presence of Virulence Genes and Antibiotic Resistance in Clinical\u003cem\u003eKlebsiella pneumoniae\u003c/em\u003eIsolates. \u003cem\u003eLaboratory Medicine\u003c/em\u003e, \u003cem\u003e47\u003c/em\u003e(4), 306\u0026ndash;311. https://doi.org/10.1093/labmed/lmw030\u003c/li\u003e\n\u003cli\u003ePaczosa, M. K., \u0026amp; Mecsas, J. (2016, September). \u003cem\u003eKlebsiella pneumoniae\u003c/em\u003e: Going on the Offense with a Strong Defense. \u003cem\u003eMicrobiology and Molecular Biology Reviews\u003c/em\u003e, \u003cem\u003e80\u003c/em\u003e(3), 629\u0026ndash;661. https://doi.org/10.1128/mmbr.00078-15\u003c/li\u003e\n\u003cli\u003eFisher, S. L. (2008, May 11). Glutamate racemase as a target for drug discovery. \u003cem\u003eMicrobial Biotechnology\u003c/em\u003e, \u003cem\u003e1\u003c/em\u003e(5), 345\u0026ndash;360. https://doi.org/10.1111/j.1751-7915.2008.00031.x\u003c/li\u003e\n\u003cli\u003ePandey, R., Mishra, S. K., \u0026amp; Shrestha, A. (2021, June). Characterisation of ESKAPE Pathogens with Special Reference to Multidrug Resistance and Biofilm Production in a Nepalese Hospital. \u003cem\u003eInfection and Drug Resistance\u003c/em\u003e, \u003cem\u003eVolume 14\u003c/em\u003e, 2201\u0026ndash;2212. https://doi.org/10.2147/idr.s306688\u003c/li\u003e\n\u003cli\u003eBlair, J. M. A., Webber, M. A., Baylay, A. J., Ogbolu, D. O., \u0026amp; Piddock, L. J. V. (2014, December 1). Molecular mechanisms of antibiotic resistance. \u003cem\u003eNature Reviews Microbiology\u003c/em\u003e, \u003cem\u003e13\u003c/em\u003e(1), 42\u0026ndash;51. https://doi.org/10.1038/nrmicro3380\u003c/li\u003e\n\u003cli\u003ePendleton, J. N., Gorman, S. P., \u0026amp; Gilmore, B. F. (2013, March). Clinical relevance of the ESKAPE pathogens. \u003cem\u003eExpert Review of Anti-Infective Therapy\u003c/em\u003e, \u003cem\u003e11\u003c/em\u003e(3), 297\u0026ndash;308. https://doi.org/10.1586/eri.13.12\u003c/li\u003e\n\u003cli\u003eBoucher, H., Talbot, G., Bradley, J., Edwards, J., Gilbert, D., Rice, L., Scheld, M., Spellberg, B., \u0026amp; Bartlett, J. (2009, January). Bad Bugs, No Drugs: No ESKAPE! An Update from the Infectious Diseases Society of America. \u003cem\u003eClinical Infectious Diseases\u003c/em\u003e, \u003cem\u003e48\u003c/em\u003e(1), 1\u0026ndash;12. https://doi.org/10.1086/595011\u003c/li\u003e\n\u003c/ol\u003e"}],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":true,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"hideJournal":false,"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":"bmc-bioinformatics","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"binf","sideBox":"Learn more about [BMC Bioinformatics](http://bmcbioinformatics.biomedcentral.com/)","snPcode":"","submissionUrl":"https://www.editorialmanager.com/binf","title":"BMC Bioinformatics","twitterHandle":"@BMC_Bioinformatics","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"em","reportingPortfolio":"BMC Series","inReviewEnabled":true,"inReviewRevisionsEnabled":true},"keywords":"K. pneumoniae, Glutamate racemase (MurI), MDR, antibiotics","lastPublishedDoi":"10.21203/rs.3.rs-3811412/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-3811412/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003e\u003cem\u003eKlebsiella pneumoniae\u003c/em\u003e is a bacterium that gives rise to infections in humans as well as animals. It is found in the environment, including in soil and water, and can also be present in the human microbiome, particularly in the gastrointestinal tract. \u003cem\u003eKlebsiella pneumoniae\u003c/em\u003e can lead to a range of illnesses, including pneumonia, infections of the urinary tract, and wound infections. It is more typically found in patients with compromised immune systems, such as those who are hospitalized, have underlying medical conditions, or are taking certain medications that suppress the immune system. Antibiotic-resistant strains of \u003cem\u003eKlebsiella pneumoniae\u003c/em\u003e, such as those that are resistant to carbapenem antibiotics, have become a significant public health concern in recent years. These strains can be difficult to treat and can lead to severe infections and high mortality rates. MurI is an enzyme found in the bacterial species \u003cem\u003eKlebsiella pneumoniae\u003c/em\u003e that is implicated in the production of peptidoglycan, a key component of the bacterial cell wall. Inhibiting the activity of MurI has been shown to be an effective technique to establish new antibiotics for the treatment of infections caused by \u003cem\u003eK. pneumoniae\u003c/em\u003e. In this study, we used homology modeling and docking techniques to identify novel inhibitors of MurI. Homology modeling is a computational method that uses the structure of a similar protein to predict the structure of a target protein. Docking is a method that predicts how well a small molecule will fit into the active site of a protein. To identify potential inhibitors of MurI, we first built a homology model of the enzyme using the structure of a related protein as a template. We then used this model to perform docking studies with a large database of small molecules. The docking results allowed us to identify several compounds that had good binding affinity for the active site of MurI. We then performed further experiments to confirm the inhibitory activity of these compounds against MurI in vitro. Overall, our study demonstrates the utility of homology modeling and docking in the identification of novel inhibitors of MurI. These compounds may have the ability as new antibiotics for the treatment of \u003cem\u003eKlebsiella pneumoniae\u003c/em\u003e infections.\u003c/p\u003e","manuscriptTitle":"Identification of Novel Inhibitors Against Glutamate Racemase of Klebsiella Pneumoniae Through Homology Modeling and Docking Studies","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2024-01-03 01:46:28","doi":"10.21203/rs.3.rs-3811412/v1","editorialEvents":[{"type":"communityComments","content":0},{"type":"editorAssigned","content":"","date":"2023-12-28T08:13:29+00:00","index":"","fulltext":""},{"type":"checksComplete","content":"","date":"2023-12-28T08:13:28+00:00","index":"","fulltext":""},{"type":"submitted","content":"BMC Bioinformatics","date":"2023-12-27T08:46:17+00:00","index":"","fulltext":""}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"bmc-bioinformatics","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"binf","sideBox":"Learn more about [BMC Bioinformatics](http://bmcbioinformatics.biomedcentral.com/)","snPcode":"","submissionUrl":"https://www.editorialmanager.com/binf","title":"BMC Bioinformatics","twitterHandle":"@BMC_Bioinformatics","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"em","reportingPortfolio":"BMC Series","inReviewEnabled":true,"inReviewRevisionsEnabled":true}}],"origin":"","ownerIdentity":"f6ea3f83-b0b2-4e31-bdcd-34769c59174d","owner":[],"postedDate":"January 3rd, 2024","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"under-review","subjectAreas":[],"tags":[],"updatedAt":"2024-01-03T01:46:28+00:00","versionOfRecord":[],"versionCreatedAt":"2024-01-03 01:46:28","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-3811412","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-3811412","identity":"rs-3811412","version":["v1"]},"buildId":"qtupq5eGEP_6zYnWcrvyt","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}