New insights about the serine/threonine protein kinase substrates from Mycobacterium tuberculosis using molecular docking, quantum similarity analysis and DFT calculations

New insights about the serine/threonine protein... | F1000Research "use strict";function _typeof(t){return(_typeof="function"==typeof Symbol&&"symbol"==typeof Symbol.iterator?function(t){return typeof t}:function(t){return t&&"function"==typeof Symbol&&t.constructor===Symbol&&t!==Symbol.prototype?"symbol":typeof t})(t)}!function(){var t=function(){var t,e,o=[],n=window,r=n;for(;r;){try{if(r.frames.__tcfapiLocator){t=r;break}}catch(t){}if(r===n.top)break;r=r.parent}t||(!function t(){var e=n.document,o=!!n.frames.__tcfapiLocator;if(!o)if(e.body){var r=e.createElement("iframe");r.style.cssText="display:none",r.name="__tcfapiLocator",e.body.appendChild(r)}else setTimeout(t,5);return!o}(),n.__tcfapi=function(){for(var t=arguments.length,n=new Array(t),r=0;r 3&&2===parseInt(n[1],10)&&"boolean"==typeof n[3]&&(e=n[3],"function"==typeof n[2]&&n[2]("set",!0)):"ping"===n[0]?"function"==typeof n[2]&&n[2]({gdprApplies:e,cmpLoaded:!1,cmpStatus:"stub"}):o.push(n)},n.addEventListener("message",(function(t){var e="string"==typeof t.data,o={};if(e)try{o=JSON.parse(t.data)}catch(t){}else o=t.data;var n="object"===_typeof(o)&&null!==o?o.__tcfapiCall:null;n&&window.__tcfapi(n.command,n.version,(function(o,r){var a={__tcfapiReturn:{returnValue:o,success:r,callId:n.callId}};t&&t.source&&t.source.postMessage&&t.source.postMessage(e?JSON.stringify(a):a,"*")}),n.parameter)}),!1))};"undefined"!=typeof module?module.exports=t:t()}(); dataLayer = dataLayer || []; // Standard GTM initialization - Google Consent Mode handles consent automatically (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+ '>m_auth=hzk0Vc3qFsQYhCrIoHz68A>m_preview=env-1>m_cookies_win=x';f.parentNode.insertBefore(j,f); })(window,document,'script','dataLayer','GTM-MWFK8L5J'); ;window.NREUM||(NREUM={});NREUM.init={distributed_tracing:{enabled:true},privacy:{cookies_enabled:true},ajax:{deny_list:["bam.nr-data.net"]}}; ;NREUM.loader_config={accountID:"438030",trustKey:"438030",agentID:"772317073",licenseKey:"97f8f67f26",applicationID:"772317073"} ;NREUM.info={beacon:"bam.nr-data.net",errorBeacon:"bam.nr-data.net",licenseKey:"97f8f67f26",applicationID:"772317073",sa:1} ;/*! For license information please see nr-loader-spa-1.236.0.min.js.LICENSE.txt */ (()=>{"use strict";var e,t,r={5763:(e,t,r)=>{r.d(t,{P_:()=>l,Mt:()=>g,C5:()=>s,DL:()=>v,OP:()=>T,lF:()=>D,Yu:()=>y,Dg:()=>h,CX:()=>c,GE:()=>b,sU:()=>_});var n=r(8632),i=r(9567);const o={beacon:n.ce.beacon,errorBeacon:n.ce.errorBeacon,licenseKey:void 0,applicationID:void 0,sa:void 0,queueTime:void 0,applicationTime:void 0,ttGuid:void 0,user:void 0,account:void 0,product:void 0,extra:void 0,jsAttributes:{},userAttributes:void 0,atts:void 0,transactionName:void 0,tNamePlain:void 0},a={};function s(e){if(!e)throw new Error("All info objects require an agent identifier!");if(!a[e])throw new Error("Info for ".concat(e," was never set"));return a[e]}function c(e,t){if(!e)throw new Error("All info objects require an agent identifier!");a[e]=(0,i.D)(t,o),(0,n.Qy)(e,a[e],"info")}var u=r(7056);const d=()=>{const e={blockSelector:"[data-nr-block]",maskInputOptions:{password:!0}};return{allow_bfcache:!0,privacy:{cookies_enabled:!0},ajax:{deny_list:void 0,enabled:!0,harvestTimeSeconds:10},distributed_tracing:{enabled:void 0,exclude_newrelic_header:void 0,cors_use_newrelic_header:void 0,cors_use_tracecontext_headers:void 0,allowed_origins:void 0},session:{domain:void 0,expiresMs:u.oD,inactiveMs:u.Hb},ssl:void 0,obfuscate:void 0,jserrors:{enabled:!0,harvestTimeSeconds:10},metrics:{enabled:!0},page_action:{enabled:!0,harvestTimeSeconds:30},page_view_event:{enabled:!0},page_view_timing:{enabled:!0,harvestTimeSeconds:30,long_task:!1},session_trace:{enabled:!0,harvestTimeSeconds:10},harvest:{tooManyRequestsDelay:60},session_replay:{enabled:!1,harvestTimeSeconds:60,sampleRate:.1,errorSampleRate:.1,maskTextSelector:"*",maskAllInputs:!0,get blockClass(){return"nr-block"},get ignoreClass(){return"nr-ignore"},get maskTextClass(){return"nr-mask"},get blockSelector(){return e.blockSelector},set blockSelector(t){e.blockSelector+=",".concat(t)},get maskInputOptions(){return e.maskInputOptions},set maskInputOptions(t){e.maskInputOptions={...t,password:!0}}},spa:{enabled:!0,harvestTimeSeconds:10}}},f={};function l(e){if(!e)throw new Error("All configuration objects require an agent identifier!");if(!f[e])throw new Error("Configuration for ".concat(e," was never set"));return f[e]}function h(e,t){if(!e)throw new Error("All configuration objects require an agent identifier!");f[e]=(0,i.D)(t,d()),(0,n.Qy)(e,f[e],"config")}function g(e,t){if(!e)throw new Error("All configuration objects require an agent identifier!");var r=l(e);if(r){for(var n=t.split("."),i=0;i {r.d(t,{D:()=>i});var n=r(50);function i(e,t){try{if(!e||"object"!=typeof e)return(0,n.Z)("Setting a Configurable requires an object as input");if(!t||"object"!=typeof t)return(0,n.Z)("Setting a Configurable requires a model to set its initial properties");const r=Object.create(Object.getPrototypeOf(t),Object.getOwnPropertyDescriptors(t)),o=0===Object.keys(r).length?e:r;for(let a in o)if(void 0!==e[a])try{"object"==typeof e[a]&&"object"==typeof t[a]?r[a]=i(e[a],t[a]):r[a]=e[a]}catch(e){(0,n.Z)("An error occurred while setting a property of a Configurable",e)}return r}catch(e){(0,n.Z)("An error occured while setting a Configurable",e)}}},6818:(e,t,r)=>{r.d(t,{Re:()=>i,gF:()=>o,q4:()=>n});const n="1.236.0",i="PROD",o="CDN"},385:(e,t,r)=>{r.d(t,{FN:()=>a,IF:()=>u,Nk:()=>f,Tt:()=>s,_A:()=>o,il:()=>n,pL:()=>c,v6:()=>i,w1:()=>d});const n="undefined"!=typeof window&&!!window.document,i="undefined"!=typeof WorkerGlobalScope&&("undefined"!=typeof self&&self instanceof WorkerGlobalScope&&self.navigator instanceof WorkerNavigator||"undefined"!=typeof globalThis&&globalThis instanceof WorkerGlobalScope&&globalThis.navigator instanceof WorkerNavigator),o=n?window:"undefined"!=typeof WorkerGlobalScope&&("undefined"!=typeof self&&self instanceof WorkerGlobalScope&&self||"undefined"!=typeof globalThis&&globalThis instanceof WorkerGlobalScope&&globalThis),a=""+o?.location,s=/iPad|iPhone|iPod/.test(navigator.userAgent),c=s&&"undefined"==typeof SharedWorker,u=(()=>{const e=navigator.userAgent.match(/Firefox[/\s](\d+\.\d+)/);return Array.isArray(e)&&e.length>=2?+e[1]:0})(),d=Boolean(n&&window.document.documentMode),f=!!navigator.sendBeacon},1117:(e,t,r)=>{r.d(t,{w:()=>o});var n=r(50);const i={agentIdentifier:"",ee:void 0};class o{constructor(e){try{if("object"!=typeof e)return(0,n.Z)("shared context requires an object as input");this.sharedContext={},Object.assign(this.sharedContext,i),Object.entries(e).forEach((e=>{let[t,r]=e;Object.keys(i).includes(t)&&(this.sharedContext[t]=r)}))}catch(e){(0,n.Z)("An error occured while setting SharedContext",e)}}}},8e3:(e,t,r)=>{r.d(t,{L:()=>d,R:()=>c});var n=r(2177),i=r(1284),o=r(4322),a=r(3325);const s={};function c(e,t){const r={staged:!1,priority:a.p[t]||0};u(e),s[e].get(t)||s[e].set(t,r)}function u(e){e&&(s[e]||(s[e]=new Map))}function d(){let e=arguments.length>0&&void 0!==arguments[0]?arguments[0]:"",t=arguments.length>1&&void 0!==arguments[1]?arguments[1]:"feature";if(u(e),!e||!s[e].get(t))return a(t);s[e].get(t).staged=!0;const r=[...s[e]];function a(t){const r=e?n.ee.get(e):n.ee,a=o.X.handlers;if(r.backlog&&a){var s=r.backlog[t],c=a[t];if(c){for(var u=0;s&&u {let[t,r]=e;return r.staged}))&&(r.sort(((e,t)=>e[1].priority-t[1].priority)),r.forEach((e=>{let[t]=e;a(t)})))}function f(e,t){var r=e[1];(0,i.D)(t[r],(function(t,r){var n=e[0];if(r[0]===n){var i=r[1],o=e[3],a=e[2];i.apply(o,a)}}))}},2177:(e,t,r)=>{r.d(t,{c:()=>f,ee:()=>u});var n=r(8632),i=r(2210),o=r(1284),a=r(5763),s="nr@context";let c=(0,n.fP)();var u;function d(){}function f(e){return(0,i.X)(e,s,l)}function l(){return new d}function h(){u.aborted=!0,u.backlog={}}c.ee?u=c.ee:(u=function e(t,r){var n={},c={},f={},g=!1;try{g=16===r.length&&(0,a.OP)(r).isolatedBacklog}catch(e){}var p={on:b,addEventListener:b,removeEventListener:y,emit:v,get:x,listeners:w,context:m,buffer:A,abort:h,aborted:!1,isBuffering:E,debugId:r,backlog:g?{}:t&&"object"==typeof t.backlog?t.backlog:{}};return p;function m(e){return e&&e instanceof d?e:e?(0,i.X)(e,s,l):l()}function v(e,r,n,i,o){if(!1!==o&&(o=!0),!u.aborted||i){t&&o&&t.emit(e,r,n);for(var a=m(n),s=w(e),d=s.length,f=0;fn,p:()=>i});var n=r(2177).ee.get("handle");function i(e,t,r,i,o){o?(o.buffer([e],i),o.emit(e,t,r)):(n.buffer([e],i),n.emit(e,t,r))}},4322:(e,t,r)=>{r.d(t,{X:()=>o});var n=r(5546);o.on=a;var i=o.handlers={};function o(e,t,r,o){a(o||n.E,i,e,t,r)}function a(e,t,r,i,o){o||(o="feature"),e||(e=n.E);var a=t[o]=t[o]||{};(a[r]=a[r]||[]).push([e,i])}},3239:(e,t,r)=>{r.d(t,{bP:()=>s,iz:()=>c,m$:()=>a});var n=r(385);let i=!1,o=!1;try{const e={get passive(){return i=!0,!1},get signal(){return o=!0,!1}};n._A.addEventListener("test",null,e),n._A.removeEventListener("test",null,e)}catch(e){}function a(e,t){return i||o?{capture:!!e,passive:i,signal:t}:!!e}function s(e,t){let r=arguments.length>2&&void 0!==arguments[2]&&arguments[2],n=arguments.length>3?arguments[3]:void 0;window.addEventListener(e,t,a(r,n))}function c(e,t){let r=arguments.length>2&&void 0!==arguments[2]&&arguments[2],n=arguments.length>3?arguments[3]:void 0;document.addEventListener(e,t,a(r,n))}},4402:(e,t,r)=>{r.d(t,{Ht:()=>u,M:()=>c,Rl:()=>a,ky:()=>s});var n=r(385);const i="xxxxxxxx-xxxx-4xxx-yxxx-xxxxxxxxxxxx";function o(e,t){return e?15&e[t]:16*Math.random()|0}function a(){const e=n._A?.crypto||n._A?.msCrypto;let t,r=0;return e&&e.getRandomValues&&(t=e.getRandomValues(new Uint8Array(31))),i.split("").map((e=>"x"===e?o(t,++r).toString(16):"y"===e?(3&o()|8).toString(16):e)).join("")}function s(e){const t=n._A?.crypto||n._A?.msCrypto;let r,i=0;t&&t.getRandomValues&&(r=t.getRandomValues(new Uint8Array(31)));const a=[];for(var s=0;s {r.d(t,{Bq:()=>n,Hb:()=>o,oD:()=>i});const n="NRBA",i=144e5,o=18e5},7894:(e,t,r)=>{function n(){return Math.round(performance.now())}r.d(t,{z:()=>n})},7243:(e,t,r)=>{r.d(t,{e:()=>o});var n=r(385),i={};function o(e){if(e in i)return i[e];if(0===(e||"").indexOf("data:"))return{protocol:"data"};let t;var r=n._A?.location,o={};if(n.il)t=document.createElement("a"),t.href=e;else try{t=new URL(e,r.href)}catch(e){return o}o.port=t.port;var a=t.href.split("://");!o.port&&a[1]&&(o.port=a[1].split("/")[0].split("@").pop().split(":")[1]),o.port&&"0"!==o.port||(o.port="https"===a[0]?"443":"80"),o.hostname=t.hostname||r.hostname,o.pathname=t.pathname,o.protocol=a[0],"/"!==o.pathname.charAt(0)&&(o.pathname="/"+o.pathname);var s=!t.protocol||":"===t.protocol||t.protocol===r.protocol,c=t.hostname===r.hostname&&t.port===r.port;return o.sameOrigin=s&&(!t.hostname||c),"/"===o.pathname&&(i[e]=o),o}},50:(e,t,r)=>{function n(e,t){"function"==typeof console.warn&&(console.warn("New Relic: ".concat(e)),t&&console.warn(t))}r.d(t,{Z:()=>n})},2587:(e,t,r)=>{r.d(t,{N:()=>c,T:()=>u});var n=r(2177),i=r(5546),o=r(8e3),a=r(3325);const s={stn:[a.D.sessionTrace],err:[a.D.jserrors,a.D.metrics],ins:[a.D.pageAction],spa:[a.D.spa],sr:[a.D.sessionReplay,a.D.sessionTrace]};function c(e,t){const r=n.ee.get(t);e&&"object"==typeof e&&(Object.entries(e).forEach((e=>{let[t,n]=e;void 0===u[t]&&(s[t]?s[t].forEach((e=>{n?(0,i.p)("feat-"+t,[],void 0,e,r):(0,i.p)("block-"+t,[],void 0,e,r),(0,i.p)("rumresp-"+t,[Boolean(n)],void 0,e,r)})):n&&(0,i.p)("feat-"+t,[],void 0,void 0,r),u[t]=Boolean(n))})),Object.keys(s).forEach((e=>{void 0===u[e]&&(s[e]?.forEach((t=>(0,i.p)("rumresp-"+e,[!1],void 0,t,r))),u[e]=!1)})),(0,o.L)(t,a.D.pageViewEvent))}const u={}},2210:(e,t,r)=>{r.d(t,{X:()=>i});var n=Object.prototype.hasOwnProperty;function i(e,t,r){if(n.call(e,t))return e[t];var i=r();if(Object.defineProperty&&Object.keys)try{return Object.defineProperty(e,t,{value:i,writable:!0,enumerable:!1}),i}catch(e){}return e[t]=i,i}},1284:(e,t,r)=>{r.d(t,{D:()=>n});const n=(e,t)=>Object.entries(e||{}).map((e=>{let[r,n]=e;return t(r,n)}))},4351:(e,t,r)=>{r.d(t,{P:()=>o});var n=r(2177);const i=()=>{const e=new WeakSet;return(t,r)=>{if("object"==typeof r&&null!==r){if(e.has(r))return;e.add(r)}return r}};function o(e){try{return JSON.stringify(e,i())}catch(e){try{n.ee.emit("internal-error",[e])}catch(e){}}}},3960:(e,t,r)=>{r.d(t,{K:()=>a,b:()=>o});var n=r(3239);function i(){return"undefined"==typeof document||"complete"===document.readyState}function o(e,t){if(i())return e();(0,n.bP)("load",e,t)}function a(e){if(i())return e();(0,n.iz)("DOMContentLoaded",e)}},8632:(e,t,r)=>{r.d(t,{EZ:()=>u,Qy:()=>c,ce:()=>o,fP:()=>a,gG:()=>d,mF:()=>s});var n=r(7894),i=r(385);const o={beacon:"bam.nr-data.net",errorBeacon:"bam.nr-data.net"};function a(){return i._A.NREUM||(i._A.NREUM={}),void 0===i._A.newrelic&&(i._A.newrelic=i._A.NREUM),i._A.NREUM}function s(){let e=a();return e.o||(e.o={ST:i._A.setTimeout,SI:i._A.setImmediate,CT:i._A.clearTimeout,XHR:i._A.XMLHttpRequest,REQ:i._A.Request,EV:i._A.Event,PR:i._A.Promise,MO:i._A.MutationObserver,FETCH:i._A.fetch}),e}function c(e,t,r){let i=a();const o=i.initializedAgents||{},s=o[e]||{};return Object.keys(s).length||(s.initializedAt={ms:(0,n.z)(),date:new Date}),i.initializedAgents={...o,[e]:{...s,[r]:t}},i}function u(e,t){a()[e]=t}function d(){return function(){let e=a();const t=e.info||{};e.info={beacon:o.beacon,errorBeacon:o.errorBeacon,...t}}(),function(){let e=a();const t=e.init||{};e.init={...t}}(),s(),function(){let e=a();const t=e.loader_config||{};e.loader_config={...t}}(),a()}},7956:(e,t,r)=>{r.d(t,{N:()=>i});var n=r(3239);function i(e){let t=arguments.length>1&&void 0!==arguments[1]&&arguments[1],r=arguments.length>2?arguments[2]:void 0,i=arguments.length>3?arguments[3]:void 0;return void(0,n.iz)("visibilitychange",(function(){if(t)return void("hidden"==document.visibilityState&&e());e(document.visibilityState)}),r,i)}},1214:(e,t,r)=>{r.d(t,{em:()=>v,u5:()=>N,QU:()=>S,_L:()=>I,Gm:()=>L,Lg:()=>M,gy:()=>U,BV:()=>Q,Kf:()=>ee});var n=r(2177);const i="nr@original";var o=Object.prototype.hasOwnProperty,a=!1;function s(e,t){return e||(e=n.ee),r.inPlace=function(e,t,n,i,o){n||(n="");var a,s,c,u="-"===n.charAt(0);for(c=0;c 2?n-2:0),o=2;o {r(A[T],e,w),r(E[T],e,w)})),r(l._A,"fetch",y),t.on(y+"end",(function(e,r){var n=this;if(r){var i=r.headers.get("content-length");null!==i&&(n.rxSize=i),t.emit(y+"done",[null,r],n)}else t.emit(y+"done",[e],n)})),t}const O={},j=["pushState","replaceState"];function S(e){const t=function(e){return(e||n.ee).get("history")}(e);return!l.il||O[t.debugId]++||(O[t.debugId]=1,s(t).inPlace(window.history,j,"-")),t}var P=r(3239);const C={},R=["appendChild","insertBefore","replaceChild"];function I(e){const t=function(e){return(e||n.ee).get("jsonp")}(e);if(!l.il||C[t.debugId])return t;C[t.debugId]=!0;var r=s(t),i=/[?&](?:callback|cb)=([^&#]+)/,o=/(.*)\.([^.]+)/,a=/^(\w+)(\.|$)(.*)$/;function c(e,t){var r=e.match(a),n=r[1],i=r[3];return i?c(i,t[n]):t[n]}return r.inPlace(Node.prototype,R,"dom-"),t.on("dom-start",(function(e){!function(e){if(!e||"string"!=typeof e.nodeName||"script"!==e.nodeName.toLowerCase())return;if("function"!=typeof e.addEventListener)return;var n=(a=e.src,s=a.match(i),s?s[1]:null);var a,s;if(!n)return;var u=function(e){var t=e.match(o);if(t&&t.length>=3)return{key:t[2],parent:c(t[1],window)};return{key:e,parent:window}}(n);if("function"!=typeof u.parent[u.key])return;var d={};function f(){t.emit("jsonp-end",[],d),e.removeEventListener("load",f,(0,P.m$)(!1)),e.removeEventListener("error",l,(0,P.m$)(!1))}function l(){t.emit("jsonp-error",[],d),t.emit("jsonp-end",[],d),e.removeEventListener("load",f,(0,P.m$)(!1)),e.removeEventListener("error",l,(0,P.m$)(!1))}r.inPlace(u.parent,[u.key],"cb-",d),e.addEventListener("load",f,(0,P.m$)(!1)),e.addEventListener("error",l,(0,P.m$)(!1)),t.emit("new-jsonp",[e.src],d)}(e[0])})),t}var k=r(5763);const H={};function L(e){const t=function(e){return(e||n.ee).get("mutation")}(e);if(!l.il||H[t.debugId])return t;H[t.debugId]=!0;var r=s(t),i=k.Yu.MO;return i&&(window.MutationObserver=function(e){return this instanceof i?new i(r(e,"fn-")):i.apply(this,arguments)},MutationObserver.prototype=i.prototype),t}const z={};function M(e){const t=function(e){return(e||n.ee).get("promise")}(e);if(z[t.debugId])return t;z[t.debugId]=!0;var r=n.c,o=s(t),a=k.Yu.PR;return a&&function(){function e(r){var n=t.context(),i=o(r,"executor-",n,null,!1);const s=Reflect.construct(a,[i],e);return t.context(s).getCtx=function(){return n},s}l._A.Promise=e,Object.defineProperty(e,"name",{value:"Promise"}),e.toString=function(){return a.toString()},Object.setPrototypeOf(e,a),["all","race"].forEach((function(r){const n=a[r];e[r]=function(e){let i=!1;[...e||[]].forEach((e=>{this.resolve(e).then(a("all"===r),a(!1))}));const o=n.apply(this,arguments);return o;function a(e){return function(){t.emit("propagate",[null,!i],o,!1,!1),i=i||!e}}}})),["resolve","reject"].forEach((function(r){const n=a[r];e[r]=function(e){const r=n.apply(this,arguments);return e!==r&&t.emit("propagate",[e,!0],r,!1,!1),r}})),e.prototype=a.prototype;const n=a.prototype.then;a.prototype.then=function(){var e=this,i=r(e);i.promise=e;for(var a=arguments.length,s=new Array(a),c=0;c e())),t};function m(e,t){i.inPlace(t,["onreadystatechange"],"fn-",E)}function b(){var e=this,t=r.context(e);e.readyState>3&&!t.resolved&&(t.resolved=!0,r.emit("xhr-resolved",[],e)),i.inPlace(e,f,"fn-",E)}if(function(e,t){for(var r in e)t[r]=e[r]}(o,p),p.prototype=o.prototype,i.inPlace(p.prototype,J,"-xhr-",E),r.on("send-xhr-start",(function(e,t){m(e,t),function(e){h.push(e),a&&(y?y.then(A):u?u(A):(w=-w,x.data=w))}(t)})),r.on("open-xhr-start",m),a){var y=c&&c.resolve();if(!u&&!c){var w=1,x=document.createTextNode(w);new a(A).observe(x,{characterData:!0})}}else t.on("fn-end",(function(e){e[0]&&e[0].type===d||A()}));function A(){for(var e=0;e {r.d(t,{t:()=>n});const n=r(3325).D.ajax},6660:(e,t,r)=>{r.d(t,{A:()=>i,t:()=>n});const n=r(3325).D.jserrors,i="nr@seenError"},3081:(e,t,r)=>{r.d(t,{gF:()=>o,mY:()=>i,t9:()=>n,vz:()=>s,xS:()=>a});const n=r(3325).D.metrics,i="sm",o="cm",a="storeSupportabilityMetrics",s="storeEventMetrics"},4649:(e,t,r)=>{r.d(t,{t:()=>n});const n=r(3325).D.pageAction},7633:(e,t,r)=>{r.d(t,{Dz:()=>i,OJ:()=>a,qw:()=>o,t9:()=>n});const n=r(3325).D.pageViewEvent,i="firstbyte",o="domcontent",a="windowload"},9251:(e,t,r)=>{r.d(t,{t:()=>n});const n=r(3325).D.pageViewTiming},3614:(e,t,r)=>{r.d(t,{BST_RESOURCE:()=>i,END:()=>s,FEATURE_NAME:()=>n,FN_END:()=>u,FN_START:()=>c,PUSH_STATE:()=>d,RESOURCE:()=>o,START:()=>a});const n=r(3325).D.sessionTrace,i="bstResource",o="resource",a="-start",s="-end",c="fn"+a,u="fn"+s,d="pushState"},7836:(e,t,r)=>{r.d(t,{BODY:()=>A,CB_END:()=>E,CB_START:()=>u,END:()=>x,FEATURE_NAME:()=>i,FETCH:()=>_,FETCH_BODY:()=>v,FETCH_DONE:()=>m,FETCH_START:()=>p,FN_END:()=>c,FN_START:()=>s,INTERACTION:()=>l,INTERACTION_API:()=>d,INTERACTION_EVENTS:()=>o,JSONP_END:()=>b,JSONP_NODE:()=>g,JS_TIME:()=>T,MAX_TIMER_BUDGET:()=>a,REMAINING:()=>f,SPA_NODE:()=>h,START:()=>w,originalSetTimeout:()=>y});var n=r(5763);const i=r(3325).D.spa,o=["click","submit","keypress","keydown","keyup","change"],a=999,s="fn-start",c="fn-end",u="cb-start",d="api-ixn-",f="remaining",l="interaction",h="spaNode",g="jsonpNode",p="fetch-start",m="fetch-done",v="fetch-body-",b="jsonp-end",y=n.Yu.ST,w="-start",x="-end",A="-body",E="cb"+x,T="jsTime",_="fetch"},5938:(e,t,r)=>{r.d(t,{W:()=>o});var n=r(5763),i=r(2177);class o{constructor(e,t,r){this.agentIdentifier=e,this.aggregator=t,this.ee=i.ee.get(e,(0,n.OP)(this.agentIdentifier).isolatedBacklog),this.featureName=r,this.blocked=!1}}},9144:(e,t,r)=>{r.d(t,{j:()=>m});var n=r(3325),i=r(5763),o=r(5546),a=r(2177),s=r(7894),c=r(8e3),u=r(3960),d=r(385),f=r(50),l=r(3081),h=r(8632);function g(){const e=(0,h.gG)();["setErrorHandler","finished","addToTrace","inlineHit","addRelease","addPageAction","setCurrentRouteName","setPageViewName","setCustomAttribute","interaction","noticeError","setUserId"].forEach((t=>{e[t]=function(){for(var r=arguments.length,n=new Array(r),i=0;i 1?r-1:0),i=1;i {e.exposed&&e.api[t]&&o.push(e.api[t](...n))})),o.length>1?o:o[0]}(t,...n)}}))}var p=r(2587);function m(e){let t=arguments.length>1&&void 0!==arguments[1]?arguments[1]:{},m=arguments.length>2?arguments[2]:void 0,v=arguments.length>3?arguments[3]:void 0,{init:b,info:y,loader_config:w,runtime:x={loaderType:m},exposed:A=!0}=t;const E=(0,h.gG)();y||(b=E.init,y=E.info,w=E.loader_config),(0,i.Dg)(e,b||{}),(0,i.GE)(e,w||{}),(0,i.sU)(e,x),y.jsAttributes??={},d.v6&&(y.jsAttributes.isWorker=!0),(0,i.CX)(e,y),g();const T=function(e,t){t||(0,c.R)(e,"api");const h={};var g=a.ee.get(e),p=g.get("tracer"),m="api-",v=m+"ixn-";function b(t,r,n,o){const a=(0,i.C5)(e);return null===r?delete a.jsAttributes[t]:(0,i.CX)(e,{...a,jsAttributes:{...a.jsAttributes,[t]:r}}),x(m,n,!0,o||null===r?"session":void 0)(t,r)}function y(){}["setErrorHandler","finished","addToTrace","inlineHit","addRelease"].forEach((e=>h[e]=x(m,e,!0,"api"))),h.addPageAction=x(m,"addPageAction",!0,n.D.pageAction),h.setCurrentRouteName=x(m,"routeName",!0,n.D.spa),h.setPageViewName=function(t,r){if("string"==typeof t)return"/"!==t.charAt(0)&&(t="/"+t),(0,i.OP)(e).customTransaction=(r||"http://custom.transaction")+t,x(m,"setPageViewName",!0)()},h.setCustomAttribute=function(e,t){let r=arguments.length>2&&void 0!==arguments[2]&&arguments[2];if("string"==typeof e){if(["string","number"].includes(typeof t)||null===t)return b(e,t,"setCustomAttribute",r);(0,f.Z)("Failed to execute setCustomAttribute.\nNon-null value must be a string or number type, but a type of was provided."))}else(0,f.Z)("Failed to execute setCustomAttribute.\nName must be a string type, but a type of was provided."))},h.setUserId=function(e){if("string"==typeof e||null===e)return b("enduser.id",e,"setUserId",!0);(0,f.Z)("Failed to execute setUserId.\nNon-null value must be a string type, but a type of was provided."))},h.interaction=function(){return(new y).get()};var w=y.prototype={createTracer:function(e,t){var r={},i=this,a="function"==typeof t;return(0,o.p)(v+"tracer",[(0,s.z)(),e,r],i,n.D.spa,g),function(){if(p.emit((a?"":"no-")+"fn-start",[(0,s.z)(),i,a],r),a)try{return t.apply(this,arguments)}catch(e){throw p.emit("fn-err",[arguments,this,"string"==typeof e?new Error(e):e],r),e}finally{p.emit("fn-end",[(0,s.z)()],r)}}}};function x(e,t,r,i){return function(){return(0,o.p)(l.xS,["API/"+t+"/called"],void 0,n.D.metrics,g),i&&(0,o.p)(e+t,[(0,s.z)(),...arguments],r?null:this,i,g),r?void 0:this}}function A(){r.e(439).then(r.bind(r,7438)).then((t=>{let{setAPI:r}=t;r(e),(0,c.L)(e,"api")})).catch((()=>(0,f.Z)("Downloading runtime APIs failed...")))}return["actionText","setName","setAttribute","save","ignore","onEnd","getContext","end","get"].forEach((e=>{w[e]=x(v,e,void 0,n.D.spa)})),h.noticeError=function(e,t){"string"==typeof e&&(e=new Error(e)),(0,o.p)(l.xS,["API/noticeError/called"],void 0,n.D.metrics,g),(0,o.p)("err",[e,(0,s.z)(),!1,t],void 0,n.D.jserrors,g)},d.il?(0,u.b)((()=>A()),!0):A(),h}(e,v);return(0,h.Qy)(e,T,"api"),(0,h.Qy)(e,A,"exposed"),(0,h.EZ)("activatedFeatures",p.T),T}},3325:(e,t,r)=>{r.d(t,{D:()=>n,p:()=>i});const n={ajax:"ajax",jserrors:"jserrors",metrics:"metrics",pageAction:"page_action",pageViewEvent:"page_view_event",pageViewTiming:"page_view_timing",sessionReplay:"session_replay",sessionTrace:"session_trace",spa:"spa"},i={[n.pageViewEvent]:1,[n.pageViewTiming]:2,[n.metrics]:3,[n.jserrors]:4,[n.ajax]:5,[n.sessionTrace]:6,[n.pageAction]:7,[n.spa]:8,[n.sessionReplay]:9}}},n={};function i(e){var t=n[e];if(void 0!==t)return t.exports;var o=n[e]={exports:{}};return r[e](o,o.exports,i),o.exports}i.m=r,i.d=(e,t)=>{for(var r in t)i.o(t,r)&&!i.o(e,r)&&Object.defineProperty(e,r,{enumerable:!0,get:t[r]})},i.f={},i.e=e=>Promise.all(Object.keys(i.f).reduce(((t,r)=>(i.f[r](e,t),t)),[])),i.u=e=>(({78:"page_action-aggregate",147:"metrics-aggregate",242:"session-manager",317:"jserrors-aggregate",348:"page_view_timing-aggregate",412:"lazy-feature-loader",439:"async-api",538:"recorder",590:"session_replay-aggregate",675:"compressor",733:"session_trace-aggregate",786:"page_view_event-aggregate",873:"spa-aggregate",898:"ajax-aggregate"}[e]||e)+"."+{78:"ac76d497",147:"3dc53903",148:"1a20d5fe",242:"2a64278a",317:"49e41428",348:"bd6de33a",412:"2f55ce66",439:"30bd804e",538:"1b18459f",590:"cf0efb30",675:"ae9f91a8",733:"83105561",786:"06482edd",860:"03a8b7a5",873:"e6b09d52",898:"998ef92b"}[e]+"-1.236.0.min.js"),i.o=(e,t)=>Object.prototype.hasOwnProperty.call(e,t),e={},t="NRBA:",i.l=(r,n,o,a)=>{if(e[r])e[r].push(n);else{var s,c;if(void 0!==o)for(var u=document.getElementsByTagName("script"),d=0;d {s.onerror=s.onload=null,clearTimeout(h);var i=e[r];if(delete e[r],s.parentNode&&s.parentNode.removeChild(s),i&&i.forEach((e=>e(n))),t)return t(n)},h=setTimeout(l.bind(null,void 0,{type:"timeout",target:s}),12e4);s.onerror=l.bind(null,s.onerror),s.onload=l.bind(null,s.onload),c&&document.head.appendChild(s)}},i.r=e=>{"undefined"!=typeof Symbol&&Symbol.toStringTag&&Object.defineProperty(e,Symbol.toStringTag,{value:"Module"}),Object.defineProperty(e,"__esModule",{value:!0})},i.j=364,i.p="https://js-agent.newrelic.com/",(()=>{var e={364:0,953:0};i.f.j=(t,r)=>{var n=i.o(e,t)?e[t]:void 0;if(0!==n)if(n)r.push(n[2]);else{var o=new Promise(((r,i)=>n=e[t]=[r,i]));r.push(n[2]=o);var a=i.p+i.u(t),s=new Error;i.l(a,(r=>{if(i.o(e,t)&&(0!==(n=e[t])&&(e[t]=void 0),n)){var o=r&&("load"===r.type?"missing":r.type),a=r&&r.target&&r.target.src;s.message="Loading chunk "+t+" failed.\n("+o+": "+a+")",s.name="ChunkLoadError",s.type=o,s.request=a,n[1](s)}}),"chunk-"+t,t)}};var t=(t,r)=>{var n,o,[a,s,c]=r,u=0;if(a.some((t=>0!==e[t]))){for(n in s)i.o(s,n)&&(i.m[n]=s[n]);if(c)c(i)}for(t&&t(r);u {i.r(o);var e=i(3325),t=i(5763);const r=Object.values(e.D);function n(e){const n={};return r.forEach((r=>{n[r]=function(e,r){return!1!==(0,t.Mt)(r,"".concat(e,".enabled"))}(r,e)})),n}var a=i(9144);var s=i(5546),c=i(385),u=i(8e3),d=i(5938),f=i(3960),l=i(50);class h extends d.W{constructor(e,t,r){let n=!(arguments.length>3&&void 0!==arguments[3])||arguments[3];super(e,t,r),this.auto=n,this.abortHandler,this.featAggregate,this.onAggregateImported,n&&(0,u.R)(e,r)}importAggregator(){let e=arguments.length>0&&void 0!==arguments[0]?arguments[0]:{};if(this.featAggregate||!this.auto)return;const r=c.il&&!0===(0,t.Mt)(this.agentIdentifier,"privacy.cookies_enabled");let n;this.onAggregateImported=new Promise((e=>{n=e}));const o=async()=>{let t;try{if(r){const{setupAgentSession:e}=await Promise.all([i.e(860),i.e(242)]).then(i.bind(i,3228));t=e(this.agentIdentifier)}}catch(e){(0,l.Z)("A problem occurred when starting up session manager. This page will not start or extend any session.",e)}try{if(!this.shouldImportAgg(this.featureName,t))return void(0,u.L)(this.agentIdentifier,this.featureName);const{lazyFeatureLoader:r}=await i.e(412).then(i.bind(i,8582)),{Aggregate:o}=await r(this.featureName,"aggregate");this.featAggregate=new o(this.agentIdentifier,this.aggregator,e),n(!0)}catch(e){(0,l.Z)("Downloading and initializing ".concat(this.featureName," failed..."),e),this.abortHandler?.(),n(!1)}};c.il?(0,f.b)((()=>o()),!0):o()}shouldImportAgg(r,n){return r!==e.D.sessionReplay||!1!==(0,t.Mt)(this.agentIdentifier,"session_trace.enabled")&&(!!n?.isNew||!!n?.state.sessionReplay)}}var g=i(7633),p=i(7894);class m extends h{static featureName=g.t9;constructor(r,n){let i=!(arguments.length>2&&void 0!==arguments[2])||arguments[2];if(super(r,n,g.t9,i),("undefined"==typeof PerformanceNavigationTiming||c.Tt)&&"undefined"!=typeof PerformanceTiming){const n=(0,t.OP)(r);n[g.Dz]=Math.max(Date.now()-n.offset,0),(0,f.K)((()=>n[g.qw]=Math.max((0,p.z)()-n[g.Dz],0))),(0,f.b)((()=>{const t=(0,p.z)();n[g.OJ]=Math.max(t-n[g.Dz],0),(0,s.p)("timing",["load",t],void 0,e.D.pageViewTiming,this.ee)}))}this.importAggregator()}}var v=i(1117),b=i(1284);class y extends v.w{constructor(e){super(e),this.aggregatedData={}}store(e,t,r,n,i){var o=this.getBucket(e,t,r,i);return o.metrics=function(e,t){t||(t={count:0});return t.count+=1,(0,b.D)(e,(function(e,r){t[e]=w(r,t[e])})),t}(n,o.metrics),o}merge(e,t,r,n,i){var o=this.getBucket(e,t,n,i);if(o.metrics){var a=o.metrics;a.count+=r.count,(0,b.D)(r,(function(e,t){if("count"!==e){var n=a[e],i=r[e];i&&!i.c?a[e]=w(i.t,n):a[e]=function(e,t){if(!t)return e;t.c||(t=x(t.t));return t.min=Math.min(e.min,t.min),t.max=Math.max(e.max,t.max),t.t+=e.t,t.sos+=e.sos,t.c+=e.c,t}(i,a[e])}}))}else o.metrics=r}storeMetric(e,t,r,n){var i=this.getBucket(e,t,r);return i.stats=w(n,i.stats),i}getBucket(e,t,r,n){this.aggregatedData[e]||(this.aggregatedData[e]={});var i=this.aggregatedData[e][t];return i||(i=this.aggregatedData[e][t]={params:r||{}},n&&(i.custom=n)),i}get(e,t){return t?this.aggregatedData[e]&&this.aggregatedData[e][t]:this.aggregatedData[e]}take(e){for(var t={},r="",n=!1,i=0;i t.max&&(t.max=e),e 2&&void 0!==arguments[2])||arguments[2];super(e,r,j.t,n),c.il&&((0,t.OP)(e).initHidden=Boolean("hidden"===document.visibilityState),(0,N.N)((()=>(0,s.p)("docHidden",[(0,p.z)()],void 0,j.t,this.ee)),!0),(0,O.bP)("pagehide",(()=>(0,s.p)("winPagehide",[(0,p.z)()],void 0,j.t,this.ee))),this.importAggregator())}}var P=i(3081);class C extends h{static featureName=P.t9;constructor(e,t){let r=!(arguments.length>2&&void 0!==arguments[2])||arguments[2];super(e,t,P.t9,r),this.importAggregator()}}var R,I=i(2210),k=i(1214),H=i(2177),L={};try{R=localStorage.getItem("__nr_flags").split(","),console&&"function"==typeof console.log&&(L.console=!0,-1!==R.indexOf("dev")&&(L.dev=!0),-1!==R.indexOf("nr_dev")&&(L.nrDev=!0))}catch(e){}function z(e){try{L.console&&z(e)}catch(e){}}L.nrDev&&H.ee.on("internal-error",(function(e){z(e.stack)})),L.dev&&H.ee.on("fn-err",(function(e,t,r){z(r.stack)})),L.dev&&(z("NR AGENT IN DEVELOPMENT MODE"),z("flags: "+(0,b.D)(L,(function(e,t){return e})).join(", ")));var M=i(6660);class B extends h{static featureName=M.t;constructor(r,n){let i=!(arguments.length>2&&void 0!==arguments[2])||arguments[2];super(r,n,M.t,i),this.skipNext=0;try{this.removeOnAbort=new AbortController}catch(e){}const o=this;o.ee.on("fn-start",(function(e,t,r){o.abortHandler&&(o.skipNext+=1)})),o.ee.on("fn-err",(function(t,r,n){o.abortHandler&&!n[M.A]&&((0,I.X)(n,M.A,(function(){return!0})),this.thrown=!0,(0,s.p)("err",[n,(0,p.z)()],void 0,e.D.jserrors,o.ee))})),o.ee.on("fn-end",(function(){o.abortHandler&&!this.thrown&&o.skipNext>0&&(o.skipNext-=1)})),o.ee.on("internal-error",(function(t){(0,s.p)("ierr",[t,(0,p.z)(),!0],void 0,e.D.jserrors,o.ee)})),this.origOnerror=c._A.onerror,c._A.onerror=this.onerrorHandler.bind(this),c._A.addEventListener("unhandledrejection",(t=>{const r=function(e){let t="Unhandled Promise Rejection: ";if(e instanceof Error)try{return e.message=t+e.message,e}catch(t){return e}if(void 0===e)return new Error(t);try{return new Error(t+(0,D.P)(e))}catch(e){return new Error(t)}}(t.reason);(0,s.p)("err",[r,(0,p.z)(),!1,{unhandledPromiseRejection:1}],void 0,e.D.jserrors,this.ee)}),(0,O.m$)(!1,this.removeOnAbort?.signal)),(0,k.gy)(this.ee),(0,k.BV)(this.ee),(0,k.em)(this.ee),(0,t.OP)(r).xhrWrappable&&(0,k.Kf)(this.ee),this.abortHandler=this.#e,this.importAggregator()}#e(){this.removeOnAbort?.abort(),this.abortHandler=void 0}onerrorHandler(t,r,n,i,o){"function"==typeof this.origOnerror&&this.origOnerror(...arguments);try{this.skipNext?this.skipNext-=1:(0,s.p)("err",[o||new F(t,r,n),(0,p.z)()],void 0,e.D.jserrors,this.ee)}catch(t){try{(0,s.p)("ierr",[t,(0,p.z)(),!0],void 0,e.D.jserrors,this.ee)}catch(e){}}return!1}}function F(e,t,r){this.message=e||"Uncaught error with no additional information",this.sourceURL=t,this.line=r}let U=1;const q="nr@id";function G(e){const t=typeof e;return!e||"object"!==t&&"function"!==t?-1:e===c._A?0:(0,I.X)(e,q,(function(){return U++}))}function V(e){if("string"==typeof e&&e.length)return e.length;if("object"==typeof e){if("undefined"!=typeof ArrayBuffer&&e instanceof ArrayBuffer&&e.byteLength)return e.byteLength;if("undefined"!=typeof Blob&&e instanceof Blob&&e.size)return e.size;if(!("undefined"!=typeof FormData&&e instanceof FormData))try{return(0,D.P)(e).length}catch(e){return}}}var X=i(7243);class W{constructor(e){this.agentIdentifier=e,this.generateTracePayload=this.generateTracePayload.bind(this),this.shouldGenerateTrace=this.shouldGenerateTrace.bind(this)}generateTracePayload(e){if(!this.shouldGenerateTrace(e))return null;var r=(0,t.DL)(this.agentIdentifier);if(!r)return null;var n=(r.accountID||"").toString()||null,i=(r.agentID||"").toString()||null,o=(r.trustKey||"").toString()||null;if(!n||!i)return null;var a=(0,_.M)(),s=(0,_.Ht)(),c=Date.now(),u={spanId:a,traceId:s,timestamp:c};return(e.sameOrigin||this.isAllowedOrigin(e)&&this.useTraceContextHeadersForCors())&&(u.traceContextParentHeader=this.generateTraceContextParentHeader(a,s),u.traceContextStateHeader=this.generateTraceContextStateHeader(a,c,n,i,o)),(e.sameOrigin&&!this.excludeNewrelicHeader()||!e.sameOrigin&&this.isAllowedOrigin(e)&&this.useNewrelicHeaderForCors())&&(u.newrelicHeader=this.generateTraceHeader(a,s,c,n,i,o)),u}generateTraceContextParentHeader(e,t){return"00-"+t+"-"+e+"-01"}generateTraceContextStateHeader(e,t,r,n,i){return i+"@nr=0-1-"+r+"-"+n+"-"+e+"----"+t}generateTraceHeader(e,t,r,n,i,o){if(!("function"==typeof c._A?.btoa))return null;var a={v:[0,1],d:{ty:"Browser",ac:n,ap:i,id:e,tr:t,ti:r}};return o&&n!==o&&(a.d.tk=o),btoa((0,D.P)(a))}shouldGenerateTrace(e){return this.isDtEnabled()&&this.isAllowedOrigin(e)}isAllowedOrigin(e){var r=!1,n={};if((0,t.Mt)(this.agentIdentifier,"distributed_tracing")&&(n=(0,t.P_)(this.agentIdentifier).distributed_tracing),e.sameOrigin)r=!0;else if(n.allowed_origins instanceof Array)for(var i=0;i 2&&void 0!==arguments[2])||arguments[2];super(r,n,Z.t,i),(0,t.OP)(r).xhrWrappable&&(this.dt=new W(r),this.handler=(e,t,r,n)=>(0,s.p)(e,t,r,n,this.ee),(0,k.u5)(this.ee),(0,k.Kf)(this.ee),function(r,n,i,o){function a(e){var t=this;t.totalCbs=0,t.called=0,t.cbTime=0,t.end=E,t.ended=!1,t.xhrGuids={},t.lastSize=null,t.loadCaptureCalled=!1,t.params=this.params||{},t.metrics=this.metrics||{},e.addEventListener("load",(function(r){_(t,e)}),(0,O.m$)(!1)),c.IF||e.addEventListener("progress",(function(e){t.lastSize=e.loaded}),(0,O.m$)(!1))}function s(e){this.params={method:e[0]},T(this,e[1]),this.metrics={}}function u(e,n){var i=(0,t.DL)(r);i.xpid&&this.sameOrigin&&n.setRequestHeader("X-NewRelic-ID",i.xpid);var a=o.generateTracePayload(this.parsedOrigin);if(a){var s=!1;a.newrelicHeader&&(n.setRequestHeader("newrelic",a.newrelicHeader),s=!0),a.traceContextParentHeader&&(n.setRequestHeader("traceparent",a.traceContextParentHeader),a.traceContextStateHeader&&n.setRequestHeader("tracestate",a.traceContextStateHeader),s=!0),s&&(this.dt=a)}}function d(e,t){var r=this.metrics,i=e[0],o=this;if(r&&i){var a=V(i);a&&(r.txSize=a)}this.startTime=(0,p.z)(),this.listener=function(e){try{"abort"!==e.type||o.loadCaptureCalled||(o.params.aborted=!0),("load"!==e.type||o.called===o.totalCbs&&(o.onloadCalled||"function"!=typeof t.onload)&&"function"==typeof o.end)&&o.end(t)}catch(e){try{n.emit("internal-error",[e])}catch(e){}}};for(var s=0;s 1?e[1]=i:e.push(i)}else e[0]&&e[0].headers&&s(e[0].headers,n)&&(this.dt=n);function s(e,t){var r=!1;return t.newrelicHeader&&(e.set("newrelic",t.newrelicHeader),r=!0),t.traceContextParentHeader&&(e.set("traceparent",t.traceContextParentHeader),t.traceContextStateHeader&&e.set("tracestate",t.traceContextStateHeader),r=!0),r}}function x(e,t){this.params={},this.metrics={},this.startTime=(0,p.z)(),this.dt=t,e.length>=1&&(this.target=e[0]),e.length>=2&&(this.opts=e[1]);var r,n=this.opts||{},i=this.target;"string"==typeof i?r=i:"object"==typeof i&&i instanceof Y?r=i.url:c._A?.URL&&"object"==typeof i&&i instanceof URL&&(r=i.href),T(this,r);var o=(""+(i&&i instanceof Y&&i.method||n.method||"GET")).toUpperCase();this.params.method=o,this.txSize=V(n.body)||0}function A(t,r){var n;this.endTime=(0,p.z)(),this.params||(this.params={}),this.params.status=r?r.status:0,"string"==typeof this.rxSize&&this.rxSize.length>0&&(n=+this.rxSize);var o={txSize:this.txSize,rxSize:n,duration:(0,p.z)()-this.startTime};i("xhr",[this.params,o,this.startTime,this.endTime,"fetch"],this,e.D.ajax)}function E(t){var r=this.params,n=this.metrics;if(!this.ended){this.ended=!0;for(var o=0;o 2&&void 0!==arguments[2])||arguments[2];super(e,t,we.t,r),this.importAggregator()}}new class{constructor(e){let t=arguments.length>1&&void 0!==arguments[1]?arguments[1]:(0,_.ky)(16);c._A?(this.agentIdentifier=t,this.sharedAggregator=new y({agentIdentifier:this.agentIdentifier}),this.features={},this.desiredFeatures=new Set(e.features||[]),this.desiredFeatures.add(m),Object.assign(this,(0,a.j)(this.agentIdentifier,e,e.loaderType||"agent")),this.start()):(0,l.Z)("Failed to initial the agent. Could not determine the runtime environment.")}get config(){return{info:(0,t.C5)(this.agentIdentifier),init:(0,t.P_)(this.agentIdentifier),loader_config:(0,t.DL)(this.agentIdentifier),runtime:(0,t.OP)(this.agentIdentifier)}}start(){const t="features";try{const r=n(this.agentIdentifier),i=[...this.desiredFeatures];i.sort(((t,r)=>e.p[t.featureName]-e.p[r.featureName])),i.forEach((t=>{if(r[t.featureName]||t.featureName===e.D.pageViewEvent){const n=function(t){switch(t){case e.D.ajax:return[e.D.jserrors];case e.D.sessionTrace:return[e.D.ajax,e.D.pageViewEvent];case e.D.sessionReplay:return[e.D.sessionTrace];case e.D.pageViewTiming:return[e.D.pageViewEvent];default:return[]}}(t.featureName);n.every((e=>r[e]))||(0,l.Z)("".concat(t.featureName," is enabled but one or more dependent features has been disabled (").concat((0,D.P)(n),"). This may cause unintended consequences or missing data...")),this.features[t.featureName]=new t(this.agentIdentifier,this.sharedAggregator)}})),(0,T.Qy)(this.agentIdentifier,this.features,t)}catch(e){(0,l.Z)("Failed to initialize all enabled instrument classes (agent aborted) -",e);for(const e in this.features)this.features[e].abortHandler?.();const r=(0,T.fP)();return delete r.initializedAgents[this.agentIdentifier]?.api,delete r.initializedAgents[this.agentIdentifier]?.[t],delete this.sharedAggregator,r.ee?.abort(),delete r.ee?.get(this.agentIdentifier),!1}}}({features:[J,m,S,class extends h{static featureName=oe;constructor(t,r){if(super(t,r,oe,!(arguments.length>2&&void 0!==arguments[2])||arguments[2]),!c.il)return;const n=this.ee;let i;(0,k.QU)(n),this.eventsEE=(0,k.em)(n),this.eventsEE.on(se,(function(e,t){this.bstStart=(0,p.z)()})),this.eventsEE.on(ae,(function(t,r){(0,s.p)("bst",[t[0],r,this.bstStart,(0,p.z)()],void 0,e.D.sessionTrace,n)})),n.on(ce+ne,(function(e){this.time=(0,p.z)(),this.startPath=location.pathname+location.hash})),n.on(ce+ie,(function(t){(0,s.p)("bstHist",[location.pathname+location.hash,this.startPath,this.time],void 0,e.D.sessionTrace,n)}));try{i=new PerformanceObserver((t=>{const r=t.getEntries();(0,s.p)(te,[r],void 0,e.D.sessionTrace,n)})),i.observe({type:re,buffered:!0})}catch(e){}this.importAggregator({resourceObserver:i})}},C,xe,B,class extends h{static featureName=de;constructor(e,r){if(super(e,r,de,!(arguments.length>2&&void 0!==arguments[2])||arguments[2]),!c.il)return;if(!(0,t.OP)(e).xhrWrappable)return;try{this.removeOnAbort=new AbortController}catch(e){}let n,i=0;const o=this.ee.get("tracer"),a=(0,k._L)(this.ee),s=(0,k.Lg)(this.ee),u=(0,k.BV)(this.ee),d=(0,k.Kf)(this.ee),f=this.ee.get("events"),l=(0,k.u5)(this.ee),h=(0,k.QU)(this.ee),g=(0,k.Gm)(this.ee);function m(e,t){h.emit("newURL",[""+window.location,t])}function v(){i++,n=window.location.hash,this[ve]=(0,p.z)()}function b(){i--,window.location.hash!==n&&m(0,!0);var e=(0,p.z)();this[pe]=~~this[pe]+e-this[ve],this[ye]=e}function y(e,t){e.on(t,(function(){this[t]=(0,p.z)()}))}this.ee.on(ve,v),s.on(be,v),a.on(be,v),this.ee.on(ye,b),s.on(ge,b),a.on(ge,b),this.ee.buffer([ve,ye,"xhr-resolved"],this.featureName),f.buffer([ve],this.featureName),u.buffer(["setTimeout"+le,"clearTimeout"+fe,ve],this.featureName),d.buffer([ve,"new-xhr","send-xhr"+fe],this.featureName),l.buffer([me+fe,me+"-done",me+he+fe,me+he+le],this.featureName),h.buffer(["newURL"],this.featureName),g.buffer([ve],this.featureName),s.buffer(["propagate",be,ge,"executor-err","resolve"+fe],this.featureName),o.buffer([ve,"no-"+ve],this.featureName),a.buffer(["new-jsonp","cb-start","jsonp-error","jsonp-end"],this.featureName),y(l,me+fe),y(l,me+"-done"),y(a,"new-jsonp"),y(a,"jsonp-end"),y(a,"cb-start"),h.on("pushState-end",m),h.on("replaceState-end",m),window.addEventListener("hashchange",m,(0,O.m$)(!0,this.removeOnAbort?.signal)),window.addEventListener("load",m,(0,O.m$)(!0,this.removeOnAbort?.signal)),window.addEventListener("popstate",(function(){m(0,i>1)}),(0,O.m$)(!0,this.removeOnAbort?.signal)),this.abortHandler=this.#e,this.importAggregator()}#e(){this.removeOnAbort?.abort(),this.abortHandler=void 0}}],loaderType:"spa"})})(),window.NRBA=o})(); window.jQuery || document.write(' ') CKEDITOR_BASEPATH='https://f1000research.com/js/vendor/ckeditor/' window.reactTheme = 'research'; window.MathJax = { CommonHTML: { linebreaks: { automatic: true } }, 'HTML-CSS': { linebreaks: { automatic: true } }, SVG: { linebreaks: { automatic: true } }, AuthorInit: function() { MathJax.Hub.Register.MessageHook('End Process', function () { let timeout = false; // holder for timeout id const delay = 250; // delay after event is "complete" to run callback const reflowMath = function() { const dispFormulas = document.querySelectorAll('.disp-formula.panel'); if (!dispFormulas) { return; } for (const dispFormula of dispFormulas) { const child = dispFormula.querySelector('.MathJax_Preview').nextSibling.firstChild; const isMultiline = MathJax.Hub.getAllJax(dispFormula)[0].root.isMultiline; if (dispFormula.offsetWidth < child.offsetWidth || isMultiline) { MathJax.Hub.Queue(['Rerender', MathJax.Hub, dispFormula]); } } }; window.addEventListener('resize', function() { clearTimeout(timeout); // clear the timeout timeout = setTimeout(reflowMath, delay); // start timing for event "completion" }); }); }, }; if (window.location.hash == '#_=_'){ window.location = window.location.href.split('#')[0] } !function(f,b,e,v,n,t,s){if(f.fbq)return;n=f.fbq=function() {n.callMethod? n.callMethod.apply(n,arguments):n.queue.push(arguments)} ;if(!f._fbq)f._fbq=n; n.push=n;n.loaded=!0;n.version='2.0';n.queue=[];t=b.createElement(e);t.async=!0; t.src=v;s=b.getElementsByTagName(e)[0];s.parentNode.insertBefore(t,s)}(window, document,'script','https://connect.facebook.net/en_US/fbevents.js'); fbq('init', '1641728616063202'); fbq('track', "PixelInitialized", {}); (function(h,o,t,j,a,r){ h.hj=h.hj||function(){(h.hj.q=h.hj.q||[]).push(arguments)}; h._hjSettings={hjid:2318163,hjsv:6}; a=o.getElementsByTagName('head')[0]; r=o.createElement('script');r.async=1; r.src=t+h._hjSettings.hjid+j+h._hjSettings.hjsv; a.appendChild(r); })(window,document,'https://static.hotjar.com/c/hotjar-','.js?sv='); search file_upload Submit your research search menu close search Browse Gateways & Collections How to Publish Submit your Research My Submissions Article Guidelines Article Guidelines (New Versions) Open Data, Software and Code Guidelines Open Data and Accessible Source Materials Guidelines (HSS) Open Data, Software and Code Guidelines (PSE) Prepublication Checks Production Process Posters and Slides Guidelines Document Guidelines Article Processing Charges Peer Review Finding Article Reviewers About How it Works For Reviewers Our Advisors Policies Glossary FAQs For Developers Newsroom Contact My Research Submissions Content and Tracking Alerts My Details Sign In file_upload Submit your research <input type="hidden" id="meta-article-title" value="New insights about the serine/threonine protein kinase substrates from Mycobacterium tuberculosis using molecular docking, quantum similarity analysis and DFT calculations" /> { "@context": "https://schema.org", "@type": "ScholarlyArticle", "mainEntityOfPage": { "@type": "WebPage", "@id": "https://f1000research.com/articles/10-66" }, "headline": "New insights about the serine/threonine protein kinase substrates from Mycobacterium tuberculosis using...", "datePublished": "2021-02-03T11:57:43", "dateModified": "2021-02-03T11:57:43", "author": [ { "@type": "Person", "name": "Alejandro Morales-Bayuelo" }, { "@type": "Person", "name": "Jesús Sánchez-Márquez" } ], "publisher": { "@type": "Organization", "name": "F1000Research", "logo": { "@type": "ImageObject", "url": "https://f1000research.com/img/AMP/F1000Research_image.png", "height": 480, "width": 60 } }, "image": { "@type": "ImageObject", "url": "https://f1000research.com/img/AMP/F1000Research_image.png", "height": 1200, "width": 150 }, "description": "Background: The protein kinases present in the human body have received a lot of attention because of the interest in their use as therapeutic targets. However, little is known about the protein kinases associated with tuberculosis. For these reasons, this research investigates a new point of view regarding the crystallized serine/threonine protein kinases Pkn A, B and G of Mycobacterium tuberculosis. Methods: The conformational analysis shows a DFG-in motif in Pkn B and G and a DFG-out motif in Pkn A. For all the protein kinases that have been studied, the gatekeeper residue is methionine. A study of the protein kinases with their ligands was also conducted to find new insights on the binding site with a series of ligands associated to protein kinases Pkn A, B and G through molecular docking. The residues with hydrogen bonds on the hinge zone of Pkn A are GLU96 and VAL 98, of Pkn B are GLU 93 and VAL 95 and of Pkn G are GLU233 and VAL235. Results: The results show the H-bond acceptor and H-bond donor sites on the hinge zone to all ligands, establishing a structural model of the ligands on the active site with two or three interactions in this zone. This interaction model was validated using density functional theory calculations (by means of net charges and images of the electrostatic potential) and molecular quantum similarity analysis, showing a high correlation between the electronic and steric effects in each ATP complex studied. Conclusions: In this work we can see that the interactions of the hinge zone are characterized by the key factor of one or two H-bonds acceptors and one H-bond donor in the ligands of this zone. The quantum similarity analysis shows good correlation between the steric and electronic effects in each ATP complex." } { "@context": "http://schema.org", "@type": "BreadcrumbList", "itemListElement": [ { "@type": "ListItem", "position": "1", "item": { "@id": "https://f1000research.com/", "name": "Home" } }, { "@type": "ListItem", "position": "2", "item": { "@id": "https://f1000research.com/browse/articles", "name": "Browse" } }, { "@type": "ListItem", "position": "3", "item": { "@id": "https://f1000research.com/articles/10-66/v1", "name": "New insights about the serine/threonine protein kinase substrates..." } } ] } Home Browse New insights about the serine/threonine protein kinase substrates... ALL Metrics - Views Downloads Get PDF Get XML Cite How to cite this article Morales-Bayuelo A and Sánchez-Márquez J. New insights about the serine/threonine protein kinase substrates from Mycobacterium tuberculosis using molecular docking, quantum similarity analysis and DFT calculations [version 1; peer review: 1 approved] . F1000Research 2021, 10 :66 ( https://doi.org/10.12688/f1000research.28078.1 ) NOTE: If applicable, it is important to ensure the information in square brackets after the title is included in all citations of this article. Close Copy Citation Details Export Export Citation Sciwheel EndNote Ref. Manager Bibtex ProCite Sente EXPORT Select a format first Track Share ▬ ✚ Research Article New insights about the serine/threonine protein kinase substrates from Mycobacterium tuberculosis using molecular docking, quantum similarity analysis and DFT calculations [version 1; peer review: 1 approved] Alejandro Morales-Bayuelo https://orcid.org/0000-0001-9385-7414 1 , Jesús Sánchez-Márquez 2 Alejandro Morales-Bayuelo https://orcid.org/0000-0001-9385-7414 1 , Jesús Sánchez-Márquez 2 PUBLISHED 03 Feb 2021 Author details Author details 1 Centro de Investigación de Procesos del Tecnológico Comfenalco (CIPTEC), Fundación UNiversitaria Tecnologico Comfenalco, Cartagena de Indias, Colombia 2 Departamento de Química-Física, Facultad de Ciencias, Universidad de Cádiz, Cádiz, Spain Alejandro Morales-Bayuelo Roles: Conceptualization, Formal Analysis, Investigation, Methodology Jesús Sánchez-Márquez Roles: Conceptualization, Formal Analysis, Investigation OPEN PEER REVIEW DETAILS REVIEWER STATUS This article is included in the Cheminformatics gateway. Abstract Background : The protein kinases present in the human body have received a lot of attention because of the interest in their use as therapeutic targets. However, little is known about the protein kinases associated with tuberculosis. For these reasons, this research investigates a new point of view regarding the crystallized serine/threonine protein kinases Pkn A, B and G of Mycobacterium tuberculosis . Methods : The conformational analysis shows a DFG-in motif in Pkn B and G and a DFG-out motif in Pkn A. For all the protein kinases that have been studied, the gatekeeper residue is methionine. A study of the protein kinases with their ligands was also conducted to find new insights on the binding site with a series of ligands associated to protein kinases Pkn A, B and G through molecular docking. The residues with hydrogen bonds on the hinge zone of Pkn A are GLU96 and VAL 98, of Pkn B are GLU 93 and VAL 95 and of Pkn G are GLU233 and VAL235. Results : The results show the H-bond acceptor and H-bond donor sites on the hinge zone to all ligands, establishing a structural model of the ligands on the active site with two or three interactions in this zone. This interaction model was validated using density functional theory calculations (by means of net charges and images of the electrostatic potential) and molecular quantum similarity analysis, showing a high correlation between the electronic and steric effects in each ATP complex studied. Conclusions: In this work we can see that the interactions of the hinge zone are characterized by the key factor of one or two H-bonds acceptors and one H-bond donor in the ligands of this zone. The quantum similarity analysis shows good correlation between the steric and electronic effects in each ATP complex. READ ALL READ LESS Keywords Mycobacterium tuberculosis, Serine/Threonine Protein Kinases A, B, G, Molecular Docking, Molecular Quantum Similarity Analysis, Electrostatic Interactions. Corresponding Author(s) Alejandro Morales-Bayuelo ( [email protected] ) Jesús Sánchez-Márquez ( [email protected] ) Close Corresponding authors: Alejandro Morales-Bayuelo, Jesús Sánchez-Márquez Competing interests: No competing interests were disclosed. Grant information: Fundación Universitaria Tecnológico Comfenalco (Cartagena, Colombia), Project Inv-2020. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Copyright: © 2021 Morales-Bayuelo A and Sánchez-Márquez J. This is an open access article distributed under the terms of the Creative Commons Attribution License , which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. How to cite: Morales-Bayuelo A and Sánchez-Márquez J. New insights about the serine/threonine protein kinase substrates from Mycobacterium tuberculosis using molecular docking, quantum similarity analysis and DFT calculations [version 1; peer review: 1 approved] . F1000Research 2021, 10 :66 ( https://doi.org/10.12688/f1000research.28078.1 ) First published: 03 Feb 2021, 10 :66 ( https://doi.org/10.12688/f1000research.28078.1 ) Latest published: 03 Feb 2021, 10 :66 ( https://doi.org/10.12688/f1000research.28078.1 ) Introduction Protein kinases (PKs) are a key in controlling proliferation and differentiation in eukaryotic cells in living organisms. They are enzymes that catalyze the protein phosphorylation process. An important reason to analyse the protein phosphorylation process is that it represents an attractive drug target in a variety of fatal diseases such as cancer 1 . The PKs present in the human body have been widely used in the field of drug design because they play an important role as therapeutic targets in these diseases. However, little is known about the serine/threonine protein kinases (STPKs) involved in tuberculosis. For this reason, we propose a study about crystalized STPKs Pkn A, B and G, to gain new insights in the mechanism of the phosphorylation process. To date, one of the main questions in the tuberculosis field is ‘what are the protein substrates of the STPKs?’ According to Av-Gay et al. 2 , to deal with this topic we need to study the interactions of crystalized STPKs Pkn A, B and G with a particular series of ligands to each PK. The competitive ATP ligands used are a series of compounds for Pkn A reported by Sipos et al. 3 , ligands for Pkn B reported by Székely et al. 4 , Loughheed et al. 5 and Chapman et al. 6 and ligands for Pkn G reported by Sipos et al. 3 and Pato et al. 7 . These ligands were selected with the goal of finding new insights into the inhibition of oxidative phosphorylation. Therefore, we are researching new pharmacological alternatives for this disease through the structural models of the ligands on the ATP sites. Another aim of this study is to conduct molecular quantum similarity (MQS) analysis using a quantum similarity field to understand the electronic and structural patterns involved in stabilization of the active site of the inhibitors for each PK studied. Therefore, a hybrid quantum mechanics/molecular mechanics (QM/MM) approach was used to carry out a structure-activity relationship analysis of the inhibitor set for Pkn A, Pkn B and Pkn G. Methods Pkn A, B and G: docking of their ATP-competitive inhibitors The crystal structures of Pkn A (PBD code: 4OW8 , resolution: 2.03 Å 8 ), Pkn B1 (PDB code: 3F69 , resolution: 2.80 Å 9(a) ), Pkn B2 (PDB code: 1MRU , resolution: 3.0 Å 9(b) ), Pkn B3 (PDB code: 2FUM , resolution: 2.89 Å 9(c) ) and Pkn G (PBD code: 2PZI , resolution: 2.40 Å 10 ) were selected for the preparation process using Schrödinger Suite 2014-1’s Protein Preparation Wizard module 11 , which refines the protein structure and optimizes the hydrogen bond (H-bond) network. The open-source software AutoDock Vina could also be used to perform these steps. Protonation states were identified using PropKa utility at a physiological pH 12 . After, restrained molecular minimization using the Impact Refinement (Impref) module 13 was carried out, taking into account the heavy atoms restrained within a root-mean-square deviation (RMSD) of 0.18 Å from the initial coordinates. The main characteristics of Pkn A and B consist of a transmembrane receptor with a tyrosine kinase domain protruding into the cytoplasm. For Pkn G, the unique multidomain topology of this PK reveals a central kinase domain that is flanked by N- and C-terminal rubredoxin and tetratrico-peptide repeat domains, respectively 13 , 14 . The molecular datasets used for the docking study were reported by Sipos et al. 4 , Székely et al. 5 , Lougheed et al. 6 , Chapman et al. 7 and finally Pato et al. 8 (see Table 1 – Table 6 ). To select this molecular dataset, the structural diversity and uniform distribution of IC 50 was taken into account. Logarithmic IC 50 (μM) (pIC 50 =−log IC 50 ) was employed as the dependent variable instead of IC 50 . The 3D molecular structures of the compounds were drawn and optimized using Maestro 15 and then prepared with the LigPrep module 16 , where ionization/tautomeric states were predicted at physiological pH conditions using Epik 17 . Afterwards, energy minimization was performed using Macromodel 18 with the OPLS2005 force field. The open-source software AutoDock Vina could also be used to perform these steps. Table 1. Structures and pIC 50 values of the Pkn A ligands. Compound a Structure pIC 50 1 -1.568 2 -1.839 3 -1.875 4 -1.934 a Compounds to Pkn A reported by Sipos et al. 4 Table 2. Structures and pIC 50 values of the Pkn B ligands. Compound Structure pIC 50 5 a , b -0.585 Pkn G:1.301 6 a 0.569 7 a 0.086 8 a 0.585 9 a 0.237 10 c -0.375 11 d 1.276 12 d 1.252 13 d 1.046 14 d 0.285 15 d -1.219 16 d -0.1758 17 d 0.462 18 d 1.259 19 d 1.017 20 d 1.036 21 d -0.792 22 d 1.187 a Compounds to Pkn A reported by Sipos et al. 4 b This compound has biological activity to Pkn B and G. Sipos et al. 4 c Compound to Pkn B reported by Székely et al. 5 d Compound to Pkn B reported by Loughheed et al. 6 Table 3. Structures and pIC 50 values of the Pkn B ligands. Compound a R 1 NHR 2 pIC 50 23 0.492 24 0.344 25 -0.065 26 0.652 27 0.357 28 0.971 29 0,369 30 - 0.426 31 - 0,416 32 - 0.406 33 - 1.066 34 - 0.618 35 - 1.060 36 - 0.695 37 - 1.076 38 - 0.451 39 - 0.146 40 - 1.130 41 - 1.194 42 - 0.664 43 - 0.939 a Compounds to Pkn B reported by Chapman et al. 7 Table 4. Structures and pIC 50 values of the Pkn B ligands. Compound a NR 1 R 2 or OR 1 R 3 pIC 50 44 - 1.056 45 - 0.917 46 - 1.260 47 - 1.137 48 - 1.276 49 - 1.252 50 CN 1.252 51 CN 1.409 52 CN 1.638 53 SO 2 Me 1.398 a Compounds to Pkn B reported by Chapman et al. 7 Table 5. Structures and pIC 50 values of the Pkn B ligands. Compound a R 1 R 2 pIC 50 54 H CN -0.299 55 OMe H -0.053 56 Cl H 0.754 57 CF 3 CN 1.398 a Compounds to Pkn B reported by Chapman et al. 7 Table 6. Structures and pIC 50 values of the Pkn G ligands. C R 1 R 2 R 3 R 4 R 5 X Bond C 3 -X Bond C 1 -C 2 pIC 50 58 a cyclopropyl H H H NH C C 3 -X C 1 -C 2 0.523 59 a cyclohexyl H - H NH O C 3 -X C 1 -C 2 0.167 60 a cyclopropyl H - H NH O C 3 -X C 1 -C 2 0.276 61 a isopropyl H -OH H NH C C 3 =X C 1 =C 2 1.523 62 a cyclopropyl Br -OH H NH C C 3 =X C 1 =C 2 1.699 63 a methy-cyclopropyl Cl -OH H NH C C 3 =X C 1 =C 2 1.699 64 a methy-cyclopropyl Cl -OH H NH C C 3 =X C 1 =C 2 1.699 65 a cyclopropyl Cl -OCH 3 Cl NH C C 3 =X C 1 =C 2 1.398 66 a 1,3-benzodioxole Cl -OH H NH C C 3 =X C 1 =C 2 2.000 67 a methy-cyclopropyl H -OH H NH C C 3 =X C 1 =C 2 1.301 68 a methy-cyclopropyl H -OH H NH C C 3 =X C 1 =C 2 1.301 69 b p-methylbenzoate H H H NH C C 3 -X C 1 -C 2 0.699 70 b isopropyl H H H NH C C 3 -X C 1 -C 2 -0.478 71 b Cyclobutyl H H H NH C C 3 -X C 1 -C 2 -0.477 72 b methyl-isopropyl H H H NH C C 3 -X C 1 -C 2 -1.176 73 b cyclopropyl H -Me H NH C C 3 -X C 1 -C 2 0.046 74 b -Me H -Me H NH C C 3 -X C 1 -C 2 -1.079 75 b cyclopropyl H H H NH S C 3 -X C 1 -C 2 -0.301 76 b Furanyl H H H C 2 H 4 OH C C 3 -X C 1 -C 2 -1.204 77 b cyclopropyl H H H OH C C 3 -X C 1 -C 2 -1.279 a Compounds to Pkn G reported by Sipos et al. 4 b Compounds to Pkn G reported by Pato et al. 8 Docking studies were performed with the software Glide 18 using standard precision (SP) mode and default parameters. The open-source software AutoDock Vina could also be used to obtain similar results. The docking grid was generated with standard protocol centered at the co-crystallized ligand. Due to that, the scaling factor for the van der Waals interactions is very important it was taken as 0.8. The radii of nonpolar protein atoms were selected to allow the binding of larger ligands. Further, the induced fit docking (IFD) workflow 19 was also used to generate a good number of conformations of the receptor suitable for binding ligands that had strange orientations. It allows the protein to undergo side-chain movements, backbone movements, or both, upon ligand docking. The docking procedure has four steps where accuracy is ensured by Glide’s scoring function and Prime’s: (i) The first step for Glide docking is carry out into the rigid receptor to generate a good ensemble of poses. (ii) Analysis of the protein using Prime 21 . Taking into account side-chain prediction module followed by a structure energy minimization of each protein/ligand complex pose. (iii) Analysis through re-docking of the ligand into low energy induced-fit structures taking in account the previous step using default Glide settings (no vdW scaling). (iv) Finally, the binding energy is estimated using (IFDScore) by accounting for the docking energy (GScore), as well as receptor strain and some solvation terms (Prime energy). To obtain the docking outcomes, the dynamics simulation of 100ns in vacuo using the GROMOS11 force field set was used on the protein–ligand complex, using Gromacs 5.1.2 20 to analyze the stability of the protein–ligand complexes 22 . MQS analysis In recent studies, MQS methodology has shown good results in understanding steric and electronic effects of ligands 23 , 24 . The MQS field was introduced by Carbó and co-workers 30 years ago 25 – 30 and has been used to understand the steric and electronic effect on the molecular sets. The mathematic relationship to obtain quantum similarity Z AB between two compounds A and B, with electron density ρ A ( r 1 ) and ρ B ( r 2 ) is defined using the minimization of the expression for the Euclidean distance as: D A B = ( ∫ | ρ A ( r ) − ρ B ( r ) | 2 d r ) 1 / 2 = ( ∫ ( ρ A ( r 1 ) ) 2 d r 1 + ∫ ( ρ B ( r 2 ) ) 2 d r 2 − 2 ∫ ρ A ( r 1 ) ρ B ( r 2 ) d r 1 d r 2 ) 1 / 2 = ( Z A A + Z B B − 2 Z A B ) 1 / 2 ( 1 ) Therefore, the Euclidean distance is the square root of the integral on the squared differences between the densities ρ A ( r 1 ) and ρ B ( r 2 ). In this context, Z AB represents the similarity measure between the electronic densities of the compounds A and B, and Z AA and Z BB are the self-similarity of compounds A and B 31 . The similarity index very often used is the Carbó index 31 . This index is expressed as follows: I A B = ∫ ρ A ( r 1 ) ρ B ( r 2 ) d r 1 d r 2 ( ∫ ( ρ A ( r 1 ) ) 2 d r 1 ∫ ( ρ B ( r 2 ) ) 2 d r 2 ) 1 / 2 = Z A B ( Ω ) ( Z A A ( Ω ) Z B B ( Ω )) 1 / 2 ( 2 ) In Equation 2 , (Ω) represents an operator. A simple way to make quantum similarity measures (QSM) 29 – 31 involving two density functions, in the most usual form, is expressed as an integral: Z A B ( Ω ) = ∫ ∫ ( ρ A ( r 1 ) Ω ( r 1 , r 2 ) ρ B ( r 2 ) d r 1 d r 2 ( 3 ) In this equation ρ A ( r 1 ) and ρ B ( r 2 ) are the density functions to quantum objects A and B, while Ω ( r 1 , r 2 ) is a positive operator that defines weight. The Dirac delta function: δ ( r 1 – r 2 ) is used to obtain the overlap similarity measure and to measure the Coulomb similarity the Coulomb operator: | r 1 – r 2 | -1 is used. These operators are the most useful for obtaining similarity comparisons between ligands. Molecular alignment An important factor when carrying out the QSM is an optimal molecular alignment. As the integrals associated to the QSM produce, in any case, real positive results, the relative position problem can be approached using a maximal QSM. An overlap QSM can be expressed according to the equation: max ⁡ T ; ϕ Z A B ( T ; ϕ ) = max ⁡ T ; ϕ ∫ ρ A ( r ) ρ B ( r | T ; ϕ ) d r ( 4 ) In this equation, it is implicitly supposed that ρ B ( r ) is translated and rotated by the six possible ways: (T;φ) and are shown as explicit parameters in this integral 31 . This key factor was applied using the topo geometrical superposition algorithm (TGSA) 31 . Density functional theory (DFT) calculations The calculations of this study were performed with the GAUSSIAN 09 program 32 . The open-source software AutoDock Vina could also be used to obtain similar results. The structures were optimized using the B3LYP functional (DFT exchange-correlation method) 33 , 34 and the 6-31G(d,p) basis set 35 . The contour lines of the molecular electrostatic potential have been obtained with the GaussView program 36 . Results and discussion Pkn A, B and G: docking of their ATP-competitive inhibitors The conformational analysis of the STPKs defines the active and inactive form. These forms are also known as the DFG-in and DFG-out states. They are distinguishable by a flip of the Asp and Phe orientation in the activation loop as well as conformational changes in the surrounding loops 37 . The main difference between DFG-in and DFG-out conformations is that the different position of the DFG residue in the “out” form results in the opening of an additional cavity, the allosteric site, which can be hydrophobic in nature according to Zuccotto et al. 38 . In Pkn A the Asp side chain is buried and the Phe side chain is flipped outside the pocket. Therefore, Pkn A becomes DFG-out. However, in the STPKs Pkn B1 (crystal: 1MRU), Pkn B2 (crystal: 2FUM) and Pkn B3 (crystal: 3F69), the Asp side chain is exposed and the Phe side chain is buried (DFG-in), allowing ATP binding. Pkn G has DLG (Asp-Leu-Gly) instead of DFG (see Figure 1 ); the conformation is DLG-in. An important residue of STPKs is the gatekeeper. Their size determines the access of small, medium and large inhibitors to the back cavity even from the DFG-in state. In these crystallized PKs, the gatekeeper residues are MET95 for Pkn A, MET92 for Pkn B1 (crystal: 3F69), Pkn B2 (crystal: 1MRU), Pkn B3 (crystal: 2FUM), and MET232 for Pkn G. The methionine is a medium gatekeeper residue, according to Zuccotto et al. 38 and allows access to small, medium and large inhibitors. This characteristic is important because it increases the range of molecular diversity in the development of new inhibitors. Figure 1. DFG conformational analysis and gatekeeper residues to STPKs crystalized from Mycobacterium tuberculosis for ( A ) Pkn A, ( B ) Pkn B and ( C ) Pkn G. Hydrogen-bond-acceptor map (red mesh) for ( D ) Pkn A, ( E ) Pkn B and ( F ) Pkn G. Hydrogen-bond donor map (blue mesh) for ( G ) Pkn A, ( H ) Pkn B and ( I ) Pkn G. Hydrophobic map for ( J ) Pkn, ( K ) Pkn B and ( L ) Pkn G. Note: map sites were calculated using SiteMAP in Maestro. The open-source software AutoDock Vina could also be used to obtain similar results. In Figure 1D, 1E and 1F we can see the hydrogen-bond-acceptor maps in red mesh. Pkn A shows a small red contour on the hinge zone ( Figure 1D ), a medium contour near to the DFG motif and a large contour near to the helix-αC and C-terminal loop. This is unlike Pkn B, which, using the crystal 3F69 ( Figure 1E ), shows only acceptor maps near to the DFG motif and in the C-terminal loop. Pkn G ( Figure 1F ) has large acceptor contours involving the hinge zone, DLG zone, helix-αC and C-terminal loop. Figure 1G, 1H and 1I shows the hydrogen-bond donor maps in blue mesh. In Pkn A ( Figure 1G ) we can see medium contours to hydrogen-bond donor on the hinge zone and C-terminal loop and a large contour near the DFG motif. In contrast, Pkn B ( Figure 1H ) shows only a large contour near to the DFG motif. Pkn G ( Figure 1I ) has small contours to hydrogen-bond donors along the hinge zone and near the DLG motif, helix-αC, C-terminal and N-terminal loops. Analyses of hydrophobicity are shown in Figure 1J, 1K and 1L . Figure 1J shows a large contour of hydrophobicity for Pkn A near to the hinge zone and small contours on the C-terminal loop. Pkn B ( Figure 1K ) has only a small contour on the C-terminal loop. In contrast, Pkn G ( Figure 1J ) shows a large contour near the hinge zone, DLG motif and small contours near to the helix-αC and C-terminal loop. These physical-chemistry properties are important to describe the non-covalent stabilization on the active sites and selectivity of the ligands in the active pocket. Pkn A: Descriptions of the structural characteristics of ATP binding sites and docking of inhibitors To obtain the docking outcomes, hydrogen bonds on the hinge zone and non-covalent interactions near the “gatekeeper door”, helix-αC, C-terminal and N-terminal were analyzed. An important insight are the non-covalent interactions. Theses interactions involved backbone, side chain hydrogen bonds and aromatic-aromatic interactions. On the other hand, the ligands with high scores have these characteristics in their non-covalent interactions. The ligands with lower scores have few to no interaction forces. Further, some of the higher scoring ligands forming hydrogen bonds and aromatic-aromatic interactions with the amino acid residues are related to the hinge zone. Figure 2 shows the docking interactions of the Pkn A inhibitors from Table 1 . These compounds have groups with electron withdrawing resonance effects such as nitro, amine, carbonyl groups and electron donating groups such as methylene. Figure 2. Interactions on the hinge zone of compound 1 ( A ) and compounds 2-4 aligned ( B ), from Table 1 . In Figure 2A we can see the hydrogen bonds on the hinge zone to compound 1 ( Table 1 ). This compound has two interactions on the hinge zone with the residues Glu96, Val98 of 2.29 Å and 2.54 Å, respectively. Another hydrogen bond can be formed with the residue Asn104 of 1.98 Å. Compounds 2, 3 and 4, see Figure 2B , have differences only in the substituent group, in the case of 3, this is a pyrrole ring and in 4, is the dimethyl-amine group. In this series, the most active compound is 2, with pIC 50 -1.839. These compounds show two hydrogen bonds on the hinge zone with residues Glu96 and Val98 of 1.31 Å and 2.30 Å to 2, 1.71 Å and 2.35 Å to 3 and 1.81 Å and 2.21 Å to 4. Another hydrogen bond can also be formed with the residue Gly145 of 2.22 Å to 2, 1.81 Å to 3 and 1.95 Å to 4. From these results, we can see the key factor to the stabilization of the active site in this ligand set, with the main characteristic of one H-bond acceptor and H-bond donor in this zone. Figure 3 (left) and Figure 4 show, respectively, the atomic charges calculated by the CHelpG population and electrostatic potential analyses of compound 1 in some areas of special interest. The net charges obtained for H22, O24, O30 and O31 are consistent with the formation of hydrogen bonds shown in Figure 2A . The electrostatic potential surfaces shown in Figure 4 also justify the formation of hydrogen bonds with Glu96, Val98 and Asn104. Figure 3 (right) and Figure 5 show, respectively, the atomic charges and electrostatic potential of compound 4. The atomic charges of H27, H42 and H15 justify very well the formation of hydrogen bonds with Glu96, Val98 and Asn104 that can be seen in Figure 2B . An equivalent conclusion can be found from the electrostatic potential surfaces shown in Figure 5 . Figure 3. CHelpG charges calculated for compounds 1 (left) and 4 (right). Figure 4. Molecular electrostatic potential contour lines of compound 1. Figure 5. Molecular electrostatic potential contour lines of compound 4. Pkn B: Descriptions of the structural characteristics of ATP binding sites and docking of inhibitors The compounds to Pkn B have groups with electron withdrawing resonance effects, such as carbonyl, hydroxyl, amine and methoxy groups, with big rings central to its stabilization on the active site. Figure 6 shows the docking results of the Pkn B inhibitors from Table 2 – Table 5 , grouped by series, taking into account their functional groups and structural similarities. Figure 6A shows compound 5, which has interactions in the hinge zone with the residues Glu93 (2.63Å) and Val95 (-CO: 2.46Å, -NH: 1.99Å, 2.16Å), see Table 7 . Compound 5 has dual effects, interacting with Pkn B (pIC 50 : -0.585) and Pkn G (pIC 50 : 1.301), see Table 2 . Figure 6B shows the interaction with compound 6, which has interactions with the residue Val95 (-CO: 1.31Å, -NH: 2.48Å). In these interactions the -NH is H-bond donor and the –CO is H-bond acceptor; these interactions can be related to the pIC 50 of 0.569 for this compound. Figure 6. Interactions in the hinge zone with compound 5 ( A ); compound 6 ( B ); compounds 7, 8, 9 ( C ); compound 10 ( D ); compounds 11, 12, 17, 18, 19, 20 and 23-53 ( E ); compounds 13 and 22 ( F ); and compounds 14, 15, 16, 21 and 54-57 ( G ), from Table 2 – Table 5 . Table 7. Hydrogen bonds in the hinge zone and other zones to the Pkn B inhibitors ( Table 2 ), distance in Å. Compound Hinge zone Others (–H bonds) Crystal PDB ID Glu93 Val95 (-C=O) Val95 (-NH) 5 2.63 1.99 2.46, 2.16 Asp96:1.97 1MRU 6 - 1.31 2.48 Leu17:1.97 Lys401.75 1MRU 7 2.31 2.15 - - 2FUM 8 2.15 1.80 - - 2FUM 9 2.22 2.07 - - 2FUM 10 2.33 2.09 - Asp96:1.71 Lys140:2.01 Asp102:2.42 (-C=O), 2.10 (-OH) 3F69 11 1.94 2.51 2.16 3F69 12 2.42 2.34 2.42 3F69 13 - 2.39 2.42 - 3F69 14 - 2.40 2.45 - 3F69 15 - 1.98 2.40 Glu15:2.73 2FUM 16 - 2.08 2.25 - 2FUM 17 1.94 2.38 2.09 - 3F69 18 1.89 2.73 2.32 - 3F69 19 2.56 2.65 2.18 - 1MRU 20 2.46 2.19 2.02 - 1MRU 21 - 2.30 2.38 - 1MRU 22 - 2.27 1.90 Gly97:2.02 3F69 23 1.93 - 2.27 - 3F69 24 1.72 - 2.21 - 3F69 25 1.88 - 2.44 - 3F69 26 1.97 - 2.28 - 3F69 27 1.93 - 2.28 - 3F69 28 1.87 - 2.39 - 3F69 29 1.98 - 2.14 - 3F69 30 1.91 2.27 2.09 - 3F69 31 1.91 2.44 2.13 - 3F69 32 1.93 2.25 2.05 - 3F69 33 1.91 2.31 2.12 - 3F69 34 1.91 2.21 2.07 - 3F69 35 1.92 2.16 2.08 - 3F69 36 1.91 2.23 2.07 - 3F69 37 1.91 2.24 2.08 - 3F69 38 1.94 2.10 2.10 - 3F69 39 1.91 2.20 2.07 - 3F69 40 1.91 2.21 2.08 - 3F69 41 2.19 2.05 2.20 - 3F69 42 1.99 1.96 2.06 - 3F69 43 1.92 2.16 2.09 - 3F69 44 1.96 2.14 2.13 Gly97:2.01 3F69 45 1.92 2.42 2.13 - 3F69 46 1.91 2.34 2.11 Gly97:2.19 3F69 47 1.93 2.35 2.19 Gly97:2.21 3F69 48 1.59 2.46 2.05 - 3F69 49 2.64 2.67 2.13 - 1MRU 50 2.07 2.26 1.80 - 1MRU 51 1.94 2.20 2.16 Gly97:2.04 1MRU 52 2.21 2.33 1.85 - 1MRU 53 2.27 2.19 2.27 - 3F69 54 - 2.72 2.44 - 1MRU 55 - 2.46 2.04 - 2FUM 56 - 2.23 2.12 - 1MRU 57 - 2.58 2.39 - 1MRU Figure 6C shows the interaction in the hinge zone to of compounds 7, 8 and 9. These compounds have two interactions in the hinge zone with the residue Val95. The most active compound of this series is 8 (pIC 50 : 0.585) with its interactions with the residue Val95 (-CO: 1.80Å, -NH: 2.15Å), see Table 7 . Figure 6D shows the interactions of the compound 10; this compound has two interactions in the hinge zone with the residue Val95 (-NH: 2.33Å, -C=O: 2.09Å). Another H-bond happens with the residues Asp96 (1.71Å) Asp102 (-C=O: 2.42Å, -OH: 2.10Å) and Lys140 (2.01Å). The interactions with the two guanidine groups are through the aspartates. This is very interesting because these kinds of interactions could differentiate one kinase from another. Figure 6E shows the interactions in the hinge zone of the compounds 11, 12, 17, 18, 19, 20 and 23–53. This series of compounds have three H-bonds in the hinge zone with the residues Glu93 and Val95. The most active compound from this series is 52 (pIC 50 : 1.638). It has interactions with residues Glu93 (2.21Å) and Val95 (-CO: 2.33Å, -NH: 1.85Å), see Table 7 . In this series there are two –CO H bond acceptors and one -NH H bond acceptor. Figure 6F shows the interactions in the hinge zone of the compounds 13 and 22; these compounds have two interactions in the hinge zone with the residue Val95 (-CO: 2.39Å, -NH: 2.42Å for 13 and -CO: 2.27Å, -NH: 1.90Å for 22), see Table 7 . The most active compound is 22 (pIC 50 : 1.187). Finally, Figure 6G shows the interactions in the hinge zone of the compounds 14, 15, 16, 21 and 54–57. This series of compounds also has three interactions in the hinge zone with the residues Glu93 and Val95. The most active compound in this series is 57 (pIC 50 : 1.398), see Table 5 . Taking in account the results from Table 7 , the key factor to the stabilization of the active site of these ligands is one or two –CO (H bond acceptor) and one -NH (H bond acceptor) groups in this zone. Figure 7 shows the atomic charges calculated with the CHelpG population analysis (upper left) and the electrostatic potential (upper right and down) of compound 5 in some areas of special interest. The net charges obtained for H11, O13, H21 and H22 are consistent with the formation of hydrogen bonds shown in Figure 6A . The electrostatic potential of surfaces shown in Figure 7 also justify the formation of hydrogen bonds with Glu93 and Val95. Figure 7. CHelpG charges (left) and molecular electrostatic potential contour lines (right and down) of compound 5. Figure 8 shows the atomic charges calculated by CHelpG population analysis (left) and the electrostatic potential (right) of compound 6 in some areas of special interest. The net charges obtained for H40 and O41 are consistent with the formation of hydrogen bonds shown in Figure 6B . The electrostatic potential of surfaces shown in Figure 8 also justify the formation of hydrogen bonds with Val95. Figure 8. CHelpG Charges (left) and molecular electrostatic potential contour lines (right) of compound 6. Figure 9 shows the atomic charges calculated by CHelpG population analysis (left) and the electrostatic potential (right) of compound 8 in some areas of special interest. The net charges obtained for N9 and H13 are consistent with the formation of hydrogen bonds shown in Figure 6C . The electrostatic potential of surfaces shown in Figure 9 also justify the formation of hydrogen bonds with Val95. Figure 9. CHelpG charges (left) and molecular electrostatic potential contour lines (right) of compound 8. Figure 10 shows the atomic charges calculated by CHelpG population analysis (left) and the electrostatic potential (upper right and lower) of compound 10 in some areas of special interest. The net charges obtained for O29, N31, N16, H64 and H76 are consistent with the formation of hydrogen bonds shown in Figure 6D . The electrostatic potential of surfaces shown in Figure 10 also justify the formation of hydrogen bonds with Val95 (O29 and N31), Lys140 (N16) and Asp102 (H64 and H76). Figure 10. CHelpG charges (left) and molecular electrostatic potential contour lines (right and down) of compound 10. Figure 11 shows the electrostatic potential generated by compound 13 in some areas of special interest. The electrostatic potential of surfaces shown in Figure 11 are consistent with the interactions shown in Figure 6F and justify the formation of hydrogen bonds of H34 and N36 with Val95. Figure 11. Molecular electrostatic potential contour lines of compound 13. Figure 12 shows the atomic charges calculated with the CHelpG population analysis (left) and the electrostatic potential (right) of compound 15. The net charges obtained for H31, H38 and N39 are consistent with the formation of hydrogen bonds shown in Figure 3G . The electrostatic potential of surfaces shown in Figure 12 also justify the formation of hydrogen bonds with Glu93 (H38) and Val95 (H31 and N39). Figure 12. CHelpG charges (left) and molecular electrostatic potential contour lines (right) of compound 15. Pkn G: Descriptions of the structural characteristics of ATP binding sites and docking of inhibitors The Pkn G inhibitors from Table 6 have a common structure and three interactions in the hinge zone with the residues Glu233 and Val 235 (see Figure 13 ). Figure 13. Interactions in the hinge zone of compounds 58-75 with Pkn G, from Table 6 . The most active compound of this series is 66 (pIC 50 : 2.000). This compound has interactions with the residue Glu93 (2.59Å) and Val95 (-CO: 2.24Å, -NH: 2.17Å), see Table 8 . Other compounds with good reactivity are 62, 63C1 and 63C2 (pIC 50 : 1.699). These compounds have interactions with the residues Glu93 (2.18Å), Val95 (-CO: 2.56Å, -NH:1.78 Å); Glu93 (2.36Å), Val95 (-CO: 2.18Å, -NH:1.90 Å) and Glu93 (2.10Å), Val95 (-CO: 2.22Å, -NH:1.89 Å), respectively. In these ligands the key factors are two –CO (H bond acceptor) and one -NH (H bond acceptor) groups for stabilizing the ATP active site. Table 8. Hydrogen bonds in the hinge zone and other zones with the Pkn G inhibitors ( Table 6 ), distance in Å. Compound Hinge zone Others (–H bonds) Glu233 Val235 (-C=O) Val235 (-NH) 58 1.99 2.37 1.80 - 59 2.27 2.74 2.36 - 60 2.07 2.51 1.88 - 61 2.57 2.57 2.18 - 62 2.18 2.56 1.78 - 63C1 a 2.36 2.18 1.90 Lys181:2.33 64C2 a 2.10 2.22 1.89 Asp293:1.68 65 2.69 2.64 1.93 Lys181:2.31 66 2.59 2.24 2.17 Lys181:2.16 67C1 a 2.47 2.61 1.93 Asp293:2.00 68C2 a 2.28 - 1.98 Asp293:1.81 69 2.43 2.67 1.87 - 70 1.96 2.60 1.73 - 71 2.60 2.56 1.79 - 72 2.00 2.49 1.80 - 73 2.27 2.06 1.94 - 74 2.43 2.74 2.24 - 75 2.07 2.60 1.80 - 76 2.47 - 2.56 - 77 2.03 2.55 1.82 - a Conformations with respect to the methyl in the cyclopropyl group. Figure 14 shows the atomic charges calculated by CHelpG population analysis (left) and the electrostatic potential (right) of compound 58. The net charges obtained for H16, O11 and H14 are consistent with the formation of the hydrogen bonds shown in Figure 13 . The electrostatic potential of surfaces shown in Figure 14 also justify the formation of hydrogen bonds with Glu233 (H16) and Val235 (O11 and H14). Figure 14. CHelpG charges (left) and molecular electrostatic potential contour lines (right) of compound 58. MQS analysis The MQS analysis was conducted to understand the correlation between the ATP ligands associated to each kinase studied and the stabilization process in the active site. This correlation allows postulation of the structural models of the ATP complexes. For the Pkn A ligands (see Figure 15 ), the correlation between the steric and electronic effects is R 2 =0,9487 using the coulomb and overlap operators to determine electronic and steric effects, respectively. This correlation shows the nature of the stabilization of these ligands on the active site and its non-covalent character. Figure 15. Electronic and steric effect correlation to Pkn A ligands. Figure 16 shows the correlation of Pkn B ligands (see Table 2 – Table 5 ). This correlation shows the electronic and steric effects along the ligand set associated with the active site. The high values in the Carbó indexes give an idea about the ATP complex generated and stabilized. Figure 16. Electronic and steric effects correlation to Pkn B ligands. In Figure 17 is shown the correlation between the steric and electronic effects associated with the ATP complex of Pkn G (see Table 6 ). This complex has a correlation of R 2 =0,7357. In this complex, the steric and electronic effects also are very relevant and the stabilization in the active site has a high non-covalent character. Figure 17. Electronic and steric effects correlation to Pkn G ligands. In Figure 15 – Figure 17 a strong correlation between the two operators used to determine electronic and steric effects is shown. These effects can be related to the stabilization process and non-covalent interactions. In this way, the quantum similarity analysis allows us study the ATP complex and understand the steric and electronic relationship along the ligand set. Conclusions Inadequate dosing and incomplete treatment regimens, coupled with the ability of the tuberculosis bacilli to cause latent infections that are tolerant of currently used drugs, have fueled the rise of multi-drug resistant tuberculosis. To deal with this problem, there is currently an increased interest in kinase inhibitors with the main aim of proposing new anti-tuberculosis drugs. For these reasons, in this work we conducted a study of the crystalized STPKs Pkn A, B1, B2, B3 and G. The conformational analysis shows the DFG-in state of Pkn B, G, and DFG-out state of Pkn A. Methionine is the gatekeeper residue in all the kinases studied. To understand the interactions of the active site of the protein kinases from Mycobacterium tuberculosis, a docking study using the protein kinases Pkn A, B and G was conducted. In these protein kinases, the C-term domain is extracellular and N-term is cytosolic. The cytosolic domain is almost the same for all the kinases and the extracellular domain is different. Ligands bind to the kinase through the formation of two to three hydrogen bonds with the backbone residues of the hinge region connecting the kinase N- and C-terminal loops. The residues with hydrogen bonds on the hinge zone of Pkn A are GLU96 and VAL 98, of Pkn B are GLU 93 and VAL 95, and finally of Pkn G are GLU233 and VAL235. From these results, it is possible to see that the interactions of the hinge zone are characterized by the key factor of one or two H-bonds acceptors and one H-bond donor in the ligands of this zone. On the other hand, the DFT calculations performed with some of the most representative compounds have supported the previous conclusions. Finally, the quantum similarity analysis shows good correlation between the steric and electronic effects in each ATP complex. In this sense, the outcomes presented in this work can be used to develop new protein substrates of the STPKs and find new tuberculosis treatments. Data availability All data underlying the results are available as part of the article and no additional source data are required. Acknowledgements Thanks to Fundación Universitaria Tecnológico Comfenalco (Cartagena, Colombia) for their support of this work. Many of the calculations were performed through CICA (Centro Informático Científico de Andalucía, https://www.cica.es/ ). Faculty Opinions recommended References 1. Hallows KR, Alzamora R, Li H: AMP-activated protein kinase inhibits alkaline pH- and PKA-induced apical vacuolar H+-ATPase accumulation in epididymal clear cells. Am J Physiol Cell Physiol. 2009; 296 (4): C672–81. PubMed Abstract | Publisher Full Text | Free Full Text 2. Av-Gay F, Everett M: The eukaryotic-like Ser/Thr protein kinases of Mycobacterium tuberculosis . Trends in microbiology. 2000; 8 (5): 238–244. 3. Sipos A, Pató J, Székely R, et al. : Lead selection and characterization of antitubercular compounds using the Nested Chemical Library. Tuberculosis (Edinb). 2015; 95 Suppl 1 : S200–6. PubMed Abstract | Publisher Full Text 4. Székely R, Wáczek F, Szabadkai I, et al. : A novel drug discovery concept for tuberculosis: inhibition of bacterial and host cell signalling. Immunol Lett. 2008; 116 (2): 225–31. PubMed Abstract | Publisher Full Text 5. Lougheed KEA, Osborne SA, Saxty B, et al. : Effective inhibitors of the essential kinase PknB and their potential as anti-mycobacterial agents. Tuberculosis (Edinb). 2011; 91 (4): 277–86. PubMed Abstract | Publisher Full Text | Free Full Text 6. Chapman TM, Bouloc N, Buxton RS, et al. : Substituted aminopyrimidine protein kinase B (PknB) inhibitors show activity against Mycobacterium tuberculosis . Bioorg Med Chem Lett. 2012; 22 (9): 3349–53. PubMed Abstract | Publisher Full Text | Free Full Text 7. Pato J, Orfi L, Waczek F, et al. : United States Patent Application Publication. Pub: No.:US 2004/0171603 A1. 2004. 8. Ravala SK, Singh S, Yadav GS, et al. : Evidence that phosphorylation of threonine in the GT motif triggers activation of PknA, a eukaryotic-type serine/threonine kinase from Mycobacterium tuberculosis . FEBS J. 2015; 282 (8): 1419–31. PubMed Abstract | Publisher Full Text 9(a). (3f69) Mieczkowski C, Lavarone AT, Alber T: Auto-activation mechanism of the Mycobacterium tuberculosis PknB receptor Ser/Thr kinase. Embo J. 2008; 27 (23): 3186–3197. PubMed Abstract | Publisher Full Text | Free Full Text (b). (2mru) Young TA, Delagoutte B, Endrizzi JA, et al. : Structure of Mycobacterium tuberculosis PknB supports a universal activation mechanism for Ser/Thr protein kinases. Nat Struct Biol. 2003; 10 (3): 168–74. PubMed Abstract | Publisher Full Text (c). (2fum) Wehenkel A, Fernandez P, Bellinzoni M, et al. : The structure of PknB in complex with mitoxantrone, an ATP-competitive inhibitor, suggests a mode of protein kinase regulation in mycobacteria. Embo J. 2006; 580 (13): 3018–22. PubMed Abstract | Publisher Full Text 10. Scherr N, Honnappa S, Kunz G, et al. : Structural basis for the specific inhibition of protein kinase G, a virulence factor of Mycobacterium tuberculosis . Proc Natl Acad Sci U S A. 2007; 104 (29): 12151–6. PubMed Abstract | Publisher Full Text | Free Full Text 11. Schrödinger Suite 2014-1 Protein Preparation Wizard; Epik version 2,7. Schrödinger, LLC, New York, NY, 2013. Impact version 6,2, Schrödinger, LLC, New York, NY, 2014; Prime version 3,5, Schrödinger, LLC, New York, NY, 2014; (n,d,). 12. Olsson MHM, Søndergaard CR, Rostkowski M, et al. : PROPKA3: Consistent Treatment of Internal and Surface Residues in Empirical pKa Predictions. J Chem Theo Comp. 2011; 7 (2): 525–537. PubMed Abstract | Publisher Full Text 13. Banks JL, Beard HS, Cao Y, et al. : Integrated Modeling Program, Applied Chemical Theory (IMPACT). J Comput Chem. 2005; 26 (16): 1752–80. PubMed Abstract | Publisher Full Text | Free Full Text 14. Malhotra V, Arteaga-Cortés LT, Clay G, et al. : Mycobacterium tuberculosis protein kinase K confers survival advantage during early infection in mice and regulates growth in culture and during persistent infection: implications for immune modulation. Microbiology (Reading). 2010; 156 (Pt 9): 2829–2841. PubMed Abstract | Publisher Full Text | Free Full Text 15. Maestro, version 9,7. Schrödinger, LLC, New York, NY. 2014; (n,d,). 16. LigPrep, version 2,9. Schrödinger, LLC, New York, NY. 2014; (n,d,). 17. Epik, version 2,7. Schrödinger, LLC New York, NY. 2014; (n,d,). 18. Schrödinger Suite 2014-2 Induced Fit Docking protocol; Glide, version 6.2. Schrödinger, LLC, New York, NY. 2014. 19. Sherman W, Day T, Jacobson MP, et al. : Novel procedure for modeling ligand/receptor induced fit effects. J Med Chem. 2006; 49 (2): 534–553. PubMed Abstract | Publisher Full Text 20. Schrödinger Release 2016-3: Prime. Schrödinger, LLC, New York, NY, 2016. 21. https://www.pdc.kth.se/software/software/GROMACS/centos7/5.1.2/index.html 22. Karplus M, McCammon JA: Molecular dynamics simulations of biomolecules. Nat Struct Biol. 2001; 9 (9): 646–52. PubMed Abstract | Publisher Full Text 23. Carbó R, Leyda L, Arnau M: How similar is a molecule to another? An electron density measure of similarity between two molecular structures. Int J Quantum Chem. 1980; 17 (6): 1185–1189. Publisher Full Text 24. Amat L, Carbó-Dorca R: Use of promolecular ASA density functions as a general algorithm to obtain starting MO in SCF calculations. Int J Quantum Chem. 2002; 87 (2): 59–67. Publisher Full Text 25. Gironés X, Carbó-Dorca R: Modelling Toxicity using Molecular Quantum Similarity Measures. QSAR Comb Sci. 2006; 25 (7): 579–589. Publisher Full Text 26. Carbó-Dorca R, Gironés X: Foundation of quantum similarity measures and their relationship to QSPR: Density function structure, approximations, and application examples. QSAR Comb Sci. 2006; 101 (1): 8–20. Publisher Full Text 27. Morales-Bayuelo A, Torres J, Vivas-Reyes R: Quantum molecular similarity analysis and quantitative definition of catecholamines with respect to biogenic monoamines associated: Scale alpha and beta of quantitative convergence. Int J Quant Chem. 2012; 112 (14): 2637–2642. Publisher Full Text 28. Morales-Bayuelo A, Vivas-Reyes R: Topological model to quantify the global reactivity indexes as local in Diels–Alder reactions, using density function theory (DFT) and local quantum similarity (LQS). J Math Chem. 2013; 51 : 125–143. Publisher Full Text 29. Morales-Bayuelo A, Torres J, Baldiris R, et al. : Theoretical study of the chemical reactivity and molecular quantum similarity in a series of derivatives of 2‐adamantyl‐thiazolidine‐4‐one using density functional theory and the topo‐geometrical superposition approach. Int J Quant Chem. 2012; 112 : 2681–2687. Publisher Full Text 30. Morales-Bayuelo A, Torres J, Vivas-Reyes R: Hückel treatment of pyrrole and pentalene as a function of cyclopentadienyl using local quantum similarity index (LQSI) and the Topo-Geometrical Superposition Approach (TGSA). J Theo Comp Chem. 2012; 11 (1): 223–239. Publisher Full Text 31. Gironés; X, Robert D, Carbó-Dorca R: TGSA: A molecular superposition program based on topo‐geometrical considerations. J Comput Chem. 2001; 22 (2): 255–263. <a target="xrefwindow" id="d549313e7300" href="https://doi.org/10.1002/1096-987X(20010130)22:2 Publisher Full Text 32. Frisch MJG, Trucks W, Schlegel HB, et al. : GAUSSIAN 09, Revision C.01, Gaussian; Inc., Wallingford, 2010. Reference Source 33. Beeke AD: Density‐functional thermochemistry. III. The role of exact exchange. J Chem Phys. 1993; 98 : 5648. Publisher Full Text 34. Lee C, Yang W, Parr RG: Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. Phys Rev B. 1988; 37 : 785. PubMed Abstract | Publisher Full Text 35. Krishnan R, Binkley JS, Seeger R, et al. : Self‐consistent molecular orbital methods. XX. A basis set for correlated wave functions. J Chem Phys. 1980; 72 : 650. Publisher Full Text 36. R. Dennington, Inc: Wallingford, CT, 2008. 37. Malhotra V, Arteaga-Cortés LT, Clay G, et al. : Mycobacterium tuberculosis protein kinase K confers survival advantage during early infection in mice and regulates growth in culture and during persistent infection: implications for immune modulation. Microbiology (Reading). 2010; 156 (Pt 9): 2829–2841. PubMed Abstract | Publisher Full Text | Free Full Text 38. Zuccotto F, Ardini E, Casale E, et al. : Through the "gatekeeper door": exploiting the active kinase conformation. J Med Chem. 2010; 53 (7): 2681–2694. PubMed Abstract | Publisher Full Text Comments on this article Comments (0) Version 1 VERSION 1 PUBLISHED 03 Feb 2021 ADD YOUR COMMENT Comment Author details Author details 1 Centro de Investigación de Procesos del Tecnológico Comfenalco (CIPTEC), Fundación UNiversitaria Tecnologico Comfenalco, Cartagena de Indias, Colombia 2 Departamento de Química-Física, Facultad de Ciencias, Universidad de Cádiz, Cádiz, Spain Alejandro Morales-Bayuelo Roles: Conceptualization, Formal Analysis, Investigation, Methodology Jesús Sánchez-Márquez Roles: Conceptualization, Formal Analysis, Investigation Competing interests No competing interests were disclosed. Grant information Fundación Universitaria Tecnológico Comfenalco (Cartagena, Colombia), Project Inv-2020. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Article Versions (1) version 1 Published: 03 Feb 2021, 10:66 https://doi.org/10.12688/f1000research.28078.1 Copyright © 2021 Morales-Bayuelo A and Sánchez-Márquez J. This is an open access article distributed under the terms of the Creative Commons Attribution License , which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Download Export To Sciwheel Bibtex EndNote ProCite Ref. Manager (RIS) Sente metrics Views Downloads F1000Research - - PubMed Central info_outline Data from PMC are received and updated monthly. - - Citations open_in_new 0 open_in_new 0 open_in_new SEE MORE DETAILS CITE how to cite this article Morales-Bayuelo A and Sánchez-Márquez J. New insights about the serine/threonine protein kinase substrates from Mycobacterium tuberculosis using molecular docking, quantum similarity analysis and DFT calculations [version 1; peer review: 1 approved] . F1000Research 2021, 10 :66 ( https://doi.org/10.12688/f1000research.28078.1 ) NOTE: If applicable, it is important to ensure the information in square brackets after the title is included in all citations of this article. COPY CITATION DETAILS track receive updates on this article Track an article to receive email alerts on any updates to this article. TRACK THIS ARTICLE Share Open Peer Review Current Reviewer Status: ? Key to Reviewer Statuses VIEW HIDE Approved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested Approved with reservations A number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit. Not approved Fundamental flaws in the paper seriously undermine the findings and conclusions Version 1 VERSION 1 PUBLISHED 03 Feb 2021 Views 0 Cite How to cite this report: Fraga H. Reviewer Report For: New insights about the serine/threonine protein kinase substrates from Mycobacterium tuberculosis using molecular docking, quantum similarity analysis and DFT calculations [version 1; peer review: 1 approved] . F1000Research 2021, 10 :66 ( https://doi.org/10.5256/f1000research.31058.r78802 ) The direct URL for this report is: https://f1000research.com/articles/10-66/v1#referee-response-78802 NOTE: it is important to ensure the information in square brackets after the title is included in this citation. Close Copy Citation Details Reviewer Report 24 Feb 2021 Hugo Fraga , Faculdade de Medicina da Universidade do Porto - FMUP, Porto, Portugal Approved VIEWS 0 https://doi.org/10.5256/f1000research.31058.r78802 Although the scientific question is interesting - I don’t understand how the question stated in the introduction: “what are the protein substrates of the STPKs?” can be directly answered by studying ATP competitive inhibitors. We already know ATP is a ... Continue reading READ ALL Although the scientific question is interesting - I don’t understand how the question stated in the introduction: “what are the protein substrates of the STPKs?” can be directly answered by studying ATP competitive inhibitors. We already know ATP is a binder - what we don’t know are the proteins that are targets for the kinases. Perhaps, by having specific inhibitors that would help in the identification of the targets but this is not stated in the introduction. Nevertheless, this does not reduce the interest of the study per se – to study the binding surface of putative kinase inhibitors is itself relevant. While this is a computational study, and the methodology and results look sound, I feel that some experimental data would be required to validate the exercise. It would be interesting to test if the residues identified – by mutating etc – do influence the IC50 of the compounds tested – but don’t know how easy is to express the proteins and if the researchers have the know-how to perform such a task. Something is missing in the sentence: “The compounds to Pkn B have groups with electron withdraw- ing resonance effects, such as carbonyl, hydroxyl, amine and methoxy groups, with big rings central to its stabilization on the active site.” Is the work clearly and accurately presented and does it cite the current literature? Yes Is the study design appropriate and is the work technically sound? Yes Are sufficient details of methods and analysis provided to allow replication by others? Yes If applicable, is the statistical analysis and its interpretation appropriate? I cannot comment. A qualified statistician is required. Are all the source data underlying the results available to ensure full reproducibility? Yes Are the conclusions drawn adequately supported by the results? Yes Competing Interests: No competing interests were disclosed. Reviewer Expertise: Tuberculosis, Drug Development I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard. Close READ LESS CITE CITE HOW TO CITE THIS REPORT Fraga H. Reviewer Report For: New insights about the serine/threonine protein kinase substrates from Mycobacterium tuberculosis using molecular docking, quantum similarity analysis and DFT calculations [version 1; peer review: 1 approved] . F1000Research 2021, 10 :66 ( https://doi.org/10.5256/f1000research.31058.r78802 ) The direct URL for this report is: https://f1000research.com/articles/10-66/v1#referee-response-78802 NOTE: it is important to ensure the information in square brackets after the title is included in all citations of this article. COPY CITATION DETAILS Report a concern Author Response 24 Feb 2021 Ph. D. Alejandro Morales-Bayuelo , Centro de Investigación de Procesos del Tecnológico Comfenalco (CIPTEC), Fundación UNiversitaria Tecnologico Comfenalco, Cartagena de Indias, Colombia 24 Feb 2021 Author Response Ok, thank you very much by the sugestions. PKs (or PK domains within a larger protein) are generally made up of two lobes separated by a large cavity capable of ... Continue reading Ok, thank you very much by the sugestions. PKs (or PK domains within a larger protein) are generally made up of two lobes separated by a large cavity capable of including the substrate and a smaller cavity capable of including Adenosine TriphosPhate (ATP). The N-terminal lobe is mainly made up of β sheets and a conserved helix called the “C-helix”. The C-terminal lobe is larger and is made up mostly of α-helices. In general, molecules that are designed with the intention of inhibiting PKs compete with ATP. For this reason, the inhibitors with higher activity has been selected inthis work for the PKs selected. It has been reported that there is a relationship between the characteristics found at the ATP binding site and the pharmacology associated with this site. In the current work, a characterization of the 3D structures of the PKs involved in tuberculosis was made. To study these protein kinases, the components that make up the ATP binding site were also taken into account, such as the hinge zone residues, gatekeeper residue, presence or absence of the domain (DFG) and position of the glutamate residue conserved in the C-helix. On the other hand, For the future, the experimental studies to extrapolate the conclusions are being consolidated. However, for the moment this study uses the experimental data of the activities and performs computational analyzes. Best regards __________________________________ Alejandro Morales-Bayuelo. Chemist. Molecular Physical Chemistry Ph. D. Molecular Physical-Chemistry Post-doctoral Molecular Biophysics Post-doctoral Academic Researcher. Cartagena de Indias, Colombia. Ok, thank you very much by the sugestions. PKs (or PK domains within a larger protein) are generally made up of two lobes separated by a large cavity capable of including the substrate and a smaller cavity capable of including Adenosine TriphosPhate (ATP). The N-terminal lobe is mainly made up of β sheets and a conserved helix called the “C-helix”. The C-terminal lobe is larger and is made up mostly of α-helices. In general, molecules that are designed with the intention of inhibiting PKs compete with ATP. For this reason, the inhibitors with higher activity has been selected inthis work for the PKs selected. It has been reported that there is a relationship between the characteristics found at the ATP binding site and the pharmacology associated with this site. In the current work, a characterization of the 3D structures of the PKs involved in tuberculosis was made. To study these protein kinases, the components that make up the ATP binding site were also taken into account, such as the hinge zone residues, gatekeeper residue, presence or absence of the domain (DFG) and position of the glutamate residue conserved in the C-helix. On the other hand, For the future, the experimental studies to extrapolate the conclusions are being consolidated. However, for the moment this study uses the experimental data of the activities and performs computational analyzes. Best regards __________________________________ Alejandro Morales-Bayuelo. Chemist. Molecular Physical Chemistry Ph. D. Molecular Physical-Chemistry Post-doctoral Molecular Biophysics Post-doctoral Academic Researcher. Cartagena de Indias, Colombia. Competing Interests: No competing interests were disclosed. Close Report a concern Respond or Comment COMMENTS ON THIS REPORT Author Response 24 Feb 2021 Ph. D. Alejandro Morales-Bayuelo , Centro de Investigación de Procesos del Tecnológico Comfenalco (CIPTEC), Fundación UNiversitaria Tecnologico Comfenalco, Cartagena de Indias, Colombia 24 Feb 2021 Author Response Ok, thank you very much by the sugestions. PKs (or PK domains within a larger protein) are generally made up of two lobes separated by a large cavity capable of ... Continue reading Ok, thank you very much by the sugestions. PKs (or PK domains within a larger protein) are generally made up of two lobes separated by a large cavity capable of including the substrate and a smaller cavity capable of including Adenosine TriphosPhate (ATP). The N-terminal lobe is mainly made up of β sheets and a conserved helix called the “C-helix”. The C-terminal lobe is larger and is made up mostly of α-helices. In general, molecules that are designed with the intention of inhibiting PKs compete with ATP. For this reason, the inhibitors with higher activity has been selected inthis work for the PKs selected. It has been reported that there is a relationship between the characteristics found at the ATP binding site and the pharmacology associated with this site. In the current work, a characterization of the 3D structures of the PKs involved in tuberculosis was made. To study these protein kinases, the components that make up the ATP binding site were also taken into account, such as the hinge zone residues, gatekeeper residue, presence or absence of the domain (DFG) and position of the glutamate residue conserved in the C-helix. On the other hand, For the future, the experimental studies to extrapolate the conclusions are being consolidated. However, for the moment this study uses the experimental data of the activities and performs computational analyzes. Best regards __________________________________ Alejandro Morales-Bayuelo. Chemist. Molecular Physical Chemistry Ph. D. Molecular Physical-Chemistry Post-doctoral Molecular Biophysics Post-doctoral Academic Researcher. Cartagena de Indias, Colombia. Ok, thank you very much by the sugestions. PKs (or PK domains within a larger protein) are generally made up of two lobes separated by a large cavity capable of including the substrate and a smaller cavity capable of including Adenosine TriphosPhate (ATP). The N-terminal lobe is mainly made up of β sheets and a conserved helix called the “C-helix”. The C-terminal lobe is larger and is made up mostly of α-helices. In general, molecules that are designed with the intention of inhibiting PKs compete with ATP. For this reason, the inhibitors with higher activity has been selected inthis work for the PKs selected. It has been reported that there is a relationship between the characteristics found at the ATP binding site and the pharmacology associated with this site. In the current work, a characterization of the 3D structures of the PKs involved in tuberculosis was made. To study these protein kinases, the components that make up the ATP binding site were also taken into account, such as the hinge zone residues, gatekeeper residue, presence or absence of the domain (DFG) and position of the glutamate residue conserved in the C-helix. On the other hand, For the future, the experimental studies to extrapolate the conclusions are being consolidated. However, for the moment this study uses the experimental data of the activities and performs computational analyzes. Best regards __________________________________ Alejandro Morales-Bayuelo. Chemist. Molecular Physical Chemistry Ph. D. Molecular Physical-Chemistry Post-doctoral Molecular Biophysics Post-doctoral Academic Researcher. Cartagena de Indias, Colombia. Competing Interests: No competing interests were disclosed. Close Report a concern COMMENT ON THIS REPORT Comments on this article Comments (0) Version 1 VERSION 1 PUBLISHED 03 Feb 2021 ADD YOUR COMMENT Comment keyboard_arrow_left keyboard_arrow_right Open Peer Review Reviewer Status info_outline Alongside their report, reviewers assign a status to the article: Approved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested Approved with reservations A number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit. Not approved Fundamental flaws in the paper seriously undermine the findings and conclusions Reviewer Reports Invited Reviewers 1 Version 1 03 Feb 21 read Hugo Fraga , Faculdade de Medicina da Universidade do Porto - FMUP, Porto, Portugal Comments on this article All Comments (0) Add a comment Sign up for content alerts Sign Up You are now signed up to receive this alert Browse by related subjects keyboard_arrow_left Back to all reports Reviewer Report 0 Views copyright © 2021 Fraga H. This is an open access peer review report distributed under the terms of the Creative Commons Attribution License , which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. 24 Feb 2021 | for Version 1 Hugo Fraga , Faculdade de Medicina da Universidade do Porto - FMUP, Porto, Portugal 0 Views copyright © 2021 Fraga H. This is an open access peer review report distributed under the terms of the Creative Commons Attribution License , which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. format_quote Cite this report speaker_notes Responses (1) Approved info_outline Alongside their report, reviewers assign a status to the article: Approved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested Approved with reservations A number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit. Not approved Fundamental flaws in the paper seriously undermine the findings and conclusions Although the scientific question is interesting - I don’t understand how the question stated in the introduction: “what are the protein substrates of the STPKs?” can be directly answered by studying ATP competitive inhibitors. We already know ATP is a binder - what we don’t know are the proteins that are targets for the kinases. Perhaps, by having specific inhibitors that would help in the identification of the targets but this is not stated in the introduction. Nevertheless, this does not reduce the interest of the study per se – to study the binding surface of putative kinase inhibitors is itself relevant. While this is a computational study, and the methodology and results look sound, I feel that some experimental data would be required to validate the exercise. It would be interesting to test if the residues identified – by mutating etc – do influence the IC50 of the compounds tested – but don’t know how easy is to express the proteins and if the researchers have the know-how to perform such a task. Something is missing in the sentence: “The compounds to Pkn B have groups with electron withdraw- ing resonance effects, such as carbonyl, hydroxyl, amine and methoxy groups, with big rings central to its stabilization on the active site.” Is the work clearly and accurately presented and does it cite the current literature? Yes Is the study design appropriate and is the work technically sound? Yes Are sufficient details of methods and analysis provided to allow replication by others? Yes If applicable, is the statistical analysis and its interpretation appropriate? I cannot comment. A qualified statistician is required. Are all the source data underlying the results available to ensure full reproducibility? Yes Are the conclusions drawn adequately supported by the results? Yes Competing Interests No competing interests were disclosed. Reviewer Expertise Tuberculosis, Drug Development I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard. reply Respond to this report Responses (1) Author Response 24 Feb 2021 Ph. D. Alejandro Morales-Bayuelo, Centro de Investigación de Procesos del Tecnológico Comfenalco (CIPTEC), Fundación UNiversitaria Tecnologico Comfenalco, Cartagena de Indias, Colombia Ok, thank you very much by the sugestions. PKs (or PK domains within a larger protein) are generally made up of two lobes separated by a large cavity capable of including the substrate and a smaller cavity capable of including Adenosine TriphosPhate (ATP). The N-terminal lobe is mainly made up of β sheets and a conserved helix called the “C-helix”. The C-terminal lobe is larger and is made up mostly of α-helices. In general, molecules that are designed with the intention of inhibiting PKs compete with ATP. For this reason, the inhibitors with higher activity has been selected inthis work for the PKs selected. It has been reported that there is a relationship between the characteristics found at the ATP binding site and the pharmacology associated with this site. In the current work, a characterization of the 3D structures of the PKs involved in tuberculosis was made. To study these protein kinases, the components that make up the ATP binding site were also taken into account, such as the hinge zone residues, gatekeeper residue, presence or absence of the domain (DFG) and position of the glutamate residue conserved in the C-helix. On the other hand, For the future, the experimental studies to extrapolate the conclusions are being consolidated. However, for the moment this study uses the experimental data of the activities and performs computational analyzes. Best regards __________________________________ Alejandro Morales-Bayuelo. Chemist. Molecular Physical Chemistry Ph. D. Molecular Physical-Chemistry Post-doctoral Molecular Biophysics Post-doctoral Academic Researcher. Cartagena de Indias, Colombia. View more View less Competing Interests No competing interests were disclosed. reply Respond Report a concern Fraga H. Peer Review Report For: New insights about the serine/threonine protein kinase substrates from Mycobacterium tuberculosis using molecular docking, quantum similarity analysis and DFT calculations [version 1; peer review: 1 approved] . F1000Research 2021, 10 :66 ( https://doi.org/10.5256/f1000research.31058.r78802) NOTE: it is important to ensure the information in square brackets after the title is included in this citation. The direct URL for this report is: https://f1000research.com/articles/10-66/v1#referee-response-78802 Alongside their report, reviewers assign a status to the article: Approved - the paper is scientifically sound in its current form and only minor, if any, improvements are suggested Approved with reservations - A number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit. Not approved - fundamental flaws in the paper seriously undermine the findings and conclusions Adjust parameters to alter display View on desktop for interactive features Includes Interactive Elements View on desktop for interactive features Competing Interests Policy Provide sufficient details of any financial or non-financial competing interests to enable users to assess whether your comments might lead a reasonable person to question your impartiality. Consider the following examples, but note that this is not an exhaustive list: Examples of 'Non-Financial Competing Interests' Within the past 4 years, you have held joint grants, published or collaborated with any of the authors of the selected paper. You have a close personal relationship (e.g. parent, spouse, sibling, or domestic partner) with any of the authors. You are a close professional associate of any of the authors (e.g. scientific mentor, recent student). You work at the same institute as any of the authors. You hope/expect to benefit (e.g. favour or employment) as a result of your submission. You are an Editor for the journal in which the article is published. Examples of 'Financial Competing Interests' You expect to receive, or in the past 4 years have received, any of the following from any commercial organisation that may gain financially from your submission: a salary, fees, funding, reimbursements. You expect to receive, or in the past 4 years have received, shared grant support or other funding with any of the authors. You hold, or are currently applying for, any patents or significant stocks/shares relating to the subject matter of the paper you are commenting on. Stay Updated Sign up for content alerts and receive a weekly or monthly email with all newly published articles Register with F1000Research Already registered? Sign in Not now, thanks close PLEASE NOTE If you are an AUTHOR of this article, please check that you signed in with the account associated with this article otherwise we cannot automatically identify your role as an author and your comment will be labelled as a “User Comment”. If you are a REVIEWER of this article, please check that you have signed in with the account associated with this article and then go to your account to submit your report, please do not post your review here. If you do not have access to your original account, please contact us . All commenters must hold a formal affiliation as per our Policies . The information that you give us will be displayed next to your comment. User comments must be in English, comprehensible and relevant to the article under discussion. We reserve the right to remove any comments that we consider to be inappropriate, offensive or otherwise in breach of the User Comment Terms and Conditions . Commenters must not use a comment for personal attacks. When criticisms of the article are based on unpublished data, the data should be made available. I accept the User Comment Terms and Conditions Please confirm that you accept the User Comment Terms and Conditions. Affiliation ✕ refresh Please enter your institution. Note: To add your institution or organisation, start typing the name and then select the correct name from the list. Where applicable, the name will appear in both the original language and in English. Do not paste in the name. If the name does not appear in the drop-down list, we will display the information you have entered. ✕ refresh Country/Region * USA UK Canada China France Germany Afghanistan Aland Islands Albania Algeria American Samoa Andorra Angola Anguilla Antarctica Antigua and Barbuda Argentina Armenia Aruba Australia Austria Azerbaijan Bahamas Bahrain Bangladesh Barbados Belarus Belgium Belize Benin Bermuda Bhutan Bolivia Bosnia and Herzegovina Botswana Bouvet Island Brazil British Indian Ocean Territory British Virgin Islands Brunei Bulgaria Burkina Faso Burundi Cambodia Cameroon Canada Cape Verde Cayman Islands Central African Republic Chad Chile China Christmas Island Cocos (Keeling) Islands Colombia Comoros Congo Cook Islands Costa Rica Cote d'Ivoire Croatia Cuba Cyprus Czech Republic Democratic Republic of the Congo Denmark Djibouti Dominica Dominican Republic Ecuador Egypt El Salvador Equatorial Guinea Eritrea Estonia Ethiopia Falkland Islands Faroe Islands Federated States of Micronesia Fiji Finland France French Guiana French Polynesia French Southern Territories Gabon Georgia Germany Ghana Gibraltar Greece Greenland Grenada Guadeloupe Guam Guatemala Guernsey Guinea Guinea-Bissau Guyana Haiti Heard Island and Mcdonald Islands Holy See (Vatican City State) Honduras Hong Kong Hungary Iceland India Indonesia Iran Iraq Ireland Israel Italy Jamaica Japan Jersey Jordan Kazakhstan Kenya Kiribati Kosovo (Serbia and Montenegro) Kuwait Kyrgyzstan Lao People's Democratic Republic Latvia Lebanon Lesotho Liberia Libya Liechtenstein Lithuania Luxembourg Macao Madagascar Malawi Malaysia Maldives Mali Malta Marshall Islands Martinique Mauritania Mauritius Mayotte Mexico Minor Outlying Islands of the United States Moldova Monaco Mongolia Montenegro Montserrat Morocco Mozambique Myanmar Namibia Nauru Nepal Netherlands Antilles New Caledonia New Zealand Nicaragua Niger Nigeria Niue Norfolk Island North Korea North Macedonia Northern Mariana Islands Norway Oman Pakistan Palau Palestinian Territory Panama Papua New Guinea Paraguay Peru Philippines Pitcairn Poland Portugal Puerto Rico Qatar Reunion Romania Russian Federation Rwanda Saint Helena Saint Kitts and Nevis Saint Lucia Saint Pierre and Miquelon Saint Vincent and the Grenadines Samoa San Marino Sao Tome and Principe Saudi Arabia Senegal Serbia Seychelles Sierra Leone Singapore Slovakia Slovenia Solomon Islands Somalia South Africa South Georgia and the South Sandwich Is South Korea South Sudan Spain Sri Lanka Sudan Suriname Svalbard and Jan Mayen Swaziland Sweden Switzerland Syria Taiwan Tajikistan Tanzania Thailand The Gambia The Netherlands Timor-Leste Togo Tokelau Tonga Trinidad and Tobago Tunisia Turkey Turkmenistan Turks and Caicos Islands Tuvalu UK USA Uganda Ukraine United Arab Emirates United States Virgin Islands Uruguay Uzbekistan Vanuatu Venezuela Vietnam Wallis and Futuna West Bank and Gaza Strip Western Sahara Yemen Zambia Zimbabwe Please select your country/region. You must enter a comment. Competing Interests Please disclose any competing interests that might be construed to influence your judgment of the article's or peer review report's validity or importance. Competing Interests Policy Provide sufficient details of any financial or non-financial competing interests to enable users to assess whether your comments might lead a reasonable person to question your impartiality. Consider the following examples, but note that this is not an exhaustive list: Examples of 'Non-Financial Competing Interests' Within the past 4 years, you have held joint grants, published or collaborated with any of the authors of the selected paper. You have a close personal relationship (e.g. parent, spouse, sibling, or domestic partner) with any of the authors. You are a close professional associate of any of the authors (e.g. scientific mentor, recent student). You work at the same institute as any of the authors. You hope/expect to benefit (e.g. favour or employment) as a result of your submission. You are an Editor for the journal in which the article is published. Examples of 'Financial Competing Interests' You expect to receive, or in the past 4 years have received, any of the following from any commercial organisation that may gain financially from your submission: a salary, fees, funding, reimbursements. You expect to receive, or in the past 4 years have received, shared grant support or other funding with any of the authors. You hold, or are currently applying for, any patents or significant stocks/shares relating to the subject matter of the paper you are commenting on. Please state your competing interests The comment has been saved. An error has occurred. Please try again. Cancel Post var lTitle = "New insights about the serine\/threonine...".replace("'", ''); var linkedInUrl = "http://www.linkedin.com/shareArticle?url=https://f1000research.com/articles/10-66/v1" + "&title=" + encodeURIComponent(lTitle) + "&summary=" + encodeURIComponent('Read the article by '); var deliciousUrl = "https://del.icio.us/post?url=https://f1000research.com/articles/10-66/v1&title=" + encodeURIComponent(lTitle); var redditUrl = "http://reddit.com/submit?url=https://f1000research.com/articles/10-66/v1" + "&title=" + encodeURIComponent(lTitle); linkedInUrl += encodeURIComponent('Morales-Bayuelo A and Sánchez-Márquez J'); var offsetTop = /chrome/i.test( navigator.userAgent ) ? 4 : -10; var addthis_config = { ui_offset_top: offsetTop, services_compact : "facebook,twitter,www.linkedin.com,www.mendeley.com,reddit.com", services_expanded : "facebook,twitter,www.linkedin.com,www.mendeley.com,reddit.com", services_custom : [ { name: "LinkedIn", url: linkedInUrl, icon:"/img/icon/at_linkedin.svg" }, { name: "Mendeley", url: "http://www.mendeley.com/import/?url=https://f1000research.com/articles/10-66/v1/mendeley", icon:"/img/icon/at_mendeley.svg" }, { name: "Reddit", url: redditUrl, icon:"/img/icon/at_reddit.svg" }, ] }; var addthis_share = { url: "https://f1000research.com/articles/10-66", templates : { twitter : "New insights about the serine\/threonine protein kinase substrates.... Morales-Bayuelo A and Sánchez-Márquez J, published by " + "@F1000Research" + ", https://f1000research.com/articles/10-66/v1" } }; if (typeof(addthis) != "undefined"){ addthis.addEventListener('addthis.ready', checkCount); addthis.addEventListener('addthis.menu.share', checkCount); } $(".f1r-shares-twitter").attr("href", "https://twitter.com/intent/tweet?text=" + addthis_share.templates.twitter); $(".f1r-shares-facebook").attr("href", "https://www.facebook.com/sharer/sharer.php?u=" + addthis_share.url); $(".f1r-shares-linkedin").attr("href", addthis_config.services_custom[0].url); $(".f1r-shares-reddit").attr("href", addthis_config.services_custom[2].url); $(".f1r-shares-mendelay").attr("href", addthis_config.services_custom[1].url); function checkCount(){ setTimeout(function(){ $(".addthis_button_expanded").each(function(){ var count = $(this).text(); if (count !== "" && count != "0") $(this).removeClass("is-hidden"); else $(this).addClass("is-hidden"); }); }, 1000); } close How to cite this report {{reportCitation}} Cancel Copy Citation Details $(function(){R.ui.buttonDropdowns('.dropdown-for-downloads');}); $(function(){R.ui.toolbarDropdowns('.toolbar-dropdown-for-downloads');}); $.get("/articles/acj/28078/31058") new F1000.Clipboard(); new F1000.ThesaurusTermsDisplay("articles", "article", "31058"); $(document).ready(function() { $( "#frame1" ).on('load', function() { var mydiv = $(this).contents().find("div"); var h = mydiv.height(); console.log(h) }); var tooltipLivingFigure = jQuery(".interactive-living-figure-label .icon-more-info"), titleLivingFigure = tooltipLivingFigure.attr("title"); tooltipLivingFigure.simpletip({ fixed: true, position: ["-115", "30"], baseClass: 'small-tooltip', content:titleLivingFigure + " " }); tooltipLivingFigure.removeAttr("title"); $("body").on("click", ".cite-living-figure", function(e) { e.preventDefault(); var ref = $(this).attr("data-ref"); $(this).closest(".living-figure-list-container").find("#" + ref).fadeIn(200); }); $("body").on("click", ".close-cite-living-figure", function(e) { e.preventDefault(); $(this).closest(".popup-window-wrapper").fadeOut(200); }); $(document).on("mouseup", function(e) { var metricsContainer = $(".article-metrics-popover-wrapper"); if (!metricsContainer.is(e.target) && metricsContainer.has(e.target).length === 0) { $(".article-metrics-close-button").click(); } }); var articleId = $('#articleId').val(); if($("#main-article-count-box").attachArticleMetrics) { $("#main-article-count-box").attachArticleMetrics(articleId, { articleMetricsView: true }); } }); var figshareWidget = $(".new_figshare_widget"); if (figshareWidget.length > 0) { window.figshare.load("f1000", function(Widget) { // Select a tag/tags defined in your page. In this tag we will place the widget. _.map(figshareWidget, function(el){ var widget = new Widget({ articleId: $(el).attr("figshare_articleId") //height:300 // this is the height of the viewer part. [Default: 550] }); widget.initialize(); // initialize the widget widget.mount(el); // mount it in a tag that's on your page // this will save the widget on the global scope for later use from // your JS scripts. This line is optional. //window.widget = widget; }); }); } close Error Close Add Reset F1000.MICROSERVICES.AFFILIATION = ''; $(document).ready(function () { $('.js-affiliations-form').each((index, form) => { new AffiliationForm({ formId: form.id, institutionErrorSelector: '.comment-enter-institution', departmentErrorSelector: '.comment-enter-department', placeSelector: '.js-add-comment-place', stateSelector: '.js-add-comment-state', zipCodeSelector: '.js-add-comment-zipcode', countrySelector: '.js-add-comment-country', countryErrorSelector: '.comment-enter-country', }); }); }); $(document).ready(function () { var reportIds = { "80713": 0, "78797": 0, "78799": 0, "78798": 0, "78801": 0, "78800": 0, "78803": 0, "78802": 17, "78805": 0, "78804": 0, "122205": 0, "122204": 0, "122467": 0, "122210": 0, "122469": 0, "122468": 0, "122471": 0, "122470": 0, "122473": 0, "122472": 0, "81640": 0, "122474": 0, "122218": 0, "83564": 0, "122220": 0, "122223": 0, "122222": 0, "122225": 0, "122227": 0, "122226": 0, "83706": 0, }; $(".referee-response-container,.js-referee-report").each(function(index, el) { var reportId = $(el).attr("data-reportid"), reportCount = reportIds[reportId] || 0; $(el).find(".comments-count-container,.js-referee-report-views").html(reportCount); }); var uuidInput = $("#article_uuid"), oldUUId = uuidInput.val(), newUUId = "93ef7343-1839-44e2-ab23-838e9fc921c7"; uuidInput.val(newUUId); $("a[href*='article_uuid=']").each(function(index, el) { var newHref = $(el).attr("href").replace(oldUUId, newUUId); $(el).attr("href", newHref); }); }); An innovative open access publishing platform offering rapid publication and open peer review, whilst supporting data deposition and sharing. Browse Gateways Collections How it Works Contact For Developers Cookie Notice Privacy Notice RSS Submit Your Research Follow us © 2012-2026 F1000 Research Ltd. ISSN 2046-1402 | Legal | Partner of Research4Life • CrossRef • ORCID • FAIRSharing R.templateTests.simpleTemplate = R.template(' $text $text $text $text $text '); R.templateTests.runTests(); var F1000platform = new F1000.Platform({ name: "f1000research", displayName: "F1000Research", hostName: "f1000research.com", id: "1", editorialEmail: "[email protected]", infoEmail: "[email protected]", usePmcStats: true }); $(function(){R.ui.dropdowns('.dropdown-for-authors, .dropdown-for-about, .dropdown-for-myresearch');}); // $(function(){R.ui.dropdowns('.dropdown-for-referees');}); $(document).ready(function () { if ($(".cookie-warning").is(":visible")) { $(".sticky").css("margin-bottom", "35px"); $(".devices").addClass("devices-and-cookie-warning"); } $(".cookie-warning .close-button").click(function (e) { $(".devices").removeClass("devices-and-cookie-warning"); $(".sticky").css("margin-bottom", "0"); }); $("#tweeter-feed .tweet-message").each(function (i, message) { var self = $(message); self.html(linkify(self.html())); }); $(".partner").on("mouseenter mouseleave", function() { $(this).find(".gray-scale, .colour").toggleClass("is-hidden"); }); }); Sign In Remember me Forgotten your password? Sign In Cancel Email or password not correct. Please try again Please wait... $(function(){ // Note: All the setup needs to run against a name attribute and *not* the id due the clonish // nature of facebox... $("a[id=googleSignInButton]").click(function(event){ event.preventDefault(); $("input[id=oAuthSystem]").val("GOOGLE"); $("form[id=oAuthForm]").submit(); }); $("a[id=facebookSignInButton]").click(function(event){ event.preventDefault(); $("input[id=oAuthSystem]").val("FACEBOOK"); $("form[id=oAuthForm]").submit(); }); $("a[id=orcidSignInButton]").click(function(event){ event.preventDefault(); $("input[id=oAuthSystem]").val("ORCID"); $("form[id=oAuthForm]").submit(); }); }); If you've forgotten your password, please enter your email address below and we'll send you instructions on how to reset your password. The email address should be the one you originally registered with F1000. Email address not valid, please try again You registered with F1000 via Google, so we cannot reset your password. To sign in, please click here . If you still need help with your Google account password, please click here . You registered with F1000 via Facebook, so we cannot reset your password. To sign in, please click here . If you still need help with your Facebook account password, please click here . Code not correct, please try again Reset password Cancel Email us for further assistance. Server error, please try again. If your email address is registered with us, we will email you instructions to reset your password. If you think you should have received this email but it has not arrived, please check your spam filters and/or contact for further assistance. Please wait... Register $(document).ready(function () { signIn.createSignInAsRow($("#sign-in-form-gfb-popup")); $(".target-field").each(function () { var uris = $(this).val().split("/"); if (uris.pop() === "login") { $(this).val(uris.toString().replace(",","/")); } }); });