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Deshmukh N, Talkal R, Lakshmi B. In silico screening of potential inhibitors from Cordyceps species against SARS-CoV-2 main protease. J Biomol Struct Dyn 2024; 42:4395-4411. [PMID: 37325819 DOI: 10.1080/07391102.2023.2225110] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 06/05/2023] [Indexed: 06/17/2023]
Abstract
Coronavirus disease 2019 (COVID-19) is a result of a retroviral infection of SARS-CoV-2. Due to its virulence and high infection rate, it is a matter of serious concern and a global health emergency. Currently available COVID-19 vaccines approved by regulatory bodies around the world have been shown to provide significant protection against COVID-19. But no vaccine is 100% effective at preventing infection, also they have varying efficacy rates and different side effects. However, the main protease (Mpro) of SARS-CoV-2 has been identified as a key drug target due to its essential role in viral infection and its minimal similarity with human proteases. Cordyceps mushrooms have been found to have various therapeutic properties that could effectively combat SARS-CoV-2, including improve lung functioning, anti-viral, immunomodulators, anti-infectious, and anti-inflammatory. The present study aims to screen and evaluate the inhibitory potential of the bioactive molecules from the Cordyceps species against the Mpro of SARS-CoV-2. The bioactive molecules were screened based on their docking score, molecular interactions in the binding pocket, ADME properties, toxicity, carcinogenicity, and mutagenicity. Among all the molecules that were tested, cordycepic acid was the most effective and promising candidate, with a binding affinity of -8.10 kcal/mol against Mpro. The molecular dynamics (MD) simulation and free binding energy calculations revealed that the cordycepic acid-Mpro complex was highly stable and showed fewer conformational fluctuations. These findings need to be investigated further through in-vitro and in-vivo studies for additional validation.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Niketan Deshmukh
- L J School of Applied Sciences, L J University, Ahmedabad, India
| | - Reshma Talkal
- Gujarat Biotechnology Research Centre, Gandhinagar, India
| | - Bhaskaran Lakshmi
- Department of Biotechnology, Kadi Sarva Vishwavidyalaya, Gandhinagar, India
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Srivastava A, Ahmad R, Wani IA, Siddiqui S, Yadav K, Trivedi A, Upadhyay S, Husain I, Ahamad T, Dudhagi SS. Steroidal lactones from Withania somnifera effectively target Beta, Gamma, Delta and Omicron variants of SARS-CoV-2 and reveal a decreased susceptibility to viral infection and perpetuation: a polypharmacology approach. In Silico Pharmacol 2024; 12:14. [PMID: 38419919 PMCID: PMC10897645 DOI: 10.1007/s40203-023-00184-y] [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: 01/06/2023] [Accepted: 12/14/2023] [Indexed: 03/02/2024] Open
Abstract
Prevention from disease is presently the cornerstone of the fight against COVID-19. With the rapid emergence of novel SARS-CoV-2 variants, there is an urgent need for novel or repurposed agents to strengthen and fortify the immune system. Existing vaccines induce several systemic and local side-effects that can lead to severe consequences. Moreover, elevated cytokines in COVID-19 patients with cancer as co-morbidity represent a significant bottleneck in disease prognosis and therapy. Withania somnifera (WS) and its phytoconstituent(s) have immense untapped immunomodulatory and therapeutic potential and the anticancer potential of WS is well documented. To this effect, WS methanolic extract (WSME) was characterized using HPLC. Withanolides were identified as the major phytoconstituents. In vitro cytotoxicity of WSME was determined against human breast MDA-MB-231 and normal Vero cells using MTT assay. WSME displayed potent cytotoxicity against MDA-MB-231 cells (IC50: 66 µg/mL) and no effect on Vero cells in the above range. MD simulations of Withanolide A with SARS-CoV-2 main protease and spike receptor-binding domain as well as Withanolide B with SARS-CoV spike glycoprotein and SARS-CoV-2 papain-like protease were performed using Schrödinger. Stability of complexes followed the order 6M0J-Withanolide A > 6W9C-Withnaolide B > 5WRG-Withanolide B > 6LU7-Withanolide A. Maximum stable interaction(s) were observed between Withanolides A and B with SARS-CoV-2 and SARS-CoV spike glycoproteins, respectively. Withanolides A and B also displayed potent binding to pro-inflammatory markers viz. serum ferritin and IL-6. Thus, WS phytoconstituents have the potential to be tested further in vitro and in vivo as novel antiviral agents against COVID-19 patients having cancer as a co-morbidity. Graphical abstract Supplementary Information The online version contains supplementary material available at 10.1007/s40203-023-00184-y.
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Affiliation(s)
- Aditi Srivastava
- Department of Biochemistry, Era’s Lucknow Medical College & Hospital, Era University, Sarfarazganj, Hardoi Road, Lucknow, UP 226003 India
| | - Rumana Ahmad
- Department of Biochemistry, Era’s Lucknow Medical College & Hospital, Era University, Sarfarazganj, Hardoi Road, Lucknow, UP 226003 India
| | - Irshad A. Wani
- Department of Cardiology, Era University, Sarfarazganj, Hardoi Road, Lucknow, UP 226003 India
| | - Sahabjada Siddiqui
- Department of Biotechnology, Era University, Sarfarazganj, Hardoi Road, Lucknow, UP 226003 India
| | - Kusum Yadav
- Department of Biochemistry, University of Lucknow, Lucknow, UP 226007 India
| | - Anchal Trivedi
- Department of Biochemistry, Era’s Lucknow Medical College & Hospital, Era University, Sarfarazganj, Hardoi Road, Lucknow, UP 226003 India
| | - Shivbrat Upadhyay
- Department of Biotechnology, Era University, Sarfarazganj, Hardoi Road, Lucknow, UP 226003 India
| | - Ishrat Husain
- Department of Biochemistry, Era’s Lucknow Medical College & Hospital, Era University, Sarfarazganj, Hardoi Road, Lucknow, UP 226003 India
| | - Tanveer Ahamad
- Department of Biotechnology, Era University, Sarfarazganj, Hardoi Road, Lucknow, UP 226003 India
| | - Shivanand S. Dudhagi
- Plant Physiology Laboratory, CSIR-National Botanical Research Institute, Lucknow, UP 226001 India
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Gupta D, Sharma P, Singh M, Kumar M, Ethayathulla AS, Kaur P. Structural and functional insights into the spike protein mutations of emerging SARS-CoV-2 variants. Cell Mol Life Sci 2021; 78:7967-7989. [PMID: 34731254 PMCID: PMC11073194 DOI: 10.1007/s00018-021-04008-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 10/20/2021] [Accepted: 10/22/2021] [Indexed: 02/07/2023]
Abstract
Since the emergence of the first case of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus (SARS-CoV-2), the viral genome has constantly undergone rapid mutations for better adaptation in the host system. These newer mutations have given rise to several lineages/ variants of the virus that have resulted in high transmission and virulence rates compared to the previously circulating variants. Owing to this, the overall caseload and related mortality have tremendously increased globally to > 233 million infections and > 4.7 million deaths as of Sept. 28th, 2021. SARS-CoV-2, Spike (S) protein binds to host cells by recognizing human angiotensin-converting enzyme 2 (hACE2) receptor. The viral S protein contains S1 and S2 domains that constitute the binding and fusion machinery, respectively. Structural analysis of viral S protein reveals that the virus undergoes conformational flexibility and dynamicity to interact with the hACE2 receptor. The SARS-CoV-2 variants and mutations might be associated with affecting the conformational plasticity of S protein, potentially linked to its altered affinity, infectivity, and immunogenicity. This review focuses on the current circulating variants of SARS-CoV-2 and the structure-function analysis of key S protein mutations linked with increased affinity, higher infectivity, enhanced transmission rates, and immune escape against this infection.
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Affiliation(s)
- Deepali Gupta
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi,, Delhi, 110029, India
| | - Priyanka Sharma
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi,, Delhi, 110029, India
| | - Mandeep Singh
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi,, Delhi, 110029, India
| | - Mukesh Kumar
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi,, Delhi, 110029, India
| | - A S Ethayathulla
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi,, Delhi, 110029, India
| | - Punit Kaur
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi,, Delhi, 110029, India.
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Siddiqui AJ, Khan MF, Hamadou WS, Goyal M, Jahan S, Jamal A, Ashraf SA, Sharma P, Sachidanandan M, Badraoui R, Chaubey KK, Snoussi M, Adnan M. Molecular Docking and Dynamics Simulation Revealed Ivermectin as Potential Drug against Schistosoma-Associated Bladder Cancer Targeting Protein Signaling: Computational Drug Repositioning Approach. MEDICINA (KAUNAS, LITHUANIA) 2021; 57:1058. [PMID: 34684095 PMCID: PMC8539496 DOI: 10.3390/medicina57101058] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 09/26/2021] [Accepted: 09/29/2021] [Indexed: 12/29/2022]
Abstract
Urogenital schistosomiasis is caused by Schistosoma haematobium (S. haematobium) infection, which has been linked to the development of bladder cancer. In this study, three repurposing drugs, ivermectin, arteether and praziquantel, were screened to find the potent drug-repurposing candidate against the Schistosoma-associated bladder cancer (SABC) in humans by using computational methods. The biology of most glutathione S-transferases (GSTs) proteins and vascular endothelial growth factor (VEGF) is complex and multifaceted, according to recent evidence, and these proteins actively participate in many tumorigenic processes such as cell proliferation, cell survival and drug resistance. The VEGF and GSTs are now widely acknowledged as an important target for antitumor therapy. Thus, in this present study, ivermectin displayed promising inhibition of bladder cancer cells via targeting VEGF and GSTs signaling. Moreover, molecular docking and molecular dynamics (MD) simulation analysis revealed that ivermectin efficiently targeted the binding pockets of VEGF receptor proteins and possessed stable dynamics behavior at binding sites. Therefore, we proposed here that these compounds must be tested experimentally against VEGF and GST signaling in order to control SABC. Our study lies within the idea of discovering repurposing drugs as inhibitors against the different types of human cancers by targeting essential pathways in order to accelerate the drug development cycle.
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Affiliation(s)
- Arif Jamal Siddiqui
- Department of Biology, College of Science, University of Hail, Hail 2440, Saudi Arabia; (W.S.H.); (A.J.); (R.B.); (M.S.); (M.A.)
| | - Mohammad Faheem Khan
- Department of Biotechnology, Era’s Lucknow Medical College, Era University, Lucknow 226003, India;
| | - Walid Sabri Hamadou
- Department of Biology, College of Science, University of Hail, Hail 2440, Saudi Arabia; (W.S.H.); (A.J.); (R.B.); (M.S.); (M.A.)
| | - Manish Goyal
- Molecular Parasitology and Immunology Division, CSIR-Central Drug Research Institute, Lucknow 226031, India; (M.G.); (P.S.)
| | - Sadaf Jahan
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Al Majmaah 11952, Saudi Arabia;
| | - Arshad Jamal
- Department of Biology, College of Science, University of Hail, Hail 2440, Saudi Arabia; (W.S.H.); (A.J.); (R.B.); (M.S.); (M.A.)
| | - Syed Amir Ashraf
- Department of Clinical Nutrition, College of Applied Medial Sciences, University of Hail, Hail 2440, Saudi Arabia;
| | - Pankaj Sharma
- Molecular Parasitology and Immunology Division, CSIR-Central Drug Research Institute, Lucknow 226031, India; (M.G.); (P.S.)
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Manojkumar Sachidanandan
- Department of Oral Radiology, College of Dentistry, University of Hail, Hail 2440, Saudi Arabia;
| | - Riadh Badraoui
- Department of Biology, College of Science, University of Hail, Hail 2440, Saudi Arabia; (W.S.H.); (A.J.); (R.B.); (M.S.); (M.A.)
- Section of Histology-Cytology, Medicine Faculty of Tunis, University of Tunis El Manar, Tunis 1017, Tunisia
| | - Kundan Kumar Chaubey
- Department of Biotechnology, Academic Block VI, GLA University, Mathura 281406, India;
| | - Mejdi Snoussi
- Department of Biology, College of Science, University of Hail, Hail 2440, Saudi Arabia; (W.S.H.); (A.J.); (R.B.); (M.S.); (M.A.)
- Laboratory of Genetics, Biodiversity and Valorization of Bio-Resources (LR11ES41), University of Monastir, Higher Institute of Biotechnology of Monastir, Avenue Tahar Haddas BP74, Monastir 5000, Tunisia
| | - Mohd Adnan
- Department of Biology, College of Science, University of Hail, Hail 2440, Saudi Arabia; (W.S.H.); (A.J.); (R.B.); (M.S.); (M.A.)
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