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Majrashi TA, El Hassab MA, Mahmoud SH, Mostafa A, Wahsh EA, Elkaeed EB, Hassan FE, Eldehna WM, Abdelgawad SM. In vitro biological evaluation and in silico insights into the antiviral activity of standardized olive leaves extract against SARS-CoV-2. PLoS One 2024; 19:e0301086. [PMID: 38662719 PMCID: PMC11045091 DOI: 10.1371/journal.pone.0301086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Accepted: 03/08/2024] [Indexed: 04/28/2024] Open
Abstract
There is still a great global need for efficient treatments for the management of SARS-CoV-2 illness notwithstanding the availability and efficacy of COVID-19 vaccinations. Olive leaf is an herbal remedy with a potential antiviral activity that could improve the recovery of COVID-19 patients. In this work, the olive leaves major metabolites were screened in silico for their activity against SARS-CoV-2 by molecular docking on several viral targets such as methyl transferase, helicase, Plpro, Mpro, and RdRp. The results of in silico docking study showed that olive leaves phytoconstituents exhibited strong potential antiviral activity against SARS-CoV-2 selected targets. Verbacoside demonstrated a strong inhibition against methyl transferase, helicase, Plpro, Mpro, and RdRp (docking scores = -17.2, -20, -18.2, -19.8, and -21.7 kcal/mol.) respectively. Oleuropein inhibited 5rmm, Mpro, and RdRp (docking scores = -15, -16.6 and -18.6 kcal/mol., respectively) respectively. Apigenin-7-O-glucoside exhibited activity against methyl transferase and RdRp (docking score = -16.1 and -19.4 kcal/mol., respectively) while Luteolin-7-O-glucoside inhibited Plpro and RdRp (docking score = -15.2 and -20 kcal/mol., respectively). The in vitro antiviral assay was carried out on standardized olive leaf extract (SOLE) containing 20% oleuropein and IC50 was calculated. The results revealed that 20% SOLE demonstrated a moderate antiviral activity against SARS-CoV-2 with IC50 of 118.3 μg /mL. Accordingly, olive leaf could be a potential herbal therapy against SARS-CoV-2 but more in vivo and clinical investigations are recommended.
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Affiliation(s)
- Taghreed A. Majrashi
- Department of Pharmacognosy, College of Pharmacy, King Khalid University, Asir, Saudi Arabia
| | - Mahmoud A. El Hassab
- Department of Medicinal Chemistry, Faculty of Pharmacy, King Salman International University (KSIU), South Sinai, Egypt
| | - Sara H. Mahmoud
- Center of Scientific Excellence for Influenza Viruses, National Research Centre, Giza, Egypt
| | - Ahmed Mostafa
- Center of Scientific Excellence for Influenza Viruses, National Research Centre, Giza, Egypt
| | - Engy A. Wahsh
- Clinical Pharmacy Department, Faculty of Pharmacy, October 6 University, Giza Governorate, Egypt
| | - Eslam B. Elkaeed
- Department of Pharmaceutical Sciences, College of Pharmacy, AlMaarefa University, Riyadh, Saudi Arabia
| | - Fatma E. Hassan
- Department of Physiology, General Medicine Practice Program, Batterjee Medical College, Jeddah, Saudi Arabia
- Medical Physiology Department, Kasr Alainy, Faculty of Medicine, Cairo University, Giza, Egypt
| | - Wagdy M. Eldehna
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh, Egypt
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Zaidi AK, Singh RB, A A Rizvi S, Dehgani-Mobaraki P, Palladino N. COVID-19 pathogenesis. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024; 202:67-112. [PMID: 38237991 DOI: 10.1016/bs.pmbts.2023.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2024]
Abstract
The pathogenesis of COVID-19 involves a complex interplay between host factors and the SARS-CoV-2 virus, leading to a multitude of clinical manifestations beyond the respiratory system. This chapter provides an overview of the risk factors, genetic predisposition, and multisystem manifestations of COVID-19, shedding light on the underlying mechanisms that contribute to extrapulmonary manifestations. The chapter discusses the direct invasion of SARS-CoV-2 into various organs as well as the indirect mechanisms such as dysregulation of the renin-angiotensin-aldosterone system (RAAS), immune response dysfunctions within the innate and adaptive immune systems, endothelial damage, and immunothrombosis. Furthermore, the multisystem manifestations of COVID-19 across different organ systems, including the cardiovascular, renal, gastrointestinal, hepatobiliary, nervous, endocrine and metabolic, ophthalmic, ear-nose-throat, reproductive, hematopoietic, and immune systems are discussed in detail. Each system exhibits unique manifestations that contribute to the complexity of the disease.
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Affiliation(s)
| | - Rohan Bir Singh
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, United States; Department of Population, Policy and Practice, Greater Ormond Street Institute of Child Health, University College London, United Kingdom; Discipline of Ophthalmology and Visual Sciences, Adelaide Medical School, University of Adelaide, Australia
| | - Syed A A Rizvi
- College of Biomedical Sciences, Larkin University, Miami, Florida, United States.
| | - Puya Dehgani-Mobaraki
- Founder and President, Associazione Naso Sano, Ringgold Institution ID 567754, San Mariano, Italy.
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Chan LC, Mat Yassim AS, Ahmad Fuaad AAH, Leow TC, Sabri S, Radin Yahaya RS, Abu Bakar AMS. Inhibition of SARS-CoV-2 3CL protease by the anti-viral chimeric protein RetroMAD1. Sci Rep 2023; 13:20178. [PMID: 37978223 PMCID: PMC10656507 DOI: 10.1038/s41598-023-47511-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 11/14/2023] [Indexed: 11/19/2023] Open
Abstract
COVID-19 results from SARS-CoV-2, which mutates frequently, challenging current treatments. Therefore, it is critical to develop new therapeutic drugs against this disease. This study explores the interaction between SARS-CoV-2 3CLpro and RetroMAD1, a well-characterized coronavirus protein and potential drug target, using in-silico methods. The analysis through the HDOCK server showed stable complex formation with a binding energy of -12.3, the lowest among reference drugs. The RetroMAD1-3CLpro complex underwent a 100 ns molecular dynamics simulation (MDS) in an explicit solvation system, generating various trajectories, including RMSD, RMSF, hydrogen bonding, radius of gyration, and ligand binding energy. MDS results confirmed intact interactions within the RetroMAD1-3CLpro complex during simulations. In vitro experiments validated RetroMAD1's ability to inhibit 3CLpro enzyme activity and prevent SARS-CoV-2 infection in human bronchial cells. RetroMAD1 exhibited antiviral efficacy comparable to Remdesivir without cytotoxicity at effective concentrations. These results suggest RetroMAD1 as a potential drug candidate against SARS-CoV-2, warranting further in vivo and clinical studies to assess its efficiency.
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Affiliation(s)
- Lee-Chin Chan
- Biovalence Sdn. Bhd., 22, Jalan SS 25/34, Taman Mayang, 47301, Petaling Jaya, Selangor, Malaysia
- Biovalence Technologies Pte. Ltd., #06-307 The Plaza, 7500A Beach Road, Singapore, 199591, Singapore
| | - Aini Syahida Mat Yassim
- Biovalence Sdn. Bhd., 22, Jalan SS 25/34, Taman Mayang, 47301, Petaling Jaya, Selangor, Malaysia.
- Biovalence Technologies Pte. Ltd., #06-307 The Plaza, 7500A Beach Road, Singapore, 199591, Singapore.
- School of Health Science, Universiti Sains Malaysia, 16150 Kubang Kerian, Kelantan, Malaysia.
| | - Abdullah Al Hadi Ahmad Fuaad
- Centre of Fundamental and Frontier Sciences in Self-Assembly (FSSA), Department of Chemistry, Faculty of Science, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
| | - Thean Chor Leow
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
- Enzyme and Microbial Technology Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
- Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Suriana Sabri
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
- Enzyme and Microbial Technology Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Radin Shafierul Radin Yahaya
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Awang Muhammad Sagaf Abu Bakar
- Jabatan Perkhidmatan Veterinar Sabah, Aras 3, Blok B, Wisma Pertanian Sabah, Jalan Tasik, Luyang (Off Jln Maktab Gaya), Beg Berkunci 2051, 88999, Kota Kinabalu, Sabah, Malaysia.
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Wildner G, Tucci AR, Prestes ADS, Muller T, Rosa ADS, Borba NRR, Ferreira VN, Rocha JBT, Miranda MD, Barbosa NV. Ebselen and Diphenyl Diselenide Inhibit SARS-CoV-2 Replication at Non-Toxic Concentrations to Human Cell Lines. Vaccines (Basel) 2023; 11:1222. [PMID: 37515038 PMCID: PMC10384302 DOI: 10.3390/vaccines11071222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 06/18/2023] [Accepted: 06/25/2023] [Indexed: 07/30/2023] Open
Abstract
The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was the causative agent of the COVID-19 pandemic, a global public health problem. Despite the numerous studies for drug repurposing, there are only two FDA-approved antiviral agents (Remdesivir and Nirmatrelvir) for non-hospitalized patients with mild-to-moderate COVID-19 symptoms. Consequently, it is pivotal to search for new molecules with anti-SARS-CoV-2 activity and to study their effects in the human immune system. Ebselen (Eb) is an organoselenium compound that is safe for humans and has antioxidant, anti-inflammatory, and antimicrobial properties. Diphenyl diselenide ((PhSe)2) shares several pharmacological properties with Eb and is of low toxicity to mammals. Herein, we investigated Eb and (PhSe)2 anti-SARS-CoV-2 activity in a human pneumocytes cell model (Calu-3) and analyzed their toxic effects on human peripheral blood mononuclear cells (PBMCs). Both compounds significantly inhibited the SARS-CoV-2 replication in Calu-3 cells. The EC50 values for Eb and (PhSe)2 after 24 h post-infection (hpi) were 3.8 µM and 3.9 µM, respectively, and after 48 hpi were 2.6 µM and 3.4 µM. These concentrations are safe for non-infected cells, since the CC50 values found for Eb and (PhSe)2 on Calu-3 were greater than 200 µM. Importantly, the concentration rates tested on viral replication were not toxic to human PBMCs. Therefore, our findings reinforce the efficacy of Eb and demonstrate (PhSe)2 as a new candidate to be tested in future trials against SARS-CoV-2 infection/inflammation conditions.
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Affiliation(s)
- Guilherme Wildner
- Programa de Pós-Graduação em Bioquímica Toxicológica, Universidade Federal de Santa Maria, Santa Maria 97105-900, RS, Brazil
| | - Amanda Resende Tucci
- Laboratório de Morfologia e Morfogênese Viral, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21041-250, RJ, Brazil
- Programa de Pós-Graduação em Biologia Celular e Molecular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21041-250, RJ, Brazil
| | - Alessandro de Souza Prestes
- Programa de Pós-Graduação em Bioquímica Toxicológica, Universidade Federal de Santa Maria, Santa Maria 97105-900, RS, Brazil
| | - Talise Muller
- Programa de Pós-Graduação em Bioquímica Toxicológica, Universidade Federal de Santa Maria, Santa Maria 97105-900, RS, Brazil
| | - Alice Dos Santos Rosa
- Laboratório de Morfologia e Morfogênese Viral, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21041-250, RJ, Brazil
- Programa de Pós-Graduação em Biologia Celular e Molecular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21041-250, RJ, Brazil
| | - Nathalia Roberto R Borba
- Laboratório de Morfologia e Morfogênese Viral, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21041-250, RJ, Brazil
| | - Vivian Neuza Ferreira
- Laboratório de Morfologia e Morfogênese Viral, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21041-250, RJ, Brazil
| | - João Batista Teixeira Rocha
- Programa de Pós-Graduação em Bioquímica Toxicológica, Universidade Federal de Santa Maria, Santa Maria 97105-900, RS, Brazil
| | - Milene Dias Miranda
- Laboratório de Morfologia e Morfogênese Viral, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21041-250, RJ, Brazil
- Programa de Pós-Graduação em Biologia Celular e Molecular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21041-250, RJ, Brazil
| | - Nilda Vargas Barbosa
- Programa de Pós-Graduação em Bioquímica Toxicológica, Universidade Federal de Santa Maria, Santa Maria 97105-900, RS, Brazil
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Rungruangmaitree R, Phoochaijaroen S, Chimprasit A, Saparpakorn P, Pootanakit K, Tanramluk D. Structural analysis of the coronavirus main protease for the design of pan-variant inhibitors. Sci Rep 2023; 13:7055. [PMID: 37120654 PMCID: PMC10148699 DOI: 10.1038/s41598-023-34305-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 04/27/2023] [Indexed: 05/01/2023] Open
Abstract
With the rapid rate of SARS-CoV-2 Main protease (Mpro) structures deposition, a computational method that can combine all the useful structural features becomes crucial. This research focuses on the frequently occurring atoms and residues to find a generalized strategy for inhibitor design given a large amount of protein complexes from SARS-CoV in contrast to SARS-CoV-2 Mpro. By superposing large numbers of the ligands onto the protein template and grid box, we can analyse which part of the structure is conserved from position-specific interaction for both data sets for the development of pan-Mpro antiviral design. The difference in conserved recognition sites from the crystal structures can be used to determine specificity determining residues for designing selective drugs. We can display pictures of the imaginary shape of the ligand by unionising all atoms from the ligand. We also pinpoint the most probable atom adjustments to imitate the frequently found densities from the ligand atoms statistics. With molecular docking, Molecular Dynamics simulation, and MM-PBSA methods, a carbonyl replacement at the nitrile warhead (N5) of Paxlovid's Nirmatrelvir (PF-07321332) was suggested. By gaining insights into the selectivity and promiscuity regions for proteins and ligands, crucial residues are highlighted, and the antiviral design strategies are proposed.
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Affiliation(s)
| | - Sakao Phoochaijaroen
- Integrative Computational BioScience (ICBS) Center, Mahidol University, Salaya, Nakhon Pathom, 73170, Thailand
| | - Aunlika Chimprasit
- Department of Chemistry, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand
| | - Patchreenart Saparpakorn
- Department of Chemistry, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand
| | - Kusol Pootanakit
- Institute of Molecular Biosciences, Mahidol University, Salaya, Nakhon Pathom, 73170, Thailand
| | - Duangrudee Tanramluk
- Institute of Molecular Biosciences, Mahidol University, Salaya, Nakhon Pathom, 73170, Thailand.
- Integrative Computational BioScience (ICBS) Center, Mahidol University, Salaya, Nakhon Pathom, 73170, Thailand.
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6
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Ouyang Y, Chen Y, Shang J, Sun S, Wang X, Huan S, Xiong B, Zhang XB. Virus-like Plasmonic Nanoprobes for Quick Analysis of Antiviral Efficacy and Mutation-Induced Drug Resistance. Anal Chem 2023; 95:5009-5017. [PMID: 36893130 DOI: 10.1021/acs.analchem.2c05464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/10/2023]
Abstract
As the pathogenic viruses and the variants of concern greatly threaten human health and global public safety, the development of convenient and robust strategies enabling rapid analysis of antiviral drug efficacy and mutation-induced resistance is quite important to prevent the spread of human epidemics. Herein, we introduce a simple single-particle detection strategy for quick analysis of anti-infective drugs against SARS-CoV-2 and mutation-induced drug resistance, by using the wild-type and mutant spike protein-functionalized AuNPs as virus-like plasmonic nanoprobes. Both the wild-type and mutant virus-like plasmonic nanoprobes can form core-satellite nanoassemblies with the ACE2@AuNPs, providing the opportunity to detect the drug efficacy and mutation-induced resistance by detecting the changes of nanoassemblies upon drug treatment with dark-field microscopy. As a demonstration, we applied the single-particle detection strategy for quantitative determination of antiviral efficacy and mutation-induced resistance of ceftazidime and rhein. The mutations in the receptor-binding domain of Omicron variant could lead to an increase of EC50 values of ceftazidime and rhein, formerly from 49 and 57 μM against wild-type SARS-CoV-2, to 121 and 340 μM, respectively. The mutation-induced remarkable decline in the inhibitory efficacy of drugs was validated with molecule docking analysis and virus-like plasmonic nanoprobe-based cell-incubation assay. Due to the generality and feasibility of the strategy for the preparation of virus-like plasmonic nanoprobes and single-particle detection, we anticipated that this simple and robust method is promising for the discovery and efficacy evaluation of anti-infective drugs against different pathogenic viruses.
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Affiliation(s)
- Yuzhi Ouyang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Yancao Chen
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Jinhui Shang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Shijie Sun
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Xiangbin Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Shuangyan Huan
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Bin Xiong
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Xiao-Bing Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
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7
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Leitzke M. Is the post-COVID-19 syndrome a severe impairment of acetylcholine-orchestrated neuromodulation that responds to nicotine administration? Bioelectron Med 2023; 9:2. [PMID: 36650574 PMCID: PMC9845100 DOI: 10.1186/s42234-023-00104-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 12/30/2022] [Indexed: 01/19/2023] Open
Abstract
Following a SARS-CoV-2 infection, many individuals suffer from post-COVID-19 syndrome. It makes them unable to proceed with common everyday activities due to weakness, memory lapses, pain, dyspnea and other unspecific physical complaints. Several investigators could demonstrate that the SARS-CoV-2 related spike glycoprotein (SGP) attaches not only to ACE-2 receptors but also shows DNA sections highly affine to nicotinic acetylcholine receptors (nAChRs). The nAChR is the principal structure of cholinergic neuromodulation and is responsible for coordinated neuronal network interaction. Non-intrinsic viral nAChR attachment compromises integrative interneuronal communication substantially. This explains the cognitive, neuromuscular and mood impairment, as well as the vegetative symptoms, characterizing post-COVID-19 syndrome. The agonist ligand nicotine shows an up to 30-fold higher affinity to nACHRs than acetylcholine (ACh). We therefore hypothesize that this molecule could displace the virus from nAChR attachment and pave the way for unimpaired cholinergic signal transmission. Treating several individuals suffering from post-COVID-19 syndrome with a nicotine patch application, we witnessed improvements ranging from immediate and substantial to complete remission in a matter of days.
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Affiliation(s)
- Marco Leitzke
- Department of Anesthesiology, Helios Clinics, Colditzer Straße 48, 04703, Leisnig, Germany.
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8
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Kim H, Hauner D, Laureanti JA, Agustin K, Raugei S, Kumar N. Mechanistic investigation of SARS-CoV-2 main protease to accelerate design of covalent inhibitors. Sci Rep 2022; 12:21037. [PMID: 36470873 PMCID: PMC9722715 DOI: 10.1038/s41598-022-23570-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 11/02/2022] [Indexed: 12/12/2022] Open
Abstract
Targeted covalent inhibition represents one possible strategy to block the function of SARS-CoV-2 Main Protease (MPRO), an enzyme that plays a critical role in the replication of the novel SARS-CoV-2. Toward the design of covalent inhibitors, we built a covalent inhibitor dataset using deep learning models followed by high throughput virtual screening of these candidates against MPRO. Two top-ranking inhibitors were selected for mechanistic investigations-one with an activated ester warhead that has a piperazine core and the other with an acrylamide warhead. Specifically, we performed a detailed analysis of the free energetics of covalent inhibition by hybrid quantum mechanics/molecular mechanics simulations. Cleavage of a fragment of the non-structured protein (NSP) from the SARS-CoV-2 genome was also simulated for reference. Simulations show that both candidates form more stable enzyme-inhibitor (E-I) complexes than the chosen NSP. It was found that both the NSP fragment and the activated ester inhibitor react with CYS145 of MPRO in a concerted manner, whereas the acrylamide inhibitor follows a stepwise mechanism. Most importantly, the reversible reaction and the subsequent hydrolysis reaction from E-I complexes are less probable when compared to the reactions with an NSP fragment, showing promise for these candidates to be the base for efficient MPRO inhibitors.
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Affiliation(s)
- Hoshin Kim
- grid.451303.00000 0001 2218 3491Physical and Computational Science Directorate, Pacific Northwest National Laboratory, Richland, WA 99352 USA
| | - Darin Hauner
- grid.451303.00000 0001 2218 3491Earth and Biological Science Directorate, Pacific Northwest National Laboratory, Richland, WA 99352 USA
| | - Joseph A. Laureanti
- grid.451303.00000 0001 2218 3491Physical and Computational Science Directorate, Pacific Northwest National Laboratory, Richland, WA 99352 USA
| | - Kruel Agustin
- grid.451303.00000 0001 2218 3491Earth and Biological Science Directorate, Pacific Northwest National Laboratory, Richland, WA 99352 USA
| | - Simone Raugei
- grid.451303.00000 0001 2218 3491Physical and Computational Science Directorate, Pacific Northwest National Laboratory, Richland, WA 99352 USA
| | - Neeraj Kumar
- grid.451303.00000 0001 2218 3491Earth and Biological Science Directorate, Pacific Northwest National Laboratory, Richland, WA 99352 USA
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Efficacy of Dexamethasone and Methylprednisolone in Hospitalization Outcomes of COVID-19 Patients: A Comparative Retrospective Study. ARCHIVES OF CLINICAL INFECTIOUS DISEASES 2022. [DOI: 10.5812/archcid-129727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Background: Control of the COVID-19 pandemic, its treatment, and prevention of mortality and morbidity have been the main focus of researchers over the past two years. Due to disagreement on the usefulness of different corticosteroids in the treatment of COVID-19, this work compared the efficacy of dexamethasone and methylprednisolone in the treatment outcomes of intensive critical care (ICU) patients. Methods: The present retrospective cohort study examined clinical records of 105 COVID-19 patients hospitalized in the ICUs of Firoozabadi Hospital in 2021. Clinical outcomes, including the length of hospital stay, the need for a ventilator, and mortality, were compared between patients who received either dexamethasone (DXM) or methylprednisolone (MP). Data were analyzed by SPSS V.20 software at P < 0.05 as statistical significance. Results: The mean ± SD ages of the patients in the DXM and MP groups were 58.82 ± 19.29 and 60.66 ± 14.17 years, respectively, without a statistically significant difference (P > 0.05). The mean duration of hospitalization was 8.14 ± 4.36 days in the DXM group and 6.80 ± 3.34 days in the MP group (P = 0.295). Also, 19 (33.3%) cases in the DXM group an, 19 (39.6%) in the MP group needed mechanical ventilation during hospitalization (P = 0.546). Finally, 30 (52.6%) patients in the DXM group and 27 (56.2%) in the MP group died. Conclusions: The findings indicated no significant difference in the mean duration of hospitalization, the need for a ventilator, and mortality in COVID-19 ICU patients treated with methylprednisolone or dexamethasone. There is a need to perform meta-analyses owing to conflicting results regarding the effects of different corticosteroids on the COVID-19 course.
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Delgado CP, Rocha JBT, Orian L, Bortoli M, Nogara PA. In silico studies of M pro and PL pro from SARS-CoV-2 and a new class of cephalosporin drugs containing 1,2,4-thiadiazole. Struct Chem 2022; 33:2205-2220. [PMID: 36106095 PMCID: PMC9463509 DOI: 10.1007/s11224-022-02036-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 08/09/2022] [Indexed: 11/29/2022]
Abstract
The SARS-CoV-2 proteases Mpro and PLpro are important targets for the development of antivirals against COVID-19. The functional group 1,2,4-thiadiazole has been indicated to inhibit cysteinyl proteases, such as papain and cathepsins. Of note, the 1,2,4-thiadiazole moiety is found in a new class of cephalosporin FDA-approved antibiotics: ceftaroline fosamil, ceftobiprole, and ceftobiprole medocaril. Here we investigated the interaction of these new antibiotics and their main metabolites with the SARS-CoV-2 proteases by molecular docking, molecular dynamics (MD), and density functional theory (DFT) calculations. Our results indicated the PLpro enzyme as a better in silico target for the new antibacterial cephalosporins. The results with ceftaroline fosamil and the dephosphorylate metabolite compounds should be tested as potential inhibitor of PLpro, Mpro, and SARS-CoV-2 replication in vitro. In addition, the data here reported can help in the design of new potential drugs against COVID-19 by exploiting the S atom reactivity in the 1,2,4-thiadiazole moiety. Supplementary Information The online version contains supplementary material available at 10.1007/s11224-022-02036-5.
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Affiliation(s)
- Cássia Pereira Delgado
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Santa Maria (UFSM), Santa Maria, RS 97105-900 Brazil
| | - João Batista Teixeira Rocha
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Santa Maria (UFSM), Santa Maria, RS 97105-900 Brazil
| | - Laura Orian
- Dipartimento di Scuenze Chimiche, Università degli Studi di Padova, Via Marzolo 1, 35131 Padua, Italy
| | - Marco Bortoli
- Institut de Química Computacionali Catàlisi (IQCC), Departament de Química, Facultat de Ciències, Universitat de Girona, C/M. A. Capmany 69, 17003 Girona, Spain
| | - Pablo Andrei Nogara
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Santa Maria (UFSM), Santa Maria, RS 97105-900 Brazil
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Fath MK, Naderi M, Hamzavi H, Ganji M, Shabani S, Ghahroodi FN, Khalesi B, Pourzardosht N, Hashemi ZS, Khalili S. Molecular mechanisms and therapeutic effects of different vitamins and minerals in COVID-19 patients. J Trace Elem Med Biol 2022; 73:127044. [PMID: 35901669 PMCID: PMC9297660 DOI: 10.1016/j.jtemb.2022.127044] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 07/10/2022] [Accepted: 07/18/2022] [Indexed: 12/12/2022]
Abstract
COVID-19 is a rapidly spreading disease, which has caught the world by surprise. Millions of people suffer from illness, and the mortality rates are dramatically high. Currently, there is no specific and immediate treatment for this disease. Remedies are limited to supportive regiments and few antiviral and anti-inflammatory drugs. The lack of a definite cure for COVID-19 is the reason behind its high mortality and global prevalence. COVID-19 can lead to a critical illness with severe respiratory distress and cytokine release. Increased oxidative stress and excessive production of inflammatory cytokines are vital components of severe COVID-19. Micronutrients, metalloids, and vitamins such as iron, manganese, selenium, Zinc, Copper, vitamin A, B family, and C are among the essential and trace elements that play a pivotal role in human nutrition and health. They participate in metabolic processes that lead to energy production. In addition, they support immune functions and act as antioxidants. Therefore, maintaining an optimal level of micronutrients intake, particularly those with antioxidant activities, is essential to fight against oxidative stress, modulate inflammation, and boost the immune system. Therefore, these factors could play a crucial role in COVID-19 prevention and treatment. In this review, we aimed to summarize antiviral properties of different vitamins and minerals. Moreover, we will investigate the correlation between them and their effects in COVID-19 patients.
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Affiliation(s)
- Mohsen Karami Fath
- Department of Cellular and Molecular Biology, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran
| | - Malihe Naderi
- Department of Microbiology and Microbial Biotechnology, Faculty of life Science and Biotechnology, Shahid Beheshti University, Tehran, Iran; Infectious Diseases Research Center, Golestan University of Medical Sciences, Gorgan, Iran
| | - Hosna Hamzavi
- Department of Biology, Shahed University, Tehran, Iran
| | - Mahmoud Ganji
- Department of Medical Biotechnology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Shima Shabani
- Department of Medical Biotechnology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Faezeh Noorabad Ghahroodi
- Department of Clinical Biochemistry, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Bahman Khalesi
- Department of Research and Production of Poultry Viral Vaccine, Razi Vaccine and Serum Research Institute, Agricultural Research Education and Extension Organization, Karaj, Iran
| | - Navid Pourzardosht
- Biochemistry Department, Guilan University of Medical Sciences, Rasht, Iran
| | - Zahra Sadat Hashemi
- ATMP Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran. Iran.
| | - Saeed Khalili
- Department of Biology Sciences, Shahid Rajaee Teacher Training University, Tehran, Iran.
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12
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Chen F, Liu Q, Xiong Y, Xu L. Nucleic acid strategies for infectious disease treatments: The nanoparticle-based oral delivery route. Front Pharmacol 2022; 13:984981. [PMID: 36105233 PMCID: PMC9465296 DOI: 10.3389/fphar.2022.984981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 08/08/2022] [Indexed: 11/13/2022] Open
Abstract
Therapies based on orally administrated nucleic acids have significant potential for the treatment of infectious diseases, including chronic inflammatory diseases such as inflammatory bowel disease (IBD)-associated with the gastrointestinal (GI) tract, and infectious and acute contagious diseases like coronavirus disease 2019 (COVID-19). This is because nucleic acids could precisely regulate susceptibility genes in regulating the pro- and anti-inflammatory cytokines expression related to the infections. Unfortunately, gene delivery remains a major hurdle due to multiple intracellular and extracellular barriers. This review thoroughly discusses the challenges of nanoparticle-based nucleic acid gene deliveries and strategies for overcoming delivery barriers to the inflammatory sites. Oral nucleic acid delivery case studies were also present as vital examples of applications in infectious diseases such as IBD and COVID-19.
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Affiliation(s)
- Fengqian Chen
- Translational Research Program, Department of Anesthesiology and Center for Shock Trauma Anesthesiology Research, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Qi Liu
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Yang Xiong
- College of Pharmaceutical Science, Zhejiang Chinese Medical University, Hangzhou, China
| | - Li Xu
- Department of Anorectal Surgery, the First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, China
- *Correspondence: Li Xu,
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13
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Deroubaix A, Kramvis A. Imaging Techniques: Essential Tools for the Study of SARS-CoV-2 Infection. Front Cell Infect Microbiol 2022; 12:794264. [PMID: 35937687 PMCID: PMC9355083 DOI: 10.3389/fcimb.2022.794264] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 06/21/2022] [Indexed: 01/08/2023] Open
Abstract
The world has seen the emergence of a new virus in 2019, SARS-CoV-2, causing the COVID-19 pandemic and millions of deaths worldwide. Microscopy can be much more informative than conventional detection methods such as RT-PCR. This review aims to present the up-to-date microscopy observations in patients, the in vitro studies of the virus and viral proteins and their interaction with their host, discuss the microscopy techniques for detection and study of SARS-CoV-2, and summarize the reagents used for SARS-CoV-2 detection. From basic fluorescence microscopy to high resolution techniques and combined technologies, this article shows the power and the potential of microscopy techniques, especially in the field of virology.
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Affiliation(s)
- Aurélie Deroubaix
- Hepatitis Virus Diversity Research Unit, Department of Internal Medicine, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Life Sciences Imaging Facility, University of the Witwatersrand, Johannesburg, South Africa
| | - Anna Kramvis
- Hepatitis Virus Diversity Research Unit, Department of Internal Medicine, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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14
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Abdizadeh R, Hadizadeh F, Abdizadeh T. Evaluation of apigenin-based biflavonoid derivatives as potential therapeutic agents against viral protease (3CLpro) of SARS-CoV-2 via molecular docking, molecular dynamics and quantum mechanics studies. J Biomol Struct Dyn 2022:1-31. [PMID: 35848354 DOI: 10.1080/07391102.2022.2098821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is the causative agent of the pandemic COVID-19 disease that affects human respiratory function. Despite the scientific progression made in the development of the vaccine, there is an urgent need for the discovery of antiviral drugs for better performance at different stages of SARS-CoV-2 reproduction. The main protease (Mpro or 3CLpro) plays a pivotal role in the life cycle of the virus, making it an attractive target for the development of antiviral agents effective against the new strains of coronaviruses (CoVs). In this study, a series of apigenin-based natural biflavonoid derivatives as potential inhibitors of coronaviruses 3CLpro was investigated by in silico approaches. For this purpose, the molecular docking was performed to analyze the interaction of the natural biflavonoids with SARS-Cov-2 main protease and for further investigation, docking to the 3CLpro of SARS-CoV and MERS-CoV. Based on docking scores and comparison with the reference inhibitors (ritonavir and lopinavir), more than half of the biflavonoids had strong interactions with the residues of the binding pocket of the coronaviruses 3CLpro and exhibited better binding affinities toward the main protease than ritonavir and lopinavir. The top biflavonoids were further explored through molecular dynamics simulation, binding free energy calculation and residual energy contributions estimated by the MM-PBSA. Also, drug likeness property investigation by Swiss ADME tools and density functional theory (DFT) calculations were performed. The results confirmed that the 3CLpro-amentoflavone, 3CLpro-bilobetin, 3CLpro-ginkgetin, and 3CLpro-sotetsuflavone complexes possess a large amount of dynamic properties such as high stability, significant binding energy and fewer conformation fluctuations. Also, the pharmacokinetics and drug-likeness studies and HOMO-LUMO and DFT descriptor values indicated a promising result of the selected natural biflavonoids. Overall findings indicate that the apigenin-based biflavonoids may inhibit COVID-19 by significant interactions in the binding pocket and those results can pave the way in drug discovery although the effectiveness of these bioactive compounds should be further validated by in-vitro and in-vivo investigations. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Rahman Abdizadeh
- Department of Medical Parasitology and Mycology, Faculty of Medicine, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Farzin Hadizadeh
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Tooba Abdizadeh
- Clinical Biochemistry Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
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15
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Popoola TD, Segun PA, Ekuadzi E, Dickson RA, Awotona OR, Nahar L, Sarker SD, Fatokun AA. West African medicinal plants and their constituent compounds as treatments for viral infections, including SARS-CoV-2/COVID-19. Daru 2022; 30:191-210. [PMID: 35476297 PMCID: PMC9043090 DOI: 10.1007/s40199-022-00437-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 02/16/2022] [Indexed: 12/13/2022] Open
Abstract
OBJECTIVES The recent emergence of the COVID-19 pandemic (caused by SARS-CoV-2) and the experience of its unprecedented alarming toll on humanity have shone a fresh spotlight on the weakness of global preparedness for pandemics, significant health inequalities, and the fragility of healthcare systems in certain regions of the world. It is imperative to identify effective drug treatments for COVID-19. Therefore, the objective of this review is to present a unique and contextualised collection of antiviral natural plants or remedies from the West African sub-region as existing or potential treatments for viral infections, including COVID-19, with emphasis on their mechanisms of action. EVIDENCE ACQUISITION Evidence was synthesised from the literature using appropriate keywords as search terms within scientific databases such as Scopus, PubMed, Web of Science and Google Scholar. RESULTS While some vaccines and small-molecule drugs are now available to combat COVID-19, access to these therapeutic entities in many countries is still quite limited. In addition, significant aspects of the symptomatology, pathophysiology and long-term prognosis of the infection yet remain unknown. The existing therapeutic armamentarium, therefore, requires significant expansion. There is evidence that natural products with antiviral effects have been used in successfully managing COVID-19 symptoms and could be developed as anti-COVID-19 agents which act through host- and virus-based molecular targets. CONCLUSION Natural products could be successfully exploited for treating viral infections/diseases, including COVID-19. Strengthening natural products research capacity in developing countries is, therefore, a key strategy for reducing health inequalities, improving global health, and enhancing preparedness for future pandemics.
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Affiliation(s)
- Temidayo D Popoola
- Centre for Natural Products Discovery (CNPD), School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, James Parsons Building, Byrom Street, Liverpool, L3 3AF, UK
| | - Peter A Segun
- Department of Pharmacognosy, Faculty of Pharmacy, Olabisi Onabanjo University, Ogun State, Sagamu Campus, Nigeria
| | - Edmund Ekuadzi
- Department of Pharmacognosy, Faculty of Pharmacy and Pharmaceutical Sciences, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Rita A Dickson
- Department of Pharmacognosy, Faculty of Pharmacy and Pharmaceutical Sciences, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Olanrewaju R Awotona
- Department of Pharmacy and Pharmaceutical Sciences, College of Health Sciences, Legacy University, No. 55, Kairaba Avenue, Fajara, Banjul, The Gambia
| | - Lutfun Nahar
- Laboratory of Growth Regulators, Institute of Experimental Botany, ASCR & Palacký University, Šlechtitelů 27, 78371, Olomouc, Czech Republic
| | - Satyajit D Sarker
- Centre for Natural Products Discovery (CNPD), School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, James Parsons Building, Byrom Street, Liverpool, L3 3AF, UK
| | - Amos A Fatokun
- Centre for Natural Products Discovery (CNPD), School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, James Parsons Building, Byrom Street, Liverpool, L3 3AF, UK.
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16
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Kumar S, Paul P, Yadav P, Kaul R, Maitra SS, Jha SK, Chaari A. A multi-targeted approach to identify potential flavonoids against three targets in the SARS-CoV-2 life cycle. Comput Biol Med 2022; 142:105231. [PMID: 35032740 PMCID: PMC8750703 DOI: 10.1016/j.compbiomed.2022.105231] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 01/08/2022] [Accepted: 01/08/2022] [Indexed: 02/07/2023]
Abstract
The advent and persistence of the Severe Acute Respiratory Syndrome Coronavirus - 2 (SARS-CoV-2)-induced Coronavirus Disease (COVID-19) pandemic since December 2019 has created the largest public health emergency in over a century. Despite the administration of multiple vaccines across the globe, there continues to be a lack of approved efficacious non-prophylactic interventions for the disease. Flavonoids are a class of phytochemicals with historically established antiviral, anti-inflammatory and antioxidative properties that are effective against cancers, type 2 diabetes mellitus, and even other human coronaviruses. To identify the most promising bioactive flavonoids against the SARS-CoV-2, this article screened a virtual library of 46 bioactive flavonoids against three promising targets in the SARS-CoV-2 life cycle: human TMPRSS2 protein, 3CLpro, and PLpro. By examining the effects of glycosylation and other structural-activity relationships, the presence of sugar moiety in flavonoids significantly reduces its binding energy. It increases the solubility of flavonoids leading to reduced toxicity and higher bioavailability. Through protein-ligand contact profiling, it was concluded that naringin formed more hydrogen bonds with TMPRSS2 and 3CLpro. In contrast, hesperidin formed a more significant number of hydrogen bonds with PLpro. These observations were complimented by the 100 ns molecular dynamics simulation and binding free energy analysis, which showed a considerable stability of docked bioflavonoids in the active site of SARS-CoV-2 target proteins. Finally, the binding affinity and stability of the selected docked complexes were compared with the reference ligands (camostat for TMPRSS2, GC376 for 3CLpro, and GRL0617 for PLpro) that strongly inhibit their respective SARS-COV-2 targets. Overall analysis revealed that the selected flavonoids could be potential therapeutic agents against SARS-CoV-2. Naringin showed better affinity and stability for TMPRSS2 and 3CLpro, whereas hesperidin showed a better binding relationship and stability for PLpro.
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Affiliation(s)
- Sanjay Kumar
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067, India; Center for Bioinformatics, Computational and Systems Biology, Pathfinder Research and Training Foundation, Greater Noida, India.
| | - Pradipta Paul
- Weill Cornell Medicine-Qatar, Education City, Qatar Foundation, Doha, 24144, Qatar.
| | - Pardeep Yadav
- Center for Bioinformatics, Computational and Systems Biology, Pathfinder Research and Training Foundation, Greater Noida, India; Department of Biotechnology, School of Engineering & Technology, Sharda University, Greater Noida, Uttar Pradesh, 201310, India.
| | - Ridhima Kaul
- Weill Cornell Medicine-Qatar, Education City, Qatar Foundation, Doha, 24144, Qatar.
| | - S S Maitra
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067, India.
| | - Saurabh Kumar Jha
- Department of Biotechnology, School of Engineering & Technology, Sharda University, Greater Noida, Uttar Pradesh, 201310, India.
| | - Ali Chaari
- Weill Cornell Medicine-Qatar, Education City, Qatar Foundation, Doha, 24144, Qatar.
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17
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Louis TJ, Qasem A, Abdelli LS, Naser SA. Extra-Pulmonary Complications in SARS-CoV-2 Infection: A Comprehensive Multi Organ-System Review. Microorganisms 2022; 10:153. [PMID: 35056603 PMCID: PMC8781813 DOI: 10.3390/microorganisms10010153] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 01/07/2022] [Accepted: 01/10/2022] [Indexed: 02/07/2023] Open
Abstract
Coronavirus disease (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, is typically presented with acute symptoms affecting upper and lower respiratory systems. As the current pandemic progresses, COVID-19 patients are experiencing a series of nonspecific or atypical extra-pulmonary complications such as systemic inflammation, hypercoagulability state, and dysregulation of the renin-angiotensin-aldosterone system (RAAS). These manifestations often delay testing, diagnosis, and the urge to seek effective treatment. Although the pathophysiology of these complications is not clearly understood, the incidence of COVID-19 increases with age and the presence of pre-existing conditions. This review article outlines the pathophysiology and clinical impact of SARS-CoV-2 infection on extra-pulmonary systems. Understanding the broad spectrum of atypical extra-pulmonary manifestations of COVID-19 should increase disease surveillance, restrict transmission, and most importantly prevent multiple organ-system complications.
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Affiliation(s)
- Taylor J Louis
- Division of Molecular Microbiology, Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL 32816, USA
| | - Ahmad Qasem
- Division of Molecular Microbiology, Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL 32816, USA
| | - Latifa S Abdelli
- Division of Molecular Microbiology, Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL 32816, USA
| | - Saleh A Naser
- Division of Molecular Microbiology, Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL 32816, USA
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18
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Liana D, Phanumartwiwath A. Leveraging knowledge of Asian herbal medicine and its active compounds as COVID-19 treatment and prevention. J Nat Med 2022; 76:20-37. [PMID: 34623617 PMCID: PMC8498083 DOI: 10.1007/s11418-021-01575-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 09/29/2021] [Indexed: 12/24/2022]
Abstract
The outbreak of COVID-19 disease has led to a search for effective vaccines or drugs. However, insufficient vaccine supplies to meet global demand and no effective approved prescribed drugs for COVID-19 have led some people to consider the use of alternative or complementary medicines, such as traditional herbal medicine. Medicinal plants have various therapeutic properties that depend on the active compounds they contain. Obviously, herbal medicine has had an essential role in treatment and prevention during COVID-19 outbreak, especially in Asian cultures. Hence, we reviewed the uses of herbal medicine in Asian cultures and described the prominent families and species that are sources of antiviral agents against COVID-19 on the basis of case reports, community surveys, and guidelines available in the literature databases. Antiviral efficacy as determined in laboratory testing was assessed, and several promising active compounds with their molecular targets in cell models against SARS-CoV-2 viral infection will be discussed. Our review findings revealed the highly frequent use of Lamiaceae family members, Zingiber officinale, and Glycyrrhiza spp. as medicinal sources for treatment of COVID-19. In addition, several plant bioactive compounds derived from traditional herbal medicine, including andrographolide, panduratin A, baicalein, digoxin, and digitoxin, have shown potent SARS-CoV-2 antiviral activity as compared with some repurposed FDA-approved drugs. These commonly used plants and promising compounds are recommended for further exploration of their safety and efficacy against COVID-19.
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Affiliation(s)
- Desy Liana
- College of Public Health Sciences, Chulalongkorn University, Pathumwan, Bangkok, 10330, Thailand
| | - Anuchit Phanumartwiwath
- College of Public Health Sciences, Chulalongkorn University, Pathumwan, Bangkok, 10330, Thailand.
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19
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Azam F, Eid EEM, Almutairi A. Targeting SARS-CoV-2 main protease by teicoplanin: A mechanistic insight by docking, MM/GBSA and molecular dynamics simulation. J Mol Struct 2021; 1246:131124. [PMID: 34305175 PMCID: PMC8286173 DOI: 10.1016/j.molstruc.2021.131124] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 07/05/2021] [Accepted: 07/14/2021] [Indexed: 12/16/2022]
Abstract
First emerged in late December 2019, the outbreak of novel severe acute respiratory syndrome corona virus-2 (SARS-CoV-2) pandemic has instigated public-health emergency around the globe. Till date there is no specific therapeutic agent for this disease and hence, the world is craving to identify potential antiviral agents against SARS-CoV-2. The main protease (MPro) is considered as an attractive drug target for rational drug design against SARS-CoV-2 as it is known to play a crucial role in the viral replication and transcription. Teicoplanin is a glycopeptide class of antibiotic which is regularly used for treating Gram-positive bacterial infections, has shown potential therapeutic efficacy against SARS-CoV-2 in vitro. Therefore, in this study, a mechanistic insight of intermolecular interactions between teicoplanin and SARS-CoV-2 MPro has been scrutinized by molecular docking. Both monomeric and dimeric forms of MPro was used in docking involving blind as well as defined binding site based on the known inhibitor. Binding energies of teicoplanin-MPro complexes were estimated by Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) computations from docking and simulated trajectories. The dynamic and thermodynamics constraints of docked drug in complex with target proteins under specific physiological conditions was ascertained by all-atom molecular dynamics simulation of 100 ns trajectory. Root mean square deviation and fluctuation of carbon α chain justified the stability of the bound complex in biological environments. The outcomes of current study are supposed to be fruitful in rational design of antiviral drugs against SARS-CoV-2.
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20
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A photoactivable natural product with broad antiviral activity against enveloped viruses including highly pathogenic coronaviruses. Antimicrob Agents Chemother 2021; 66:e0158121. [PMID: 34807755 PMCID: PMC8846325 DOI: 10.1128/aac.01581-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreak has highlighted the need for broad-spectrum antivirals against coronaviruses (CoVs). Here, pheophorbide a (Pba) was identified as a highly active antiviral molecule against human CoV-229E after bioguided fractionation of plant extracts. The antiviral activity of Pba was subsequently shown for SARS-CoV-2 and Middle East respiratory syndrome coronavirus (MERS-CoV), and its mechanism of action was further assessed, showing that Pba is an inhibitor of coronavirus entry by directly targeting the viral particle. Interestingly, the antiviral activity of Pba depends on light exposure, and Pba was shown to inhibit virus-cell fusion by stiffening the viral membrane, as demonstrated by cryoelectron microscopy. Moreover, Pba was shown to be broadly active against several other enveloped viruses and reduced SARS-CoV-2 and MERS-CoV replication in primary human bronchial epithelial cells. Pba is the first described natural antiviral against SARS-CoV-2 with direct photosensitive virucidal activity that holds potential for COVID-19 therapy or disinfection of SARS-CoV-2-contaminated surfaces.
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21
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Wang C, Konecki DM, Marciano DC, Govindarajan H, Williams AM, Wastuwidyaningtyas B, Bourquard T, Katsonis P, Lichtarge O. Identification of evolutionarily stable functional and immunogenic sites across the SARS-CoV-2 proteome and greater coronavirus family. Bioinformatics 2021; 37:4033-4040. [PMID: 34043002 PMCID: PMC8243408 DOI: 10.1093/bioinformatics/btab406] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 05/10/2021] [Accepted: 05/26/2021] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Since the first recognized case of COVID-19, more than 100 million people have been infected worldwide. Global efforts in drug and vaccine development to fight the disease have yielded vaccines and drug candidates to cure COVID-19. However, the spread of SARS-CoV-2 variants threatens the continued efficacy of these treatments. In order to address this, we interrogate the evolutionary history of the entire SARS-CoV-2 proteome to identify evolutionarily conserved functional sites that can inform the search for treatments with broader coverage across the coronavirus family. RESULTS Combining coronavirus family sequence information with the mutations observed in the current COVID-19 outbreak, we systematically and comprehensively define evolutionarily stable sites that may provide useful drug and vaccine targets and which are less likely to be compromised by the emergence of new virus strains. Several experimentally validated effective drugs interact with these proposed target sites. In addition, the same evolutionary information can prioritize cross reactive antigens that are useful in directing multi-epitope vaccine strategies to illicit broadly neutralizing immune responses to the betacoronavirus family. Although the results are focused on SARS-CoV-2, these approaches stem from evolutionary principles that are agnostic to the organism or infective agent. AVAILABILITY AND IMPLEMENTATION The results of this work are made interactively available at http://cov.lichtargelab.org. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Chen Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Daniel M Konecki
- Quantitative and Computational Biosciences Graduate Program, Baylor College of Medicine, Houston, TX 77030, USA
| | - David C Marciano
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Harikumar Govindarajan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Amanda M Williams
- Cancer and Cell Biology Graduate Program, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Thomas Bourquard
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Panagiotis Katsonis
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Olivier Lichtarge
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Quantitative and Computational Biosciences Graduate Program, Baylor College of Medicine, Houston, TX 77030, USA
- Cancer and Cell Biology Graduate Program, Baylor College of Medicine, Houston, TX 77030, USA
- Computational and Integrative Biomedical Research Center, Baylor College of Medicine, Houston, TX 77030, USA
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22
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Yadav DK, Singh DD, Han I, Kumar Y, Choi EH. Current Potential Therapeutic Approaches against SARS-CoV-2: A Review. Biomedicines 2021; 9:biomedicines9111620. [PMID: 34829850 PMCID: PMC8615922 DOI: 10.3390/biomedicines9111620] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/23/2021] [Accepted: 10/30/2021] [Indexed: 12/13/2022] Open
Abstract
The ongoing SARS-CoV-2 pandemic is a serious threat to public health worldwide and, to date, no effective treatment is available. Thus, we herein review the pharmaceutical approaches to SARS-CoV-2 infection treatment. Numerous candidate medicines that can prevent SARS-CoV-2 infection and replication have been proposed. These medicines include inhibitors of serine protease TMPRSS2 and angiotensin converting enzyme 2 (ACE2). The S protein of SARS-CoV-2 binds to the receptor in host cells. ACE2 inhibitors block TMPRSS2 and S protein priming, thus preventing SARS-CoV-2 entry to host cells. Moreover, antiviral medicines (including the nucleotide analogue remdesivir, the HIV protease inhibitors lopinavir and ritonavir, and wide-spectrum antiviral antibiotics arbidol and favipiravir) have been shown to reduce the dissemination of SARS-CoV-2 as well as morbidity and mortality associated with COVID-19.
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Affiliation(s)
- Dharmendra Kumar Yadav
- Gachon Institute of Pharmaceutical Science and Department of Pharmacy, College of Pharmacy, Gachon University, Hambakmoeiro 191, Yeonsu-gu, Incheon 21924, Korea
- Correspondence: (D.K.Y.); (E.-H.C.); Tel.: +82-32-820-4947 (E.-H.C.)
| | - Desh Deepak Singh
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur 303002, India;
| | - Ihn Han
- Plasma Bioscience Research Center, Applied Plasma Medicine Center, Department of Electrical & Biological Physics, Kwangwoon University, Seoul 01897, Korea;
| | - Yogesh Kumar
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Martinistrasse 52/Gebäude N27, 20246 Hamburg, Germany;
| | - Eun-Ha Choi
- Plasma Bioscience Research Center, Applied Plasma Medicine Center, Department of Electrical & Biological Physics, Kwangwoon University, Seoul 01897, Korea;
- Correspondence: (D.K.Y.); (E.-H.C.); Tel.: +82-32-820-4947 (E.-H.C.)
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23
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Kaul R, Paul P, Kumar S, Büsselberg D, Dwivedi VD, Chaari A. Promising Antiviral Activities of Natural Flavonoids against SARS-CoV-2 Targets: Systematic Review. Int J Mol Sci 2021; 22:11069. [PMID: 34681727 PMCID: PMC8539743 DOI: 10.3390/ijms222011069] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 10/08/2021] [Accepted: 10/10/2021] [Indexed: 12/13/2022] Open
Abstract
The ongoing COVID-19 pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) became a globally leading public health concern over the past two years. Despite the development and administration of multiple vaccines, the mutation of newer strains and challenges to universal immunity has shifted the focus to the lack of efficacious drugs for therapeutic intervention for the disease. As with SARS-CoV, MERS-CoV, and other non-respiratory viruses, flavonoids present themselves as a promising therapeutic intervention given their success in silico, in vitro, in vivo, and more recently, in clinical studies. This review focuses on data from in vitro studies analyzing the effects of flavonoids on various key SARS-CoV-2 targets and presents an analysis of the structure-activity relationships for the same. From 27 primary papers, over 69 flavonoids were investigated for their activities against various SARS-CoV-2 targets, ranging from the promising 3C-like protease (3CLpro) to the less explored nucleocapsid (N) protein; the most promising were quercetin and myricetin derivatives, baicalein, baicalin, EGCG, and tannic acid. We further review promising in silico studies featuring activities of flavonoids against SARS-CoV-2 and list ongoing clinical studies involving the therapeutic potential of flavonoid-rich extracts in combination with synthetic drugs or other polyphenols and suggest prospects for the future of flavonoids against SARS-CoV-2.
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Affiliation(s)
- Ridhima Kaul
- Weill Cornell Medicine-Qatar, Education City, Qatar Foundation, Doha 24144, Qatar; (R.K.); (P.P.)
| | - Pradipta Paul
- Weill Cornell Medicine-Qatar, Education City, Qatar Foundation, Doha 24144, Qatar; (R.K.); (P.P.)
| | - Sanjay Kumar
- Center for Bioinformatics, Computational and Systems Biology, Pathfinder Research and Training Foundation, Greater Noida 201308, India; (S.K.); (V.D.D.)
- School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
| | - Dietrich Büsselberg
- Department of Physiology and Biophysics, Weill Cornell Medicine-Qatar, Education City, Qatar Foundation, Doha 24144, Qatar;
| | - Vivek Dhar Dwivedi
- Center for Bioinformatics, Computational and Systems Biology, Pathfinder Research and Training Foundation, Greater Noida 201308, India; (S.K.); (V.D.D.)
| | - Ali Chaari
- Weill Cornell Medicine-Qatar, Education City, Qatar Foundation, Doha 24144, Qatar; (R.K.); (P.P.)
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24
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Agrawal PK, Agrawal C, Blunden G. Pharmacological Significance of Hesperidin and Hesperetin, Two Citrus Flavonoids, as Promising Antiviral Compounds for Prophylaxis Against and Combating COVID-19. Nat Prod Commun 2021. [DOI: 10.1177/1934578x211042540] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Hesperidin and hesperetin are flavonoids that are abundantly present as constituents of citrus fruits. These compounds have attracted attention as several computational methods, mostly docking studies, have shown that hesperidin may bind to multiple regions of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (spike protein, angiotensin-converting enzyme 2, and proteases). Hesperidin has a low binding energy, both with the SARS-CoV-2 “spike” protein responsible for internalization, and also with the “PLpro” and “Mpro” responsible for transforming the early proteins of the virus into the complex responsible for viral replication. This suggests that these flavonoids could act as prophylactic agents by blocking several mechanisms of viral infection and replication, and thus helping the host cell to resist viral attack.
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Affiliation(s)
| | | | - Gerald Blunden
- School of Pharmacy & Biomedical Sciences, University of Portsmouth, Portsmouth, UK
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25
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Muhammed Y, Yusuf Nadabo A, Pius M, Sani B, Usman J, Anka Garba N, Mohammed Sani J, Opeyemi Olayanju B, Zeal Bala S, Garba Abdullahi M, Sambo M. SARS-CoV-2 spike protein and RNA dependent RNA polymerase as targets for drug and vaccine development: A review. BIOSAFETY AND HEALTH 2021; 3:249-263. [PMID: 34396086 PMCID: PMC8346354 DOI: 10.1016/j.bsheal.2021.07.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 07/04/2021] [Accepted: 07/18/2021] [Indexed: 01/18/2023] Open
Abstract
The present pandemic has posed a crisis to the economy of the world and the health sector. Therefore, the race to expand research to understand some good molecular targets for vaccine and therapeutic development for SARS-CoV-2 is inevitable. The newly discovered coronavirus 2019 (COVID-19) is a positive sense, single-stranded RNA, and enveloped virus, assigned to the beta CoV genus. The virus (SARS-CoV-2) is more infectious than the previously detected coronaviruses (MERS and SARS). Findings from many studies have revealed that S protein and RdRp are good targets for drug repositioning, novel therapeutic development (antibodies and small molecule drugs), and vaccine discovery. Therapeutics such as chloroquine, convalescent plasma, monoclonal antibodies, spike binding peptides, and small molecules could alter the ability of S protein to bind to the ACE-2 receptor, and drugs such as remdesivir (targeting SARS-CoV-2 RdRp), favipir, and emetine could prevent SASR-CoV-2 RNA synthesis. The novel vaccines such as mRNA1273 (Moderna), 3LNP-mRNAs (Pfizer/BioNTech), and ChAdOx1-S (University of Oxford/Astra Zeneca) targeting S protein have proven to be effective in combating the present pandemic. Further exploration of the potential of S protein and RdRp is crucial in fighting the present pandemic.
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Affiliation(s)
- Yusuf Muhammed
- Department of Biochemistry, Federal University, Gusau, Nigeria,Corresponding author: Department of Biochemistry, Federal University, Gusau, Nigeria
| | | | - Mkpouto Pius
- Department of Medical Genetics, University of Cambridge, CB2 1TN, United Kingdom
| | - Bashiru Sani
- Department of Microbiology, Federal University of Lafia, Nigeria
| | - Jafar Usman
- Department of Biochemistry, Federal University, Gusau, Nigeria
| | | | | | - Basit Opeyemi Olayanju
- Department of Chemistry and Biochemistry, Florida International University, FL 33199, USA
| | | | | | - Misbahu Sambo
- Department of Biochemistry, Abubakar Tafawa Balewa University Bauchi, Nigeria
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26
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Pitsillou E, Liang J, Yu Meng Huang H, Hung A, Karagiannis TC. In silico investigation to identify potential small molecule inhibitors of the RNA-dependent RNA polymerase (RdRp) nidovirus RdRp-associated nucleotidyltransferase domain. Chem Phys Lett 2021; 779:138889. [PMID: 34305155 PMCID: PMC8273049 DOI: 10.1016/j.cplett.2021.138889] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 05/30/2021] [Accepted: 07/08/2021] [Indexed: 01/18/2023]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA-dependent RNA polymerase (RdRp) is a promising target for antiviral drugs. In this study, a chemical library (n = 300) was screened against the nidovirus RdRp-associated nucleotidyltransferase (NiRAN) domain. Blind docking was performed using a selection of 30 compounds and nine ligands were chosen based on their docking scores, safety profile, and availability. Using cluster analysis on a 10 microsecond molecular dynamics simulation trajectory (from D.E. Shaw Research), the compounds were docked to the different conformations. On the basis of our modelling studies, oleuropein was identified as a potential lead compound.
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Affiliation(s)
- Eleni Pitsillou
- Epigenomic Medicine, Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC 3004, Australia,School of Science, STEM College, RMIT University, VIC 3001, Australia
| | - Julia Liang
- Epigenomic Medicine, Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC 3004, Australia,School of Science, STEM College, RMIT University, VIC 3001, Australia
| | - Helen Yu Meng Huang
- Epigenomic Medicine, Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC 3004, Australia,Department of Microbiology and Immunology, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Andrew Hung
- School of Science, STEM College, RMIT University, VIC 3001, Australia
| | - Tom C. Karagiannis
- Epigenomic Medicine, Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC 3004, Australia,Department of Clinical Pathology, The University of Melbourne, Parkville, VIC 3052, Australia,Corresponding author
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27
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Valdés-Aguayo JJ, Garza-Veloz I, Badillo-Almaráz JI, Bernal-Silva S, Martínez-Vázquez MC, Juárez-Alcalá V, Vargas-Rodríguez JR, Gaeta-Velasco ML, González-Fuentes C, Ávila-Carrasco L, Martinez-Fierro ML. Mitochondria and Mitochondrial DNA: Key Elements in the Pathogenesis and Exacerbation of the Inflammatory State Caused by COVID-19. ACTA ACUST UNITED AC 2021; 57:medicina57090928. [PMID: 34577851 PMCID: PMC8471487 DOI: 10.3390/medicina57090928] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 08/21/2021] [Accepted: 09/01/2021] [Indexed: 12/15/2022]
Abstract
Background and Objectives. The importance of mitochondria in inflammatory pathologies, besides providing energy, is associated with the release of mitochondrial damage products, such as mitochondrial DNA (mt-DNA), which may perpetuate inflammation. In this review, we aimed to show the importance of mitochondria, as organelles that produce energy and intervene in multiple pathologies, focusing mainly in COVID-19 and using multiple molecular mechanisms that allow for the replication and maintenance of the viral genome, leading to the exacerbation and spread of the inflammatory response. The evidence suggests that mitochondria are implicated in the replication of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which forms double-membrane vesicles and evades detection by the cell defense system. These mitochondrion-hijacking vesicles damage the integrity of the mitochondrion’s membrane, releasing mt-DNA into circulation and triggering the activation of innate immunity, which may contribute to an exacerbation of the pro-inflammatory state. Conclusions. While mitochondrial dysfunction in COVID-19 continues to be studied, the use of mt-DNA as an indicator of prognosis and severity is a potential area yet to be explored.
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Affiliation(s)
- José J. Valdés-Aguayo
- Molecular Medicine Laboratory, Unidad Académica de Medicina Humana y C.S., Universidad Autónoma de Zacatecas, Carretera Zacatecas-Guadalajara Km.6. Ejido la Escondida, Zacatecas 98160, Mexico; (J.J.V.-A.); (I.G.-V.); (J.I.B.-A.); (M.C.M.-V.); (V.J.-A.); (J.R.V.-R.); (L.Á.-C.)
| | - Idalia Garza-Veloz
- Molecular Medicine Laboratory, Unidad Académica de Medicina Humana y C.S., Universidad Autónoma de Zacatecas, Carretera Zacatecas-Guadalajara Km.6. Ejido la Escondida, Zacatecas 98160, Mexico; (J.J.V.-A.); (I.G.-V.); (J.I.B.-A.); (M.C.M.-V.); (V.J.-A.); (J.R.V.-R.); (L.Á.-C.)
| | - José I. Badillo-Almaráz
- Molecular Medicine Laboratory, Unidad Académica de Medicina Humana y C.S., Universidad Autónoma de Zacatecas, Carretera Zacatecas-Guadalajara Km.6. Ejido la Escondida, Zacatecas 98160, Mexico; (J.J.V.-A.); (I.G.-V.); (J.I.B.-A.); (M.C.M.-V.); (V.J.-A.); (J.R.V.-R.); (L.Á.-C.)
| | - Sofia Bernal-Silva
- Microbiology Department, Facultad de Medicina, Universidad Autónoma de San Luis Potosí, Avenida Venustiano Carranza 2405, San Luis Potosí 78210, Mexico;
| | - Maria C. Martínez-Vázquez
- Molecular Medicine Laboratory, Unidad Académica de Medicina Humana y C.S., Universidad Autónoma de Zacatecas, Carretera Zacatecas-Guadalajara Km.6. Ejido la Escondida, Zacatecas 98160, Mexico; (J.J.V.-A.); (I.G.-V.); (J.I.B.-A.); (M.C.M.-V.); (V.J.-A.); (J.R.V.-R.); (L.Á.-C.)
| | - Vladimir Juárez-Alcalá
- Molecular Medicine Laboratory, Unidad Académica de Medicina Humana y C.S., Universidad Autónoma de Zacatecas, Carretera Zacatecas-Guadalajara Km.6. Ejido la Escondida, Zacatecas 98160, Mexico; (J.J.V.-A.); (I.G.-V.); (J.I.B.-A.); (M.C.M.-V.); (V.J.-A.); (J.R.V.-R.); (L.Á.-C.)
| | - José R. Vargas-Rodríguez
- Molecular Medicine Laboratory, Unidad Académica de Medicina Humana y C.S., Universidad Autónoma de Zacatecas, Carretera Zacatecas-Guadalajara Km.6. Ejido la Escondida, Zacatecas 98160, Mexico; (J.J.V.-A.); (I.G.-V.); (J.I.B.-A.); (M.C.M.-V.); (V.J.-A.); (J.R.V.-R.); (L.Á.-C.)
| | - María L. Gaeta-Velasco
- Hospital General de Zacatecas “Luz González Cosío”, Circuito Ciudad Gobierno 410, Col. Ciudad Gobierno, Zacatecas 98160, Mexico; (M.L.G.-V.); (C.G.-F.)
| | - Carolina González-Fuentes
- Hospital General de Zacatecas “Luz González Cosío”, Circuito Ciudad Gobierno 410, Col. Ciudad Gobierno, Zacatecas 98160, Mexico; (M.L.G.-V.); (C.G.-F.)
| | - Lorena Ávila-Carrasco
- Molecular Medicine Laboratory, Unidad Académica de Medicina Humana y C.S., Universidad Autónoma de Zacatecas, Carretera Zacatecas-Guadalajara Km.6. Ejido la Escondida, Zacatecas 98160, Mexico; (J.J.V.-A.); (I.G.-V.); (J.I.B.-A.); (M.C.M.-V.); (V.J.-A.); (J.R.V.-R.); (L.Á.-C.)
| | - Margarita L. Martinez-Fierro
- Molecular Medicine Laboratory, Unidad Académica de Medicina Humana y C.S., Universidad Autónoma de Zacatecas, Carretera Zacatecas-Guadalajara Km.6. Ejido la Escondida, Zacatecas 98160, Mexico; (J.J.V.-A.); (I.G.-V.); (J.I.B.-A.); (M.C.M.-V.); (V.J.-A.); (J.R.V.-R.); (L.Á.-C.)
- Correspondence: ; Tel.: +52-(492)-925669 (ext. 4511)
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28
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Nogara PA, Omage FB, Bolzan GR, Delgado CP, Aschner M, Orian L, Teixeira Rocha JB. In silico Studies on the Interaction between Mpro and PLpro From SARS-CoV-2 and Ebselen, its Metabolites and Derivatives. Mol Inform 2021; 40:e2100028. [PMID: 34018687 PMCID: PMC8236915 DOI: 10.1002/minf.202100028] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 04/11/2021] [Indexed: 12/20/2022]
Abstract
The COVID-19 pandemic caused by the SARS-CoV-2 has mobilized scientific attention in search of a treatment. The cysteine-proteases, main protease (Mpro) and papain-like protease (PLpro) are important targets for antiviral drugs. In this work, we simulate the interactions between the Mpro and PLpro with Ebselen, its metabolites and derivatives with the aim of finding molecules that can potentially inhibit these enzymes. The docking data demonstrate that there are two main interactions between the thiol (-SH) group of Cys (from the protease active sites) and the electrophilic centers of the organoselenium molecules, i. e. the interaction with the carbonyl group (O=C… SH) and the interaction with the Se moiety (Se… SH). Both interactions may lead to an adduct formation and enzyme inhibition. Density Functional Theory (DFT) calculations with Ebselen indicate that the energetics of the thiol nucleophilic attack is more favorable on Se than on the carbonyl group, which is in accordance with experimental data (Jin et al. Nature, 2020, 582, 289-293). Therefore, organoselenium molecules should be further explored as inhibitors of the SARS-CoV-2 proteases. Furthermore, we suggest that some metabolites of Ebselen (e. g. Ebselen diselenide and methylebselenoxide) and derivatives ethaselen and ebsulfur should be tested in vitro as inhibitors of virus replication and its proteases.
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Affiliation(s)
- Pablo Andrei Nogara
- Departamento de Bioquímica e Biologia MolecularUniversidade Federal de Santa Maria (UFSM)Santa Maria97105-900RSBrazil
| | - Folorunsho Bright Omage
- Departamento de Bioquímica e Biologia MolecularUniversidade Federal de Santa Maria (UFSM)Santa Maria97105-900RSBrazil
| | - Gustavo Roni Bolzan
- Departamento de Bioquímica e Biologia MolecularUniversidade Federal de Santa Maria (UFSM)Santa Maria97105-900RSBrazil
| | - Cássia Pereira Delgado
- Departamento de Bioquímica e Biologia MolecularUniversidade Federal de Santa Maria (UFSM)Santa Maria97105-900RSBrazil
| | - Michael Aschner
- Department of Molecular PharmacologyAlbert Einstein College of Medicine1300 Morris Park Avenue, BronxNY10461USA
| | - Laura Orian
- Dipartimento di Scienze ChimicheUniversità degli Studi di PadovaVia Marzolo 135131PadovaItaly
| | - João Batista Teixeira Rocha
- Departamento de Bioquímica e Biologia MolecularUniversidade Federal de Santa Maria (UFSM)Santa Maria97105-900RSBrazil
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29
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Toward the Identification of Potential α-Ketoamide Covalent Inhibitors for SARS-CoV-2 Main Protease: Fragment-Based Drug Design and MM-PBSA Calculations. Processes (Basel) 2021. [DOI: 10.3390/pr9061004] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Since December 2019, the world has been facing the outbreak of the SARS-CoV-2 pandemic that has infected more than 149 million and killed 3.1 million people by 27 April 2021, according to WHO statistics. Safety measures and precautions taken by many countries seem insufficient, especially with no specific approved drugs against the virus. This has created an urgent need to fast track the development of new medication against the virus in order to alleviate the problem and meet public expectations. The SARS-CoV-2 3CL main protease (Mpro) is one of the most attractive targets in the virus life cycle, which is responsible for the processing of the viral polyprotein and is a key for the ribosomal translation of the SARS-CoV-2 genome. In this work, we targeted this enzyme through a structure-based drug design (SBDD) protocol, which aimed at the design of a new potential inhibitor for Mpro. The protocol involves three major steps: fragment-based drug design (FBDD), covalent docking and molecular dynamics (MD) simulation with the calculation of the designed molecule binding free energy at a high level of theory. The FBDD step identified five molecular fragments, which were linked via a suitable carbon linker, to construct our designed compound RMH148. The mode of binding and initial interactions between RMH148 and the enzyme active site was established in the second step of our protocol via covalent docking. The final step involved the use of MD simulations to test for the stability of the docked RMH148 into the Mpro active site and included precise calculations for potential interactions with active site residues and binding free energies. The results introduced RMH148 as a potential inhibitor for the SARS-CoV-2 Mpro enzyme, which was able to achieve various interactions with the enzyme and forms a highly stable complex at the active site even better than the co-crystalized reference.
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30
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Remington JM, McKay KT, Ferrell JB, Schneebeli ST, Li J. Enhanced sampling protocol to elucidate fusion peptide opening of SARS-CoV-2 spike protein. Biophys J 2021; 120:2848-2858. [PMID: 34087207 PMCID: PMC8169235 DOI: 10.1016/j.bpj.2021.05.022] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 04/14/2021] [Accepted: 05/05/2021] [Indexed: 12/20/2022] Open
Abstract
Large-scale conformational transitions in the spike protein S2 domain are required during host-cell infection of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus. Although conventional molecular dynamics simulations have been extensively used to study therapeutic targets of SARS-CoV-2, it is still challenging to gain molecular insight into the key conformational changes because of the size of the spike protein and the long timescale required to capture these transitions. In this work, we have developed an efficient simulation protocol that leverages many short simulations, a dynamic selection algorithm, and Markov state models to interrogate the structural changes of the S2 domain. We discovered that the conformational flexibility of the dynamic region upstream of the fusion peptide in S2 is coupled to the proteolytic cleavage state of the spike protein. These results suggest that opening of the fusion peptide likely occurs on a submicrosecond timescale after cleavage at the S2' site. Building on the structural and dynamical information gained to date about S2 domain dynamics, we provide proof of principle that a small molecule bound to a seam neighboring the fusion peptide can slow the opening of the fusion peptide, leading to a new inhibition strategy for experiments to confirm. In aggregate, these results will aid the development of drug cocktails to inhibit infections caused by SARS-CoV-2 and other coronaviruses.
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Affiliation(s)
| | - Kyle T McKay
- Department of Chemistry, University of Vermont, Burlington, Vermont
| | | | | | - Jianing Li
- Department of Chemistry, University of Vermont, Burlington, Vermont.
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31
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Bendre AD, Peters PJ, Kumar J. Recent Insights into the Structure and Function of Mycobacterial Membrane Proteins Facilitated by Cryo-EM. J Membr Biol 2021; 254:321-341. [PMID: 33954837 PMCID: PMC8099146 DOI: 10.1007/s00232-021-00179-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Accepted: 03/23/2021] [Indexed: 12/26/2022]
Abstract
Mycobacterium tuberculosis (Mtb) is one of the deadliest pathogens encountered by humanity. Over the decades, its characteristic membrane organization and composition have been understood. However, there is still limited structural information and mechanistic understanding of the constituent membrane proteins critical for drug discovery pipelines. Recent advances in single-particle cryo-electron microscopy and cryo-electron tomography have provided the much-needed impetus towards structure determination of several vital Mtb membrane proteins whose structures were inaccessible via X-ray crystallography and NMR. Important insights into membrane composition and organization have been gained via a combination of electron tomography and biochemical and biophysical assays. In addition, till the time of writing this review, 75 new structures of various Mtb proteins have been reported via single-particle cryo-EM. The information obtained from these structures has improved our understanding of the mechanisms of action of these proteins and the physiological pathways they are associated with. These structures have opened avenues for structure-based drug design and vaccine discovery programs that might help achieve global-TB control. This review describes the structural features of selected membrane proteins (type VII secretion systems, Rv1819c, Arabinosyltransferase, Fatty Acid Synthase, F-type ATP synthase, respiratory supercomplex, ClpP1P2 protease, ClpB disaggregase and SAM riboswitch), their involvement in physiological pathways, and possible use as a drug target. Tuberculosis is a deadly disease caused by Mycobacterium tuberculosis. The Cryo-EM and tomography have simplified the understanding of the mycobacterial membrane organization. Some proteins are located in the plasma membrane; some span the entire envelope, while some, like MspA, are located in the mycomembrane. Cryo-EM has made the study of such membrane proteins feasible.
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Affiliation(s)
- Ameya D Bendre
- Laboratory of Membrane Protein Biology, National Centre for Cell Science, NCCS Complex, S. P. Pune University Campus, Ganeshkhind, Pune, Maharashtra, 411007, India
| | - Peter J Peters
- The Maastricht Multimodal Molecular Imaging Institute (M4I), Division of Nanoscopy, Maastricht University, Maastricht, The Netherlands
| | - Janesh Kumar
- Laboratory of Membrane Protein Biology, National Centre for Cell Science, NCCS Complex, S. P. Pune University Campus, Ganeshkhind, Pune, Maharashtra, 411007, India.
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32
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Tenofovir, Another Inexpensive, Well-Known and Widely Available Old Drug Repurposed for SARS-COV-2 Infection. Pharmaceuticals (Basel) 2021; 14:ph14050454. [PMID: 34064831 PMCID: PMC8150375 DOI: 10.3390/ph14050454] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/01/2021] [Accepted: 05/05/2021] [Indexed: 12/18/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is spreading worldwide with different clinical manifestations. Age and comorbidities may explain severity in critical cases and people living with human immunodeficiency virus (HIV) might be at particularly high risk for severe progression. Nonetheless, current data, although sometimes contradictory, do not confirm higher morbidity, risk of more severe COVID-19 or higher mortality in HIV-infected people with complete access to antiretroviral therapy (ART). A possible protective role of ART has been hypothesized to explain these observations. Anti-viral drugs used to treat HIV infection have been repurposed for COVID-19 treatment; this is also based on previous studies on severe acute respiratory syndrome virus (SARS-CoV) and Middle East respiratory syndrome virus (MERS-CoV). Among them, lopinavir/ritonavir, an inhibitor of viral protease, was extensively used early in the pandemic but it was soon abandoned due to lack of effectiveness in clinical trials. However, remdesivir, a nucleotide analog that acts as reverse-transcriptase inhibitor, which was tested early during the pandemic because of its wide range of antiviral activity against several RNA viruses and its safety profile, is currently the only antiviral medication approved for COVID-19. Tenofovir, another nucleotide analog used extensively for HIV treatment and pre-exposure prophylaxis (PrEP), has also been hypothesized as effective in COVID-19. No data on tenofovir's efficacy in coronavirus infections other than COVID-19 are currently available, although information relating to SARS-CoV-2 infection is starting to come out. Here, we review the currently available evidence on tenofovir's efficacy against SARS-CoV-2.
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33
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Mohebbi A, Askari FS, Sammak AS, Ebrahimi M, Najafimemar Z. Druggability of cavity pockets within SARS-CoV-2 spike glycoprotein and pharmacophore-based drug discovery. Future Virol 2021; 16:10.2217/fvl-2020-0394. [PMID: 34099962 PMCID: PMC8176656 DOI: 10.2217/fvl-2020-0394] [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: 11/30/2020] [Accepted: 05/19/2021] [Indexed: 01/02/2023]
Abstract
Aim: Virus spike glycoprotein of SARS-CoV-2 is a good target for drug discovery. Objective: To examine the potential for druggability of spike protein for pharmacophore-based drug discovery and to investigate the binding affinity of natural products with SARS-CoV-2 spike protein. Methods: Druggable cavities were searched though CavityPlus. A pharmacophore was built and used for hit identification. Autodock Vina was used to evaluate the hits' affinities. 10 chemical derivatives were also made from the chemical backbone to optimize the lead compound. Results: 10 druggable cavities were found within the glycoprotein spike. Only one cavity with the highest score at the binding site was selected for pharmacophore extraction. Hit identification resulted in the identification of 410 hits. Discussion: This study provides a druggable region within viral glycoprotein and a candidate compound to block viral entry.
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Affiliation(s)
- Alireza Mohebbi
- Department of Microbiology, School of Medicine, Golestan University of Medical Sciences, Gorgan 4934174515, Iran
| | - Fatemeh Sana Askari
- Student Research Committee, School of Medicine, Golestan University of Medical Sciences, Gorgan 4934174515, Iran
| | - Ali Salehnia Sammak
- Department of Microbiology, Faculty of Basic Sciences, Rasht Branch, Islamic Azad University, Rasht, Gilan 4147654919, Iran
| | - Mohsen Ebrahimi
- Children's Research Center, Golestan University of Medical Sciences, Gorgan, Iran
| | - Zahra Najafimemar
- Department of Microbiology, School of Medicine, Golestan University of Medical Sciences, Gorgan 4934174515, Iran
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Galvez J, Zanni R, Galvez-Llompart M, Benlloch JM. Macrolides May Prevent Severe Acute Respiratory Syndrome Coronavirus 2 Entry into Cells: A Quantitative Structure Activity Relationship Study and Experimental Validation. J Chem Inf Model 2021; 61:2016-2025. [PMID: 33734704 PMCID: PMC7986980 DOI: 10.1021/acs.jcim.0c01394] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Indexed: 02/07/2023]
Abstract
The global pandemic caused by the emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is threatening the health and economic systems worldwide. Despite the enormous efforts of scientists and clinicians around the world, there is still no drug or vaccine available worldwide for the treatment and prevention of the infection. A rapid strategy for the identification of new treatments is based on repurposing existing clinically approved drugs that show antiviral activity against SARS-CoV-2 infection. In this study, after developing a quantitative structure activity relationship analysis based on molecular topology, several macrolide antibiotics are identified as promising SARS-CoV-2 spike protein inhibitors. To confirm the in silico results, the best candidates were tested against two human coronaviruses (i.e., 229E-GFP and SARS-CoV-2) in cell culture. Time-of-addition experiments and a surrogate model of viral cell entry were used to identify the steps in the virus life cycle inhibited by the compounds. Infection experiments demonstrated that azithromycin, clarithromycin, and lexithromycin reduce the intracellular accumulation of viral RNA and virus spread as well as prevent virus-induced cell death, by inhibiting the SARS-CoV-2 entry into cells. Even though the three macrolide antibiotics display a narrow antiviral activity window against SARS-CoV-2, it may be of interest to further investigate their effect on the viral spike protein and their potential in combination therapies for the coronavirus disease 19 early stage of infection.
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Affiliation(s)
- Jorge Galvez
- Molecular Topology and Drug Design
Unit, Department of Physical Chemistry, Universitat de
Valencia, Burjassot 46100,
Spain
| | - Riccardo Zanni
- Molecular Topology and Drug Design
Unit, Department of Physical Chemistry, Universitat de
Valencia, Burjassot 46100,
Spain
| | - Maria Galvez-Llompart
- Molecular Topology and Drug Design
Unit, Department of Physical Chemistry, Universitat de
Valencia, Burjassot 46100,
Spain
- Instituto de Tecnología
Química, UPV-CSIC, Universidad Politícnica
de Valencia, Valencia 46022,
Spain
| | - Jose Maria Benlloch
- Instituto de Instrumentación para
Imagen Molecular, Centro Mixto CSIC—Universitat
Politècnica de València, Valencia
46022, Spain
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35
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Ullah A, Ullah K. Inhibition of SARS-CoV-2 3CL M pro by Natural and Synthetic Inhibitors: Potential Implication for Vaccine Production Against COVID-19. Front Mol Biosci 2021; 8:640819. [PMID: 33912587 PMCID: PMC8072276 DOI: 10.3389/fmolb.2021.640819] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Accepted: 03/10/2021] [Indexed: 12/24/2022] Open
Abstract
COVID-19 has created a pandemic situation all over the world. It has spread in nearly every continent. Researchers all over the world are trying to produce an effective vaccine against this virus, however; no specific treatment for COVID-19 has been discovered -so far. The current work describes the inhibition study of the SARS-CoV-2 main proteinase or 3CL Mpro by natural and synthetic inhibitors, which include 2S albumin and flocculating protein from Moringa oleifera (M. oleifera) and Suramin. Molecular Docking study was carried out using the programs like AutoDock 4.0, HADDOCK2.4, patchdock, pardock, and firedock. The global binding energy of Suramin, 2S albumin, and flocculating proteins were −41.96, −9.12, and −14.78 kJ/mol, respectively. The docking analysis indicates that all three inhibitors bind at the junction of domains II and III. The catalytic function of 3CL Mpro is dependent on its dimeric form, and the flexibility of domain III is considered important for this dimerization. Our study showed that all three inhibitors reduce this flexibility and restrict their motion. The decrease in flexibility of domain III was further confirmed by analysis coming from Molecular dynamic simulation. The analysis results indicate that the temperature B-factor of the enzyme decreases tremendously when the inhibitors bind to it. This study will further explore the possibility of producing an effective treatment against COVID-19.
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Affiliation(s)
- Anwar Ullah
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Kifayat Ullah
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
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36
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Bhowmick S, Saha A, Osman SM, Alasmary FA, Almutairi TM, Islam MA. Structure-based identification of SARS-CoV-2 main protease inhibitors from anti-viral specific chemical libraries: an exhaustive computational screening approach. Mol Divers 2021; 25:1979-1997. [PMID: 33844135 PMCID: PMC8039805 DOI: 10.1007/s11030-021-10214-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Accepted: 03/21/2021] [Indexed: 12/19/2022]
Abstract
Abstract Worldwide coronavirus disease 2019 (COVID-19) outbreak is still threatening global health since its outbreak first reported in the late 2019. The causative novel virus has been designated as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Although COVID-19 emergent with significant mortality, there is no availability of definite treatment measures. It is now extremely desirable to identify potential chemical entities against SARS-CoV-2 for the treatment of COVID-19. In the present study, a state-of-art virtual screening protocol was implemented on three anti-viral specific chemical libraries against SARS-CoV-2 main protease (Mpro). Particularly, viewing the large-scale biological role of Mpro in the viral replication process it has been considered as a prospective anti-viral drug target. Herein, on collected 79,892 compounds, hierarchical multistep docking followed by relative binding free energy estimation has been performed. Thereafter, implying a user-defined XP-dock and MM-GBSA cut-off scores as −8.00 and −45.00 kcal/mol, chemical space has been further reduced. Exhaustive molecular binding interactions analyses and various pharmacokinetics profiles assessment suggested four compounds (ChemDiv_D658-0159, ChemDiv_F431-0433, Enamine_Z3019991843 and Asinex_LAS_51389260) as potent inhibitors/modulators of SARS-CoV-2 Mpro. In-depth protein–ligand interactions stability in the dynamic state has been evaluated by 100 ns molecular dynamics (MD) simulation studies along with MM-GBSA-based binding free energy estimations of entire simulation trajectories that have revealed strong binding affinity of all identified compounds towards Mpro. Hence, all four identified compounds might be considered as promising candidates for future drug development specifically targeting the SARS-CoV-2 Mpro; however, they also need experimental assessment for a better understanding of molecular interaction mechanisms. Graphic abstract ![]()
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Affiliation(s)
- Shovonlal Bhowmick
- Department of Chemical Technology, University of Calcutta, 92, A.P.C. Road, Kolkata- 700009, India
| | - Achintya Saha
- Department of Chemical Technology, University of Calcutta, 92, A.P.C. Road, Kolkata- 700009, India.
| | - Sameh Mohamed Osman
- Chemistry Department, College of Science, King Saud University, P.O. Box 2455, Riyadh, 11451, Saudi Arabia.
| | - Fatmah Ali Alasmary
- Chemistry Department, College of Science, King Saud University, P.O. Box 2455, Riyadh, 11451, Saudi Arabia
| | - Tahani Mazyad Almutairi
- Chemistry Department, College of Science, King Saud University, P.O. Box 2455, Riyadh, 11451, Saudi Arabia
| | - Md Ataul Islam
- Division of Pharmacy and Optometry, School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester, M13 9PL, UK. .,Department of Chemical Pathology, Faculty of Health Sciences, University of Pretoria and National Health Laboratory Service Tshwane Academic Division, Pretoria, South Africa.
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37
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Colombani T, Rogers ZJ, Eggermont LJ, Bencherif SA. Harnessing biomaterials for therapeutic strategies against COVID-19. EMERGENT MATERIALS 2021; 4:9-18. [PMID: 33842840 PMCID: PMC8022295 DOI: 10.1007/s42247-021-00171-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 01/24/2021] [Indexed: 05/16/2023]
Abstract
With the emergence of the coronavirus disease 2019 (COVID-19), the world is experiencing a profound human health crisis. The number of infections and deaths due to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to increase every minute, pinpointing major shortcomings in our ability to prevent viral outbreaks. Although several COVID-19 vaccines have been recently approved for emergency use, therapeutic options remain limited, and their long-term potency has yet to be validated. Biomaterials science has a pivotal role to play in pushing the boundaries of emerging technologies for antiviral research and treatment. In this perspective, we discuss how biomaterials can be harnessed to develop accurate COVID-19 infection models, enhance antiviral drug delivery, foster new antiviral strategies, and boost vaccine efficacy. These efforts will not only contribute to stop or mitigate the current pandemic but will also provide unorthodox platforms to understand, prevent, and protect us from future viral outbreaks.
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Affiliation(s)
- Thibault Colombani
- Department of Chemical Engineering, Northeastern University, Boston, MA 02115 USA
| | - Zachary J. Rogers
- Department of Chemical Engineering, Northeastern University, Boston, MA 02115 USA
| | - Loek J. Eggermont
- Department of Chemical Engineering, Northeastern University, Boston, MA 02115 USA
| | - Sidi A. Bencherif
- Department of Chemical Engineering, Northeastern University, Boston, MA 02115 USA
- Department of Bioengineering, Northeastern University, Boston, MA 02115 USA
- Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138 USA
- Biomechanics and Bioengineering (BMBI), UTC CNRS UMR 7338, University of Technology of Compiègne, Sorbonne University, 60203 Compiègne, France
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38
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Yan H, Li Y, Cheng S, Zeng Y. Advances in Analytical Technologies for Extracellular Vesicles. Anal Chem 2021; 93:4739-4774. [PMID: 33635060 DOI: 10.1021/acs.analchem.1c00693] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- He Yan
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Yutao Li
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Shibo Cheng
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Yong Zeng
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States.,University of Florida Health Cancer Center, Gainesville, Florida 32610, United States
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39
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Pavel A, del Giudice G, Federico A, Di Lieto A, Kinaret PAS, Serra A, Greco D. Integrated network analysis reveals new genes suggesting COVID-19 chronic effects and treatment. Brief Bioinform 2021; 22:1430-1441. [PMID: 33569598 PMCID: PMC7929418 DOI: 10.1093/bib/bbaa417] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 11/13/2020] [Accepted: 12/19/2020] [Indexed: 01/08/2023] Open
Abstract
The COVID-19 disease led to an unprecedented health emergency, still ongoing worldwide. Given the lack of a vaccine or a clear therapeutic strategy to counteract the infection as well as its secondary effects, there is currently a pressing need to generate new insights into the SARS-CoV-2 induced host response. Biomedical data can help to investigate new aspects of the COVID-19 pathogenesis, but source heterogeneity represents a major drawback and limitation. In this work, we applied data integration methods to develop a Unified Knowledge Space (UKS) and used it to identify a new set of genes associated with SARS-CoV-2 host response, both in vitro and in vivo. Functional analysis of these genes reveals possible long-term systemic effects of the infection, such as vascular remodelling and fibrosis. Finally, we identified a set of potentially relevant drugs targeting proteins involved in multiple steps of the host response to the virus.
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Affiliation(s)
- Alisa Pavel
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- BioMediTech Institute, Tampere University, Tampere, Finland
| | - Giusy del Giudice
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- BioMediTech Institute, Tampere University, Tampere, Finland
| | - Antonio Federico
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- BioMediTech Institute, Tampere University, Tampere, Finland
| | - Antonio Di Lieto
- Department of Forensic Psychiatry, Aarhus University, Aarhus, Denmark
| | - Pia A S Kinaret
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Angela Serra
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- BioMediTech Institute, Tampere University, Tampere, Finland
| | - Dario Greco
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- BioMediTech Institute, Tampere University, Tampere, Finland
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
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40
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Waman VP, Sen N, Varadi M, Daina A, Wodak SJ, Zoete V, Velankar S, Orengo C. The impact of structural bioinformatics tools and resources on SARS-CoV-2 research and therapeutic strategies. Brief Bioinform 2021; 22:742-768. [PMID: 33348379 PMCID: PMC7799268 DOI: 10.1093/bib/bbaa362] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 11/06/2020] [Accepted: 11/09/2020] [Indexed: 01/18/2023] Open
Abstract
SARS-CoV-2 is the causative agent of COVID-19, the ongoing global pandemic. It has posed a worldwide challenge to human health as no effective treatment is currently available to combat the disease. Its severity has led to unprecedented collaborative initiatives for therapeutic solutions against COVID-19. Studies resorting to structure-based drug design for COVID-19 are plethoric and show good promise. Structural biology provides key insights into 3D structures, critical residues/mutations in SARS-CoV-2 proteins, implicated in infectivity, molecular recognition and susceptibility to a broad range of host species. The detailed understanding of viral proteins and their complexes with host receptors and candidate epitope/lead compounds is the key to developing a structure-guided therapeutic design. Since the discovery of SARS-CoV-2, several structures of its proteins have been determined experimentally at an unprecedented speed and deposited in the Protein Data Bank. Further, specialized structural bioinformatics tools and resources have been developed for theoretical models, data on protein dynamics from computer simulations, impact of variants/mutations and molecular therapeutics. Here, we provide an overview of ongoing efforts on developing structural bioinformatics tools and resources for COVID-19 research. We also discuss the impact of these resources and structure-based studies, to understand various aspects of SARS-CoV-2 infection and therapeutic development. These include (i) understanding differences between SARS-CoV-2 and SARS-CoV, leading to increased infectivity of SARS-CoV-2, (ii) deciphering key residues in the SARS-CoV-2 involved in receptor-antibody recognition, (iii) analysis of variants in host proteins that affect host susceptibility to infection and (iv) analyses facilitating structure-based drug and vaccine design against SARS-CoV-2.
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Affiliation(s)
| | | | | | - Antoine Daina
- Molecular Modeling Group at SIB, Swiss Institute of Bioinformatics
| | | | - Vincent Zoete
- Department of Fundamental Oncology at the University of Lausanne and Group leader at SIB
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41
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El Hassab MA, Ibrahim TM, Al-Rashood ST, Alharbi A, Eskandrani RO, Eldehna WM. In silico identification of novel SARS-COV-2 2'-O-methyltransferase (nsp16) inhibitors: structure-based virtual screening, molecular dynamics simulation and MM-PBSA approaches. J Enzyme Inhib Med Chem 2021; 36:727-736. [PMID: 33685335 PMCID: PMC7946047 DOI: 10.1080/14756366.2021.1885396] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The novel coronavirus disease COVID-19, caused by the virus SARS CoV-2, has exerted a significant unprecedented economic and medical crisis, in addition to its impact on the daily life and health care systems all over the world. Regrettably, no vaccines or drugs are currently available for this new critical emerging human disease. Joining the global fight against COVID-19, in this study we aim at identifying a potential novel inhibitor for SARS COV-2 2'-O-methyltransferase (nsp16) which is one of the most attractive targets in the virus life cycle, responsible for the viral RNA protection via a cap formation process. Firstly, nsp16 enzyme bound to Sinefungin was retrieved from the protein data bank (PDB ID: 6WKQ), then, a 3D pharmacophore model was constructed to be applied to screen 48 Million drug-like compounds of the Zinc database. This resulted in only 24 compounds which were subsequently docked into the enzyme. The best four score-ordered hits from the docking outcome exhibited better scores compared to Sinefungin. Finally, three molecular dynamics (MD) simulation experiments for 150 ns were carried out as a refinement step for our proposed approach. The MD and MM-PBSA outputs revealed compound 11 as the best potential nsp16 inhibitor herein identified, as it displayed a better stability and average binding free energy for the ligand-enzyme complex compared to Sinefungin.
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Affiliation(s)
- Mahmoud A El Hassab
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr City, Egypt
| | - Tamer M Ibrahim
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh, Egypt
| | - Sara T Al-Rashood
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Amal Alharbi
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Razan O Eskandrani
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Wagdy M Eldehna
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh, Egypt
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42
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Wang C, Konecki DM, Marciano DC, Govindarajan H, Williams AM, Wastuwidyaningtyas B, Bourquard T, Katsonis P, Lichtarge O. Identification of evolutionarily stable functional and immunogenic sites across the SARS-CoV-2 proteome and the greater coronavirus family. RESEARCH SQUARE 2021:rs.3.rs-95030. [PMID: 33106800 PMCID: PMC7587783 DOI: 10.21203/rs.3.rs-95030/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Since the first recognized case of COVID-19, more than 100 million people have been infected worldwide. Global efforts in drug and vaccine development to fight the disease have yielded vaccines and drug candidates to cure COVID-19. However, the spread of SARS-CoV-2 variants threatens the continued efficacy of these treatments. In order to address this, we interrogate the evolutionary history of the entire SARS-CoV-2 proteome to identify evolutionarily conserved functional sites that can inform the search for treatments with broader coverage across the coronavirus family. Combining this information with the mutations observed in the current COVID-19 outbreak, we systematically and comprehensively define evolutionarily stable sites that may provide useful drug and vaccine targets and which are less likely to be compromised by the emergence of new virus strains. Several experimentally-validated effective drugs interact with these proposed target sites. In addition, the same evolutionary information can prioritize cross reactive antigens that are useful in directing multi-epitope vaccine strategies to illicit broadly neutralizing immune responses to the betacoronavirus family. Although the results are focused on SARS-CoV-2, these approaches stem from evolutionary principles that are agnostic to the organism or infective agent.
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Affiliation(s)
- Chen Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Daniel M. Konecki
- Quantitative and Computational Biosciences Graduate Program, Baylor College of Medicine, Houston, TX 77030, USA
| | - David C. Marciano
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Harikumar Govindarajan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Amanda M. Williams
- Cancer and Cell Biology Graduate Program, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Thomas Bourquard
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- MAbSilico, Nouzilly, Centre, France, EU
| | - Panagiotis Katsonis
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Olivier Lichtarge
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Quantitative and Computational Biosciences Graduate Program, Baylor College of Medicine, Houston, TX 77030, USA
- Cancer and Cell Biology Graduate Program, Baylor College of Medicine, Houston, TX 77030, USA
- Computational and Integrative Biomedical Research Center, Baylor College of Medicine, Houston, TX 77030, USA
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43
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Wang C, Konecki DM, Marciano DC, Govindarajan H, Williams AM, Wastuwidyaningtyas B, Bourquard T, Katsonis P, Lichtarge O. Identification of evolutionarily stable functional and immunogenic sites across the SARS-CoV-2 proteome and the greater coronavirus family. RESEARCH SQUARE 2021:rs.3.rs-95030. [PMID: 36575762 PMCID: PMC9793837 DOI: 10.21203/rs.3.rs-95030/v3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Since the first recognized case of COVID-19, more than 100 million people have been infected worldwide. Global efforts in drug and vaccine development to fight the disease have yielded vaccines and drug candidates to cure COVID-19. However, the spread of SARS-CoV-2 variants threatens the continued efficacy of these treatments. In order to address this, we interrogate the evolutionary history of the entire SARS-CoV-2 proteome to identify evolutionarily conserved functional sites that can inform the search for treatments with broader coverage across the coronavirus family. Combining this information with the mutations observed in the current COVID-19 outbreak, we systematically and comprehensively define evolutionarily stable sites that may provide useful drug and vaccine targets and which are less likely to be compromised by the emergence of new virus strains. Several experimentally-validated effective drugs interact with these proposed target sites. In addition, the same evolutionary information can prioritize cross reactive antigens that are useful in directing multi-epitope vaccine strategies to illicit broadly neutralizing immune responses to the betacoronavirus family. Although the results are focused on SARS-CoV-2, these approaches stem from evolutionary principles that are agnostic to the organism or infective agent.
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Affiliation(s)
- Chen Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Daniel M. Konecki
- Quantitative and Computational Biosciences Graduate Program, Baylor College of Medicine, Houston, TX 77030, USA
| | - David C. Marciano
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA,Correspondence: (D.C.M), (O.L.)
| | - Harikumar Govindarajan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Amanda M. Williams
- Cancer and Cell Biology Graduate Program, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Thomas Bourquard
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA,MAbSilico, Nouzilly, Centre, France, EU
| | - Panagiotis Katsonis
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Olivier Lichtarge
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA,Quantitative and Computational Biosciences Graduate Program, Baylor College of Medicine, Houston, TX 77030, USA,Cancer and Cell Biology Graduate Program, Baylor College of Medicine, Houston, TX 77030, USA,Computational and Integrative Biomedical Research Center, Baylor College of Medicine, Houston, TX 77030, USA,Correspondence: (D.C.M), (O.L.)
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44
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Selvaraj C, Panwar U, Dinesh DC, Boura E, Singh P, Dubey VK, Singh SK. Microsecond MD Simulation and Multiple-Conformation Virtual Screening to Identify Potential Anti-COVID-19 Inhibitors Against SARS-CoV-2 Main Protease. Front Chem 2021; 8:595273. [PMID: 33585398 PMCID: PMC7873971 DOI: 10.3389/fchem.2020.595273] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Accepted: 11/19/2020] [Indexed: 12/14/2022] Open
Abstract
The recent pandemic outbreak of COVID-19, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), raised global health and economic concerns. Phylogenetically, SARS-CoV-2 is closely related to SARS-CoV, and both encode the enzyme main protease (Mpro/3CLpro), which can be a potential target inhibiting viral replication. Through this work, we have compiled the structural aspects of Mpro conformational changes, with molecular modeling and 1-μs MD simulations. Long-scale MD simulation resolves the mechanism role of crucial amino acids involved in protein stability, followed by ensemble docking which provides potential compounds from the Traditional Chinese Medicine (TCM) database. These lead compounds directly interact with active site residues (His41, Gly143, and Cys145) of Mpro, which plays a crucial role in the enzymatic activity. Through the binding mode analysis in the S1, S1′, S2, and S4 binding subsites, screened compounds may be functional for the distortion of the oxyanion hole in the reaction mechanism, and it may lead to the inhibition of Mpro in SARS-CoV-2. The hit compounds are naturally occurring compounds; they provide a sustainable and readily available option for medical treatment in humans infected by SARS-CoV-2. Henceforth, extensive analysis through molecular modeling approaches explained that the proposed molecules might be promising SARS-CoV-2 inhibitors for the inhibition of COVID-19, subjected to experimental validation.
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Affiliation(s)
- Chandrabose Selvaraj
- Computer Aided Drug Design and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi, India
| | - Umesh Panwar
- Computer Aided Drug Design and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi, India
| | - Dhurvas Chandrasekaran Dinesh
- Section of Molecular Biology and Biochemistry, Institute of Organic Chemistry and Biochemistry AS CR, v.v.i., Prague, Czechia
| | - Evzen Boura
- Section of Molecular Biology and Biochemistry, Institute of Organic Chemistry and Biochemistry AS CR, v.v.i., Prague, Czechia
| | - Poonam Singh
- Corrosion and Materials Protection Division, Council of Scientific and Industrial Research (CSIR)-Central Electrochemical Research Institute, Karaikudi, India
| | - Vikash Kumar Dubey
- School of Biochemical Engineering, Indian Institute of Technology (BHU), Varanasi, India
| | - Sanjeev Kumar Singh
- Computer Aided Drug Design and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi, India
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Carro B. SARS-CoV-2 mechanisms of action and impact on human organism, risk factors and potential treatments. An exhaustive survey. ALL LIFE 2021. [DOI: 10.1080/26895293.2021.1977186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Affiliation(s)
- Belén Carro
- Department of Signal Theory and Communications, Universidad de Valladolid, Valladolid, Spain
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Pitsillou E, Liang J, Ververis K, Lim KW, Hung A, Karagiannis TC. Identification of Small Molecule Inhibitors of the Deubiquitinating Activity of the SARS-CoV-2 Papain-Like Protease: in silico Molecular Docking Studies and in vitro Enzymatic Activity Assay. Front Chem 2020; 8:623971. [PMID: 33364229 PMCID: PMC7753156 DOI: 10.3389/fchem.2020.623971] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 11/16/2020] [Indexed: 12/14/2022] Open
Abstract
COVID-19 is an ongoing pandemic caused by the SARS-CoV-2 virus with important political, socio-economic, and public health consequences. Inhibiting replication represents an important antiviral approach, and in this context two viral proteases, the SARS-CoV-2 main and papain-like proteases (PLpro), which cleave pp1a and pp1ab polypeptides, are critical. Along with protease activity, the PLpro possesses deubiquitinating activity, which is important in immune regulation. Naphthalene-based inhibitors, such as the well-investigated GRL-0617 compound, have been shown to possess dual effects, inhibiting both protease and deubiquitinating activity of the PLpro. Rather than binding to the canonical catalytic triad, these type of non-covalent inhibitors target an adjacent pocket, the naphthalene-inhibitor binding site. Using a high-throughput screen, we have previously identified the dietary hypericin, rutin, and cyanidin-3-O-glucoside compounds as potential protease inhibitors targeting the naphthalene-inhibitor binding site. Here, our aim was to investigate the binding characteristics of these compounds to the PLpro, and to evaluate deubiquitinating activity, by analyzing seven different PLpro crystal structures. Molecular docking highlighted the relatively high affinity of GRL-0617 and dietary compounds. In contrast binding of the small molecules was abolished in the presence of ubiquitin in the palm subdomain of the PLpro. Further, docking the small molecules in the naphthalene-inhibitor binding site, followed by protein-protein docking revealed displacement of ubiquitin in a conformation inconsistent with functional activity. Finally, the deubiquitinating activity was validated in vitro using an enzymatic activity assay. The findings indicated that the dietary compounds inhibited deubiquitinase activity in the micromolar range with an order of activity of GRL-0167, hypericin >> rutin, cyanidin-3-O-glucoside > epigallocatechin gallate, epicatechin gallate, and cefotaxime. Our findings are in accordance with mechanisms and potential antiviral effects of the naphthalene-based, GRL-0617 inhibitor, which is currently progressing in preclinical trials. Further, our findings indicate that in particular hypericin, rutin, and cyanidin-3-O-glucoside, represent suitable candidates for subsequent evaluation as PLpro inhibitors.
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Affiliation(s)
- Eleni Pitsillou
- Epigenomic Medicine, Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC, Australia
- School of Science, College of Science, Engineering and Health, RMIT University, Melbourne, VIC, Australia
| | - Julia Liang
- Epigenomic Medicine, Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC, Australia
- School of Science, College of Science, Engineering and Health, RMIT University, Melbourne, VIC, Australia
| | - Katherine Ververis
- Epigenomic Medicine, Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - Kah Wai Lim
- Epigenomic Medicine, Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC, Australia
- Department of Microbiology and Immunology, The University of Melbourne, Parkville, VIC, Australia
| | - Andrew Hung
- School of Science, College of Science, Engineering and Health, RMIT University, Melbourne, VIC, Australia
| | - Tom C. Karagiannis
- Epigenomic Medicine, Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC, Australia
- Department of Clinical Pathology, The University of Melbourne, Parkville, VIC, Australia
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Singh DD, Han I, Choi EH, Yadav DK. Recent Advances in Pathophysiology, Drug Development and Future Perspectives of SARS-CoV-2. Front Cell Dev Biol 2020; 8:580202. [PMID: 33240881 PMCID: PMC7677140 DOI: 10.3389/fcell.2020.580202] [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: 07/05/2020] [Accepted: 09/22/2020] [Indexed: 12/15/2022] Open
Abstract
The coronavirus (SARS-CoV-2) pandemic is a rapidly transmitting and highly pathogenic disease. The spike protein of SARS-CoV-2 binds to the surface of angiotensin-converting enzyme-2 (ACE2) receptors along the upper respiratory tract and intestinal epithelial cells. SARS-CoV-2 patients develop acute respiratory distress, lymphocytic myocarditis, disseminated intravascular coagulation, lymphocytic infiltration, and other serious complications. A SARS-CoV-2 diagnosis is conducted using quantitative reverse-transcription PCR and computed tomography (CT) imaging. In addition, IgM or IgG antibodies are used to identify acute and convalescent illness. Recent clinical data have been generated by health workers and researchers and have shown that there is an urgent requirement in the effective clinical and treatment of patients, as well as other developments for dealing with SARS-CoV-2 infection. A broad spectrum of clinical trials of different vaccines and drug treatment has been evaluated for use against SARS-CoV-2. This review includes the emergence of SARS-CoV-2 pneumonia as a way to recognize and eliminate any barriers that affect rapid patient care and public health management against the SARS-CoV-2 epidemic based on the natural history of the disease, its transmission, pathogenesis, immune response, epidemiology, diagnosis, clinical presentation, possible treatment, drug and vaccine development, prevention, and future perspective.
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Affiliation(s)
- Desh Deepak Singh
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India
| | - Ihn Han
- Plasma Bioscience Research Center, Applied Plasma Medicine Center, Department of Electrical and Biological Physics, Kwangwoon University, Seoul, South Korea
| | - Eun-Ha Choi
- Plasma Bioscience Research Center, Applied Plasma Medicine Center, Department of Electrical and Biological Physics, Kwangwoon University, Seoul, South Korea
| | - Dharmendra K. Yadav
- College of Pharmacy, Gachon University of Medicine and Science, Incheon, South Korea
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Li Q, Kang C. Progress in Developing Inhibitors of SARS-CoV-2 3C-Like Protease. Microorganisms 2020; 8:E1250. [PMID: 32824639 PMCID: PMC7463875 DOI: 10.3390/microorganisms8081250] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 08/12/2020] [Accepted: 08/12/2020] [Indexed: 12/23/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The viral outbreak started in late 2019 and rapidly became a serious health threat to the global population. COVID-19 was declared a pandemic by the World Health Organization in March 2020. Several therapeutic options have been adopted to prevent the spread of the virus. Although vaccines have been developed, antivirals are still needed to combat the infection of this virus. SARS-CoV-2 is an enveloped virus, and its genome encodes polyproteins that can be processed into structural and nonstructural proteins. Maturation of viral proteins requires cleavages by proteases. Therefore, the main protease (3 chymotrypsin-like protease (3CLpro) or Mpro) encoded by the viral genome is an attractive drug target because it plays an important role in cleaving viral polyproteins into functional proteins. Inhibiting this enzyme is an efficient strategy to block viral replication. Structural studies provide valuable insight into the function of this protease and structural basis for rational inhibitor design. In this review, we describe structural studies on the main protease of SARS-CoV-2. The strategies applied in developing inhibitors of the main protease of SARS-CoV-2 and currently available protein inhibitors are summarized. Due to the availability of high-resolution structures, structure-guided drug design will play an important role in developing antivirals. The availability of high-resolution structures, potent peptidic inhibitors, and diverse compound scaffolds indicate the feasibility of developing potent protease inhibitors as antivirals for COVID-19.
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Affiliation(s)
- Qingxin Li
- Guangdong Provincial Engineering Laboratory of Biomass High Value Utilization, Institute of Bioengineering, Guangdong Academy of Sciences, Guangzhou 510316, China
| | - CongBao Kang
- Experimental Drug Development Centre (EDDC), Agency for Science, Technology and Research (A*STAR), 10 Biopolis Road, Chromos, #05-01, Singapore 138670, Singapore
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