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Tahir Khan M, Dumont E, Chaudhry AR, Wei DQ. Free energy landscape and thermodynamics properties of novel mutations in PncA of pyrazinamide resistance isolates of Mycobacterium tuberculosis. J Biomol Struct Dyn 2023:1-12. [PMID: 37837425 DOI: 10.1080/07391102.2023.2268216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 09/29/2023] [Indexed: 10/16/2023]
Abstract
Pyrazinamide (PZA) is one of the first-line antituberculosis therapy, active against non-replicating Mycobacterium tuberculosis (Mtb). The conversion of PZA into pyrazinoic acid (POA), the active form, required the activity of pncA gene product pyrazinamidase (PZase) activity. Mutations occurred in pncA are the primary cause behind the PZA resistance. However, the resistance mechanism is important to explore using high throughput computational approaches. Here we aimed to explore the mechanism of PZA resistance behind novel P62T, L120R, and V130M mutations in PZase using 200 ns molecular dynamics (MD) simulations. MD simulations were performed to observe the structural changes for these three mutants (MTs) compared to the wild types (WT). Root means square fluctuation, the radius of gyration, free energy landscape, root means square deviation, dynamic cross-correlation motion, and pocket volume were found in variation between WT and MTs, revealing the effects of P62T, L120R, and V130M. The free energy conformational landscape of MTs differs significantly from the WT system, lowering the binding of PZA. The geometric shape complementarity of the drug (PZA) and target protein (PZase) further confirmed that P62T, L120R, and V130M affect the protein structure. These effects on PZase may cause vulnerability to convert PZA into POA.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Muhammad Tahir Khan
- Zhongjing Research and Industrialization Institute of Chinese Medicine, Zhongguancun Scientific Park, Nanyang, PR China
- Institute of Molecular Biology and Biotechnology (IMBB), The University of Lahore, Lahore, Pakistan
| | - Elise Dumont
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice, UMR7272, Nice, France
- Institut Universitaire de France, Paris, France
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Khan A, Umbreen S, Hameed A, Fatima R, Zahoor U, Babar Z, Waseem M, Hussain Z, Rizwan M, Zaman N, Ali S, Suleman M, Shah A, Ali L, Ali SS, Wei DQ. In Silico Mutagenesis-Based Remodelling of SARS-CoV-1 Peptide (ATLQAIAS) to Inhibit SARS-CoV-2: Structural-Dynamics and Free Energy Calculations. Interdiscip Sci 2021; 13:521-534. [PMID: 34324157 PMCID: PMC8319699 DOI: 10.1007/s12539-021-00447-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 05/29/2021] [Accepted: 06/04/2021] [Indexed: 12/20/2022]
Abstract
The prolific spread of COVID-19 caused by a novel coronavirus (SARS-CoV-2) from its epicenter in Wuhan, China, to every nook and cranny of the world after December 2019, jeopardize the prevailing health system in the world and has raised serious concerns about human safety. Multi-directional efforts are made to design small molecule inhibitors, and vaccines and many other therapeutic options are practiced, but their final therapeutic potential is still to be tested. Using the old drug or vaccine or peptides could aid this process to avoid such long experimental procedures. Hence, here, we have repurposed a small peptide (ATLQAIAS) from the previous study, which reported the inhibitory effects of this peptide. We used in silico mutagenesis approach to design more peptides from the native wild peptide, which revealed that substitutions (T2W, T2Y, L3R, and A5W) could increase the binding affinity of the peptide towards the 3CLpro. Furthermore, using MD simulation and free energy calculation confirmed its dynamics stability and stronger binding affinities. Per-residue energy decomposition analysis revealed that the specified substitution significantly increased the binding affinity at the residue level. Our wide-ranging analyses of binding affinities disclosed that our designed peptide owns the potential to hinder the SARS-CoV-2 and will reduce the progression of SARS-CoV-2-borne pneumonia. Our research strongly suggests the experimental and clinical validation of these peptides to curtail the recent corona outbreak.
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Affiliation(s)
- Abbas Khan
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Shaheena Umbreen
- Department of Botany, University of Okara, Okara, Punjab, Pakistan
| | - Asma Hameed
- Department of Botany, University of Azad Jammu & Kashmir, Muzaffarabad, Azad Jammu & Kashmir, Pakistan
| | - Rida Fatima
- Department of Chemistry, Bahauddin Zakariya University, Multan, Pakistan
| | - Ujala Zahoor
- Department of Botany, Women University, Bagh, Azad Jammu & Kashmir, Pakistan
| | - Zainib Babar
- Center for Viticulture and Enology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Muhammad Waseem
- Faculty of Rehabilitation and Allied Health Science, Riphah International University, Islamabad, Pakistan
| | - Zahid Hussain
- Center for Biotechnology and Microbiology, University of Swat, Swat, Khyber Pakhtunkhwa, Pakistan
| | - Muhammad Rizwan
- Center for Biotechnology and Microbiology, University of Swat, Swat, Khyber Pakhtunkhwa, Pakistan
| | - Nasib Zaman
- Center for Biotechnology and Microbiology, University of Swat, Swat, Khyber Pakhtunkhwa, Pakistan
| | - Shahid Ali
- Center for Biotechnology and Microbiology, University of Swat, Swat, Khyber Pakhtunkhwa, Pakistan
| | - Muhammad Suleman
- Center for Biotechnology and Microbiology, University of Swat, Swat, Khyber Pakhtunkhwa, Pakistan
| | - Abdullah Shah
- Department of Biotechnology, Shaheed Benazir Bhutto University, Sheringal, Dir, Khyber Pakhtunkhwa, Pakistan
| | - Liaqat Ali
- Department of Biological Sciences, National University of Medical Sciences (NUMS), Rawalpindi, Pakistan
| | - Syed Shujait Ali
- Center for Biotechnology and Microbiology, University of Swat, Swat, Khyber Pakhtunkhwa, Pakistan
| | - Dong-Qing Wei
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China.
- State Key Laboratory of Microbial Metabolism, Shanghai-Islamabad-Belgrade Joint Innovation Center On Antibacterial Resistances, Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200030, People's Republic of China.
- Peng Cheng Laboratory, Vanke Cloud City Phase I Building 8, Xili Street, Nashan District, Shenzhen, Guangdong, 518055, People's Republic of China.
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Prospect of Anterior Gradient 2 homodimer inhibition via repurposing FDA-approved drugs using structure-based virtual screening. Mol Divers 2021; 26:1399-1409. [PMID: 34181147 DOI: 10.1007/s11030-021-10263-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 06/21/2021] [Indexed: 10/21/2022]
Abstract
Anterior Gradient 2 (AGR2) has recently been reported as a tumor biomarker in various cancers, i.e., breast, prostate and lung cancer. Predominantly, AGR2 exists as a homodimer via a dimerization domain (E60-K64); after it is self-dimerized, it helps FGF2 and VEGF to homo-dimerize and promotes the angiogenesis and the invasion of vascular endothelial cells and fibroblasts. Up till now, no small molecule has been discovered to inhibit the AGR2-AGR2 homodimer. Therefore, the present study was performed to prepare a validated 3D structure of AGR2 by homology modeling and discover a small molecule by screening the FDA-approved drugs library on AGR2 homodimer as a target protein. Thirteen different homology models of AGR2 were generated based on different templates which were narrowed down to 5 quality models sorted by their overall Z-scores. The top homology model based on PDB ID = 3PH9 was selected having the best Z-score and was further assessed by Verify-3D, ERRAT and RAMPAGE analysis. Structure-based virtual screening narrowed down the large library of FDA-approved drugs to ten potential AGR2-AGR2 homodimer inhibitors having FRED score lower than - 7.8 kcal/mol in which the top 5 drugs' binding stability was counter-validated by molecular dynamic simulation. To sum up, the present study prepared a validated 3D structure of AGR2 and, for the first time reported the discovery of 5 FDA-approved drugs to inhibit AGR2-AGR2 homodimer by using structure-based virtual screening. Moreover, the binding of the top 5 hits with AGR2 was also validated by molecular dynamic simulation. A validated 3D structure of Anterior Gradient 2 (AGR2) was prepared by homology modeling, which was used in virtual screening of FDA-approved drugs library for the discovery of prospective inhibitors of AGR2-AGR2 homodimer.
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Gogoi B, Chowdhury P, Goswami N, Gogoi N, Naiya T, Chetia P, Mahanta S, Chetia D, Tanti B, Borah P, Handique PJ. Identification of potential plant-based inhibitor against viral proteases of SARS-CoV-2 through molecular docking, MM-PBSA binding energy calculations and molecular dynamics simulation. Mol Divers 2021; 25:1963-1977. [PMID: 33856591 PMCID: PMC8047602 DOI: 10.1007/s11030-021-10211-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 03/16/2021] [Indexed: 12/05/2022]
Abstract
The Coronavirus disease 2019 (COVID-19), caused by the novel coronavirus, SARS-CoV-2, has recently emerged as a pandemic. Here, an attempt has been made through in-silico high throughput screening to explore the antiviral compounds from traditionally used plants for antiviral treatments in India namely, Tea, Neem and Turmeric, as potential inhibitors of two widely studied viral proteases, main protease (Mpro) and papain-like protease (PLpro) of the SARS-CoV-2. Molecular docking study using BIOVIA Discovery Studio 2018 revealed, (−)-epicatechin-3-O-gallate (ECG), a tea polyphenol has a binding affinity toward both the selected receptors, with the lowest CDocker energy − 46.22 kcal mol−1 for SARS-CoV-2 Mpro and CDocker energy − 44.72 kcal mol−1 for SARS-CoV-2 PLpro, respectively. The SARS-CoV-2 Mpro complexed with (−)-epicatechin-3-O-gallate, which had shown the best binding affinity was subjected to molecular dynamics simulations to validate its binding affinity, during which, the root-mean-square-deviation values of SARS-CoV-2 Mpro–Co-crystal ligand (N3) and SARS-CoV-2 Mpro- (−)-epicatechin-3-O-gallate systems were found to be more stable than SARS-CoV-2 Mpro system. Further, (−)-epicatechin-3-O-gallate was subjected to QSAR analysis which predicted IC50 of 0.3281 nM against SARS-CoV-2 Mpro. Overall, (−)-epicatechin-3-O-gallate showed a potential binding affinity with SARS-CoV-2 Mpro and could be proposed as a potential natural compound for COVID-19 treatment.
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Affiliation(s)
- Bhaskarjyoti Gogoi
- Department of Biotechnology, Royal Global University, Guwahati, Assam, 781035, India
| | - Purvita Chowdhury
- Department of Health Research, Model Rural Health Research Unit, Tripura, 799035, India
| | - Nabajyoti Goswami
- Bioinformatics Infrastructure Facility, College of Veterinary Science, Assam Agricultural University, Khanapara, Guwahati, Assam, 781025, India
| | - Neelutpal Gogoi
- Department of Pharmaceutical Sciences, Dibrugarh University, Dibrugarh, 786004, India
| | - Tufan Naiya
- Department of Biotechnology, Maulana Abul Kalam Azad University of Technology, West Bengal, 700064, India
| | - Pankaj Chetia
- Department of Life Sciences, Dibrugarh University, Dibrugarh, 786004, Assam, India
| | - Saurov Mahanta
- National Institute of Electronics and Information Technology (NIELIT), Guwahati, Assam, 781008, India.
| | - Dipak Chetia
- Department of Pharmaceutical Sciences, Dibrugarh University, Dibrugarh, 786004, India
| | - Bhaben Tanti
- Department of Botany, Gauhati University, Guwahati, Assam, 781014, India
| | - Probodh Borah
- Bioinformatics Infrastructure Facility, College of Veterinary Science, Assam Agricultural University, Khanapara, Guwahati, Assam, 781025, India
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Naiyer A, Khan B, Hussain A, Islam A, Alajmi MF, Hassan MI, Sundd M, Ahmad F. Stability of uniformly labeled ( 13C and 15N) cytochrome c and its L94G mutant. Sci Rep 2021; 11:6804. [PMID: 33762670 PMCID: PMC7990917 DOI: 10.1038/s41598-021-86332-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 02/02/2021] [Indexed: 11/21/2022] Open
Abstract
Cytochrome c (cyt c) is widely used as a model protein to study (i) folding and stability aspects of the protein folding problem and (ii) structure-function relationship from the evolutionary point of view. Databases of cyts c now contain 285 cyt c sequences from different organisms. A sequence alignment of all these proteins with respect to horse cyt c led to several important conclusions. One of them is that Leu94 is always conserved in all 30 mammalian cyts c. It is known that mutation L94G of the wild type (WT) horse cyt c is destabilizing and mutant exists as molten globule under the native condition (buffer pH 6 and 25 °C). We have expressed and purified uniformly labeled (13C and 15N) and unlabeled WT horse cyt c and its L94G mutant. We report that labeling does not affect the thermodynamic stability of proteins. To support this conclusion, the secondary and tertiary structure of each protein in labeled and unlabeled forms was determined by conventional techniques (UV-Vis absorption and circular dichroism spectroscopy).
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Affiliation(s)
- Abdullah Naiyer
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Bushra Khan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Afzal Hussain
- Department of Pharmacognosy College of Pharmacy, King Saud University, Riyadh, 11451, Kingdom of Saudi Arabia
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Mohamed F Alajmi
- Department of Pharmacognosy College of Pharmacy, King Saud University, Riyadh, 11451, Kingdom of Saudi Arabia
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Monica Sundd
- NMR-II Lab, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, 110067, India.
| | - Faizan Ahmad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India.
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In Silico Evaluation of Prospective Anti-COVID-19 Drug Candidates as Potential SARS-CoV-2 Main Protease Inhibitors. Protein J 2021; 40:296-309. [PMID: 33387249 PMCID: PMC7776322 DOI: 10.1007/s10930-020-09945-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/25/2020] [Indexed: 01/18/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a recently emanating human infectious coronavirus that causes COVID-19 disease. On 11th March 2020, it has been announced as a pandemic by the World Health Organization (WHO). Recently, several repositioned drugs have been subjected to clinical investigations as anti-COVID-19 drugs. Here, in silico drug discovery tools were utilized to evaluate the binding affinities and features of eighteen anti-COVID-19 drug candidates against SARS-CoV-2 main protease (Mpro). Molecular docking calculations using Autodock Vina showed considerable binding affinities of the investigated drugs with docking scores ranging from - 5.3 to - 8.3 kcal/mol, with higher binding affinities for HIV drugs compared to the other antiviral drugs. Molecular dynamics (MD) simulations were performed for the predicted drug-Mpro complexes for 50 ns, followed by binding energy calculations utilizing molecular mechanics-generalized Born surface area (MM-GBSA) approach. MM-GBSA calculations demonstrated promising binding affinities of TMC-310911 and ritonavir towards SARS-CoV-2 Mpro, with binding energy values of - 52.8 and - 49.4 kcal/mol, respectively. Surpass potentialities of TMC-310911 and ritonavir are returned to their capabilities of forming multiple hydrogen bonds with the proximal amino acids inside Mpro's binding site. Structural and energetic analyses involving root-mean-square deviation, binding energy per-frame, center-of-mass distance, and hydrogen bond length demonstrated the stability of TMC-310911 and ritonavir inside the Mpro's active site over the 50 ns MD simulation. This study sheds light on HIV protease drugs as prospective SARS-CoV-2 Mpro inhibitors.
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Pundir H, Joshi T, Joshi T, Sharma P, Mathpal S, Chandra S, Tamta S. Using Chou's 5-steps rule to study pharmacophore-based virtual screening of SARS-CoV-2 Mpro inhibitors. Mol Divers 2020; 25:1731-1744. [PMID: 33079314 PMCID: PMC7573527 DOI: 10.1007/s11030-020-10148-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 10/08/2020] [Indexed: 11/29/2022]
Abstract
Abstract Recently emerged SARS-CoV-2 is the cause of the ongoing outbreak of COVID-19. It is responsible for the deaths of millions of people and has caused global economic and social disruption. The numbers of COVID-19 cases are increasing exponentially across the world. Control of this pandemic disease is challenging because there is no effective drug or vaccine available against this virus and this situation demands an urgent need for the development of anti-SARS-CoV-2 potential medicines. In this regard, the main protease (Mpro) has emerged as an essential drug target as it plays a vital role in virus replication and transcription. In this research, we have identified two novel potent inhibitors of the Mpro (PubChem3408741 and PubChem4167619) from PubChem database by pharmacophore-based high-throughput virtual screening. The molecular docking, toxicity, and pharmacophore analysis indicate that these compounds may act as potential anti-viral candidates. The molecular dynamic simulation along with the binding free energy calculation by MMPBSA showed that these compounds bind to Mpro enzyme with high stability over 50 ns. Our results showed that two compounds: PubChem3408741 and PubChem4167619 had the binding free energy of − 94.02 kJ mol−1 and − 122.75 kJ mol−1, respectively, as compared to reference X77 (− 76.48 kJ mol−1). Based on our work’s findings, we propose that these compounds can be considered as lead molecules for targeting Mpro enzyme and they can be potential SARS-CoV-2 inhibitors. These inhibitors could be tested in vitro and explored for effective drug development against COVID-19. Graphic abstract ![]()
Electronic supplementary material The online version of this article (10.1007/s11030-020-10148-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hemlata Pundir
- Department of Botany, D.S.B Campus, Kumaun University, Nainital, Uttarakhand, 263002, India
| | - Tanuja Joshi
- Computational Biology and Biotechnology Laboratory, Department of Botany, Soban Singh Jeena University, Almora, Uttarakhand, India
| | - Tushar Joshi
- Department of Biotechnology, Kumaun University, Bhimtal Campus, Bhimtal, Uttarakhand, 263136, India
| | - Priyanka Sharma
- Department of Botany, D.S.B Campus, Kumaun University, Nainital, Uttarakhand, 263002, India
| | - Shalini Mathpal
- Department of Biotechnology, Kumaun University, Bhimtal Campus, Bhimtal, Uttarakhand, 263136, India
| | - Subhash Chandra
- Computational Biology and Biotechnology Laboratory, Department of Botany, Soban Singh Jeena University, Almora, Uttarakhand, India. .,Department of Botany, Kumaun University, S. S. J. Campus, Almora, Uttarakhand, India.
| | - Sushma Tamta
- Department of Botany, D.S.B Campus, Kumaun University, Nainital, Uttarakhand, 263002, India
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