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Mecanismo de la ATPasa tipo P CtpF de Mycobacterium tuberculosis como diana para nuevos antibióticos antituberculosis

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datacite.rightshttp://purl.org/coar/access_right/c_16ec
dc.contributor.advisorYosa Reyes, Juvenal
dc.contributor.advisorLeyva Rojas, Jorge Alonso
dc.contributor.authorPestana Nobles, Roberto Carlos
dc.date.accessioned2024-05-06T22:20:34Z
dc.date.available2024-05-06T22:20:34Z
dc.date.issued2024spa
dc.description.abstractMycobacterium tuberculosis (Mtb), el agente causal de la tuberculosis (TB), se clasifica predominantemente como un patógeno del sistema respiratorio, aunque tiene la capacidad de afectar otros órganos y tejidos del cuerpo. Esta enfermedad representa un desafío significativo en países con recursos económicos limitados, donde aproximadamente 1,5 millones de individuos fallecen anualmente a causa de esta. El tratamiento actual para la TB sigue las directrices establecidas por la Organización Mundial de la Salud (OMS), consistiendo principalmente en un tratamiento usando fármacos de primera línea: isoniacida (INH), rifampicina (RIF), etambutol (EMB) y pirazinamida (PZA). Una problemática central en el manejo de la TB es la interrupción prematura del tratamiento anti-TB, factor que contribuye significativamente a la aparición y propagación de cepas de Mtb resistentes a múltiples medicamentos, conocidas como Tuberculosis multi-resistente (TB-MDR) y Tuberculosis extremadamente-resistente (TB-XDR). Ante la necesidad urgente de superar las limitaciones de los tratamientos actuales y prevenir el desarrollo de resistencias bacterianas, se hace imperativo buscar y validar nuevos blancos terapéuticos que ofrezcan mecanismos alternativos de acción. En este contexto, emergen como blancos prometedores las ATPasas tipo P de Mtb, unas proteínas de membrana que catalizan el transporte de iones contra gradientes de concentración utilizando la energía derivada de la hidrólisis del ATP. Estas proteínas juegan roles esenciales en los procesos de transporte celular y en la interacción entre el patógeno y su huésped, convirtiéndose en candidatos ideales para el desarrollo de nuevas estrategias terapéuticas debido a su ubicación accesible en la membrana celular, lo cual facilita el abordaje por parte de agentes farmacológicos sin enfrentar obstáculos significativos de permeabilidad. Por lo que en este estudio se seleccionó la proteína CtpF, una bomba de eflujo específica para iones de calcio, la cual se encuentra implicada en mecanismos de defensa y supervivencia de la Mtb dentro del macrófago. Con el fin de tener una representación más fiel al entorno químico de la proteína, esta fue modelada dentro de una membrana lipídica compuesta por 1-palmitoil-2-oleoil-fosfatidilcolina (POPC) usando el servidor CHARMMGUI. Con este sistema construido se procedió a realizar una dinámica molecular gaussiana acelerada (GaMD) por 1 microsegundo, con el fin de explorar los movimientos intrínsecos de la proteína. La modelación de la proteína CtpF dentro de un ambiente simulado permitió estudiar la dinámica de la proteína y como esta se relaciona con su mecanismo enzimático, además se lograron identificar 4 compuestos con potencia inhibitoria para la proteína CtpF. A través de docking molecular, se evaluaron en total 670.000 moléculas, de las cuales 4 resultaron ser posibles inhibidores para la proteína CtpF. Estos 4 posibles inhibidores fueron evaluados usando dinámica molecular y cálculos de energía de interacción a través de MMPBSA comparando sus resultados con un ligando de referencia Ácido ciclopiazónico (CPA), energía de unión: -31.8663, donde se lograron identificar los aminoácidos que juegan un papel clave en la interacción con los ligandos. Se identificaron los siguientes compuestos, ligando L_43303, nombre IUPAC: Morfolina urea 1,2,4,5-tetraoxano, código ChEMBL: CHEMBL259023, energía libre de unión de -23.2025 kcal/mol. Ligando L_59025, nombre IUPAC: 2,2'-espirobi[6,7,8,9-tetrahidro-3H-ciclopenta[a]naftaleno]-1,1'- diona, energía libre de unión: -24.1896 kcal/mol. Ligando L_4946, nombre IUPAC: 1-[4-[3-(1-quinolin-2-ilazetidin-3-il)pirazin-2-il]piperazin-1-il]etanona, energía libre de unión: -29.358 kcal/mol. Ligando L_113260, nombre IUPAC: 10-amino-12-(3- metilfenil)-1,3,13-triazapentaciclo[11,8,0,02,11,04,9,015,20]henicosa2,4(9),10,15,17,19-hexaeno-14,21-diona, código ChEMBL: CHEMBL4213928, energía libre de unión: -30.1867 kcal/mol. Siendo el ligando L_113260 como posible punto de partida para para el diseño de nuevos fármacos mediante técnicas de hitto-lead y docking molecular basado en fragmentos. Este enfoque de la modelación molecular promete abrir nuevas vías para el desarrollo de terapias más efectivas y rápidas contra la TB, abordando así uno de los problemas de salud pública más urgente a nivel global.spa
dc.description.abstractMycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB), is primarily classified as a pathogen of the respiratory system, yet it possesses the capacity to affect other organs and body tissues. This disease presents a significant challenge in countries with limited economic resources, where approximately 1.5 million individuals die annually from it. The current TB treatment adheres to the guidelines established by the World Health Organization (WHO), mainly involving a regimen utilizing first-line drugs: isoniazid (INH), rifampicin (RIF), ethambutol (EMB), and pyrazinamide (PZA). A critical issue in TB management is the premature discontinuation of anti-TB treatment, a factor that significantly contributes to the emergence and spread of multi-drug resistant Mtb strains, known as Multi-Drug Resistant Tuberculosis (MDR-TB) and Extensively Drug-Resistant Tuberculosis (XDR-TB). Faced with the urgent need to surpass the limitations of current treatments and prevent the development of bacterial resistances, it is imperative to identify and validate new therapeutic targets that offer alternative mechanisms of action. In this regard, Mtb P-type ATPases, membrane proteins that catalyze ion transport against concentration gradients using energy from ATP hydrolysis, emerge as promising targets. These proteins play crucial roles in cellular transport processes and the pathogen-host interaction, making them ideal candidates for the development of new therapeutic strategies due to their accessible location on the cell membrane, which facilitates the approach by pharmacological agents without significant permeability obstacles. In light of the foregoing, this study selected the CtpF protein, a specific efflux pump for calcium ions involved in Mtb's defense and survival mechanisms inside the macrophage. To closely mimic the protein's chemical environment, it was modeled within a lipid membrane composed of 1-palmitoyl-2-oleoyl-phosphatidylcholine (POPC) using the CHARMMGUI server. With this constructed system, accelerated Gaussian molecular dynamics (GaMD) were conducted for 1 microsecond to explore the protein's intrinsic movements. Modeling the CtpF protein in a simulated environment allowed for the study of its dynamics and relation to its enzymatic mechanism, also enabling the identification of 4 compounds with inhibitory potential for the CtpF protein. Through molecular docking, a total of 670,000 molecules were evaluated, resulting in 4 as potential CtpF protein inhibitors. These 4 potential inhibitors were further assessed using molecular dynamics and interaction energy calculations through MMPBSA, comparing their results with a reference ligand, Cyclopiazonic Acid (CPA), with a binding energy of - 31.8663 kcal/mol, identifying key amino acids involved in the interaction with the ligands. The following compounds were identified: ligand L_43303, IUPAC name Morpholine urea 1,2,4,5-tetraoxane, ChEMBL code: CHEMBL259023, with a free binding energy of -23.2025 kcal/mol. Ligand L_59025, IUPAC name: 2,2'- spirobi[6,7,8,9-tetrahydro-3H-cyclopenta[a]naphthalene]-1,1'-dione, with a free binding energy of -24.1896 kcal/mol. Ligand L_4946, IUPAC name: 1-[4-[3-(1- quinolin-2-ylazetidin-3-yl)pyrazin-2-yl]piperazin-1-yl]ethanone, with a free binding energy of -29.358 kcal/mol. Ligand L_113260, IUPAC name: 10-amino-12-(3- methylphenyl)-1,3,13-triazapentacyclo[11,8,0,02,11,04,9,015,20]henicosa2,4(9),10,15,17,19-hexaene-14,21-dione, ChEMBL code: CHEMBL4213928, with a free binding energy of -30.1867 kcal/mol. Ligand L_113260 was identified as a potential starting point for new drug design using hit-to-lead techniques and fragment-based molecular docking. This molecular modeling approach promises to open new pathways for the development of more effective and rapid therapies against TB, thereby addressing one of the most urgent global public health issueseng
dc.format.mimetypepdf
dc.identifier.urihttps://hdl.handle.net/20.500.12442/14584
dc.language.isospa
dc.publisherEdiciones Universidad Simón Bolívarspa
dc.publisherFacultad de Ciencias Básicas y Biomédicasspa
dc.rights.accessrightsinfo:eu-repo/semantics/restrictedAccesseng
dc.subjectMycobacterium tuberculosisspa
dc.subjectDinámica molecularspa
dc.subjectDocking molecularspa
dc.subjectCtpFspa
dc.subjectInhibidoresspa
dc.subjectTuberculosisspa
dc.subjectDinámica molecular gaussiana aceleradaspa
dc.subjectATPasa tipo P.spa
dc.subjectMycobacterium tuberculosiseng
dc.subjectMolecular dyamicseng
dc.subjectMolecular dockingeng
dc.subjectCtpFeng
dc.subjectInhibitorseng
dc.subjectTuberculosiseng
dc.subjectGaussian accelerated molecular dynamicseng
dc.subjectATPase type P.eng
dc.titleMecanismo de la ATPasa tipo P CtpF de Mycobacterium tuberculosis como diana para nuevos antibióticos antituberculosisspa
dc.type.driverinfo:eu-repo/semantics/doctoralThesis
dc.type.spaTesis de doctorado
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