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Challapa-Mamani MR, Tomás-Alvarado E, Espinoza-Baigorria A, León-Figueroa DA, Sah R, Rodriguez-Morales AJ, Barboza JJ. Molecular Docking and Molecular Dynamics Simulations in Related to Leishmania donovani: An Update and Literature Review. Trop Med Infect Dis 2023; 8:457. [PMID: 37888585 PMCID: PMC10610989 DOI: 10.3390/tropicalmed8100457] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 09/19/2023] [Accepted: 09/20/2023] [Indexed: 10/28/2023] Open
Abstract
Leishmaniasis, a disease caused by Leishmania parasites and transmitted via sandflies, presents in two main forms: cutaneous and visceral, the latter being more severe. With 0.7 to 1 million new cases each year, primarily in Brazil, diagnosing remains challenging due to diverse disease manifestations. Traditionally, the identification of Leishmania species is inferred from clinical and epidemiological data. Advances in disease management depend on technological progress and the improvement of parasite identification programs. Current treatments, despite the high incidence, show limited efficacy due to factors like cost, toxicity, and lengthy regimens causing poor adherence and resistance development. Diagnostic techniques have improved but a significant gap remains between scientific progress and application in endemic areas. Complete genomic sequence knowledge of Leishmania allows for the identification of therapeutic targets. With the aid of computational tools, testing, searching, and detecting affinity in molecular docking are optimized, and strategies that assess advantages among different options are developed. The review focuses on the use of molecular docking and molecular dynamics (MD) simulation for drug development. It also discusses the limitations and advancements of current treatments, emphasizing the importance of new techniques in improving disease management.
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Affiliation(s)
- Mabel R. Challapa-Mamani
- Escuela de Medicina, Universidad Cesar Vallejo, Trujillo 13007, Peru;
- Sociedad Científica de Estudiantes de Medicina de la Universidad César Vallejo, Trujillo 13007, Peru
| | - Eduardo Tomás-Alvarado
- Hospital General Regional 17, Instituto Mexicano del Seguro Social, Cancún 75533, Mexico;
| | | | | | - Ranjit Sah
- Department of Clinical Microbiology, Institute of Medicine, Tribhuvan University Teaching Hospital, Kathmandu 44600, Nepal;
- Department of Microbiology, Dr. D. Y. Patil Medical College, Hospital and Research Centre, Dr. D. Y. Patil Vidyapeeth, Pune 411018, Maharashtra, India
| | - Alfonso J. Rodriguez-Morales
- Faculty of Health Sciences, Universidad Científica del Sur, Lima 150152, Peru;
- Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Beirut 350000, Lebanon
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Caro-Gómez LA, Rosas-Trigueros JL, Mixcoha E, Zamorano-Carrillo A, Martínez-Martínez J, Benítez-Cardoza CG. Anti-apoptotic Bcl-2 protein in apo and holo conformation anchored to the membrane: comparative molecular dynamics simulations. J Biomol Struct Dyn 2022:1-15. [DOI: 10.1080/07391102.2022.2101145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Affiliation(s)
| | - Jorge L. Rosas-Trigueros
- Laboratorio Transdisciplinario de Investigación en Sistemas Evolutivos, SEPI de la ESCOM del Instituto Politécnico Nacional, Mexico City, Mexico
| | - Edgar Mixcoha
- Catedrático-CONACYT Instituto Nacional de Psiquiatría Ramon de la Fuente Muñiz, Mexico City, Mexico
| | - Absalom Zamorano-Carrillo
- Laboratorio de Bioquímica y Biofísica Computacional, ENMH, Instituto Politécnico Nacional, Mexico City, Mexico
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Exploring the Conformational Space of Bcl-2 Protein Variants: Dynamic Contributions of the Flexible Loop Domain and Transmembrane Region. Molecules 2019; 24:molecules24213896. [PMID: 31671865 PMCID: PMC6865210 DOI: 10.3390/molecules24213896] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 10/21/2019] [Accepted: 10/27/2019] [Indexed: 11/24/2022] Open
Abstract
Members of the Bcl-2 protein family regulate apoptosis through interactions with several proteins. A critical intrinsically disordered region (IDR) present in some members of the Bcl-2 family is essential for their function. Also, the structural and conformational plasticity of disordered regions is essential for the regulation of the Bcl-2 protein’s activity. Further, some proteins of the family contain transmembrane-helical regions, which anchor them into organelle membranes. Bcl-2, the archetypical member of the family, is characterized by an IDR labeled as a flexible loop domain (FLD) and a transmembrane domain (TMD). Another member of this family is the Bcl-2A1 protein, containing a TMD but lacking the FLD. To our knowledge, this is the first report which characterizes the individual and simultaneous dynamical contributions of FLD and TMD in Bcl-2 and Bcl-2A1 using molecular dynamics simulations (MDS). We examined the conformational spaces of Bcl-2, Bcl-2A1, and two artificial constructs lacking the TMD (Bcl-2ΔTM and Bcl-2A1ΔTM). As the results show, FLD and TMD stabilized each protein independently when they are present. When they coincided, such as in Bcl-2, an additive stabilizing effect is observed. This information is crucial for understanding the structural mechanisms of interaction in the Bcl-2 family.
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Ilizaliturri-Flores I, Correa-Basurto J, Bello M, Rosas-Trigueros JL, Zamora-López B, Benítez-Cardoza CG, Zamorano-Carrillo A. Mapping the intrinsically disordered properties of the flexible loop domain of Bcl-2: a molecular dynamics simulation study. J Mol Model 2016; 22:98. [PMID: 27037822 DOI: 10.1007/s00894-016-2940-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 02/22/2016] [Indexed: 02/07/2023]
Abstract
Most of the B-cell lymphoma-2 (Bcl-2) protein structure has been elucidated; however, the conformation of its flexible loop domain (FLD) has not yet been experimentally predicted. Its high flexibility under physiological conditions is the reason. FLD behaves as an intrinsically disordered region (IDR) and can adopt regular structures in particular conditions associated with the control of Bcl-2's anti-apoptotic functions. In a previous contribution, we analyzed an engineered Bcl-2 construct (Bcl-2-Δ22Σ3) submitted to 25-ns MD and reported a disordered-to-helix transitions in a region of FLD (rFLD, residues 60-77). However, the conformational preferences in solution of rFLD in the nanosecond to microsecond scale were not analyzed. Herein, an average model was obtained for the native Bcl-2 protein by homology modeling and MD simulation techniques. From this, only the atomic coordinates corresponding to the rFLD were simulated for 1 μs by MD at 310 K. In concordance with previous studies, a disordered-to-helix transitions were exhibited, implying that this "interconversion of folding" in the rFLD suggest a possible set of conformations encoded in its sequence. Principal component analysis (PCA) showed that most of the conformational fluctuation of Bcl-2 is provided by rFLD. Dihedral PCA (dPCA) offered information about all the conformations of rFLD in the μs of the simulation, characterizing a dPCA-based free energy landscape of rFLD, and a conformational ensemble of fast interconverting conformations as other IDRs. Furthermore, despite the conformational heterogeneity of rFLD, the analysis of the dihedral angles (Φ, Ψ) showed that this region does not randomly explore the conformational space in solution.
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Affiliation(s)
| | - José Correa-Basurto
- Lab de Modelado Molecular y Diseño de Fármacos. ESM-IPN, Ciudad de México, Mexico
| | - Martiniano Bello
- Lab de Modelado Molecular y Diseño de Fármacos. ESM-IPN, Ciudad de México, Mexico
| | - Jorge L Rosas-Trigueros
- Lab Transdisciplinario de Investigación en Sistemas Evolutivos, ESCOM-IPN, Ciudad de México, Mexico
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Chen L, Li X, Wang R, Fang F, Yang W, Kan W. Thermal stability and unfolding pathways of hyperthermophilic and mesophilic periplasmic binding proteins studied by molecular dynamics simulation. J Biomol Struct Dyn 2016; 34:1576-89. [DOI: 10.1080/07391102.2015.1084480] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Lin Chen
- College of Chemistry and Chemical Engineering, Qiqihar University, Qiqihar 161006, P.R. China
| | - Xue Li
- College of Chemistry and Biology, Beihua Uuniversity, Jilin 132000, P.R. China
| | - Ruige Wang
- College of Chemistry and Chemical Engineering, Qiqihar University, Qiqihar 161006, P.R. China
| | - Fengqin Fang
- College of Chemistry and Chemical Engineering, Qiqihar University, Qiqihar 161006, P.R. China
| | - Wanli Yang
- College of Chemistry and Chemical Engineering, Qiqihar University, Qiqihar 161006, P.R. China
| | - Wei Kan
- College of Chemistry and Chemical Engineering, Qiqihar University, Qiqihar 161006, P.R. China
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Correa-Basurto J, Cuevas-Hernández RI, Phillips-Farfán BV, Martínez-Archundia M, Romo-Mancillas A, Ramírez-Salinas GL, Pérez-González ÓA, Trujillo-Ferrara J, Mendoza-Torreblanca JG. Identification of the antiepileptic racetam binding site in the synaptic vesicle protein 2A by molecular dynamics and docking simulations. Front Cell Neurosci 2015; 9:125. [PMID: 25914622 PMCID: PMC4392693 DOI: 10.3389/fncel.2015.00125] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Accepted: 03/17/2015] [Indexed: 01/21/2023] Open
Abstract
Synaptic vesicle protein 2A (SV2A) is an integral membrane protein necessary for the proper function of the central nervous system and is associated to the physiopathology of epilepsy. SV2A is the molecular target of the anti-epileptic drug levetiracetam and its racetam analogs. The racetam binding site in SV2A and the non-covalent interactions between racetams and SV2A are currently unknown; therefore, an in silico study was performed to explore these issues. Since SV2A has not been structurally characterized with X-ray crystallography or nuclear magnetic resonance, a three-dimensional (3D) model was built. The model was refined by performing a molecular dynamics simulation (MDS) and the interactions of SV2A with the racetams were determined by docking studies. A reliable 3D model of SV2A was obtained; it reached structural equilibrium during the last 15 ns of the MDS (50 ns) with remaining structural motions in the N-terminus and long cytoplasmic loop. The docking studies revealed that hydrophobic interactions and hydrogen bonds participate importantly in ligand recognition within the binding site. Residues T456, S665, W666, D670 and L689 were important for racetam binding within the trans-membrane hydrophilic core of SV2A. Identifying the racetam binding site within SV2A should facilitate the synthesis of suitable radio-ligands to study treatment response and possibly epilepsy progression.
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Affiliation(s)
- José Correa-Basurto
- Laboratorio de Modelado Molecular y Diseño de fármacos, Departamento de Bioquímica de la Escuela Superior de Medicina del Instituto Politécnico Nacional, México City Mexico
| | - Roberto I Cuevas-Hernández
- Laboratorio de Modelado Molecular y Diseño de fármacos, Departamento de Bioquímica de la Escuela Superior de Medicina del Instituto Politécnico Nacional, México City Mexico
| | - Bryan V Phillips-Farfán
- Laboratorio de Nutrición Experimental, Laboratorio de Oncología Experimental and Laboratorio de Neuroquímica, Instituto Nacional de Pediatría, México City Mexico
| | - Marlet Martínez-Archundia
- Laboratorio de Modelado Molecular y Diseño de fármacos, Departamento de Bioquímica de la Escuela Superior de Medicina del Instituto Politécnico Nacional, México City Mexico
| | - Antonio Romo-Mancillas
- División de Estudios de Posgrado, Facultad de Química, Universidad Autónoma de Querétaro, Santiago de Querétaro Mexico
| | - Gema L Ramírez-Salinas
- Laboratorio de Modelado Molecular y Diseño de fármacos, Departamento de Bioquímica de la Escuela Superior de Medicina del Instituto Politécnico Nacional, México City Mexico
| | - Óscar A Pérez-González
- Laboratorio de Nutrición Experimental, Laboratorio de Oncología Experimental and Laboratorio de Neuroquímica, Instituto Nacional de Pediatría, México City Mexico
| | - José Trujillo-Ferrara
- Laboratorio de Modelado Molecular y Diseño de fármacos, Departamento de Bioquímica de la Escuela Superior de Medicina del Instituto Politécnico Nacional, México City Mexico
| | - Julieta G Mendoza-Torreblanca
- Laboratorio de Nutrición Experimental, Laboratorio de Oncología Experimental and Laboratorio de Neuroquímica, Instituto Nacional de Pediatría, México City Mexico
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