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Rana N, Singh AK, Shuaib M, Gupta S, Habiballah MM, Alkhanani MF, Haque S, Reshi MS, Kumar S. Drug Resistance Mechanism of M46I-Mutation-Induced Saquinavir Resistance in HIV-1 Protease Using Molecular Dynamics Simulation and Binding Energy Calculation. Viruses 2022; 14:v14040697. [PMID: 35458427 PMCID: PMC9031992 DOI: 10.3390/v14040697] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/05/2022] [Accepted: 03/07/2022] [Indexed: 02/06/2023] Open
Abstract
Drug-resistance-associated mutation in essential proteins of the viral life cycle is a major concern in anti-retroviral therapy. M46I, a non-active site mutation in HIV-1 protease has been clinically associated with saquinavir resistance in HIV patients. A 100 ns molecular dynamics (MD) simulation and MM-PBSA calculations were performed to study the molecular mechanism of M46I-mutation-based saquinavir resistance. In order to acquire deeper insight into the drug-resistance mechanism, the flap curling, closed/semi-open/open conformations, and active site compactness were studied. The M46I mutation significantly affects the energetics and conformational stability of HIV-1 protease in terms of RMSD, RMSF, Rg, SASA, and hydrogen formation potential. This mutation significantly decreased van der Waals interaction and binding free energy (∆G) in the M46I–saquinavir complex and induced inward flap curling and a wider opening of the flaps for most of the MD simulation period. The predominant open conformation was reduced, but inward flap curling/active site compactness was increased in the presence of saquinavir in M46I HIV-1 protease. In conclusion, the M46I mutation induced structural dynamics changes that weaken the protease grip on saquinavir without distorting the active site of the protein. The produced information may be utilized for the discovery of inhibitor(s) against drug-resistant HIV-1 protease.
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Affiliation(s)
- Nilottam Rana
- Molecular Signaling & Drug Discovery Laboratory, Department of Biochemistry, Central University of Punjab, Bathinda 151401, Punjab, India; (N.R.); (A.K.S.); (M.S.)
| | - Atul Kumar Singh
- Molecular Signaling & Drug Discovery Laboratory, Department of Biochemistry, Central University of Punjab, Bathinda 151401, Punjab, India; (N.R.); (A.K.S.); (M.S.)
| | - Mohd Shuaib
- Molecular Signaling & Drug Discovery Laboratory, Department of Biochemistry, Central University of Punjab, Bathinda 151401, Punjab, India; (N.R.); (A.K.S.); (M.S.)
| | - Sanjay Gupta
- Department of Urology, Pharmacology and Pathology, Case Western Reserve University, Cleveland, OH 44106, USA;
| | - Mahmoud M. Habiballah
- Medical Laboratory Technology Department, Jazan University, Jazan 45142, Saudi Arabia;
- SMIRES for Consultation in Specialized Medical Laboratories, Jazan University, Jazan 45142, Saudi Arabia
| | - Mustfa F. Alkhanani
- Emergency Service Department, College of Applied Sciences, AlMaarefa University, Riyadh 11597, Saudi Arabia;
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan 45142, Saudi Arabia;
| | - Mohd Salim Reshi
- Toxicology and Pharmacology Lab., Department of Zoology, School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Rajouri 185234, Jammu & Kashmir, India;
| | - Shashank Kumar
- Molecular Signaling & Drug Discovery Laboratory, Department of Biochemistry, Central University of Punjab, Bathinda 151401, Punjab, India; (N.R.); (A.K.S.); (M.S.)
- Correspondence:
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Adinortey CA, Kwarko GB, Koranteng R, Boison D, Obuaba I, Wilson MD, Kwofie SK. Molecular Structure-Based Screening of the Constituents of Calotropis procera Identifies Potential Inhibitors of Diabetes Mellitus Target Alpha Glucosidase. Curr Issues Mol Biol 2022; 44:963-987. [PMID: 35723349 PMCID: PMC8928985 DOI: 10.3390/cimb44020064] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Revised: 01/07/2022] [Accepted: 01/09/2022] [Indexed: 01/09/2023] Open
Abstract
Diabetes mellitus is a disorder characterized by higher levels of blood glucose due to impaired insulin mechanisms. Alpha glucosidase is a critical drug target implicated in the mechanisms of diabetes mellitus and its inhibition controls hyperglycemia. Since the existing standard synthetic drugs have therapeutic limitations, it is imperative to identify new potent inhibitors of natural product origin which may slow carbohydrate digestion and absorption via alpha glucosidase. Since plant extracts from Calotropis procera have been extensively used in the treatment of diabetes mellitus, the present study used molecular docking and dynamics simulation techniques to screen its constituents against the receptor alpha glucosidase. Taraxasterol, syriogenin, isorhamnetin-3-O-robinobioside and calotoxin were identified as potential novel lead compounds with plausible binding energies of −40.2, −35.1, −34.3 and −34.3 kJ/mol against alpha glucosidase, respectively. The residues Trp481, Asp518, Leu677, Leu678 and Leu680 were identified as critical for binding and the compounds were predicted as alpha glucosidase inhibitors. Structurally similar compounds with Tanimoto coefficients greater than 0.7 were reported experimentally to be inhibitors of alpha glucosidase or antidiabetic. The structures of the molecules may serve as templates for the design of novel inhibitors and warrant in vitro assaying to corroborate their antidiabetic potential.
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Affiliation(s)
- Cynthia A. Adinortey
- Department of Molecular Biology and Biotechnology, School of Biological Sciences, University of Cape Coast, Cape Coast CC 033, Ghana;
| | - Gabriel B. Kwarko
- West African Centre for Cell Biology of Infectious Pathogens, Department of Biochemistry, Cell and Molecular Biology, College of Basic and Applied Sciences, University of Ghana, Legon, Accra LG 54, Ghana;
| | - Russell Koranteng
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic & Applied Sciences, University of Ghana, Legon, Accra LG 77, Ghana;
| | - Daniel Boison
- Department of Biochemistry, School of Biological Sciences, University of Cape Coast, Cape Coast CC 033, Ghana; (D.B.); (I.O.)
| | - Issaka Obuaba
- Department of Biochemistry, School of Biological Sciences, University of Cape Coast, Cape Coast CC 033, Ghana; (D.B.); (I.O.)
| | - Michael D. Wilson
- Department of Parasitology, Noguchi Memorial Institute for Medical Research (NMIMR), College of Health Sciences (CHS), University of Ghana, Legon, Accra LG 581, Ghana;
| | - Samuel K. Kwofie
- West African Centre for Cell Biology of Infectious Pathogens, Department of Biochemistry, Cell and Molecular Biology, College of Basic and Applied Sciences, University of Ghana, Legon, Accra LG 54, Ghana;
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic & Applied Sciences, University of Ghana, Legon, Accra LG 77, Ghana;
- Correspondence: ; Tel.: +233-203-797922
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Li B, Yue Y, Zhang Y, Yuan Z, Li P, Song N, Lin W, Liu Y, Gu L, Meng H. A Novel Enterovirus 71 (EV71) Virulence Determinant: The 69th Residue of 3C Protease Modulates Pathogenicity. Front Cell Infect Microbiol 2017; 7:26. [PMID: 28217559 PMCID: PMC5290453 DOI: 10.3389/fcimb.2017.00026] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 01/19/2017] [Indexed: 11/25/2022] Open
Abstract
Human enterovirus type 71 (EV71), the major causative agent of hand-foot-and-mouth disease, has been known to cause fatal neurological complications. Unfortunately, the reason for neurological complications that have been seen in fatal cases of the disease and the relationship between EV71 virulence and viral genetic sequences remains largely undefined. The 3C protease (3Cpro) of EV71 plays an irreplaceable role in segmenting the precursor polyprotein during viral replication, and intervening with host life activity during viral infection. In this study, for the first time, the 69th residue of 3C protease has been identified as a novel virulence determinant of EV71. The recombinant virus with single point variation, in the 69th of 3Cpro, exhibited obvious decline in replication, and virulence. We further determined the crystal structure of 3C N69D at 1.39 Ǻ resolution and found that conformation of 3C N69D demonstrated significant changes compared with a normal 3C protein, in the substrate-binding site and catalytic active site. Strikingly, one of the switch loops, essential in fixing substrates, adopts an open conformation in the 3C N69D-rupintrivir complex. Consistent with this apparent structural disruption, the catalytic activity of 3C N69D decreased sharply for host derived and viral derived substrates, detected for both in vitro and in vivo. Interestingly, in addition to EV71, Asp69 was also found in 3C proteases of other virus strains, such as CAV16, and was conserved in nearly all C type human rhinovirus. Overall, we identified a natural virulence determinant of 3C protease and revealed the mechanism of attenuated virulence is mediated by N69D substitution. Our data provides new insight into the enzymatic mechanism of a subdued 3C protease and suggests a theoretical basis for virulence determinantion of picornaviridae.
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Affiliation(s)
- Bingqing Li
- Key Laboratory of Rare and Uncommon Diseases, Department of Microbiology, Institute of Basic Medicine, Shandong Academy of Medical SciencesJinan, China
| | - Yingying Yue
- Key Laboratory of Rare and Uncommon Diseases, Department of Microbiology, Institute of Basic Medicine, Shandong Academy of Medical SciencesJinan, China
| | - Yajie Zhang
- Key Laboratory of Rare and Uncommon Diseases, Department of Microbiology, Institute of Basic Medicine, Shandong Academy of Medical SciencesJinan, China
| | - Zenglin Yuan
- State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong UniversityJinan, China
| | - Peng Li
- Key Laboratory of Rare and Uncommon Diseases, Department of Microbiology, Institute of Basic Medicine, Shandong Academy of Medical SciencesJinan, China
| | - Nannan Song
- Key Laboratory of Rare and Uncommon Diseases, Department of Microbiology, Institute of Basic Medicine, Shandong Academy of Medical SciencesJinan, China
| | - Wei Lin
- Key Laboratory of Rare and Uncommon Diseases, Department of Microbiology, Institute of Basic Medicine, Shandong Academy of Medical SciencesJinan, China
| | - Yan Liu
- Key Laboratory of Rare and Uncommon Diseases, Department of Microbiology, Institute of Basic Medicine, Shandong Academy of Medical SciencesJinan, China
| | - Lichuan Gu
- State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong UniversityJinan, China
| | - Hong Meng
- Key Laboratory of Rare and Uncommon Diseases, Department of Microbiology, Institute of Basic Medicine, Shandong Academy of Medical SciencesJinan, China
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Kaikaew A, Promptmas C, Angsuthanasombat C. Importance of Thr328 and Thr369 for functional maintenance of two receptor-binding β-hairpins of the Bacillus thuringiensis Cry4Ba toxin: Implications for synergistic interactions with Cyt2Aa2. Biochem Biophys Res Commun 2016; 469:698-703. [DOI: 10.1016/j.bbrc.2015.11.115] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 11/25/2015] [Indexed: 10/22/2022]
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