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Chandra I, Prabhu SV, Nayak C, Singh SK. E-pharmacophore based screening to identify potential HIV-1 gp120 and CD4 interaction blockers for wild and mutant types. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2021; 32:353-377. [PMID: 33832362 DOI: 10.1080/1062936x.2021.1901310] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 03/07/2021] [Indexed: 06/12/2023]
Abstract
HIV-1 gp120 provides a multistage viral entry process through the conserved CD4 binding site. Hunting of potential blockers can diminish the interaction of gp120 with the CD4 host receptor leading to the suppression of HIV-1 infection. Structure-based pharmacophore virtual screening followed by binding free energy calculation, molecular dynamics (MD) simulation and density functional theory (DFT) calculation is applied to discriminate the potential blockers from six small molecule databases. Five compounds from six databases exhibited vital interactions with key residues ASP368, GLU370, ASN425, MET426, TRP427 and GLY473 of gp120, involved in the binding with CD4, host receptor. Most importantly, compound NCI-254200 displayed strong communication with key residues of wild type and drug resistance single mutant gp120 (M426L and W427V) even in the dynamic condition, evidenced from MD simulation. This investigation provided a potential compound NCI-254200 which may show inhibitory activity against HIV-1 gp120 variant interactions with CD4 host cell receptors.
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Affiliation(s)
- I Chandra
- Computer Aided Drug Design and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi, India
| | - S V Prabhu
- Computer Aided Drug Design and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi, India
| | - C Nayak
- Computer Aided Drug Design and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi, India
| | - S K Singh
- Computer Aided Drug Design and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi, India
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Sulaiman KO, Kolapo TU, Onawole AT, Islam MA, Adegoke RO, Badmus SO. Molecular dynamics and combined docking studies for the identification of Zaire ebola virus inhibitors. J Biomol Struct Dyn 2018; 37:3029-3040. [PMID: 30058446 DOI: 10.1080/07391102.2018.1506362] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Ebola virus (EBOV) is a lethal human pathogen with a risk of global spread of its zoonotic infections, and Ebolavirus Zaire specifically has the highest fatality rate amongst other species. There is a need for continuous effort towards having therapies, as a single licensed treatment to neutralize the EBOV is yet to come into reality. This present study virtually screened the MCULE database containing almost 36 million compounds against the structure of a Zaire Ebola viral protein (VP) 35 and a consensus scoring of both MCULE and CLCDDW docking programs remarked five compounds as potential hits. These compounds, with binding energies ranging from -7.9 to -8.9 kcal/mol, were assessed for predictions of their physicochemical and bioactivity properties, as well as absorption, distribution, metabolism, excretion, and toxicity (ADMET) criteria. The results of the 50 ns molecular dynamics simulations showed the presence of dynamic stability between ligand and protein complexes, and the structures remained significantly unchanged at the ligand-binding site throughout the simulation period. Both docking analysis and molecular dynamics simulation studies suggested strong binding affinity towards the receptor cavity and these selected compounds as potential inhibitors against the Zaire Ebola VP 35. With respect to inhibition constant values, bioavailability radar and other physicochemical properties, compound A (MCULE-1018045960-0-1) appeared to be the most promising hit compound. However, the ligand efficiency and ligand efficiency scale need improvement during optimization, and also validation via in vitro and in vivo studies are necessary to finally make a lead compound in treating Ebola virus diseases. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Kazeem O Sulaiman
- a Department of Chemistry , University of Saskatchewan , Saskatoon , Saskatchewan , Canada
| | - Temitope U Kolapo
- b Department of Veterinary Parasitology and Entomology , University of Ilorin , Ilorin , Nigeria.,c Department of Veterinary Microbiology , University of Saskatchewan , Saskatchewan , Canada
| | | | - Md Ataul Islam
- e Department of Chemical Pathology Faculty of Health Sciences , University of Pretoria and National Health Laboratory Service Tshwane Academic Division , Pretoria , South Africa.,f School of Health Sciences , University of Kwazulu-Natal Westville Campus , Durban , South Africa
| | - Rukayat O Adegoke
- g Department of Pure and Applied Biology , Ladoke Akintola University of Technology , Ogbomoso , Nigeria
| | - Suaibu O Badmus
- g Department of Pure and Applied Biology , Ladoke Akintola University of Technology , Ogbomoso , Nigeria
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Amir-Hassan A, Lee VS, Baharuddin A, Othman S, Xu Y, Huang M, Yusof R, Rahman NA, Othman R. Conformational and energy evaluations of novel peptides binding to dengue virus envelope protein. J Mol Graph Model 2017; 74:273-287. [PMID: 28458006 DOI: 10.1016/j.jmgm.2017.03.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 03/15/2017] [Accepted: 03/16/2017] [Indexed: 12/13/2022]
Abstract
Effective novel peptide inhibitors which targeted the domain III of the dengue envelope (E) protein by blocking dengue virus (DENV) entry into target cells, were identified. The binding affinities of these peptides towards E-protein were evaluated by using a combination of docking and explicit solvent molecular dynamics (MD) simulation methods. The interactions of these complexes were further investigated by using the Molecular Mechanics-Poisson Boltzmann Surface Area (MMPBSA) and Molecular Mechanics Generalized Born Surface Area (MMGBSA) methods. Free energy calculations of the peptides interacting with the E-protein demonstrated that van der Waals (vdW) and electrostatic interactions were the main driving forces stabilizing the complexes. Interestingly, calculated binding free energies showed good agreement with the experimental dissociation constant (Kd) values. Our results also demonstrated that specific residues might play a crucial role in the effective binding interactions. Thus, this study has demonstrated that a combination of docking and molecular dynamics simulations can accelerate the identification process of peptides as potential inhibitors of dengue virus entry into host cells.
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Affiliation(s)
- Asfarina Amir-Hassan
- Drug Design & Development Research Group, University of Malaya, 50603 Kuala Lumpur, Malaysia; Department of Pharmacy, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Vannajan Sanghiran Lee
- Drug Design & Development Research Group, University of Malaya, 50603 Kuala Lumpur, Malaysia; Department of Chemistry, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Aida Baharuddin
- Drug Design & Development Research Group, University of Malaya, 50603 Kuala Lumpur, Malaysia; Department of Molecular Medicine, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Shatrah Othman
- Drug Design & Development Research Group, University of Malaya, 50603 Kuala Lumpur, Malaysia; Department of Molecular Medicine, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Yongtao Xu
- School of Chemistry and Chemical Engineering, Queen's University Belfast, Northern Ireland, United Kingdom; School of Biomedical Engineering, Xinxiang Medical University, Xinxiang, Henan 453003, China
| | - Meilan Huang
- School of Chemistry and Chemical Engineering, Queen's University Belfast, Northern Ireland, United Kingdom
| | - Rohana Yusof
- Drug Design & Development Research Group, University of Malaya, 50603 Kuala Lumpur, Malaysia; Department of Molecular Medicine, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Noorsaadah Abd Rahman
- Drug Design & Development Research Group, University of Malaya, 50603 Kuala Lumpur, Malaysia; Department of Chemistry, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Rozana Othman
- Drug Design & Development Research Group, University of Malaya, 50603 Kuala Lumpur, Malaysia; Department of Pharmacy, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia; Centre for Natural Product Research and Drug Discovery, University of Malaya, 50603 Kuala Lumpur, Malaysia.
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Wang L, Li Y, Xu M, Pang X, Liu Z, Tan W, Xu J. Chemical fragment-based CDK4/6 inhibitors prediction and web server. RSC Adv 2016. [DOI: 10.1039/c5ra23289a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Cyclin-dependent kinases (CDKs), a family of mammalian heterodimeric kinases, play central roles in the regulation of cell cycle progression, transcription, neuronal differentiation, and metabolism.
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Affiliation(s)
- Ling Wang
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering
- School of Bioscience and Bioengineering
- South China University of Technology
- Guangzhou 510006
- China
| | - Yecheng Li
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering
- School of Bioscience and Bioengineering
- South China University of Technology
- Guangzhou 510006
- China
| | - Mengyan Xu
- Research Center for Drug Discovery
- School of Pharmaceutical Sciences
- Sun Yat-Sen University
- Guangzhou 510006
- China
| | - Xiaoqian Pang
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering
- School of Bioscience and Bioengineering
- South China University of Technology
- Guangzhou 510006
- China
| | - Zhihong Liu
- Research Center for Drug Discovery
- School of Pharmaceutical Sciences
- Sun Yat-Sen University
- Guangzhou 510006
- China
| | - Wen Tan
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering
- School of Bioscience and Bioengineering
- South China University of Technology
- Guangzhou 510006
- China
| | - Jun Xu
- Research Center for Drug Discovery
- School of Pharmaceutical Sciences
- Sun Yat-Sen University
- Guangzhou 510006
- China
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Ahmed M, Sadek MM, Serrya RA, Kafafy AHN, Abouzid KA, Wang F. Assessment of new anti-HER2 ligands using combined docking, QM/MM scoring and MD simulation. J Mol Graph Model 2013; 40:91-8. [DOI: 10.1016/j.jmgm.2012.12.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Revised: 12/04/2012] [Accepted: 12/06/2012] [Indexed: 01/23/2023]
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