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Journal of Biomolecular Structure and Dynamics Volume 35, 2017 - Issue 13
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Research Articles

Searching the conformational complexity and binding properties of HDAC6 through docking and molecular dynamic simulations

Yudibeth Sixto-LópezLaboratorio de Modelado Molecular y Diseño de Fármacos (Laboratory of Molecular Modeling and Drug Design), Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Mexico City11340, Mexico
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Martiniano BelloLaboratorio de Modelado Molecular y Diseño de Fármacos (Laboratory of Molecular Modeling and Drug Design), Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Mexico City11340, Mexico;Laboratorio de Biofísica y Biocatálisis, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Salvador Díaz Mirón s/n, Casco de Santo Tomás, Ciudad de México11340, MexicoCorrespondence[email protected]
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Rolando Alberto Rodríguez-FonsecaLaboratorio de Modelado Molecular y Diseño de Fármacos (Laboratory of Molecular Modeling and Drug Design), Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Mexico City11340, Mexico
,
Martha Cecilia Rosales-HernándezLaboratorio de Modelado Molecular y Diseño de Fármacos (Laboratory of Molecular Modeling and Drug Design), Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Mexico City11340, Mexico;Laboratorio de Biofísica y Biocatálisis, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Salvador Díaz Mirón s/n, Casco de Santo Tomás, Ciudad de México11340, Mexico
,
Marlet Martínez-ArchundiaLaboratorio de Modelado Molecular y Diseño de Fármacos (Laboratory of Molecular Modeling and Drug Design), Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Mexico City11340, Mexico
,
José Antonio Gómez-VidalFacultad de Farmacia, Departamento de Química Farmacéutica y Orgánica, Universidad de Granada, Granada18071, Spain
&
José Correa-BasurtoLaboratorio de Modelado Molecular y Diseño de Fármacos (Laboratory of Molecular Modeling and Drug Design), Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Mexico City11340, MexicoCorrespondence[email protected]
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Pages 2794-2814 | Received 09 Mar 2016, Accepted 25 Aug 2016, Published online: 23 Sep 2016

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Yudibeth Sixto-López, José Antonio Gómez-Vidal, Nuria de Pedro, Martiniano Bello, Martha Cecilia Rosales-Hernández & José Correa-Basurto. (2022) In silico design of HDAC6 inhibitors with neuroprotective effects. Journal of Biomolecular Structure and Dynamics 40:24, pages 14204-14222.
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Malihe Hassanzadeh, Shabnam Mahernia, Gianluca Caprini, Gianluca Fossati, Mehdi Adib, Faezeh Moakedi & Massoud Amanlou. (2022) Epigenetic-based cancer therapeutics: new potential HDAC8 inhibitors. Journal of Biomolecular Structure and Dynamics 40:1, pages 297-311.
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Varun Dewaker, Pratik Narain Srivastava, Saroj Verma & Yenamandra S. Prabhakar. (2020) Molecular dynamics study of HDAC8-largazole analogues co-crystals for designing potential anticancer compounds. Journal of Biomolecular Structure and Dynamics 38:4, pages 1197-1213.
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Yudibeth Sixto-López, Martiniano Bello & José Correa-Basurto. (2019) Structural and energetic basis for the inhibitory selectivity of both catalytic domains of dimeric HDAC6. Journal of Biomolecular Structure and Dynamics 37:18, pages 4701-4720.
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Venkatesan Suryanarayanan & Sanjeev Kumar Singh. (2019) Deciphering the binding mode and mechanistic insights of pentadecylidenemalonate (1b) as activator of histone acetyltransferase PCAF. Journal of Biomolecular Structure and Dynamics 37:9, pages 2296-2309.
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Yudibeth Sixto-López, Martiniano Bello & José Correa-Basurto. (2019) Insights into structural features of HDAC1 and its selectivity inhibition elucidated by Molecular dynamic simulation and Molecular Docking. Journal of Biomolecular Structure and Dynamics 37:3, pages 584-610.
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Yijun Wang, Limei Yang, Jiaying Hou, Qing Zou, Qi Gao, Wenhui Yao, Qizheng Yao & Ji Zhang. (2019) Hierarchical virtual screening of the dual MMP-2/HDAC-6 inhibitors from natural products based on pharmacophore models and molecular docking. Journal of Biomolecular Structure and Dynamics 37:3, pages 649-670.
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Hao Zhou, Chengzhang Wang, Tao Deng, Ran Tao & Wenjun Li. (2018) Novel urushiol derivatives as HDAC8 inhibitors: rational design, virtual screening, molecular docking and molecular dynamics studies. Journal of Biomolecular Structure and Dynamics 36:8, pages 1966-1978.
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Articles from other publishers (18)

Aliki Drakontaeidi & Eleni Pontiki. (2023) A Review on Molecular Docking on HDAC Isoforms: Novel Tool for Designing Selective Inhibitors. Pharmaceuticals 16:12, pages 1639.
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Irving Balbuena-Rebolledo, Astrid M. Rivera-Antonio, Yudibeth Sixto-López, José Correa-Basurto, Martha C. Rosales-Hernández, Jessica Elena Mendieta-Wejebe, Francisco J. Martínez-Martínez, Ivonne María Olivares-Corichi, José Rubén García-Sánchez, Juan Alberto Guevara-Salazar, Martiniano Bello & Itzia I. Padilla-Martínez. (2022) Dihydropyrazole-Carbohydrazide Derivatives with Dual Activity as Antioxidant and Anti-Proliferative Drugs on Breast Cancer Targeting the HDAC6. Pharmaceuticals 15:6, pages 690.
Crossref
Yudibeth Sixto‐López & Marlet Martínez‐Archundia. (2021) Drug repositioning to target NSP15 protein on SARS‐CoV ‐2 as possible COVID ‐19 treatment . Journal of Computational Chemistry 42:13, pages 897-907.
Crossref
Yudibeth Sixto-López, José Correa-Basurto, Martiniano Bello, Bruno Landeros-Rivera, Jose Antonio Garzón-Tiznado & Sarita Montaño. (2021) Structural insights into SARS-CoV-2 spike protein and its natural mutants found in Mexican population. Scientific Reports 11:1.
Crossref
Xin-Hui Zhang, Qin-Ma, Hui-Pan Wu, Mussa Yussuf Khamis, Yi-Han Li, Li-Ying Ma & Hong-Min Liu. (2021) A Review of Progress in Histone Deacetylase 6 Inhibitors Research: Structural Specificity and Functional Diversity. Journal of Medicinal Chemistry 64:3, pages 1362-1391.
Crossref
Yudibeth Sixto-López & José Correa-Basurto. 2021. Molecular Docking for Computer-Aided Drug Design. Molecular Docking for Computer-Aided Drug Design 367 390 .
Yudibeth Sixto-López, Martiniano Bello & José Correa-Basurto. (2020) Exploring the inhibitory activity of valproic acid against the HDAC family using an MMGBSA approach. Journal of Computer-Aided Molecular Design 34:8, pages 857-878.
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Yudibeth Sixto-López, José Antonio Gómez-Vidal, Nuria de Pedro, Martiniano Bello, Martha Cecilia Rosales-Hernández & José Correa-Basurto. (2020) Hydroxamic acid derivatives as HDAC1, HDAC6 and HDAC8 inhibitors with antiproliferative activity in cancer cell lines. Scientific Reports 10:1.
Crossref
Victoriano Corpas-López, Mavys Tabraue-Chávez, Yudibeth Sixto-López, Sonia Panadero-Fajardo, Fernando Alves de Lima Franco, José F. Domínguez-Seglar, Francisco Morillas-Márquez, Francisco Franco-Montalbán, Mónica Díaz-Gavilán, José Correa-Basurto, Julián López-Viota, Margarita López-Viota, José Pérez del Palacio, Mercedes de la Cruz, Nuria de Pedro, Joaquina Martín-Sánchez & José A. Gómez-Vidal. (2020) O -Alkyl Hydroxamates Display Potent and Selective Antileishmanial Activity . Journal of Medicinal Chemistry 63:11, pages 5734-5751.
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Balázs Zoltán Zsidó & Csaba Hetényi. (2020) Molecular Structure, Binding Affinity, and Biological Activity in the Epigenome. International Journal of Molecular Sciences 21:11, pages 4134.
Crossref
Hélène Losson, Michael Schnekenburger, Mario Dicato & Marc Diederich. (2020) HDAC6—An Emerging Target Against Chronic Myeloid Leukemia?. Cancers 12:2, pages 318.
Crossref
Avinash MishraMegan CrossAndreas HofmannMark J. CosterAbdul KarimAbdul Sattar. (2019) Identification of a Novel Scaffold for Inhibition of Dipeptidyl Peptidase-4. Journal of Computational Biology 26:12, pages 1470-1486.
Crossref
Varun Chahal, Sonam Nirwan & Rita Kakkar. (2019) Combined approach of homology modeling, molecular dynamics, and docking: computer-aided drug discovery. Physical Sciences Reviews 4:10.
Crossref
A.N. Kukushkin & S. B. Svetlikova. (2019) Histone Deacetylase HDAC6 Inhibitor CAY10603 Blocks G1/S of the Cell Cycle and Promotes Senescence of Murine Fibroblasts Transformed with E1A and cHa-ras Oncogenes. Cell and Tissue Biology 13:4, pages 268-275.
Crossref
Yang Zhang, Jun Biao Ying, Jia Jun Hong, Feng Cheng Li, Ting Ting Fu, Feng Yuan Yang, Guo Xun Zheng, Xiao Jun Yao, Yan Lou, Yunqing Qiu, Wei Wei Xue & Feng Zhu. (2019) How Does Chirality Determine the Selective Inhibition of Histone Deacetylase 6? A Lesson from Trichostatin A Enantiomers Based on Molecular Dynamics. ACS Chemical Neuroscience 10:5, pages 2467-2480.
Crossref
Abdullahi Ibrahim Uba & Kemal Yelekçi. (2018) Carboxylic acid derivatives display potential selectivity for human histone deacetylase 6: Structure-based virtual screening, molecular docking and dynamics simulation studies. Computational Biology and Chemistry 75, pages 131-142.
Crossref
Marlet Martínez-Archundia, Martiniano Bello & Jose Correa-Basurto. 2018. Rational Drug Design. Rational Drug Design 403 416 .
Irving Balbuena-Rebolledo, Astrid M. Rivera-Antonio, Yudibeth Sixto-Lopez, José Correa-Basurto, Martha C. Rosales-Hernández, Jessica Elena Mendieta-Wejebe, Francisco J. Martínez-Martínez, Ivonne María Olivares-Corichi, José Ruben Garcia Sanchez, Juan Alberto Guevara-Salazar, Martiniano Bello & Itzia I. Padilla-Martínez. (2022) Dihydropyrazole-Carbohydazide Derivatives with Dual Activity as Antioxidant and Anti-Proliferative Drugs on Breast Cancer Targeting the Hdac6. SSRN Electronic Journal.
Crossref

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