1
|
Debnath U, Mitra A, Dewaker V, Prabhakar YS, Tadala R, Krishnan K, Wagh P, Velusamy U, Baliyan A, Kurpad AV, Bhattacharyya P, Mandal AK. Conformational perturbation of SARS-CoV-2 spike protein using N-acetyl cysteine: an exploration of probable mechanism of action to combat COVID-19. J Biomol Struct Dyn 2024; 42:5042-5052. [PMID: 37477247 DOI: 10.1080/07391102.2023.2234031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 06/06/2023] [Indexed: 07/22/2023]
Abstract
The infection caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) resulted in a pandemic with huge death toll and economic consequences. The virus attaches itself to the human epithelial cells through noncovalent bonding of its spike protein with the angiotensin-converting enzyme-2 (ACE2) receptor on the host cell. Based on in silico studies we hypothesized that perturbing the functionally active conformation of spike protein through the reduction of its solvent accessible disulfide bonds, thereby disintegrating its structural architecture, may be a feasible strategy to prevent infection by reducing the binding affinity towards ACE2 enzyme. Proteomics data showed that N-acetyl cysteine (NAC), an antioxidant and mucolytic agent been widely in use in clinical medicine, forms covalent conjugates with solvent accessible cysteine residues of spike protein that were disulfide bonded in the native state. Further, in silico analysis indicated that the presence of the selective covalent conjugation of NAC with Cys525 perturbed the stereo specific orientations of the interacting key residues of spike protein that resulted in threefold weakening in the binding affinity of spike protein with ACE2 receptor. Interestingly, almost all SARS-CoV-2 variants conserved cystine residues in the spike protein. Our finding results possibly provides a molecular basis for identifying NAC and/or its analogues for targeting Cys-525 of the viral spike protein as fusion inhibitor and exploring in vivo pharmaco-preventive and its therapeutic potential activity for COVID-19 disease. However, in-vitro assay and animal model-based experiment are required to validate the probable mechanism of action.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Utsab Debnath
- School of Health Science and Technology, University of Petroleum and Energy Studies, Dehradun, India
| | - Amrita Mitra
- Clinical Proteomics Unit, Division of Molecular Medicine, St. John's Research Institute, Bangalore, India
| | - Varun Dewaker
- Medicinal and Process Chemistry Division, CSIR-Central Drug Research Institute, Lucknow, India
| | - Yenamandra S Prabhakar
- Medicinal and Process Chemistry Division, CSIR-Central Drug Research Institute, Lucknow, India
| | - Raghu Tadala
- Waters India Private Limited No. 36A, Bengaluru, India
| | | | - Padmakar Wagh
- Waters India Private Limited No. 36A, Bengaluru, India
| | | | - Aastha Baliyan
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Nadia, India
| | - Anura V Kurpad
- Department of Physiology, St. John's Medical College, Bangalore, India
| | | | - Amit Kumar Mandal
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Nadia, India
| |
Collapse
|
2
|
Dewaker V, Srivastava PN, Verma S, Srivastava AK, Prabhakar YS. Non-bonding energy directed designing of HDAC2 inhibitors through molecular dynamics simulation. J Biomol Struct Dyn 2022; 40:13432-13455. [PMID: 34662251 DOI: 10.1080/07391102.2021.1989037] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Designing an inhibitor having strong affinity in the active site pocket is the cherished goal of structure based drug designing. To achieve this, it is considerably important to predict which structural scaffold is better suited for change to increase affinity. We have explored five HDAC2 co-crystals having PDB ligand code-SHH (vorinostat), LLX, 20Y, IWX (BRD4884) and 6EZ (BRD7232). For analyzing protein-ligand interaction at an atomistic level, we have employed the NAMD molecular dynamics (MD) package. The obtained 100 ns long MD trajectories were subjected to quantitative estimations of non-bonding energies (NBEs) for inferring their interactions with the whole protein or its composite active site (CAS). In addition, relative ΔGbind was calculated to rank the inhibitors. These inhibitors' NBEs reveal that the phenyl moieties are the major structural scaffold where modifications should be attempted. We designed new compounds (NCs) via introducing hydroxyl groups at 4,5 position of the phenyl moiety of 6EZ, called NC1. Improvement in NC1 further encouraged us for CAP modification by isochromane and isoindoline moieties in place of oxabicyclooctane in NC1, resulting in NC2 and NC3. We also explored trifluoromethyl oxadiazole in 6EZ (NC4 and NC5) and SHH (NC6 and NC7). This moiety acts as a ZBG in NC4 while acting as a part of the foot-pocket in the rest. NC2 and NC6 have highest favorable NBEs among all studied ligands due increased favorable electrostatic contribution. We expect these NBEs data will provide atomistic level insights and benefit in designing new and improved HDAC2 inhibitors. Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Varun Dewaker
- Medicinal and Process Chemistry Division, CSIR-Central Drug Research Institute, Lucknow, India
| | - Pratik Narain Srivastava
- Molecular Parasitology and Immunology Division, CSIR-Central Drug Research Institute, Lucknow, India
| | - Saroj Verma
- Medicinal and Process Chemistry Division, CSIR-Central Drug Research Institute, Lucknow, India.,College of Pharmacy, Shree Guru Gobind Singh Tricentenary University, Gurugram, Haryana, India
| | - Ajay K Srivastava
- Medicinal and Process Chemistry Division, CSIR-Central Drug Research Institute, Lucknow, India
| | - Yenamandra S Prabhakar
- Medicinal and Process Chemistry Division, CSIR-Central Drug Research Institute, Lucknow, India
| |
Collapse
|
3
|
Srivastava PN, Nayak B, Dewaker V, Mishra S. C-Mannosyltransferase Is Essential for Malaria Transmission in Plasmodium berghei. ACS Infect Dis 2022; 8:1116-1123. [PMID: 35594144 DOI: 10.1021/acsinfecdis.2c00239] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
C-Mannosylation of the thrombospondin type I repeat (TSR) domains is one of the most important factors involved in their function. It occurs on the first tryptophan of the WXXWXXC conserved motif where the tryptophan is usually surrounded by arginine or lysine forming the ligand-binding stretch of this sticky domain. It is found in its canonical or modified forms in many Plasmodium proteins. TSR containing proteins such as thrombospondin-like anonymous protein (TRAP), circumsporozoite protein (CSP), CSP and TRAP related protein (CTRP), and secreted protein with altered thrombospondin repeat (SPATR) have all been shown to be important for various parasite processes and life cycle stages. Here, we show that C-mannosylation catalyzing enzyme C-mannosyltransferase (CmanT) plays an essential role in malaria transmission in Plasmodium berghei. Disruption of the CmanT does not affect asexual blood stage propagation or gametocyte development but abolishes the formation of oocysts in mosquitoes. CmanT knockout (CmanT-) parasites showed normal ookinete formation; however, these ookinetes failed in their ability to glide. CmanT- was complemented by reintroducing the gene, restoring mosquito transmission to wild-type level. We also investigated the effect of C-mannosylation on the folding and heparin-binding capacity of the Plasmodium falciparum TRAP TSR domain in silico, which suggested that this phenotype should be due to its involvement in the global stabilization of TSR residue side chain interactions.
Collapse
Affiliation(s)
- Pratik Narain Srivastava
- Division of Molecular Microbiology and Immunology, CSIR-Central Drug Research Institute, Lucknow 226031, India
| | - Bandita Nayak
- Division of Molecular Microbiology and Immunology, CSIR-Central Drug Research Institute, Lucknow 226031, India
- Academy of Scientific and Innovative Research, Ghaziabad 201002, India
| | - Varun Dewaker
- Division of Medicinal and Process Chemistry, CSIR-Central Drug Research Institute, Lucknow 226031, India
| | - Satish Mishra
- Division of Molecular Microbiology and Immunology, CSIR-Central Drug Research Institute, Lucknow 226031, India
- Academy of Scientific and Innovative Research, Ghaziabad 201002, India
| |
Collapse
|
4
|
Mahajan M, Suryavanshi S, Bhowmick S, Alasmary FA, Almutairi TM, Islam MA, Kaul-Ghanekar R. Matairesinol, an active constituent of HC9 polyherbal formulation, exhibits HDAC8 inhibitory and anticancer activity. Biophys Chem 2021; 273:106588. [PMID: 33848944 DOI: 10.1016/j.bpc.2021.106588] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 03/22/2021] [Accepted: 03/29/2021] [Indexed: 02/06/2023]
Abstract
Histone deacetylase 8 (HDAC8) has emerged as a promising drug target for cancer therapeutics development. HDAC8 has been reported to regulate cancer cell proliferation, invasion and promote metastasis through modulation of cell cycle associated proteins. Of late, phytocompounds have been demonstrated to exhibit anticancer and anti-HDAC8 activity. Here, we have shown the HDAC8 inhibitory potential of an active phytocompound from HC9 (herbal composition-9), a polyherbal anticancer formulation based on the traditional Ayurvedic drug, Stanya Shodhan Kashaya. HC9 was recently reported to exhibit anticancer activity against breast cancer cells through induction of cell cycle arrest, decrease in migration and invasion as well as regulation of inflammation and chromatin modulators. In silico studies such as molecular docking, molecular dynamics (MD) simulation and binding free energy analyses showed greater binding energy values and interaction stability of MA with HDAC8 compared to other phytocompounds of HC9. Interestingly, in vitro validation confirmed the anti-HDAC8 activity of MA. Further, in vitro studies showed that MA significantly decreased the viability of breast and prostate cancer cell lines, thereby confirming its anticancer potential.
Collapse
Affiliation(s)
- Minal Mahajan
- Cancer Research Lab., Interactive Research School for Health Affairs (IRSHA), Bharati Vidyapeeth Deemed to be University, Pune-Satara Road, Pune 411043, Maharashtra, India
| | - Snehal Suryavanshi
- Cancer Research Lab., Interactive Research School for Health Affairs (IRSHA), Bharati Vidyapeeth Deemed to be University, Pune-Satara Road, Pune 411043, Maharashtra, India
| | - Shovonlal Bhowmick
- Department of Chemical Technology, University of Calcutta, 91 APC Road, Kolkata 700 009, India
| | - Fatmah Ali Alasmary
- Chemistry Department, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Tahani Mazyad Almutairi
- Chemistry Department, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Md Ataul Islam
- Division of Pharmacy and Optometry, School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester M13 9PL, UK.
| | - Ruchika Kaul-Ghanekar
- Cancer Research Lab., Interactive Research School for Health Affairs (IRSHA), Bharati Vidyapeeth Deemed to be University, Pune-Satara Road, Pune 411043, Maharashtra, India.
| |
Collapse
|
5
|
Dewaker V, Srivastava AK, Arora A, Prabhakar YS. Investigation of HDAC8-ligands’ intermolecular forces through molecular dynamics simulations: profiling of non-bonding energies to design potential compounds as new anti-cancer agents. J Biomol Struct Dyn 2020; 39:4726-4751. [DOI: 10.1080/07391102.2020.1780940] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Varun Dewaker
- Medicinal and Process Chemistry Division, CSIR-Central Drug Research Institute, Lucknow, India
| | - Ajay K. Srivastava
- Medicinal and Process Chemistry Division, CSIR-Central Drug Research Institute, Lucknow, India
| | - Ashish Arora
- Molecular & Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow, India
| | - Yenamandra S. Prabhakar
- Medicinal and Process Chemistry Division, CSIR-Central Drug Research Institute, Lucknow, India
| |
Collapse
|
6
|
Yan G, Li D, Zhong X, Liu G, Wang X, Lu Y, Qin F, Guo Y, Duan S, Li D. Identification of HDAC6 selective inhibitors: pharmacophore based virtual screening, molecular docking and molecular dynamics simulation. J Biomol Struct Dyn 2020; 39:1928-1939. [PMID: 32178584 DOI: 10.1080/07391102.2020.1743760] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
HDAC6 regulates the expression and activity of various tumor-related proteins, but currently there is no selective inhibitor targeting HDAC6 for clinical application. In order to discover novel HDAC6 inhibitors, virtual screening methods comprised of pharmacophore based virtual screening, molecular docking and molecular dynamics (MD) simulations were employed. 15 molecules were obtained after virtual screening. After in vitro bioassays, two of the hits showed inhibition activity against HDAC6, among which the inhibition activity of G1 to HDAC6 reached 81% at concentration of 20 μM. In addition, the inhibitory activity against HDAC1 and HDAC10 demonstrated that G1 and G10 were highly selective to HDAC6. The analysis of the binding modes of G1 and G10 provides a reference for further development of highly active HDAC6 inhibitors. Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Guoyi Yan
- Henan Provincial People's Hospital, Zhengzhou, Henan, China.,School of Clinical Medicine, Henan University, Zhengzhou, China
| | - Dongxiao Li
- Department of Gastroenterology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xinxin Zhong
- State Key Laboratory of Biotherapy, Collaborative Innovation Center for Biotherapy, West China Hospital, West China Medical School, Sichuan University, Sichuan, China
| | - Ge Liu
- Henan Provincial People's Hospital, Zhengzhou, Henan, China.,School of Clinical Medicine, Henan University, Zhengzhou, China
| | - Xueqin Wang
- Henan Provincial People's Hospital, Zhengzhou, Henan, China.,College of Bioengineering, Henan University of Technology, Zhengzhou, China
| | - Yuanxiang Lu
- Henan Provincial People's Hospital, Zhengzhou, Henan, China.,School of Clinical Medicine, Henan University, Zhengzhou, China
| | - Fangyuan Qin
- Henan Provincial People's Hospital, Zhengzhou, Henan, China.,School of Clinical Medicine, Henan University, Zhengzhou, China
| | - Yuqi Guo
- Henan Provincial People's Hospital, Zhengzhou, Henan, China.,School of Clinical Medicine, Henan University, Zhengzhou, China
| | - Shaofeng Duan
- School of Pharmacy, Henan University, Kaifeng, China
| | - Deyu Li
- Henan Provincial People's Hospital, Zhengzhou, Henan, China.,School of Clinical Medicine, Henan University, Zhengzhou, China
| |
Collapse
|
7
|
Uba AI, Weako J, Keskin Ö, Gürsoy A, Yelekçi K. Examining the stability of binding modes of the co-crystallized inhibitors of human HDAC8 by molecular dynamics simulation. J Biomol Struct Dyn 2019; 38:1751-1760. [PMID: 31057077 DOI: 10.1080/07391102.2019.1615989] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Histone deacetylase (HDAC) 8 has been implicated as a potential therapeutic target in a variety of cancers, neurodegenerative disorders, metabolic dysregulation and autoimmune and inflammatory diseases. Several nonselective HDAC inhibitors have been co-crystallized with HDAC8. Molecular dynamics (MD) studies may yield valuable information on the structural stabilities of the complexes over time as determined by various pharmacophore features of the co-crystallized inhibitors. Here, using 11 unmodified X-ray crystal structures of human HDAC8 (complexes) structure-based pharmacophore models were built and clustered based on distance - a function of the number of common pharmacophore features and the root-mean-squared displacement between the matching features. Based on this information, a total of seven complexes (1T64, 1W22, 3RQD, 3SFF, 3F0R, 5VI6 and 5FCW) were submitted to unrestrained 50 ns-MD simulations using nanoscale MD (NAMD) software. 1T64 (HDAC8 in complex with TSA) was found to show the highest stability over time, presumably because of the TSA's ability to span HDAC8 catalytic channel and form a strong ionic interaction with zinc metal ion. Other stable complexes were 1W22, 3SFF, 3F0R and 5FCW. However, 3RQD and 5VI6 showed relative instability over 50 ns time period. This may be attributed to bulkiness of the capping groups of both largazole thiol and trapoxin A, making them unable to fit well into the active site of HDAC8. They rather formed steric clashes with residues on loop regions near the entrance to the channel. Thus, 1T64 and similar crystal structures may be good candidates for HDAC8 structural dynamics studies and inhibitor design.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Abdullahi Ibrahim Uba
- Department of Bioinformatics and Genetics, Faculty of Engineering and Natural Science, Kadir Has University, Istanbul, Turkey
| | - Jackson Weako
- Computational Biology and Bioinformatics Department, Faculty of Science and Engineering, Koç University, Sariyer/Istanbul, Turkey
| | - Özlem Keskin
- Computational Biology and Bioinformatics Department, Faculty of Science and Engineering, Koç University, Sariyer/Istanbul, Turkey
| | - Attila Gürsoy
- Computational Biology and Bioinformatics Department, Faculty of Science and Engineering, Koç University, Sariyer/Istanbul, Turkey
| | - Kemal Yelekçi
- Department of Bioinformatics and Genetics, Faculty of Engineering and Natural Science, Kadir Has University, Istanbul, Turkey
| |
Collapse
|
8
|
Banerjee S, Adhikari N, Amin SA, Jha T. Structural exploration of tetrahydroisoquinoline derivatives as HDAC8 inhibitors through multi-QSAR modeling study. J Biomol Struct Dyn 2019; 38:1551-1564. [PMID: 31074329 DOI: 10.1080/07391102.2019.1617782] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Histone deacetylase 8 (HDAC8) is one of the crucial HDACs responsible for influencing the epigenetic functions of the body. Overexpression of HDAC8 is found to be involved in numerous disease conditions such as tumorigenesis, cell proliferation, cancer, viral infections, neuronal disorders and other epigenetic diseases. Therefore, inhibition of HDAC8 is a primary method to combat these diseases. In this article, a multi-QSAR modeling study on tetrahydroisoquinoline derivatives was conducted to identify important contributions of the structural features of these compounds toward HDAC8 inhibition. All these QSAR modeling techniques were individually validated and justified the observations of each other. The results implied that the tetrahydroisoquinoline moiety may be effective as a cap group than as a linker moiety for HDAC8 inhibition. Different substitutions at the tetrahydroisoquinoline scaffold were also found to be crucial in modulating HDAC8 inhibition.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Suvankar Banerjee
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, West Bengal, India
| | - Nilanjan Adhikari
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, West Bengal, India
- School of Pharmaceutical Technology, ADAMAS University, Kolkata, West Bengal, India
| | - Sk. Abdul Amin
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, West Bengal, India
| | - Tarun Jha
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, West Bengal, India
| |
Collapse
|