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Original Articles

Molecular Dynamics Simulation Study Explaining Inhibitor Selectivity in Different Class of Histone Deacetylases

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Pages 677-698 | Received 10 Jun 2011, Published online: 15 May 2012

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Varun Dewaker, Ajay K. Srivastava, Ashish Arora & Yenamandra S. Prabhakar. (2021) Investigation of HDAC8-ligands’ intermolecular forces through molecular dynamics simulations: profiling of non-bonding energies to design potential compounds as new anti-cancer agents. Journal of Biomolecular Structure and Dynamics 39:13, pages 4726-4751.
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Articles from other publishers (18)

Kayode Adewole, Adebayo Ishola & Ige Olaoye. (2022) In silico profiling of histone deacetylase inhibitory activity of compounds isolated from Cajanus cajan. Beni-Suef University Journal of Basic and Applied Sciences 11:1.
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Ahmad ALSULIMANI, Tulika BHARDWAJ, Essam M. JANAHI, Atiah H. ALMALKI, Brij N. TEWARI, Mohd WAHID, Mustfa F. ALKHANANI, Pallavi SOMVANSHI & Shafiul HAQUE. (2022) Systematic structure guided clustering of chemical lead compounds targeting RdRp of SARS-CoV-2. Minerva Biotechnology and Biomolecular Research 34:3.
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Ammar D. Elmezayen & Yelekçi Kemal. (2021) Structure-based virtual screening for novel potential selective inhibitors of class IIa histone deacetylases for cancer treatment. Computational Biology and Chemistry 92, pages 107491.
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Waleed A. Zalloum & Needa Zalloum. (2021) Comparative QM/MM Molecular Dynamics and Umbrella Sampling Simulations: Interaction of the Zinc-Bound Intermediate Gem-Diolate Trapoxin A Inhibitor and Acetyl- l -lysine Substrate with Histone Deacetylase 8 . The Journal of Physical Chemistry B 125:20, pages 5321-5337.
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M. S. Neiband, A. Benvidi & A. Mani-Varnosfaderani. (2019) Development of classification models for identification of important structural features of isoform-selective histone deacetylase inhibitors (class I). Molecular Diversity 24:4, pages 1077-1094.
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Loredana Cappellacci, Diego R. Perinelli, Filippo Maggi, Mario Grifantini & Riccardo Petrelli. (2020) Recent Progress in Histone Deacetylase Inhibitors as Anticancer Agents. Current Medicinal Chemistry 27:15, pages 2449-2493.
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Tulika Bhardwaj, Shafiul Haque & Pallavi Somvanshi. (2019) Comparative assessment of the therapeutic drug targets of C. botulinum ATCC 3502 and C. difficile str. 630 using in silico subtractive proteomics approach . Journal of Cellular Biochemistry 120:9, pages 16160-16184.
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Abdullahi Ibrahim Uba & Kemal Yelekçi. (2018) Pharmacophore-based virtual screening for identification of potential selective inhibitors of human histone deacetylase 6. Computational Biology and Chemistry 77, pages 318-330.
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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.
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Saif Khan, Tulika Bhardwaj, Pallavi Somvanshi, Raju K. Mandal, Sajad A. Dar, Arshad Jawed, Mohd Wahid, Naseem Akhter, Mohtashim Lohani, S. Alouffi & Shafiul Haque. (2018) Inhibition of C298S mutant of human aldose reductase for antidiabetic applications: Evidence from in silico elementary mode analysis of biological network model. Journal of Cellular Biochemistry 119:8, pages 6961-6973.
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Jeyachandran Sivakamavalli, Chandrabose Selvaraj, Sanjeev Kumar Singh & Baskaralingam Vaseeharan. (2016) Modeling of macromolecular proteins in prophenoloxidase cascade through experimental and computational approaches. Biotechnology and Applied Biochemistry 63:6, pages 779-788.
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Vikash Kumar & Mohammad Imran Siddiqi. (2016) Structural insight into inhibition of human Class II PI3K isoforms: homology modeling, binding site characterization, docking and molecular dynamics studies. RSC Advances 6:113, pages 112455-112467.
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Rodrigo Aguayo-Ortiz & Eli Fernández-de Gortari. 2016. Epi-Informatics. Epi-Informatics 21 52 .
Seyed Ahmad Ebadi, Nima Razzaghi-Asl, Mehdi Khoshneviszadeh & Ramin Miri. (2015) Detailed atomistic molecular modeling of a potent type ΙΙ p38α inhibitor. Structural Chemistry 26:4, pages 1125-1137.
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Nathalie Deschamps, Claudia Avello Simões-Pires, Pierre-Alain Carrupt & Alessandra Nurisso. (2015) How the flexibility of human histone deacetylases influences ligand binding: an overview. Drug Discovery Today 20:6, pages 736-742.
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Madhusoodanan Mottamal, Shilong Zheng, Tien Huang & Guangdi Wang. (2015) Histone Deacetylase Inhibitors in Clinical Studies as Templates for New Anticancer Agents. Molecules 20:3, pages 3898-3941.
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Subha Kalyaanamoorthy & Yi-Ping Phoebe Chen. (2014) Modelling and enhanced molecular dynamics to steer structure-based drug discovery. Progress in Biophysics and Molecular Biology 114:3, pages 123-136.
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Ahmad Ebadi, Nima Razzaghi-Asl, Mehdi Khoshneviszadeh & Ramin Miri. (2013) Comparative amino acid decomposition analysis of potent type I p38α inhibitors. DARU Journal of Pharmaceutical Sciences 21:1.
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