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Hershan AA. Pathogenesis of COVID19 and the applications of US FDA-approved repurposed antiviral drugs to combat SARS-CoV-2 in Saudi Arabia: A recent update by review of literature. Saudi J Biol Sci 2024; 31:104023. [PMID: 38799719 PMCID: PMC11127266 DOI: 10.1016/j.sjbs.2024.104023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Revised: 05/05/2024] [Accepted: 05/10/2024] [Indexed: 05/29/2024] Open
Abstract
Still, there is no cure for the highly contagious severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-caused coronavirus disease 2019 (COVID19). The COVID19 pandemic caused health emergencies which resulted in enormous medical and financial consequences worldwide including Saudi Arabia. Saudi Arabia is the largest Arab country of the Middle East. The urban setting of Saudi Arabia makes it vulnerable towards SARS-CoV-2 (SCV-2). Religious areas of this country are visited by millions of pilgrims every year for the Umrah and Hajj pilgrimage, which contributes to the potential COVID19 epidemic risk. COVID19 throws various challenges to healthcare professionals to choose the right drugs or therapy in clinical settings because of the lack of availability of newer drugs. Current drug development and discovery is an expensive, complex, and long process, which involves a high failure rate in clinical trials. While repurposing of United States Food and Drug Administration (US FDA)-approved antiviral drugs offers numerous benefits including complete pharmacokinetic and safety profiles, which significantly shorten drug development cycles and reduce costs. A range of repurposed US FDA-approved antiviral drugs including ribavirin, lopinavir/ritonavir combination, oseltamivir, darunavir, remdesivir, nirmatrelvir/ritonavir combination, and molnupiravir showed encouraging results in clinical trials in COVID19 treatment. In this article, several COVID19-related discussions have been provided including emerging variants of concern of, COVID19 pathogenesis, COVID19 pandemic scenario in Saudi Arabia, drug repurposing strategies against SCV-2, as well as repurposing of US FDA-approved antiviral drugs that might be considered to combat SCV-2 in Saudi Arabia. Moreover, drug repurposing in the context of COVID19 management along with its limitations and future perspectives have been summarized.
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Affiliation(s)
- Almonther Abdullah Hershan
- The University of Jeddah, College of Medicine, Department of Medical microbiology and parasitology, Jeddah, Saudi Arabia
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2
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Ashique S, Mishra N, Mohanto S, Garg A, Taghizadeh-Hesary F, Gowda BJ, Chellappan DK. Application of artificial intelligence (AI) to control COVID-19 pandemic: Current status and future prospects. Heliyon 2024; 10:e25754. [PMID: 38370192 PMCID: PMC10869876 DOI: 10.1016/j.heliyon.2024.e25754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 01/25/2024] [Accepted: 02/01/2024] [Indexed: 02/20/2024] Open
Abstract
The impact of the coronavirus disease 2019 (COVID-19) pandemic on the everyday livelihood of people has been monumental and unparalleled. Although the pandemic has vastly affected the global healthcare system, it has also been a platform to promote and develop pioneering applications based on autonomic artificial intelligence (AI) technology with therapeutic significance in combating the pandemic. Artificial intelligence has successfully demonstrated that it can reduce the probability of human-to-human infectivity of the virus through evaluation, analysis, and triangulation of existing data on the infectivity and spread of the virus. This review talks about the applications and significance of modern robotic and automated systems that may assist in spreading a pandemic. In addition, this study discusses intelligent wearable devices and how they could be helpful throughout the COVID-19 pandemic.
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Affiliation(s)
- Sumel Ashique
- Department of Pharmaceutical Sciences, Bengal College of Pharmaceutical Sciences & Research, Durgapur, 713212, West Bengal, India
| | - Neeraj Mishra
- Department of Pharmaceutics, Amity Institute of Pharmacy, Amity University, Gwalior, 474005, Madhya Pradesh, India
| | - Sourav Mohanto
- Department of Pharmaceutics, Yenepoya Pharmacy College & Research Centre, Yenepoya (Deemed to be University), Mangalore, Karnataka, 575018, India
| | - Ashish Garg
- Guru Ramdas Khalsa Institute of Science and Technology, Pharmacy, Jabalpur, M.P, 483001, India
| | - Farzad Taghizadeh-Hesary
- ENT and Head and Neck Research Center and Department, The Five Senses Health Institute, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
- Clinical Oncology Department, Iran University of Medical Sciences, Tehran, Iran
| | - B.H. Jaswanth Gowda
- Department of Pharmaceutics, Yenepoya Pharmacy College & Research Centre, Yenepoya (Deemed to be University), Mangalore, Karnataka, 575018, India
- School of Pharmacy, Queen's University Belfast, Medical Biology Centre, Belfast, BT9 7BL, UK
| | - Dinesh Kumar Chellappan
- Department of Life Sciences, School of Pharmacy, International Medical University, Bukit Jalil, Kuala Lumpur, 57000, Malaysia
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Sharun K, Tiwari R, Yatoo MI, Natesan S, Megawati D, Singh KP, Michalak I, Dhama K. A comprehensive review on pharmacologic agents, immunotherapies and supportive therapeutics for COVID-19. NARRA J 2022; 2:e92. [PMID: 38449903 PMCID: PMC10914132 DOI: 10.52225/narra.v2i3.92] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 12/06/2022] [Indexed: 03/08/2024]
Abstract
The emergence of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has affected many countries throughout the world. As urgency is a necessity, most efforts have focused on identifying small molecule drugs that can be repurposed for use as anti-SARS-CoV-2 agents. Although several drug candidates have been identified using in silico method and in vitro studies, most of these drugs require the support of in vivo data before they can be considered for clinical trials. Several drugs are considered promising therapeutic agents for COVID-19. In addition to the direct-acting antiviral drugs, supportive therapies including traditional Chinese medicine, immunotherapies, immunomodulators, and nutritional therapy could contribute a major role in treating COVID-19 patients. Some of these drugs have already been included in the treatment guidelines, recommendations, and standard operating procedures. In this article, we comprehensively review the approved and potential therapeutic drugs, immune cells-based therapies, immunomodulatory agents/drugs, herbs and plant metabolites, nutritional and dietary for COVID-19.
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Affiliation(s)
- Khan Sharun
- Division of Surgery, ICAR-Indian Veterinary Research Institute, Izatnagar, India
| | - Ruchi Tiwari
- Department of Veterinary Microbiology and Immunology, College of Veterinary Sciences, UP Pandit Deen Dayal Upadhayay Pashu Chikitsa Vigyan Vishwavidyalay Evum Go-Anusandhan Sansthan (DUVASU), Mathura, India
| | - Mohd I. Yatoo
- Division of Veterinary Clinical Complex, Faculty of Veterinary Sciences and Animal Husbandry, Shuhama, Alusteng Srinagar, Sher-E-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shalimar, Jammu and Kashmir, India
| | - Senthilkumar Natesan
- Department of Infectious Diseases, Indian Institute of Public Health Gandhinagar, Opp to Airforce station HQ, Gandhinagar, India
| | - Dewi Megawati
- Department of Microbiology and Parasitology, Faculty of Medicine and Health Sciences, Warmadewa University, Denpasar, Indonesia
- Department of Medical Microbiology and Immunology, University of California, Davis, California, USA
| | - Karam P. Singh
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, India
| | - Izabela Michalak
- Faculty of Chemistry, Department of Advanced Material Technologies, Wrocław University of Science and Technology, Wrocław, Poland
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, India
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Coronavirus enzyme inhibitors-experimentally proven natural compounds from plants. J Microbiol 2022; 60:347-354. [PMID: 35089586 PMCID: PMC8795716 DOI: 10.1007/s12275-022-1499-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 11/09/2021] [Accepted: 11/09/2021] [Indexed: 11/04/2022]
Abstract
Coronavirus disease (COVID-19) can cause critical conditions that require efficient therapeutics. Several medicines are derived from plants, and researchers are seeking natural compounds to ameliorate the symptoms of COVID-19. Viral enzymes are popular targets of antiviral medicines; the genome of coronaviruses encodes several enzymes, including RNA-dependent RNA polymerase and viral proteases. Various screening systems have been developed to identify potential inhibitors. In this review, we describe the natural compounds that have been shown to exert inhibitory effects on coronavirus enzymes. Although computer-aided molecular structural studies have predicted several antiviral compound candidates, the current review focuses on experimentally proven natural compounds.
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Manas Bandyopadhyay, Sengupta U, Periyasamy M, Mukhopadhyay S, Hasija A, Chopra D, Özdemir N, Said MA, Bera MK. Cu(II)(PhOMe-Salophen) Complex: Greener Pasture Biological Study, XRD/HAS Interactions, and MEP. RUSS J INORG CHEM+ 2022; 67. [PMCID: PMC10028762 DOI: 10.1134/s0036023623700274] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2023]
Abstract
PhOMe-salophen (1b) (salophen is N,N-bis(salycilidene)-1,2-phenylenediamine with two tert-butyl on each ring) and Cu(II) complex with PhOMe-salophen (1c) have been synthesized and characterized using various tools, including X-ray diffraction for the Cu(II)-complex (1c, C43H52CuN2O3)). The copper complex has been obtained by Cu2+ templated approach using 1b. PhOMe-salophen (1b) has been obtained in reasonably high yield using a mixture of the Schiff-base, 1a, Pd(OAc)2, PPh3, Na2CO3, 4-methoxyphenylboronic acid in benzene. We focus in this research work on the electronic and structural properties of the Cu–Schiff base complex. The tetra-coordinate τ4 index was calculated, indicating almost a perfect square planner in agreement with X-ray diffraction results. MEP reveals the maximum positive regions in 1/-associated with the azomethine and methoxyphenyl C–H bonds with an average value of 0.03 a.u. Hirshfeld surface analysis (HSA) was also studied to highlight the significant inter-atomic contacts and their percentage contribution through 2D Fingerprint plot. In a fair comparative molecular docking study, 1b and 1c were docked together with N-[{(5-methylisoxazol-3-yl)-carbonyl}alanyl}-l-valyl]-N1-((1R,2Z)-4-(benzyloxy)-4-oxo-1-[{(3R)-2-oxopyrrolidin-3-yl}methyl]but-2-enyl)-l-leucinamide, N3 against main protease Mpro, (PDB code 7BQY) using the same parameters and conditions. Interesting here to use the free energy, in silico, molecular docking approach, which aims to rank our molecules with respect to the well-known inhibitor, N3. The binding scores of 1b, 1c, N3 are –7.8, –9.0, and –8.4 kcal/mol, respectively. These preliminary results propose that ligands deserve additional study in the context of possible remedial agents for COVID-19.
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Affiliation(s)
- Manas Bandyopadhyay
- Department of Chemistry, Indian Institute of Engineering Science and Technology (IIEST), Shibpur P.O. Botanic Garden, 7111103 Howrah, India
| | - Utsav Sengupta
- Department of Chemistry, Indian Institute of Engineering Science and Technology (IIEST), Shibpur P.O. Botanic Garden, 7111103 Howrah, India
| | - Muthaimanoj Periyasamy
- Department of Mining Engineering, Indian Institute of Engineering Science and Technology (IIEST), Shibpur, P.O. Botanic Garden, 7111103 Howrah, India
| | - Sudipta Mukhopadhyay
- Department of Mining Engineering, Indian Institute of Engineering Science and Technology (IIEST), Shibpur, P.O. Botanic Garden, 7111103 Howrah, India
| | - Avantika Hasija
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Bhopal Bypass Rd, Bhauri, 462066 Bhopal, Madhya Pradesh India
| | - Deepak Chopra
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Bhopal Bypass Rd, Bhauri, 462066 Bhopal, Madhya Pradesh India
| | - Namık Özdemir
- Department of Mathematics and Science Education, Faculty of Education, Ondokuz Mayıs University, 55139 Samsun, Turkey
| | - Musa A. Said
- Department of Chemistry, Faculty of Science, Taibah University, 30002 Al-Madinah Al-Munawarah, Saudi Arabia
- Institut fuer Anorganische Chemie, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Mrinal K. Bera
- Department of Chemistry, Indian Institute of Engineering Science and Technology (IIEST), Shibpur P.O. Botanic Garden, 7111103 Howrah, India
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Omicron SARS-CoV-2 Variant Spike Protein Shows an Increased Affinity to the Human ACE2 Receptor: An In Silico Analysis. Pathogens 2021; 11:pathogens11010045. [PMID: 35055993 PMCID: PMC8779645 DOI: 10.3390/pathogens11010045] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 12/23/2021] [Accepted: 12/29/2021] [Indexed: 12/20/2022] Open
Abstract
The rise of SARS-CoV-2 variants, with changes that could be related to an increased virus pathogenicity, have received the interest of the scientific and medical community. In this study, we evaluated the changes that occurred in the viral spike of the SARS-CoV-2 Omicron variant and whether these changes modulate the interactions with the angiotensin-converting enzyme 2 (ACE2) host receptor. The mutations associated with the Omicron variant were retrieved from the GISAID and covariants.org databases, and a structural model was built using the SWISS-Model server. The interaction between the spike and the human ACE2 was evaluated using two different docking software, Zdock and Haddock. We found that the binding free energy was lower for the Omicron variant as compared to the WT spike. In addition, the Omicron spike protein showed an increased number of electrostatic interactions with ACE2 than the WT spike, especially the interactions related to charged residues. This study contributes to a better understanding of the changes in the interaction between the Omicron spike and the human host ACE2 receptor.
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Adhikari N, Banerjee S, Baidya SK, Ghosh B, Jha T. Ligand-based quantitative structural assessments of SARS-CoV-2 3CL pro inhibitors: An analysis in light of structure-based multi-molecular modeling evidences. J Mol Struct 2021; 1251:132041. [PMID: 34866654 PMCID: PMC8627846 DOI: 10.1016/j.molstruc.2021.132041] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 11/10/2021] [Accepted: 11/26/2021] [Indexed: 12/11/2022]
Abstract
Due to COVID-19, the whole world is undergoing a devastating situation, but treatment with no such drug candidates still has been established exclusively. In that context, 69 diverse chemicals with potential SARS-CoV-2 3CLpro inhibitory property were taken into consideration for building different internally and externally validated linear (SW-MLR and GA-MLR), non-linear (ANN and SVM) QSAR, and HQSAR models to identify important structural and physicochemical characters required for SARS-CoV-2 3CLpro inhibition. Importantly, 2-oxopyrrolidinyl methyl and benzylester functions, and methylene (hydroxy) sulphonic acid warhead group, were crucial for retaining higher SARS-CoV-2 3CLpro inhibition. These GA-MLR and HQSAR models were also applied to predict some already repurposed drugs. As per the GA-MLR model, curcumin, ribavirin, saquinavir, sepimostat, and remdesivir were found to be the potent ones, whereas according to the HQSAR model, lurasidone, saquinavir, lopinavir, elbasvir, and paritaprevir were the highly effective SARS-CoV-2 3CLpro inhibitors. The binding modes of those repurposed drugs were also justified by the molecular docking, molecular dynamics (MD) simulation, and binding energy calculations conducted by several groups of researchers. This current work, therefore, may be able to find out important structural parameters to accelerate the COVID-19 drug discovery processes in the future.
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Affiliation(s)
- Nilanjan Adhikari
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata 700032, India
| | - Suvankar Banerjee
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata 700032, India
| | - Sandip Kumar Baidya
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata 700032, India
| | - Balaram Ghosh
- Epigenetic Research Laboratory, Birla Institute of Technology and Science-Pilani Hyderabad Campus, Shamirpet, Hyderabad, India, 500078
| | - Tarun Jha
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata 700032, India
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Ahmad I, Pawara R, Surana S, Patel H. The Repurposed ACE2 Inhibitors: SARS-CoV-2 Entry Blockers of Covid-19. Top Curr Chem (Cham) 2021; 379:40. [PMID: 34623536 PMCID: PMC8498772 DOI: 10.1007/s41061-021-00353-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Accepted: 09/14/2021] [Indexed: 12/17/2022]
Abstract
The highly infectious disease COVID-19 is induced by SARS-coronavirus 2 (SARS-CoV-2), which has spread rapidly around the globe and was announced as a pandemic by the World Health Organization (WHO) in March 2020. SARS-CoV-2 binds to the host cell's angiotensin converting enzyme 2 (ACE2) receptor through the viral surface spike glycoprotein (S-protein). ACE2 is expressed in the oral mucosa and can therefore constitute an essential route for entry of SARS-CoV-2 into hosts through the tongue and lung epithelial cells. At present, no effective treatments for SARS-CoV-2 are yet in place. Blocking entry of the virus by inhibiting ACE2 is more advantageous than inhibiting the subsequent stages of the SARS-CoV-2 life cycle. Based on current published evidence, we have summarized the different in silico based studies and repurposing of anti-viral drugs to target ACE2, SARS-CoV-2 S-Protein: ACE2 and SARS-CoV-2 S-RBD: ACE2. This review will be useful to researchers looking to effectively recognize and deal with SARS-CoV-2, and in the development of repurposed ACE2 inhibitors against COVID-19.
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Affiliation(s)
- Iqrar Ahmad
- Division of Computer Aided Drug Design, Department of Pharmaceutical Chemistry, R.C. Patel Institute of Pharmaceutical Education and Research, Shirpur (Dhule), Maharashtra, 425405, India
| | - Rahul Pawara
- Division of Computer Aided Drug Design, Department of Pharmaceutical Chemistry, R.C. Patel Institute of Pharmaceutical Education and Research, Shirpur (Dhule), Maharashtra, 425405, India
| | - Sanjay Surana
- Division of Computer Aided Drug Design, Department of Pharmaceutical Chemistry, R.C. Patel Institute of Pharmaceutical Education and Research, Shirpur (Dhule), Maharashtra, 425405, India
| | - Harun Patel
- Division of Computer Aided Drug Design, Department of Pharmaceutical Chemistry, R.C. Patel Institute of Pharmaceutical Education and Research, Shirpur (Dhule), Maharashtra, 425405, India.
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Said MA, Khan DJO, Al-blewi FF, Al-Kaff NS, Ali AA, Rezki N, Aouad MR, Hagar M. New 1,2,3-Triazole Scaffold Schiff Bases as Potential Anti-COVID-19: Design, Synthesis, DFT-Molecular Docking, and Cytotoxicity Aspects. Vaccines (Basel) 2021; 9:vaccines9091012. [PMID: 34579249 PMCID: PMC8472185 DOI: 10.3390/vaccines9091012] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/24/2021] [Accepted: 09/01/2021] [Indexed: 11/16/2022] Open
Abstract
Schiff bases encompassing a 1,2,3-triazole motif were synthesized using an efficient multi-step synthesis. The formations of targeted Schiff base ligands were confirmed by different spectroscopic techniques (FT-IR, 1H NMR, 13C NMR, and CHN analysis). The spectral data analysis revealed that the newly designed hydrazones exist as a mixture of trans-E and cis-E diastereomers. Densityfunctional theory calculations (DFT) for the Schiff bases showed that the trans-trans form has the lowest energy structure with maximum stability compared to the other possible geometrical isomers that could be present due to the orientation of the amidic NH-C=O group. The energy differences between the trans-trans on one side and syn-syn and syn-trans isomers on the other side were 9.26 and 5.56 kcal/mol, respectively. A quantitative structure-activity relationship investigation was also performed in terms of density functional theory. The binding affinities of the newly synthesized bases are, maybe, attributed to the presence of hydrogen bonds together with many hydrophobic interactions between the ligands and the active amino acid residue of the receptor. The superposition of the inhibitor N3 and an example ligand into the binding pocket of 7BQY is also presented. Further interesting comparative docking analyses were performed. Quantitative structure-activity relationship calculations are presented, illustrating possible inhibitory activity. Further computer-aided cytotoxicity analysis by Drug2Way and PASS online software was carried out for Schiff base ligands against various cancer cell lines. Overall, the results of this study suggest that these Schiff base derivatives may be considered for further investigation as possible therapeutic agents for COVID-19.
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Affiliation(s)
- Musa A. Said
- Department of Chemistry, College of Science, Taibah University, Al-Madinah Al-Munawarah 30002, Saudi Arabia; (D.J.O.K.); (F.F.A.-b.); (A.A.A.); (N.R.)
- Correspondence: (M.A.S.); (M.R.A.)
| | - Daoud J. O. Khan
- Department of Chemistry, College of Science, Taibah University, Al-Madinah Al-Munawarah 30002, Saudi Arabia; (D.J.O.K.); (F.F.A.-b.); (A.A.A.); (N.R.)
| | - Fawzia F. Al-blewi
- Department of Chemistry, College of Science, Taibah University, Al-Madinah Al-Munawarah 30002, Saudi Arabia; (D.J.O.K.); (F.F.A.-b.); (A.A.A.); (N.R.)
| | - Nadia S. Al-Kaff
- Department of Biology, College of Science, Taibah University, Al-Madinah Al-Munawarah 30002, Saudi Arabia;
| | - Adeeb A. Ali
- Department of Chemistry, College of Science, Taibah University, Al-Madinah Al-Munawarah 30002, Saudi Arabia; (D.J.O.K.); (F.F.A.-b.); (A.A.A.); (N.R.)
| | - Nadjet Rezki
- Department of Chemistry, College of Science, Taibah University, Al-Madinah Al-Munawarah 30002, Saudi Arabia; (D.J.O.K.); (F.F.A.-b.); (A.A.A.); (N.R.)
| | - Mohamed Reda Aouad
- Department of Chemistry, College of Science, Taibah University, Al-Madinah Al-Munawarah 30002, Saudi Arabia; (D.J.O.K.); (F.F.A.-b.); (A.A.A.); (N.R.)
- Correspondence: (M.A.S.); (M.R.A.)
| | - Mohamed Hagar
- Chemistry Department, College of Sciences, Taibah University, Yanbu 30799, Saudi Arabia;
- Chemistry Department, Faculty of Science, Alexandria University, Alexandria 21321, Egypt
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Mahmud S, Elfiky AA, Amin A, Mohanto SC, Rahman E, Acharjee UK, Saleh A. Targeting SARS-CoV-2 nonstructural protein 15 endoribonuclease: an in silico perspective. Future Virol 2021. [PMID: 34290822 PMCID: PMC8285111 DOI: 10.2217/fvl-2020-0233] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 06/22/2021] [Indexed: 12/20/2022]
Abstract
The newly emerged human coronavirus, SARS-CoV-2, had begun to spread last year and sparked worldwide. In this study, molecular docking is utilized to test some previously approved drugs against the SARS-CoV-2 nonstructural protein 15 (Nsp15). We screened 23 drugs, from which three (saquinavir, valrubicin and aprepitant) show a paramount predicted binding affinity (-9.1, -9.6 and -9.2 kcal/mol, respectively) against SARS-CoV-2 Nsp15. Moreover, saquinavir and aprepitant make nonbonded interactions with Leu201 in the active site cavity of Nsp15, while the drug valrubicin interacts with Arg199 and Leu201. This binding pattern may be effective against the targeted protein, leading to Nsp15 blockage and virus abolition. Additionally, the pharmacological properties of the screened drugs are known since they have been approved against different viruses.
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Affiliation(s)
- Shafi Mahmud
- Genetic Engineering & Biotechnology, University of Rajshahi, Rajshahi, 6205, Bangladesh
| | - Abdo A Elfiky
- Biophysics Department, Faculty of Science, Cairo University, Giza, Egypt
| | - Al Amin
- Institute of Biological Science, University of Rajshahi, Rajshahi, 6205, Bangladesh
| | - Sumon Chandro Mohanto
- Genetic Engineering & Biotechnology, University of Rajshahi, Rajshahi, 6205, Bangladesh
| | - Ekhtiar Rahman
- Genetic Engineering & Biotechnology, University of Rajshahi, Rajshahi, 6205, Bangladesh
| | - Uzzal Kumar Acharjee
- Genetic Engineering & Biotechnology, University of Rajshahi, Rajshahi, 6205, Bangladesh
| | - Abu Saleh
- Genetic Engineering & Biotechnology, University of Rajshahi, Rajshahi, 6205, Bangladesh
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Bauso LV, Imbesi C, Irene G, Calì G, Bitto A. New Approaches and Repurposed Antiviral Drugs for the Treatment of the SARS-CoV-2 Infection. Pharmaceuticals (Basel) 2021; 14:503. [PMID: 34070359 PMCID: PMC8228036 DOI: 10.3390/ph14060503] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/02/2021] [Accepted: 05/08/2021] [Indexed: 12/15/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the virus that causes coronavirus disease 2019 (COVID-19). The outbreak of this coronavirus was first identified in Wuhan (Hubei, China) in December 2019, and it was declared as pandemic by the World Health Organization (WHO) in March 2020. Today, several vaccines against SARS-CoV-2 have been approved, and some neutralizing monoclonal antibodies are being tested as therapeutic approaches for COVID-19 but, one of the key questions is whether both vaccines and monoclonal antibodies could be effective against infections by new SARS-CoV-2 variants. Nevertheless, there are currently more than 1000 ongoing clinical trials focusing on the use and effectiveness of antiviral drugs as a possible therapeutic treatment. Among the classes of antiviral drugs are included 3CL protein inhibitors, RNA synthesis inhibitors and other small molecule drugs which target the ability of SARS-COV-2 to interact with host cells. Considering the need to find specific treatment to prevent the emergent outbreak, the aim of this review is to explain how some repurposed antiviral drugs, indicated for the treatment of other viral infections, could be potential candidates for the treatment of COVID-19.
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Affiliation(s)
- Luana Vittoria Bauso
- Department of Clinical and Experimental Medicine, University of Messina, 98125 Messina, Italy; (L.V.B.); (C.I.); (G.I.); (G.C.)
| | - Chiara Imbesi
- Department of Clinical and Experimental Medicine, University of Messina, 98125 Messina, Italy; (L.V.B.); (C.I.); (G.I.); (G.C.)
- Laboratori Campisi, Corso Vittorio Emanuele 231, 96012 Avola, Italy
| | - Gasparo Irene
- Department of Clinical and Experimental Medicine, University of Messina, 98125 Messina, Italy; (L.V.B.); (C.I.); (G.I.); (G.C.)
| | - Gabriella Calì
- Department of Clinical and Experimental Medicine, University of Messina, 98125 Messina, Italy; (L.V.B.); (C.I.); (G.I.); (G.C.)
| | - Alessandra Bitto
- Department of Clinical and Experimental Medicine, University of Messina, 98125 Messina, Italy; (L.V.B.); (C.I.); (G.I.); (G.C.)
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12
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Computational search for drug repurposing to identify potential inhibitors against SARS-COV-2 using Molecular Docking, QTAIM and IQA methods in viral Spike protein - Human ACE2 interface. J Mol Struct 2021; 1232:130076. [PMID: 33583954 PMCID: PMC7870108 DOI: 10.1016/j.molstruc.2021.130076] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 02/02/2021] [Accepted: 02/03/2021] [Indexed: 02/07/2023]
Abstract
With the advancement of the Covid-19 pandemic, this work aims to find molecules that can inhibit the attraction between the Spike proteins of the SARS-COV-2 virus and human ACE2. The results of molecular docking positioned four molecules at the interaction site Tyr-491(Spike)-Glu-37(ACE2) and one at the site Gly-488(Spike)-Lys-353(ACE2). The QTAIM and IQA data showed that the 1629 molecule had a significant inhibitory effect on the Gly488-Ly353 site, decreasing the Laplacian of the electronic density of the BCP O4-N10. The molecule 2542 showed an inhibitory effect in two regions of interaction of the Tyr491-Glu37 site, acting on the BCPs H30-H33 and O8-H31 while the ligand 2600, in conformation 26, presented a similar effect only on the BCP O8-H31 of that same interactive site. Thus, the data suggest laboratory tests of a combination of molecules that can act at two sites of interaction simultaneously, using the combination of 1629/2542 and 1629/2600 ligands.
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13
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Abdellattif MH, Abdel-Rahman AAH, Arief MMH, Mouneir SM, Ali A, Hussien MA, Okasha RM, Afifi TH, Hagar M. Novel 2-Hydroselenonicotinonitriles and Selenopheno[2, 3-b]pyridines: Efficient Synthesis, Molecular Docking-DFT Modeling, and Antimicrobial Assessment. Front Chem 2021; 9:672503. [PMID: 34041224 PMCID: PMC8141565 DOI: 10.3389/fchem.2021.672503] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 03/31/2021] [Indexed: 11/16/2022] Open
Abstract
Selenium containing heterocyclic compounds gained great interest as bioactive molecules as of late. This report explores the design, synthesis, characterization, and antimicrobial screening of new pyridine derivatives endowed with selenium moieties. A one-pot multicomponent system with a solvent-free, microwave irradiation environment was employed to afford this series. The spectroscopic techniques were exploited to verify the structures of the synthesized derivatives. Additionally, the agar diffusion method was employed to determine the antimicrobial activity of all the desired compounds. Of all the synthesized molecules, 9b, 12b, 14f, and 16d exhibited well to remarkable antibacterial and antifungal activities. Moreover, derivative 14f demonstrated the most potent antibacterial and antifungal performance. The results were also supported by molecular docking studies, utilizing the MOE (molecular operating environment) which revealed the best binding mode with the highest energy interaction within the binding pocket. Lastly, theoretical DFT calculations were carried out in a gas phase at B3LYP 6-311G (d,p) basis set to predict the molecular geometries and chemical reactivity descriptors. DFT results have been used to illustrate that molecular docking findings and biological activity assessments.
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Affiliation(s)
- Magda H Abdellattif
- Department of Chemistry, College of Science, Deanship of Scientific Research, Taif University, Taif, Saudi Arabia
| | | | | | - Samar M Mouneir
- Department of Pharmacology, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt
| | - Amena Ali
- Department of Pharmaceutical Chemistry, College of Pharmacy, Taif University, Taif, Saudi Arabia
| | - Mostafa A Hussien
- Department of Chemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia.,Department of Chemistry, Faculty of Science, Port Said University, Port Said, Egypt
| | - Rawda M Okasha
- Department of Chemistry, Faculty of Science, Taibah University, Medina, Saudi Arabia
| | - Tarek H Afifi
- Department of Chemistry, Faculty of Science, Taibah University, Medina, Saudi Arabia
| | - Mohamed Hagar
- Chemistry Department, College of Sciences, Taibah University, Yanbu, Saudi Arabia.,Chemistry Department, Faculty of Science, Alexandria University, Alexandria, Egypt
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14
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Abd-El-Aziz AS, Alsaggaf A, Assirey E, Naqvi A, Okasha RM, Afifi TH, Hagar M. A New Family of Benzo[ h]Chromene Based Azo Dye: Synthesis, In-Silico and DFT Studies with In Vitro Antimicrobial and Antiproliferative Assessment. Int J Mol Sci 2021; 22:2807. [PMID: 33802075 PMCID: PMC7998172 DOI: 10.3390/ijms22062807] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/03/2021] [Accepted: 03/03/2021] [Indexed: 12/27/2022] Open
Abstract
The high biological activity of the chromene compounds coupled with the intriguing optical features of azo chromophores prompted our desire to construct novel derivatives of chromene incorporating azo moieties 4a-l, which have been prepared via a three-component reaction of 1-naphthalenol-4-[(4-ethoxyphenyl) azo], 1, with the benzaldehyde derivatives and malononitrile. The structural identities of the azo-chromene 4a-l were confirmed on the basis of their spectral data and elemental analysis, and a UV-visible study was performed in a Dimethylformamide (DMF) solution for these molecules. Additionally, the antimicrobial activity was investigated against four human pathogens (Gram-positive and Gram-negative bacteria) and four fungi, employing an agar well diffusion method, with their minimum inhibitory concentrations being reported. Molecules 4a, 4g, and 4h were discovered to be more efficacious against Syncephalastrum racemosum (RCMB 05922) in comparison to the reference drugs, while compounds 4b and 4h demonstrated the highest inhibitory activity against Escherichia coli (E. coli) in evaluation against the reference drugs. Moreover, their cytotoxicity was assessed against three different human cell lines, including human colon carcinoma (HCT-116), human hepatocellular carcinoma (HepG-2), and human breast adenocarcinoma (MCF-7) with a selection of molecules illustrating potency against the HCT-116 and MCF-7 cell lines. Furthermore, the molecular modeling results depicted the binding interactions of the synthesized compounds 3b and 3h in the active site of the E. coli DNA gyrase B enzyme with a clear SAR (structure-activity relationship) analysis. Lastly, the density functional theory's (DFTs) theoretical calculations were performed to quantify the energy levels of the Frontier Molecular Orbitals (FMOs) and their energy gaps, dipole moments, and molecular electrostatic potentials. These data were utilized in the chemical descriptor estimations to confirm the biological activity.
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Affiliation(s)
- Alaa S. Abd-El-Aziz
- Department of Chemistry, University of Prince Edward Island, Charlottetown, PE C1A 4P3, Canada; (A.A.); (E.A.)
| | - Azhaar Alsaggaf
- Department of Chemistry, University of Prince Edward Island, Charlottetown, PE C1A 4P3, Canada; (A.A.); (E.A.)
- Department of Chemistry, Taibah University, Madinah 30002, Saudi Arabia; (A.N.); (R.M.O.)
| | - Eman Assirey
- Department of Chemistry, University of Prince Edward Island, Charlottetown, PE C1A 4P3, Canada; (A.A.); (E.A.)
- Department of Chemistry, Taibah University, Madinah 30002, Saudi Arabia; (A.N.); (R.M.O.)
| | - Arshi Naqvi
- Department of Chemistry, Taibah University, Madinah 30002, Saudi Arabia; (A.N.); (R.M.O.)
| | - Rawda M. Okasha
- Department of Chemistry, Taibah University, Madinah 30002, Saudi Arabia; (A.N.); (R.M.O.)
| | - Tarek H. Afifi
- Department of Chemistry, Taibah University, Madinah 30002, Saudi Arabia; (A.N.); (R.M.O.)
| | - Mohamed Hagar
- Department of Chemistry, College of Sciences, Taibah University, Yanbu 30799, Saudi Arabia;
- Department of Chemistry, Faculty of Science, Alexandria University, Alexandria 21321, Egypt
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15
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Sumon TA, Hussain MA, Hasan MT, Hasan M, Jang WJ, Bhuiya EH, Chowdhury AAM, Sharifuzzaman SM, Brown CL, Kwon HJ, Lee EW. A Revisit to the Research Updates of Drugs, Vaccines, and Bioinformatics Approaches in Combating COVID-19 Pandemic. Front Mol Biosci 2021; 7:585899. [PMID: 33569389 PMCID: PMC7868442 DOI: 10.3389/fmolb.2020.585899] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 12/17/2020] [Indexed: 12/19/2022] Open
Abstract
A new strain of coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) responsible for the coronavirus disease 2019 (COVID-19) pandemic was first detected in the city of Wuhan in Hubei province, China in late December 2019. To date, more than 1 million deaths and nearly 57 million confirmed cases have been recorded across 220 countries due to COVID-19, which is the greatest threat to global public health in our time. Although SARS-CoV-2 is genetically similar to other coronaviruses, i.e., SARS and Middle East respiratory syndrome coronavirus (MERS-CoV), no confirmed therapeutics are yet available against COVID-19, and governments, scientists, and pharmaceutical companies worldwide are working together in search for effective drugs and vaccines. Repurposing of relevant therapies, developing vaccines, and using bioinformatics to identify potential drug targets are strongly in focus to combat COVID-19. This review deals with the pathogenesis of COVID-19 and its clinical symptoms in humans including the most recent updates on candidate drugs and vaccines. Potential drugs (remdesivir, hydroxychloroquine, azithromycin, dexamethasone) and vaccines [mRNA-1273; measles, mumps and rubella (MMR), bacille Calmette-Guérin (BCG)] in human clinical trials are discussed with their composition, dosage, mode of action, and possible release dates according to the trial register of US National Library of Medicines (clinicaltrials.gov), European Union (clinicaltrialsregister.eu), and Chinese Clinical Trial Registry (chictr.org.cn) website. Moreover, recent reports on in silico approaches like molecular docking, molecular dynamics simulations, network-based identification, and homology modeling are included, toward repurposing strategies for the use of already approved drugs against newly emerged pathogens. Limitations of effectiveness, side effects, and safety issues of each approach are also highlighted. This review should be useful for the researchers working to find out an effective strategy for defeating SARS-CoV-2.
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Affiliation(s)
- Tofael Ahmed Sumon
- Department of Fish Health Management, Sylhet Agricultural University, Sylhet, Bangladesh
| | - Md. Ashraf Hussain
- Department of Fisheries Technology and Quality Control, Sylhet Agricultural University, Sylhet, Bangladesh
| | - Md. Tawheed Hasan
- Department of Aquaculture, Sylhet Agricultural University, Sylhet, Bangladesh
| | - Mahmudul Hasan
- Department of Pharmaceuticals and Industrial Biotechnology, Sylhet Agricultural University, Sylhet, Bangladesh
| | - Won Je Jang
- Department of Biotechnology, Pukyong National University, Busan, South Korea
| | | | | | - S. M. Sharifuzzaman
- Institute of Marine Sciences, University of Chittagong, Chittagong, Bangladesh
| | - Christopher Lyon Brown
- World Fisheries University Pilot Programme, Pukyong National University, Busan, South Korea
| | - Hyun-Ju Kwon
- Biopharmaceutical Engineering Major, Division of Applied Bioengineering, Dong-Eui University, Busan, South Korea
| | - Eun-Woo Lee
- Biopharmaceutical Engineering Major, Division of Applied Bioengineering, Dong-Eui University, Busan, South Korea
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16
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Al Sheikh Ali A, Khan D, Naqvi A, Al-blewi FF, Rezki N, Aouad MR, Hagar M. Design, Synthesis, Molecular Modeling, Anticancer Studies, and Density Functional Theory Calculations of 4-(1,2,4-Triazol-3-ylsulfanylmethyl)-1,2,3-triazole Derivatives. ACS OMEGA 2021; 6:301-316. [PMID: 33458482 PMCID: PMC7807778 DOI: 10.1021/acsomega.0c04595] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 12/09/2020] [Indexed: 05/07/2023]
Abstract
New conjugates of substituted 1,2,3-triazoles linked to 1,2,4-triazoles were synthesized starting from the appropriate S-propargylated 1,2,4-triazoles 7 and 8. Ligation of 1,2,4-triazoles to the 1,2,3-triazole core was performed through Cu(I)-catalyzed cycloaddition of 1,2,4-triazole-based alkyne side chain 7 and/or 8 with several un/functionalized alkyl- and/or aryl-substituted azides 9-15 to afford the desired 1,4-disubstituted 1,2,3-triazoles 16-27, using both classical and microwave methods. After their spectroscopic characterization (infrared, 1H, 13C nuclear magnetic resonance, and elemental analyses), an anticancer screening was carried out against some cancer cell lines including human colon carcinoma (Caco-2 and HCT116), human cervical carcinoma (HeLa), and human breast adenocarcinoma (MCF-7). The outcomes of this exploration revealed that compounds 17, 22, and 25 had a significant anticancer activity against MCF-7 and Caco-2 cancer cell lines with IC50 values of 0.31 and 4.98 μM, respectively, in relation to the standard reference drug, doxorubicin. Enzyme-docking examination was executed onto cyclin-dependent kinase 2; a promising aim for cancer medication. Synthesized compounds acquiring highest potency showcased superior interactions with the active site residue of the target protein and exhibited minimum binding energy. Finally, the density functional theory (DFT) calculations were carried out to confirm the outcomes of the molecular docking and the experimental findings. The chemical reactivity descriptors such as softness (δ), global hardness (η), electronegativity (χ), and electrophilicity were calculated from the levels of the predicted frontier molecular orbitals and their energy gap. The DFT results and the molecular docking calculation results explained the activity of the most expectedly active compounds 17, 22, and 25.
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Affiliation(s)
- Adeeb Al Sheikh Ali
- Department
of Chemistry, Faculty of Science, Taibah
University, Al-Madinah
Al-Munawarah 30002, Saudi
Arabia
| | - Daoud Khan
- Department
of Chemistry, Faculty of Science, Taibah
University, Al-Madinah
Al-Munawarah 30002, Saudi
Arabia
| | - Arshi Naqvi
- Department
of Chemistry, Faculty of Science, Taibah
University, Al-Madinah
Al-Munawarah 30002, Saudi
Arabia
| | - Fawzia Faleh Al-blewi
- Department
of Chemistry, Faculty of Science, Taibah
University, Al-Madinah
Al-Munawarah 30002, Saudi
Arabia
| | - Nadjet Rezki
- Department
of Chemistry, Faculty of Science, Taibah
University, Al-Madinah
Al-Munawarah 30002, Saudi
Arabia
| | - Mohamed Reda Aouad
- Department
of Chemistry, Faculty of Science, Taibah
University, Al-Madinah
Al-Munawarah 30002, Saudi
Arabia
| | - Mohamed Hagar
- Chemistry
Department, College of Sciences, Yanbu, Taibah University, Yanbu 30799, Saudi Arabia
- Chemistry
Department, Faculty of Science, Alexandria
University, Alexandria 21321, Egypt
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17
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Sahebnasagh A, Avan R, Saghafi F, Mojtahedzadeh M, Sadremomtaz A, Arasteh O, Tanzifi A, Faramarzi F, Negarandeh R, Safdari M, Khataminia M, Rezai Ghaleno H, Habtemariam S, Khoshi A. Pharmacological treatments of COVID-19. Pharmacol Rep 2020; 72:1446-1478. [PMID: 32816200 PMCID: PMC7439639 DOI: 10.1007/s43440-020-00152-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 07/31/2020] [Accepted: 08/10/2020] [Indexed: 02/07/2023]
Abstract
The viral infection due to the new coronavirus or coronavirus disease 2019 (COVID-19), which was reported for the first time in December 2019, was named by the World Health Organization (WHO) as Severe Acute Respiratory Syndrome-Coronavirus-2 (SARS-CoV2), because of the very similar genome and also its related symptoms to SARS-CoV1. The ongoing COVID-19 pandemic with significant mortality, morbidity, and socioeconomic impact is considered by the WHO as a global public health emergency. Since there is no specific treatment available for SARS-CoV2 infection, and or COVID-19, several clinical and sub-clinical studies are currently undertaken to find a gold-standard therapeutic regimen with high efficacy and low side effect. Based on the published scientific evidence published to date, we summarized herein the effects of different potential therapies and up-to-date clinical trials. The review is intended to help readers aware of potentially effective COVID-19 treatment and provide useful references for future studies.
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Affiliation(s)
- Adeleh Sahebnasagh
- Clinical Research Center, Department of Internal Medicine, North Khorasan University of Medical Sciences, Bojnurd, Iran
| | - Razieh Avan
- Department of Clinical Pharmacy, Medical Toxicology and Drug Abuse Research Center (MTDRC), Faculty of Pharmacy, Birjand University of Medical Sciences, Birjand, Iran
| | - Fatemeh Saghafi
- Department of Clinical Pharmacy, Faculty of Pharmacy and Pharmaceutical Sciences Research Center, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Mojataba Mojtahedzadeh
- Department of Clinical Pharmacy, Pharmaceutical Sciences Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Afsaneh Sadremomtaz
- XB20 Drug Design, Groningen Research Institute of Pharmacy, University of Groningen, 9700 AD Groningen, The Netherlands
| | - Omid Arasteh
- Department of Clinical Pharmacy, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Asal Tanzifi
- Sepanta Faragene Azma Research Laboratory. Co. LTD., Gorgan, Iran
- Department of Parasitology, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Fatemeh Faramarzi
- Clinical Pharmacy Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Reza Negarandeh
- Student Research Committee, Department of Pharmaceutics, Faculty of Pharmacy, Mazandaran University of Medical Sciences, Sari, Iran
| | - Mohammadreza Safdari
- Department of Orthopedic Surgery, Faculty of Medicine, North Khorasan University of Medical Sciences, Bojnurd, Iran
| | - Masoud Khataminia
- Student Research Committee, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Hassan Rezai Ghaleno
- Department of Surgery, Faculty of Medicine, Lorestan University of Medical Sciences, Khorramabad, Iran
| | - Solomon Habtemariam
- Pharmacognosy Research Laboratories and Herbal Analysis Services, University of Greenwich, Central Avenue, Chatham-Maritime, Kent, ME4 4TB UK
| | - Amirhosein Khoshi
- Department of Clinical Biochemistry, School of Medicine, North Khorasan University of Medical Sciences, Arkan roadway, Bojnurd, Iran
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18
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Singh TU, Parida S, Lingaraju MC, Kesavan M, Kumar D, Singh RK. Drug repurposing approach to fight COVID-19. Pharmacol Rep 2020; 72:1479-1508. [PMID: 32889701 PMCID: PMC7474498 DOI: 10.1007/s43440-020-00155-6] [Citation(s) in RCA: 248] [Impact Index Per Article: 62.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 08/20/2020] [Accepted: 08/24/2020] [Indexed: 02/07/2023]
Abstract
Currently, there are no treatment options available for the deadly contagious disease, coronavirus disease 2019 (COVID-19). Drug repurposing is a process of identifying new uses for approved or investigational drugs and it is considered as a very effective strategy for drug discovery as it involves less time and cost to find a therapeutic agent in comparison to the de novo drug discovery process. The present review will focus on the repurposing efficacy of the currently used drugs against COVID-19 and their mechanisms of action, pharmacokinetics, dosing, safety, and their future perspective. Relevant articles with experimental studies conducted in-silico, in-vitro, in-vivo, clinical trials in humans, case reports, and news archives were selected for the review. Number of drugs such as remdesivir, favipiravir, ribavirin, lopinavir, ritonavir, darunavir, arbidol, chloroquine, hydroxychloroquine, tocilizumab and interferons have shown inhibitory effects against the SARS-CoV2 in-vitro as well as in clinical conditions. These drugs either act through virus-related targets such as RNA genome, polypeptide packing and uptake pathways or target host-related pathways involving angiotensin-converting enzyme-2 (ACE2) receptors and inflammatory pathways. Using the basic knowledge of viral pathogenesis and pharmacodynamics of drugs as well as using computational tools, many drugs are currently in pipeline to be repurposed. In the current scenario, repositioning of the drugs could be considered the new avenue for the treatment of COVID-19.
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Affiliation(s)
- Thakur Uttam Singh
- Division of Pharmacology and Toxicology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, 243122, Uttar Pradesh, India.
| | - Subhashree Parida
- Division of Pharmacology and Toxicology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, 243122, Uttar Pradesh, India
| | - Madhu Cholenahalli Lingaraju
- Division of Pharmacology and Toxicology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, 243122, Uttar Pradesh, India
| | - Manickam Kesavan
- Division of Pharmacology and Toxicology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, 243122, Uttar Pradesh, India
| | - Dinesh Kumar
- Division of Pharmacology and Toxicology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, 243122, Uttar Pradesh, India
| | - Raj Kumar Singh
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, 243122, Uttar Pradesh, India
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19
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Mahdi M, Mótyán JA, Szojka ZI, Golda M, Miczi M, Tőzsér J. Analysis of the efficacy of HIV protease inhibitors against SARS-CoV-2's main protease. Virol J 2020; 17:190. [PMID: 33243253 PMCID: PMC7689640 DOI: 10.1186/s12985-020-01457-0] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 11/20/2020] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND The pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has resulted in millions of infections worldwide. While the search for an effective antiviral is still ongoing, experimental therapies based on repurposing of available antivirals is being attempted, of which HIV protease inhibitors (PIs) have gained considerable interest. Inhibition profiling of the PIs directly against the viral protease has never been attempted in vitro, and while few studies reported an efficacy of lopinavir and ritonavir in SARS-CoV-2 context, the mechanism of action of the drugs remains to be validated. METHODS We carried out an in-depth analysis of the efficacy of HIV PIs against the main protease of SARS-CoV-2 (Mpro) in cell culture and in vitro enzymatic assays, using a methodology that enabled us to focus solely on any potential inhibitory effects of the inhibitors against the viral protease. For cell culture experiments a dark-to-bright GFP reporter substrate system was designed. RESULTS Lopinavir, ritonavir, darunavir, saquinavir, and atazanavir were able to inhibit the viral protease in cell culture, albeit in concentrations much higher than their achievable plasma levels, given their current drug formulations. While inhibition by lopinavir was attributed to its cytotoxicity, ritonavir was the most effective of the panel, with IC50 of 13.7 µM. None of the inhibitors showed significant inhibition of SARS-CoV-2 Mpro in our in vitro enzymatic assays up to 100 µM concentration. CONCLUSION Targeting of SARS-CoV-2 Mpro by some of the HIV PIs might be of limited clinical potential, given the high concentration of the drugs required to achieve significant inhibition. Therefore, given their weak inhibition of the viral protease, any potential beneficial effect of the PIs in COVID-19 context might perhaps be attributed to acting on other molecular target(s), rather than SARS-CoV-2 Mpro.
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Affiliation(s)
- Mohamed Mahdi
- Laboratory of Retroviral Biochemistry, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1. Life Science Building, Debrecen, 4032, Hungary.
| | - János András Mótyán
- Laboratory of Retroviral Biochemistry, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1. Life Science Building, Debrecen, 4032, Hungary
| | - Zsófia Ilona Szojka
- Laboratory of Retroviral Biochemistry, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1. Life Science Building, Debrecen, 4032, Hungary
- Doctoral School of Molecular Cell and Immune Biology, University of Debrecen, Debrecen, Hungary
| | - Mária Golda
- Laboratory of Retroviral Biochemistry, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1. Life Science Building, Debrecen, 4032, Hungary
- Doctoral School of Molecular Cell and Immune Biology, University of Debrecen, Debrecen, Hungary
| | - Márió Miczi
- Laboratory of Retroviral Biochemistry, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1. Life Science Building, Debrecen, 4032, Hungary
- Doctoral School of Molecular Cell and Immune Biology, University of Debrecen, Debrecen, Hungary
| | - József Tőzsér
- Laboratory of Retroviral Biochemistry, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1. Life Science Building, Debrecen, 4032, Hungary
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20
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Scutellaria baicalensis Flavones as Potent Drugs against Acute Respiratory Injury during SARS-CoV-2 Infection: Structural Biology Approaches. Processes (Basel) 2020. [DOI: 10.3390/pr8111468] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection can result in severe damage to the respiratory system. With no specific treatment to date, it is crucial to identify potent inhibitors of SARS-CoV-2 Chymotrypsin-like protease (3CLpro) that could also modulate the enzymes involved in the respiratory damage that accompanies SARS-CoV-2 infection. Here, flavones isolated from Scutellaria baicalensis (baicalein, baicalin, wogonin, norwogonin, and oroxylin A) were studied as possible compounds in the treatment of SARS-CoV-2 and SARS-CoV-2-induced acute lung injuries. We used structural bioinformatics and cheminformatics to (i) identify the critical molecular features of flavones for their binding activity at human and SARS-CoV-2 enzymes; (ii) predict their drug-likeness and lead-likeness features; (iii) calculate their pharmacokinetic profile, with an emphasis on toxicology; (iv) predict their pharmacodynamic profiles, with the identification of their human body targets involved in the respiratory system injuries; and (v) dock the ligands to SARS-CoV-2 3CLpro. All flavones presented appropriate drug-like and kinetics features, except for baicalin. Flavones could bind to SARS-CoV-2 3CLpro at a similar site, but interact slightly differently with the protease. Flavones’ pharmacodynamic profiles predict that (i) wogonin strongly binds at the cyclooxygenase2 and nitric oxide synthase; (ii) baicalein and norwogonin could modulate lysine-specific demethylase 4D-like and arachidonate 15-lipoxygenase; and (iii) baicalein, wogonin, norwogonin, and oroxylin A bind to SARS-CoV-2 3CLpro. Our results propose these flavones as possible potent drugs against respiratory damage that occurs during SARS-CoV-2 infections, with a strong recommendation for baicalein.
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21
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Ortega JT, Zambrano JL, Jastrzebska B, Liprandi F, Rangel HR, Pujol FH. Understanding Severe Acute Respiratory Syndrome Coronavirus 2 Replication to Design Efficient Drug Combination Therapies. Intervirology 2020; 63:2-9. [PMID: 33099545 PMCID: PMC7649723 DOI: 10.1159/000512141] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Accepted: 09/22/2020] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its disease CO-VID-19 has strongly encouraged the search for antiviral compounds. Most of the evaluated drugs against SARS-CoV-2 derive from drug repurposing of Food and Drug Administration-approved molecules. These drugs have as target three major processes: (1) early stages of virus-cell interaction, (2) viral proteases, and (3) the viral RNA-dependent RNA polymerase. SUMMARY This review focused on the basic principles of virology and pharmacology to understand the importance of early stages of virus-cell interaction as therapeutic targets and other main processes vital for SARS-CoV-2 replication. Furthermore, we focused on describing the main targets associated with SARS-CoV-2 antiviral therapy and the rationale of drug combinations for efficiently suppressing viral replication. Key Messages: We hypothesized that blocking of both entry mechanisms could allow a more effective antiviral effect compared to the partial results obtained with chloroquine or its derivatives alone. This approach, already used to achieve an antiviral effect higher than that offered by every single drug administered separately, has been successfully applied in several viral infections such as HIV and HCV. This review will contribute to expanding the perception of the possible therapeutic targets in SARS-CoV-2 infection and highlight the benefits of using combination therapies.
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Affiliation(s)
- Joseph T Ortega
- Department of Pharmacology, Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Jose L Zambrano
- Laboratorio de Biología de Virus, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas, Venezuela
| | - Beata Jastrzebska
- Department of Pharmacology, Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Ferdinando Liprandi
- Laboratorio de Biología de Virus, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas, Venezuela
| | - Hector R Rangel
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas, Venezuela
| | - Flor H Pujol
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas, Venezuela,
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22
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Khazeei Tabari MA, Khoshhal H, Tafazoli A, Khandan M, Bagheri A. Applying computer simulations in battling with COVID-19, using pre-analyzed molecular and chemical data to face the pandemic. INFORMATICS IN MEDICINE UNLOCKED 2020; 21:100458. [PMID: 33102687 PMCID: PMC7568469 DOI: 10.1016/j.imu.2020.100458] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 10/08/2020] [Accepted: 10/14/2020] [Indexed: 12/14/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) has made many concerns for healthcare services especially, in finding useful therapeutic(s). Despite the scientists’ struggle to find and/or creating possible drugs, so far there is no treatment with high efficiency for the disease. During the pandemic, researchers have performed some molecular analyses to find potential therapeutics out of both the natural and synthetic available medicines. Computer simulations and related data have shown a significant role in drug discovery and development before. In this field, antiviral drugs, phytochemicals, anti-inflammatory agents, etc. were essential groups of compounds tested against COVID-19, using molecular modeling, molecular dynamics (MD), and docking tools. The results indicate promising effects of such compounds to be used in further experimental and clinical trials; Chloroquine, Chloroquine-OH, and Umifenovir as viral entry inhibitors, Remdesivir, Ribavirin, Lopinavir, Ritonavir, and Darunavir as viral replication inhibitors, and Sirolimus are the examples, which were tested clinically on patients after comprehensive assessments of the available data on molecular simulation. This review summarizes the outcomes of various computer simulations data in the battle against COVID-19. More knowledge of SARS-CoV-2 genomic and structural characterization is necessary. Computer simulation can find possible natural or synthetic compounds for COVID-19. Molecular docking compares binding affinity of drugs to COVID-19 related targets. Network drug repurposing determines COVID-19 associated target genes and pathways.
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Affiliation(s)
- Mohammad Amin Khazeei Tabari
- Student Research Committee, Mazandaran University of Medical Sciences, Sari, Iran.,USERN Office, Mazandaran University of Medical Sciences, Sari, Iran
| | - Hooman Khoshhal
- Student Research Committee, Mazandaran University of Medical Sciences, Sari, Iran.,USERN Office, Mazandaran University of Medical Sciences, Sari, Iran
| | - Alireza Tafazoli
- Department of Analysis and Bioanalysis of Medicines, Faculty of Pharmacy with the Division of Laboratory Medicine, Medical University of Białystok, Białystok, Poland.,Genomics Laboratory, Clinical Research Centre, Medical University of Białystok, Bialystok, Poland
| | - Mohanna Khandan
- Student Research Committee, Mazandaran University of Medical Sciences, Sari, Iran.,USERN Office, Mazandaran University of Medical Sciences, Sari, Iran
| | - Abouzar Bagheri
- Department of Clinical Biochemistry and Medical Genetics, Faculty of Medicine, Molecular and Cell Biology Research Center, Mazandaran University of Medical Sciences, Sari, Iran
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23
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Sabarimurugan S, Dharmarajan A, Warrier S, Subramanian M, Swaminathan R. Comprehensive review on the prevailing COVID-19 therapeutics and the potential of repurposing SARS-CoV-1 candidate drugs to target SARS-CoV-2 as a fast-track treatment and prevention option. ANNALS OF TRANSLATIONAL MEDICINE 2020; 8:1247. [PMID: 33178779 PMCID: PMC7607133 DOI: 10.21037/atm-20-4071] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The recent seemingly uncontrollable pandemic caused by the novel severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) has been able to spread quickly due to the non-availability of effective antivirals or vaccines. The virus has structural and non-structural proteins that are considered as possible targets. Receptor recognition is the critical determinant and preliminary phase of viral infection to enter the host cell and causes tissue tropism. We have conducted a comprehensive review of relevant publication on in vitro, in silico, in vivo and clinical evaluation of drug candidates ranging from broad-spectrum antivirals to natural molecules targeted towards viral spike protein in addition to evaluate their suitability as therapies based on an analysis of the similarities between SARS-CoV-1 and SARS-CoV-2. In general, antiviral targets are based on two strategies, either targeting the host or the host’s immune cell. We have reviewed the available details on the SARS-CoV-2 strain’s host-viral binding sites entry mechanism, alongside recently tested effective antivirals. The hypothesis of this review may provide clear insight for researchers and physicians who are struggling to narrow down scientific options to control the current pandemic. Overall, we found that the promising efficacious drug candidates reported against SARS-CoV-1 could be considered for drug repurposing; this might help to identify a potential drug for therapeutic measures and development of vaccine for COVID-19.
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Affiliation(s)
- Shanthi Sabarimurugan
- School of Biomedical Sciences, The University of Western Australia, Perth, Australia
| | - Arun Dharmarajan
- CHIRI, School of Pharmacy and Biomedical Sciences, Curtin University, Perth, WA, Australia.,Department of Biomedical Sciences, Faculty of Biomedical Sciences, Technology and Research, Sri Ramachandra Institute of Higher Education and Research, Chennai, India.,Department of Human Sciences, Faculty of Life Sciences, The University of Western Australia, Nedlands, WA, Australia
| | - Sudha Warrier
- CHIRI, School of Pharmacy and Biomedical Sciences, Curtin University, Perth, WA, Australia.,School of Regenerative Medicine, Manipal Academy of Higher Education, Bangalore, India
| | - Maheswari Subramanian
- Department of Microbiology, Centre for Research and PG Studies, Indian Academy of Degree College (Aut), Bangalore, India
| | - Rajarajan Swaminathan
- Centre for Drug Design, Discovery and Development, SRM University, Sonipat, Haryana, New Delhi, India
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24
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Yepes-Pérez AF, Herrera-Calderon O, Sánchez-Aparicio JE, Tiessler-Sala L, Maréchal JD, Cardona-G W. Investigating Potential Inhibitory Effect of Uncaria tomentosa (Cat's Claw) against the Main Protease 3CL pro of SARS-CoV-2 by Molecular Modeling. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE : ECAM 2020; 2020:4932572. [PMID: 33029165 PMCID: PMC7532411 DOI: 10.1155/2020/4932572] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 07/25/2020] [Indexed: 12/13/2022]
Abstract
COVID-19 is a disease caused by severe acute respiratory syndrome coronavirus 2. Presently, there is no effective treatment for COVID-19. As part of the worldwide efforts to find efficient therapies and preventions, it has been reported the crystalline structure of the SARS-CoV-2 main protease Mpro (also called 3CLpro) bound to a synthetic inhibitor, which represents a major druggable target. The druggability of Mpro could be used for discovering drugs to treat COVID-19. A multilevel computational study was carried out to evaluate the potential antiviral properties of the components of the medicinal herb Uncaria tomentosa (Cat's claw), focusing on the inhibition of Mpro. The in silico approach starts with protein-ligand docking of 26 Cat's claw key components, followed by ligand pathway calculations, molecular dynamics simulations, and MM-GBSA calculation of the free energy of binding for the best docked candidates. The structural bioinformatics approaches led to identification of three bioactive compounds of Uncaria tomentosa (speciophylline, cadambine, and proanthocyanidin B2) with potential therapeutic effects by strong interaction with 3CLpro. Additionally, in silico drug-likeness indices for these components were calculated and showed good predicted therapeutic profiles of these phytochemicals. Our findings suggest the potential effectiveness of Cat's claw as complementary and/or alternative medicine for COVID-19 treatment.
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Affiliation(s)
- Andres F. Yepes-Pérez
- Chemistry of Colombian Plants, Institute of Chemistry, Faculty of Exact and Natural Sciences, University of Antioquia-UdeA, Calle 70 No. 52-21, A.A 1226, Medellin, Colombia
| | - Oscar Herrera-Calderon
- Academic Department of Pharmacology, Bromatology and Toxicology, Faculty of Pharmacy and Biochemistry, Universidad Nacional Mayor de San Marcos, Jr Puno 1002, Lima 15001, Peru
| | - José-Emilio Sánchez-Aparicio
- Insilichem, Departament de Química, Universitat Autònoma de Barcelona, Edifici C.n., 08193 Cerdanyola del Vallés, Barcelona, Spain
| | - Laura Tiessler-Sala
- Insilichem, Departament de Química, Universitat Autònoma de Barcelona, Edifici C.n., 08193 Cerdanyola del Vallés, Barcelona, Spain
| | - Jean-Didier Maréchal
- Insilichem, Departament de Química, Universitat Autònoma de Barcelona, Edifici C.n., 08193 Cerdanyola del Vallés, Barcelona, Spain
| | - Wilson Cardona-G
- Chemistry of Colombian Plants, Institute of Chemistry, Faculty of Exact and Natural Sciences, University of Antioquia-UdeA, Calle 70 No. 52-21, A.A 1226, Medellin, Colombia
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25
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Rangel HR, Ortega JT, Maksoud S, Pujol FH, Serrano ML. SARS-CoV-2 host tropism: An in silico analysis of the main cellular factors. Virus Res 2020; 289:198154. [PMID: 32918944 PMCID: PMC7480320 DOI: 10.1016/j.virusres.2020.198154] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 09/01/2020] [Accepted: 09/03/2020] [Indexed: 02/06/2023]
Abstract
The role in host selectivity of ACE2, Tmprss2 and GPR78 in SARS-CoV-2 was explored. Differences in the SARS-CoV-2 RBD binding mode with ACE2 of secondary hosts could be associated with host permissiveness. Nafamostat could be considered a good inhibitor of mammalian hosts TMPRSS2 proteins. In silico studies confirm that the spike protein could interact with GRP78 in studied mammalian hosts. TMPRSS2 and GRP78 do not seem to play a role in host selectivity.
Recent reports have shown that small and big felines could be infected by SARS-CoV-2, while other animals, like swines and mice, are apparently not susceptible to this infection. These findings raise the question of the role of cell factors associated with early stages of the viral infection in host selectivity. The cellular receptor for SARS-CoV-2 is the Angiotensin Converting Enzyme (ACE2). Transmembrane protease serine 2 (TMPRSS2) has been shown to prime the viral spike for its interaction with its receptor. GRP78 has also been proposed as a possible co-receptor. In this study, we used several bioinformatics approaches to bring clues in the interaction of ACE2, TMPRSS2, and GRP78 with SARS-CoV-2. We selected several mammalian hosts that could play a key role in viral spread by acting as secondary hosts (cats, dogs, pigs, mice, and ferrets) and evaluated their predicted permissiveness by in silico analysis. Results showed that ionic pairs (salt bridges, N–O pair, and long-range interactions) produced between ACE2 and the viral spike has an essential function in the host interaction. On the other hand, TMPRSS2 and GRP78 are proteins with high homology in all the evaluated hosts. Thus, these proteins do not seem to play a role in host selectivity, suggesting that other factors may play a role in the non-permissivity in some of these hosts. These proteins represent however interesting cell targets that could be explored in order to control the virus replication in humans and in the intermediary hosts.
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Affiliation(s)
- H R Rangel
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas, Venezuela
| | - J T Ortega
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - S Maksoud
- Department of Neurology and Experimental Therapeutics and Molecular Imaging Laboratory, Massachusetts General Hospital, MA 02129, USA
| | - F H Pujol
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas, Venezuela
| | - M L Serrano
- Unidad de Química Medicinal, Facultad de Farmacia, Universidad Central de Venezuela, Caracas 1041-A, Venezuela.
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26
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Villas-Boas GR, Rescia VC, Paes MM, Lavorato SN, de Magalhães-Filho MF, Cunha MS, Simões RDC, de Lacerda RB, de Freitas-Júnior RS, Ramos BHDS, Mapeli AM, Henriques MDST, de Freitas WR, Lopes LAF, Oliveira LGR, da Silva JG, Silva-Filho SE, da Silveira APS, Leão KV, Matos MMDS, Fernandes JS, Cuman RKN, Silva-Comar FMDS, Comar JF, Brasileiro LDA, dos Santos JN, Oesterreich SA. The New Coronavirus (SARS-CoV-2): A Comprehensive Review on Immunity and the Application of Bioinformatics and Molecular Modeling to the Discovery of Potential Anti-SARS-CoV-2 Agents. Molecules 2020; 25:E4086. [PMID: 32906733 PMCID: PMC7571161 DOI: 10.3390/molecules25184086] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 09/03/2020] [Accepted: 09/04/2020] [Indexed: 02/07/2023] Open
Abstract
On March 11, 2020, the World Health Organization (WHO) officially declared the outbreak caused by the new coronavirus (SARS-CoV-2) a pandemic. The rapid spread of the disease surprised the scientific and medical community. Based on the latest reports, news, and scientific articles published, there is no doubt that the coronavirus has overloaded health systems globally. Practical actions against the recent emergence and rapid expansion of the SARS-CoV-2 require the development and use of tools for discovering new molecular anti-SARS-CoV-2 targets. Thus, this review presents bioinformatics and molecular modeling strategies that aim to assist in the discovery of potential anti-SARS-CoV-2 agents. Besides, we reviewed the relationship between SARS-CoV-2 and innate immunity, since understanding the structures involved in this infection can contribute to the development of new therapeutic targets. Bioinformatics is a technology that assists researchers in coping with diseases by investigating genetic sequencing and seeking structural models of potential molecular targets present in SARS-CoV2. The details provided in this review provide future points of consideration in the field of virology and medical sciences that will contribute to clarifying potential therapeutic targets for anti-SARS-CoV-2 and for understanding the molecular mechanisms responsible for the pathogenesis and virulence of SARS-CoV-2.
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Affiliation(s)
- Gustavo R. Villas-Boas
- Research Group on Development of Pharmaceutical Products (P&DProFar), Center for Biological and Health Sciences, Federal University of Western Bahia, Rua Bertioga, 892, Morada Nobre II, Barreiras CEP 47810-059, BA, Brazil; (V.C.R.); (M.M.P.); (S.N.L.); (M.F.d.M.-F.); (M.S.C.); (R.d.C.S.)
| | - Vanessa C. Rescia
- Research Group on Development of Pharmaceutical Products (P&DProFar), Center for Biological and Health Sciences, Federal University of Western Bahia, Rua Bertioga, 892, Morada Nobre II, Barreiras CEP 47810-059, BA, Brazil; (V.C.R.); (M.M.P.); (S.N.L.); (M.F.d.M.-F.); (M.S.C.); (R.d.C.S.)
| | - Marina M. Paes
- Research Group on Development of Pharmaceutical Products (P&DProFar), Center for Biological and Health Sciences, Federal University of Western Bahia, Rua Bertioga, 892, Morada Nobre II, Barreiras CEP 47810-059, BA, Brazil; (V.C.R.); (M.M.P.); (S.N.L.); (M.F.d.M.-F.); (M.S.C.); (R.d.C.S.)
| | - Stefânia N. Lavorato
- Research Group on Development of Pharmaceutical Products (P&DProFar), Center for Biological and Health Sciences, Federal University of Western Bahia, Rua Bertioga, 892, Morada Nobre II, Barreiras CEP 47810-059, BA, Brazil; (V.C.R.); (M.M.P.); (S.N.L.); (M.F.d.M.-F.); (M.S.C.); (R.d.C.S.)
| | - Manoel F. de Magalhães-Filho
- Research Group on Development of Pharmaceutical Products (P&DProFar), Center for Biological and Health Sciences, Federal University of Western Bahia, Rua Bertioga, 892, Morada Nobre II, Barreiras CEP 47810-059, BA, Brazil; (V.C.R.); (M.M.P.); (S.N.L.); (M.F.d.M.-F.); (M.S.C.); (R.d.C.S.)
| | - Mila S. Cunha
- Research Group on Development of Pharmaceutical Products (P&DProFar), Center for Biological and Health Sciences, Federal University of Western Bahia, Rua Bertioga, 892, Morada Nobre II, Barreiras CEP 47810-059, BA, Brazil; (V.C.R.); (M.M.P.); (S.N.L.); (M.F.d.M.-F.); (M.S.C.); (R.d.C.S.)
| | - Rafael da C. Simões
- Research Group on Development of Pharmaceutical Products (P&DProFar), Center for Biological and Health Sciences, Federal University of Western Bahia, Rua Bertioga, 892, Morada Nobre II, Barreiras CEP 47810-059, BA, Brazil; (V.C.R.); (M.M.P.); (S.N.L.); (M.F.d.M.-F.); (M.S.C.); (R.d.C.S.)
| | - Roseli B. de Lacerda
- Department of Pharmacology of the Biological Sciences Center, Federal University of Paraná, Jardim das Américas, Caixa. postal 19031, Curitiba CEP 81531-990, PR, Brazil;
| | - Renilson S. de Freitas-Júnior
- Clinical Health is Life-Integrated Health Center, Rua dos Andrades, 99, Barreirinhas, Barreiras CEP 47810-689, BA, Brazil;
| | - Bruno H. da S. Ramos
- Institute of the Spine and Pain Clinic, Rua Dr. Renato Gonçalves, 108, Renato Gonçalves, Barreiras CEP 47806-021, BA, Brazil;
| | - Ana M. Mapeli
- Research Group on Biomolecules and Catalyze, Center for Biological and Health Sciences, Federal University of Western Bahia, Rua Bertioga, 892, Morada Nobre II, Barreiras CEP 47810-059, BA, Brazil;
| | - Matheus da S. T. Henriques
- Laboratory of Pharmacology of Toxins (LabTox), Graduate Program in Pharmacology and Medicinal Chemistry (PPGFQM), Institute of Biomedical Sciences (ICB) Federal University of Rio de Janeiro (UFRJ), Avenida Carlos Chagas Filho, 373, Cidade Universitária, Rio de Janeiro CEP 21941-590, RJ, Brazil;
| | - William R. de Freitas
- Research Group on Biodiversity and Health (BIOSA), Center for Training in Health Sciences, Federal University of Southern Bahia, Praça Joana Angélica, 58, São José, Teixeira de Freitas, Teixeira de Freitas CEP 45988-058, Brazil;
| | - Luiz A. F. Lopes
- University Hospital of the Federal University of Grande Dourados (HU-UFGD), Federal University of Grande Dourados, Rua Ivo Alves da Rocha, 558, Altos do Indaiá, Dourados CEP 79823-501, MS, Brazil;
| | - Luiz G. R. Oliveira
- Nucleus of Studies on Infectious Agents and Vectors (Naive), Federal University of Western Bahia, Rua Bertioga, 892, Morada Nobre II, Barreiras CEP 47810-059, BA, Brazil;
| | - Jonatas G. da Silva
- Federal University of Western Bahia, Rua Bertioga, 892, Morada Nobre II, Barreiras CEP 47810-059, BA, Brazil; (J.G.d.S.); (K.V.L.); (J.S.F.)
| | - Saulo E. Silva-Filho
- Pharmaceutical Sciences, Food and Nutrition College, Federal University of Mato Grosso do Sul, Avenida Costa e Silva, s/nº, Bairro Universitário, Campo Grande CEP 79070-900, MS, Brazil;
| | - Ana P. S. da Silveira
- Faculty of Biological and Health Sciences, University Center Unigran Capital, Rua Balbina de Matos, 2121, Jd. University, Dourados CEP 79.824-900, MS, Brazil;
| | - Katyuscya V. Leão
- Federal University of Western Bahia, Rua Bertioga, 892, Morada Nobre II, Barreiras CEP 47810-059, BA, Brazil; (J.G.d.S.); (K.V.L.); (J.S.F.)
| | - Maria M. de S. Matos
- Health Sciences at ABC Health University Center, Avenida Príncipe de Gales, 667, Bairro Princípe de Gales, Santo André CEP 09060-870, SP, Brazil;
| | - Jamille S. Fernandes
- Federal University of Western Bahia, Rua Bertioga, 892, Morada Nobre II, Barreiras CEP 47810-059, BA, Brazil; (J.G.d.S.); (K.V.L.); (J.S.F.)
| | - Roberto K. N. Cuman
- Department of Pharmacology and Therapeutics, State University of Maringá, Avenida Colombo, nº 5790, Jardim Universitário, Maringá CEP 87020-900, PR, Brazil; (R.K.N.C.); (F.M.d.S.S.-C.)
| | - Francielli M. de S. Silva-Comar
- Department of Pharmacology and Therapeutics, State University of Maringá, Avenida Colombo, nº 5790, Jardim Universitário, Maringá CEP 87020-900, PR, Brazil; (R.K.N.C.); (F.M.d.S.S.-C.)
| | - Jurandir F. Comar
- Department of Biochemistry, State University of Maringá, Avenida Colombo, nº 5790, Jardim Universitário, Maringá CEP 87020-900, PR, Brazil;
| | - Luana do A. Brasileiro
- Nacional Cancer Institute (INCA), Rua Visconde de Santa Isabel, 274, Rio de Janeiro CEP 20560-121, RJ, Brazil;
| | | | - Silvia A. Oesterreich
- Faculty of Health Sciences, Federal University of Grande Dourados, Dourados Rodovia Dourados, Itahum Km 12, Cidade Universitaria, Caixa postal 364, Dourados CEP 79804-970, Mato Grosso do Sul, Brazil;
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27
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Gao J, Zhang L, Liu X, Li F, Ma R, Zhu Z, Zhang J, Wu J, Shi Y, Pan Y, Ge Y, Ruan K. Repurposing Low-Molecular-Weight Drugs against the Main Protease of Severe Acute Respiratory Syndrome Coronavirus 2. J Phys Chem Lett 2020; 11:7267-7272. [PMID: 32787337 PMCID: PMC7441750 DOI: 10.1021/acs.jpclett.0c01894] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 07/28/2020] [Indexed: 05/11/2023]
Abstract
The coronavirus disease pandemic caused by infection with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has affected the global healthcare system. As low-molecular-weight drugs have high potential to completely match interactions with essential SARS-CoV-2 targets, we propose a strategy to identify such drugs using the fragment-based approach. Herein, using ligand- and protein-observed fragment screening approaches, we identified niacin and hit 1 binding to the catalytic pocket of the main protease (Mpro) of SARS-CoV-2, thereby modestly inhibiting the enzymatic activity of Mpro. We further searched for low-molecular-weight drugs containing niacin or hit 1 pharmacophores with enhanced inhibiting activity, e.g., carmofur, bendamustine, triclabendazole, emedastine, and omeprazole, in which omeprazole is the only one binding to the C-terminal domain of SARS-CoV-2 Mpro. Our study demonstrates that the fragment-based approach is a feasible strategy for identifying low-molecular-weight drugs against the SARS-CoV-2 and other potential targets lacking specific drugs.
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Affiliation(s)
- Jia Gao
- Ministry of Education Key Laboratory for Membrane-less
Organelles & Cellular Dynamics, Hefei National Laboratory for
Physical Sciences at the Microscale, Division of Life Sciences and
Medicine, University of Science and Technology of
China, Huangshan Road, Hefei, Anhui 230027,
P.R. China
| | - Liang Zhang
- Ministry of Education Key Laboratory for Membrane-less
Organelles & Cellular Dynamics, Hefei National Laboratory for
Physical Sciences at the Microscale, Division of Life Sciences and
Medicine, University of Science and Technology of
China, Huangshan Road, Hefei, Anhui 230027,
P.R. China
| | - Xiaodan Liu
- Ministry of Education Key Laboratory for Membrane-less
Organelles & Cellular Dynamics, Hefei National Laboratory for
Physical Sciences at the Microscale, Division of Life Sciences and
Medicine, University of Science and Technology of
China, Huangshan Road, Hefei, Anhui 230027,
P.R. China
| | - Fudong Li
- Ministry of Education Key Laboratory for Membrane-less
Organelles & Cellular Dynamics, Hefei National Laboratory for
Physical Sciences at the Microscale, Division of Life Sciences and
Medicine, University of Science and Technology of
China, Huangshan Road, Hefei, Anhui 230027,
P.R. China
| | - Rongsheng Ma
- Ministry of Education Key Laboratory for Membrane-less
Organelles & Cellular Dynamics, Hefei National Laboratory for
Physical Sciences at the Microscale, Division of Life Sciences and
Medicine, University of Science and Technology of
China, Huangshan Road, Hefei, Anhui 230027,
P.R. China
| | - Zhongliang Zhu
- Ministry of Education Key Laboratory for Membrane-less
Organelles & Cellular Dynamics, Hefei National Laboratory for
Physical Sciences at the Microscale, Division of Life Sciences and
Medicine, University of Science and Technology of
China, Huangshan Road, Hefei, Anhui 230027,
P.R. China
| | - Jiahai Zhang
- Ministry of Education Key Laboratory for Membrane-less
Organelles & Cellular Dynamics, Hefei National Laboratory for
Physical Sciences at the Microscale, Division of Life Sciences and
Medicine, University of Science and Technology of
China, Huangshan Road, Hefei, Anhui 230027,
P.R. China
| | - Jihui Wu
- Ministry of Education Key Laboratory for Membrane-less
Organelles & Cellular Dynamics, Hefei National Laboratory for
Physical Sciences at the Microscale, Division of Life Sciences and
Medicine, University of Science and Technology of
China, Huangshan Road, Hefei, Anhui 230027,
P.R. China
| | - Yunyu Shi
- Ministry of Education Key Laboratory for Membrane-less
Organelles & Cellular Dynamics, Hefei National Laboratory for
Physical Sciences at the Microscale, Division of Life Sciences and
Medicine, University of Science and Technology of
China, Huangshan Road, Hefei, Anhui 230027,
P.R. China
| | - Yueyin Pan
- Ministry of Education Key Laboratory for Membrane-less
Organelles & Cellular Dynamics, Hefei National Laboratory for
Physical Sciences at the Microscale, Division of Life Sciences and
Medicine, University of Science and Technology of
China, Huangshan Road, Hefei, Anhui 230027,
P.R. China
| | - Yushu Ge
- Ministry of Education Key Laboratory for Membrane-less
Organelles & Cellular Dynamics, Hefei National Laboratory for
Physical Sciences at the Microscale, Division of Life Sciences and
Medicine, University of Science and Technology of
China, Huangshan Road, Hefei, Anhui 230027,
P.R. China
| | - Ke Ruan
- Ministry of Education Key Laboratory for Membrane-less
Organelles & Cellular Dynamics, Hefei National Laboratory for
Physical Sciences at the Microscale, Division of Life Sciences and
Medicine, University of Science and Technology of
China, Huangshan Road, Hefei, Anhui 230027,
P.R. China
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Tariq A, Mateen RM, Afzal MS, Saleem M. Paromomycin: A potential dual targeted drug effectively inhibits both spike (S1) and main protease of COVID-19. Int J Infect Dis 2020; 98:166-175. [PMID: 32579907 PMCID: PMC7306207 DOI: 10.1016/j.ijid.2020.06.063] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 06/12/2020] [Accepted: 06/17/2020] [Indexed: 02/02/2023] Open
Abstract
OBJECTIVES With the increasing number of people suffering from coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), there is a dire need to look for effective remedies against this pandemic. Drug repurposing seems to be the solution for the current situation. METHODS In a quest to find a potential drug against this virus, 15 antimalarial drugs (including chloroquine) and 2413 US Food and Drug Administration-approved drugs were investigated for activity against both the protease and spike proteins of SARS-CoV-2 using an in silico approach. Molecular docking analysis followed by molecular dynamics simulation was performed to estimate the binding and stability of the complexes. RESULTS This study identified a single drug - paromomycin - with activity against two targets of SARS-CoV-2, i.e., spike protein (S1) and protease domain. Paromomycin was found to have strong binding affinity for both targets of coronavirus. The results also showed that no antimalarial drug exhibited effective binding for either S1 or protease. CONCLUSIONS This study found that paromomycin may be an effective dual targeting drug against coronavirus, as it binds not only to the protease domain of the virion, but also to the spike domain, with high stability. Furthermore, none of the antimalarial drugs showed strong binding affinity for either protease or the receptor binding domain (RBD).
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Affiliation(s)
- Asma Tariq
- Institute of Biochemistry and Biotechnology, University of the Punjab, Lahore, Pakistan.
| | - Rana Muhammad Mateen
- Department of Life Sciences, School of Science, University of Management and Technology, Lahore, Pakistan.
| | - Muhammad Sohail Afzal
- Department of Life Sciences, School of Science, University of Management and Technology, Lahore, Pakistan.
| | - Mahjabeen Saleem
- Institute of Biochemistry and Biotechnology, University of the Punjab, Lahore, Pakistan.
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29
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Joshi S, Joshi M, Degani MS. Tackling SARS-CoV-2: proposed targets and repurposed drugs. Future Med Chem 2020; 12:1579-1601. [PMID: 32564623 PMCID: PMC7307730 DOI: 10.4155/fmc-2020-0147] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 06/03/2020] [Indexed: 12/15/2022] Open
Abstract
The SARS-CoV-2 pandemic, declared as a global health emergency by the WHO in February 2020, has currently infected more than 6 million people with fatalities near 371,000 and increasing exponentially, in absence of vaccines and drugs. The pathogenesis of SARS-CoV-2 is still being elucidated. Identifying potential targets and repurposing drugs as therapeutic options is the need of the hour. In this review, we focus on potential druggable targets and suitable therapeutics, currently being explored in clinical trials, to treat SARS-CoV-2 infection. A brief understanding of the complex interactions of both viral as well as host targets, and the possible repurposed drug candidates are described with an emphasis on understanding the mechanisms at the molecular level.
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Affiliation(s)
- Siddhi Joshi
- Department of Pharmaceutical Sciences & Technology, Institute of Chemical Technology, Nathalal Parekh Marg, Mumbai, 400019, Maharashtra, India
| | - Maithili Joshi
- Department of Pharmaceutical Sciences & Technology, Institute of Chemical Technology, Nathalal Parekh Marg, Mumbai, 400019, Maharashtra, India
| | - Mariam S Degani
- Department of Pharmaceutical Sciences & Technology, Institute of Chemical Technology, Nathalal Parekh Marg, Mumbai, 400019, Maharashtra, India
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30
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Gates LE, Hamed AA. The Anatomy of the SARS-CoV-2 Biomedical Literature: Introducing the CovidX Network Algorithm for Drug Repurposing Recommendation. J Med Internet Res 2020; 22:e21169. [PMID: 32735546 PMCID: PMC7474417 DOI: 10.2196/21169] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 07/09/2020] [Accepted: 07/24/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Driven by the COVID-19 pandemic and the dire need to discover an antiviral drug, we explored the landscape of the SARS-CoV-2 biomedical publications to identify potential treatments. OBJECTIVE The aims of this study are to identify off-label drugs that may have benefits for the coronavirus disease pandemic, present a novel ranking algorithm called CovidX to recommend existing drugs for potential repurposing, and validate the literature-based outcome with drug knowledge available in clinical trials. METHODS To achieve such objectives, we applied natural language processing techniques to identify drugs and linked entities (eg, disease, gene, protein, chemical compounds). When such entities are linked, they form a map that can be further explored using network science tools. The CovidX algorithm was based upon a notion that we called "diversity." A diversity score for a given drug was calculated by measuring how "diverse" a drug is calculated using various biological entities (regardless of the cardinality of actual instances in each category). The algorithm validates the ranking and awards those drugs that are currently being investigated in open clinical trials. The rationale behind the open clinical trial is to provide a validating mechanism of the PubMed results. This ensures providing up to date evidence of the fast development of this disease. RESULTS From the analyzed biomedical literature, the algorithm identified 30 possible drug candidates for repurposing, ranked them accordingly, and validated the ranking outcomes against evidence from clinical trials. The top 10 candidates according to our algorithm are hydroxychloroquine, azithromycin, chloroquine, ritonavir, losartan, remdesivir, favipiravir, methylprednisolone, rapamycin, and tilorone dihydrochloride. CONCLUSIONS The ranking shows both consistency and promise in identifying drugs that can be repurposed. We believe, however, the full treatment to be a multifaceted, adjuvant approach where multiple drugs may need to be taken at the same time.
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Affiliation(s)
| | - Ahmed Abdeen Hamed
- School of Cybersecurity, Data Science, and Computing, Norwich University, Northfield, VT, United States
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31
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Ahmed SA, Abdelrheem DA, El-Mageed HRA, Mohamed HS, Rahman AA, Elsayed KNM, Ahmed SA. Destabilizing the structural integrity of COVID-19 by caulerpin and its derivatives along with some antiviral drugs: An in silico approaches for a combination therapy. Struct Chem 2020; 31:2391-2412. [PMID: 32837118 PMCID: PMC7376526 DOI: 10.1007/s11224-020-01586-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 07/06/2020] [Indexed: 12/17/2022]
Abstract
Presently, the SARS-CoV-2 (COVID-19) pandemic has been spreading throughout the world. Some drugs such as lopinavir, simeprevir, hydroxychloroquine, chloroquine, and amprenavir have been recommended for COVID-19 treatment by some researchers, but these drugs were not effective enough against this virus. This study based on in silico approaches was aimed to increase the anti-COVID-19 activities of these drugs by using caulerpin and its derivatives as an adjunct drug against SARS-CoV-2 receptor proteins: the SARS-CoV-2 main protease and the SARS-CoV-2 spike protein. Caulerpin exhibited antiviral activities against chikungunya virus and herpes simplex virus type 1. Caulerpin and some of its derivatives showed inhibitory activity against Alzheimer’s disease. The web server ANCHOR revealed higher protein stability for the two receptors with disordered score (< 0.6). Molecular docking analysis showed that the binding energies of most of the caulerpin derivatives were higher than all the suggested drugs for the two receptors. Also, we deduced that inserting NH2, halogen, and vinyl groups can increase the binding affinity of caulerpin toward 6VYB and 6LU7, while inserting an alkyl group decreases the binding affinity of caulerpin toward 6VYB and 6LU7. So, we can modify the inhibitory effect of caulerpin against 6VYB and 6LU7 by inserting NH2, halogen, and vinyl groups. Based on the protein disordered results, the SARS-CoV-2 main protease and SARS-CoV-2 spike protein domain are highly stable proteins, so it is quite difficult to unstabilize their integrity by using individual drugs. Also, molecular dynamics (MD) simulation indicates that binding of the combination therapy of simeprevir and the candidate studied compounds to the receptors was stable and had no major effect on the flexibility of the protein throughout the simulations and provided a suitable basis for our study. So, this study suggested that caulerpin and its derivatives could be used as a combination therapy along with lopinavir, simeprevir, hydroxychloroquine, chloroquine, and amprenavir for disrupting the stability of SARS-CoV2 receptor proteins to increase the antiviral activity of these drugs.
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Affiliation(s)
- Shimaa A Ahmed
- Department of Chemistry, Faculty of Science, Beni-Suef University, Beni Suef, 62511 Egypt
| | - Doaa A Abdelrheem
- Department of Chemistry, Faculty of Science, Beni-Suef University, Beni Suef, 62511 Egypt
| | - H R Abd El-Mageed
- Micro-analysis and Environmental Research and Community Services Center, Faculty of Science, Beni-Suef University, Beni Suef, Egypt
| | - Hussein S Mohamed
- Research Institute of Medicinal and Aromatic Plants (RIMAP), Beni-Suef University, Beni Suef, Egypt
| | - Aziz A Rahman
- Department of Pharmacy, University of Rajshahi, Rajshahi, 6205 Bangladesh
| | - Khaled N M Elsayed
- Department of Botany, Faculty of Science, Beni-Suef University, Beni-Suef, 62511 Egypt
| | - Sayed A Ahmed
- Department of Chemistry, Faculty of Science, Beni-Suef University, Beni Suef, 62511 Egypt
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32
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Garza-López RA, Kozak JJ, Gray HB. Copper(II) Inhibition of the SARS-CoV-2 Main Protease. CHEMRXIV : THE PREPRINT SERVER FOR CHEMISTRY 2020:12673436. [PMID: 33200118 PMCID: PMC7668746 DOI: 10.26434/chemrxiv.12673436] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 07/21/2020] [Indexed: 05/27/2023]
Abstract
In an analysis of the structural stability of the coronavirus main protease (Mpro), we identified regions of the protein that could be disabled by cobalt(III)-cation binding to histidines and cysteines [1]. Here we have extended our work to include copper(II) chelates, which we have docked to HIS 41 and CYS 145 in the Mpro active-site region. We have found stable docked structures where Cu(II) could readily bond to the CYS 145 thiolate, which would be lethal to the enzyme.
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Affiliation(s)
- Roberto A Garza-López
- Department of Chemistry and Seaver Chemistry Laboratory, Pomona College, Claremont, CA 91711
| | - John J Kozak
- Department of Chemistry, DePaul University, Chicago IL 60604-6116
| | - Harry B Gray
- Beckman Institute, California Institute of Technology, Pasadena, CA 91125
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33
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Ortega JT, Serrano ML, Jastrzebska B. Class A G Protein-Coupled Receptor Antagonist Famotidine as a Therapeutic Alternative Against SARS-CoV2: An In Silico Analysis. Biomolecules 2020; 10:E954. [PMID: 32599963 PMCID: PMC7355875 DOI: 10.3390/biom10060954] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 06/08/2020] [Accepted: 06/22/2020] [Indexed: 12/11/2022] Open
Abstract
The pandemic associated with Severe Acute Respiratory Syndrome Coronavirus type 2 (SARS-CoV2) and its disease named COVID-19 challenged the scientific community to discover effective therapeutic solutions in a short period. Repurposing existing drugs is one viable approach that emphasizes speed during these urgent times. Famotidine, a class A G protein-coupled receptor antagonist used for the treatment of gastroesophageal reflux was recently identified in an in silico screening. Additionally, a recent retrospective clinical report showed that the treatment with famotidine provided a good outcome in patients infected with SARS-CoV2. A clinical trial testing effectiveness of famotidine in combination with hydroxychloroquine is currently ongoing in the United States (US). In the 1990s, famotidine was described as an antiviral agent against human immunodeficiency virus (HIV). Interestingly, some HIV protease inhibitors are presently being used against SARS-CoV2. However, it is not clear if famotidine could be effective against SARS-CoV2. Thus, by using a computational analysis, we aimed to examine if the antiviral effect of famotidine could be related to the inhibition of proteases involved in the virus replication. Our results showed that famotidine could interact within the catalytic site of the three proteases associated with SARS-CoV2 replication. However, weak binding affinity of famotidine to these proteases suggests that a successful famotidine therapy could likely be achieved only in combination with other antiviral drugs. Finally, analysis of famotidine's pharmacokinetic parameters indicated that its effect against SARS-CoV2 infection could be reached only upon intravenous administration. This work will contribute to the pharmacological knowledge of famotidine as an antiviral agent against SARS-CoV2.
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Affiliation(s)
- Joseph T. Ortega
- Department of Pharmacology, Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Maria Luisa Serrano
- Unidad de Química Medicinal, Facultad de Farmacia, Universidad Central de Venezuela, Caracas 1041-A, Venezuela;
| | - Beata Jastrzebska
- Department of Pharmacology, Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
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Fiesco-Sepúlveda KY, Serrano-Bermúdez LM. Contributions of Latin American researchers in the understanding of the novel coronavirus outbreak: a literature review. PeerJ 2020; 8:e9332. [PMID: 32547890 PMCID: PMC7276147 DOI: 10.7717/peerj.9332] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 05/19/2020] [Indexed: 12/13/2022] Open
Abstract
This article aimed to give the visibility of Latin American researchers' contributions to the comprehension of COVID-19; our method was a literature review. Currently, the world is facing a health and socioeconomic crisis caused by the novel coronavirus, SARS-CoV-2, and its disease COVID-19. Therefore, in less than 4 months, researchers have published a significant number of articles related to this novel virus. For instance, a search focused on the Scopus database on 10 April 2020, showed 1,224 documents published by authors with 1,797 affiliations from 80 countries. A total of 25.4%, 24.0% and 12.6% of these national affiliations were from China, Europe and the USA, respectively, making these regions leaders in COVID-19 research. In the case of Latin America, on 10 April 2020, we searched different databases, such as Scopus, PubMed and Web of Science, finding that the contribution of this region was 2.7 ± 0.6% of the total publications found. In other words, we found 153 publications related to COVID-19 with at least one Latin American researcher. We summarized and processed the information from these 153 publications, finding active participation in topics like medical, social and environmental considerations, bioinformatics and epidemiology.
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35
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Investigation of Some Antiviral N-Heterocycles as COVID 19 Drug: Molecular Docking and DFT Calculations. Int J Mol Sci 2020; 21:ijms21113922. [PMID: 32486229 PMCID: PMC7312990 DOI: 10.3390/ijms21113922] [Citation(s) in RCA: 112] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 04/29/2020] [Accepted: 04/30/2020] [Indexed: 02/07/2023] Open
Abstract
The novel coronavirus, COVID-19, caused by SARS-CoV-2, is a global health pandemic that started in December 2019. The effective drug target among coronaviruses is the main protease Mpro, because of its essential role in processing the polyproteins that are translated from the viral RNA. In this study, the bioactivity of some selected heterocyclic drugs named Favipiravir (1), Amodiaquine (2), 2'-Fluoro-2'-deoxycytidine (3), and Ribavirin (4) was evaluated as inhibitors and nucleotide analogues for COVID-19 using computational modeling strategies. The density functional theory (DFT) calculations were performed to estimate the thermal parameters, dipole moment, polarizability, and molecular electrostatic potential of the present drugs; additionally, Mulliken atomic charges of the drugs as well as the chemical reactivity descriptors were investigated. The nominated drugs were docked on SARS-CoV-2 main protease (PDB: 6LU7) to evaluate the binding affinity of these drugs. Besides, the computations data of DFT the docking simulation studies was predicted that the Amodiaquine (2) has the least binding energy (-7.77 Kcal/mol) and might serve as a good inhibitor to SARS-CoV-2 comparable with the approved medicines, hydroxychloroquine, and remdesivir which have binding affinity -6.06 and -4.96 Kcal/mol, respectively. The high binding affinity of 2 was attributed to the presence of three hydrogen bonds along with different hydrophobic interactions between the drug and the critical amino acids residues of the receptor. Finally, the estimated molecular electrostatic potential results by DFT were used to illustrate the molecular docking findings. The DFT calculations showed that drug 2 has the highest of lying HOMO, electrophilicity index, basicity, and dipole moment. All these parameters could share with different extent to significantly affect the binding affinity of these drugs with the active protein sites.
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36
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Kumar S, Zhi K, Mukherji A, Gerth K. Repurposing Antiviral Protease Inhibitors Using Extracellular Vesicles for Potential Therapy of COVID-19. Viruses 2020; 12:E486. [PMID: 32357553 PMCID: PMC7290948 DOI: 10.3390/v12050486] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 04/16/2020] [Accepted: 04/24/2020] [Indexed: 12/17/2022] Open
Abstract
In January 2020, Chinese health agencies reported an outbreak of a novel coronavirus-2 (CoV-2) which can lead to severe acute respiratory syndrome (SARS). The virus, which belongs to the coronavirus family (SARS-CoV-2), was named coronavirus disease 2019 (COVID-19) and declared a pandemic by the World Health Organization (WHO). Full-length genome sequences of SARS-CoV-2 showed 79.6% sequence identity to SARS-CoV, with 96% identity to a bat coronavirus at the whole-genome level. COVID-19 has caused over 133,000 deaths and there are over 2 million total confirmed cases as of April 15th, 2020. Current treatment plans are still under investigation due to a lack of understanding of COVID-19. One potential mechanism to slow disease progression is the use of antiviral drugs to either block the entry of the virus or interfere with viral replication and maturation. Currently, antiviral drugs, including chloroquine/hydroxychloroquine, remdesivir, and lopinavir/ritonavir, have shown effective inhibition of SARS-CoV-2 in vitro. Due to the high dose needed and narrow therapeutic window, many patients are experiencing severe side effects with the above drugs. Hence, repurposing these drugs with a proper formulation is needed to improve the safety and efficacy for COVID-19 treatment. Extracellular vesicles (EVs) are a family of natural carriers in the human body. They play a critical role in cell-to-cell communications. EVs can be used as unique drug carriers to deliver protease inhibitors to treat COVID-19. EVs may provide targeted delivery of protease inhibitors, with fewer systemic side effects. More importantly, EVs are eligible for major aseptic processing and can be upscaled for mass production. Currently, the FDA is facilitating applications to treat COVID-19, which provides a very good chance to use EVs to contribute in this combat.
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Affiliation(s)
- Santosh Kumar
- Department of Pharmaceutical Sciences, University of Tennessee Health Science Center, 881 Madison Ave, Memphis, TN 38163, USA; (A.M.); (K.G.)
| | - Kaining Zhi
- Plough Center for Sterile Drug Delivery Solutions, University of Tennessee Health Science Center, 208 South Dudley Street, Memphis, TN 38163, USA;
| | - Ahona Mukherji
- Department of Pharmaceutical Sciences, University of Tennessee Health Science Center, 881 Madison Ave, Memphis, TN 38163, USA; (A.M.); (K.G.)
| | - Kelli Gerth
- Department of Pharmaceutical Sciences, University of Tennessee Health Science Center, 881 Madison Ave, Memphis, TN 38163, USA; (A.M.); (K.G.)
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Sreepadmanabh M, Sahu AK, Chande A. COVID-19: Advances in diagnostic tools, treatment strategies, and vaccine development. J Biosci 2020; 45:148. [PMID: 33410425 PMCID: PMC7683586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 10/15/2020] [Indexed: 09/18/2023]
Abstract
An unprecedented worldwide spread of the SARS-CoV-2 has imposed severe challenges on healthcare facilities and medical infrastructure. The global research community faces urgent calls for the development of rapid diagnostic tools, effective treatment protocols, and most importantly, vaccines against the pathogen. Pooling together expertise across broad domains to innovate effective solutions is the need of the hour. With these requirements in mind, in this review, we provide detailed critical accounts on the leading efforts at developing diagnostics tools, therapeutic agents, and vaccine candidates. Importantly, we furnish the reader with a multidisciplinary perspective on how conventional methods like serology and RT-PCR, as well as cutting-edge technologies like CRISPR/Cas and artificial intelligence/machine learning, are being employed to inform and guide such investigations. We expect this narrative to serve a broad audience of both active and aspiring researchers in the field of biomedical sciences and engineering and help inspire radical new approaches towards effective detection, treatment, and prevention of this global pandemic.
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Affiliation(s)
- M Sreepadmanabh
- Molecular Virology Laboratory, Indian Institute of Science Education and Research, Bhopal, India
| | - Amit Kumar Sahu
- Molecular Virology Laboratory, Indian Institute of Science Education and Research, Bhopal, India
| | - Ajit Chande
- Molecular Virology Laboratory, Indian Institute of Science Education and Research, Bhopal, India
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