151
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Santana HS, de Souza MRP, Lopes MGM, Souza J, Silva RRO, Palma MSA, Nakano WLV, Lima GAS, Munhoz G, Noriler D, Taranto OP, Silva JL. How chemical engineers can contribute to fight the COVID-19. J Taiwan Inst Chem Eng 2020; 116:67-80. [PMID: 33282011 PMCID: PMC7698668 DOI: 10.1016/j.jtice.2020.11.024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 11/22/2020] [Accepted: 11/23/2020] [Indexed: 12/22/2022]
Abstract
The SARS-CoV-2 virus, promoter of COVID-19, already infected millions of people around the world, resulting in thousands of fatal victims. Facing this unprecedented crisis in human history, several research groups, industrial companies and governments have been spending efforts to develop vaccines and medications. People from distinct knowledge fields are doing their part in order to overcome this crisis. Chemical Engineers are also contributing in the development of actions to control the SARS-CoV-2 virus. However, many chemical engineers still do not know how to use the knowledge acquired from Chemical Engineering school to collaborate in the fight against the COVID-19. In this context, the present paper aims to discuss several knowledge fields within the Chemical Engineering and correlated areas successfully applied to create innovative and effective solutions in the fight against the COVID-19.
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Affiliation(s)
- Harrson S Santana
- University of Campinas, School of Chemical Engineering, Albert Einstein Av. 500, 13083-852 Campinas, SP, Brazil
| | - Marcos R P de Souza
- Universidade Federal do Amazonas, Faculdade de Ciências Agrárias, Departamento de Engenharia Agrícola e dos Solos, Av. General Rodrigo Otávio, 1200, 69067-005, Manaus, AM, Brazil
| | - Mariana G M Lopes
- University of Campinas, School of Chemical Engineering, Albert Einstein Av. 500, 13083-852 Campinas, SP, Brazil
| | - Johmar Souza
- University of Campinas, School of Chemical Engineering, Albert Einstein Av. 500, 13083-852 Campinas, SP, Brazil
| | - Renan R O Silva
- Department of Biochemical and Pharmaceutical Technology, Sao Paulo University, 05508-000 São Paulo, São Paulo, Brazil
| | - Mauri S A Palma
- Department of Biochemical and Pharmaceutical Technology, Sao Paulo University, 05508-000 São Paulo, São Paulo, Brazil
| | - Wilson L V Nakano
- University of Campinas, School of Chemical Engineering, Albert Einstein Av. 500, 13083-852 Campinas, SP, Brazil
| | | | | | - Dirceu Noriler
- University of Campinas, School of Chemical Engineering, Albert Einstein Av. 500, 13083-852 Campinas, SP, Brazil
| | - Osvaldir P Taranto
- University of Campinas, School of Chemical Engineering, Albert Einstein Av. 500, 13083-852 Campinas, SP, Brazil
| | - João L Silva
- Federal University of ABC, CECS - Center for Engineering, Modeling and Applied Social Sciences, Alameda da Universidade, s/n., 09606-045 São Bernardo do Campo, SP, Brazil
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152
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Haddad C, Davila-Calderon J, Tolbert BS. Integrated approaches to reveal mechanisms by which RNA viruses reprogram the cellular environment. Methods 2020; 183:50-56. [PMID: 32622045 PMCID: PMC7329689 DOI: 10.1016/j.ymeth.2020.06.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 06/16/2020] [Accepted: 06/19/2020] [Indexed: 12/12/2022] Open
Abstract
RNA viruses are major threats to global society and mass outbreaks can cause long-lasting damage to international economies. RNA and related retro viruses represent a large and diverse family that contribute to the onset of human diseases such as AIDS; certain cancers like T cell lymphoma; severe acute respiratory illnesses as seen with COVID-19; and others. The hallmark of this viral family is the storage of genetic material in the form of RNA, and upon infecting host cells, their RNA genomes reprogram the cellular environment to favor productive viral replication. RNA is a multifunctional biomolecule that not only stores and transmits heritable information, but it also has the capacity to catalyze complex biochemical reactions. It is therefore no surprise that RNA viruses use this functional diversity to their advantage to sustain chronic or lifelong infections. Efforts to subvert RNA viruses therefore requires a deep understanding of the mechanisms by which these pathogens usurp cellular machinery. Here, we briefly summarize several experimental techniques that individually inform on key physicochemical features of viral RNA genomes and their interactions with proteins. Each of these techniques provide important vantage points to understand the complexities of virus-host interactions, but we attempt to make the case that by integrating these and similar methods, more vivid descriptions of how viruses reprogram the cellular environment emerges. These vivid descriptions should expedite the identification of novel therapeutic targets.
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153
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Tomaszewski T, DeVries RS, Dong M, Bhatia G, Norsworthy MD, Zheng X, Caetano-Anollés G. New Pathways of Mutational Change in SARS-CoV-2 Proteomes Involve Regions of Intrinsic Disorder Important for Virus Replication and Release. Evol Bioinform Online 2020; 16:1176934320965149. [PMID: 33149541 PMCID: PMC7586267 DOI: 10.1177/1176934320965149] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 09/16/2020] [Indexed: 12/21/2022] Open
Abstract
The massive worldwide spread of the SARS-CoV-2 virus is fueling the COVID-19 pandemic. Since the first whole-genome sequence was published in January 2020, a growing database of tens of thousands of viral genomes has been constructed. This offers opportunities to study pathways of molecular change in the expanding viral population that can help identify molecular culprits of virulence and virus spread. Here we investigate the genomic accumulation of mutations at various time points of the early pandemic to identify changes in mutationally highly active genomic regions that are occurring worldwide. We used the Wuhan NC_045512.2 sequence as a reference and sampled 15 342 indexed sequences from GISAID, translating them into proteins and grouping them by month of deposition. The per-position amino acid frequencies and Shannon entropies of the coding sequences were calculated for each month, and a map of intrinsic disorder regions and binding sites was generated. The analysis revealed dominant variants, most of which were located in loop regions and on the surface of the proteins. Mutation entropy decreased between March and April of 2020 after steady increases at several sites, including the D614G mutation site of the spike (S) protein that was previously found associated with higher case fatality rates and at sites of the NSP12 polymerase and the NSP13 helicase proteins. Notable expanding mutations include R203K and G204R of the nucleocapsid (N) protein inter-domain linker region and G251V of the viroporin encoded by ORF3a between March and April. The regions spanning these mutations exhibited significant intrinsic disorder, which was enhanced and decreased by the N-protein and viroporin 3a protein mutations, respectively. These results predict an ongoing mutational shift from the spike and replication complex to other regions, especially to encoded molecules known to represent major β-interferon antagonists. The study provides valuable information for therapeutics and vaccine design, as well as insight into mutation tendencies that could facilitate preventive control.
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Affiliation(s)
- Tre Tomaszewski
- Department of Information Sciences, University of Illinois, Urbana, IL, USA
| | - Ryan S DeVries
- Department of Information Sciences, University of Illinois, Urbana, IL, USA
| | - Mengyi Dong
- Department of Food Science & Human Nutrition, University of Illinois, Urbana, IL, USA
| | - Gitanshu Bhatia
- Department of Agricultural & Biological Engineering, University of Illinois, Urbana, IL, USA
| | | | - Xuying Zheng
- Department of Crop Sciences, University of Illinois, Urbana, IL, USA
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154
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Patra S, Kerry RG, Maurya GK, Panigrahi B, Kumari S, Rout JR. Emerging Molecular Prospective of SARS-CoV-2: Feasible Nanotechnology Based Detection and Inhibition. Front Microbiol 2020; 11:2098. [PMID: 33193115 PMCID: PMC7606273 DOI: 10.3389/fmicb.2020.02098] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 08/10/2020] [Indexed: 12/13/2022] Open
Abstract
The rapid dissemination of SARS-CoV-2 demonstrates how vulnerable it can make communities and is why it has attained the status of global pandemic. According to the estimation from Worldometer, the SARS-CoV-2 affected cases and deaths are exponentially increasing worldwide, marking the mortality rate as ∼3.8% with no probability of its cessation till now. Despite massive attempts and races among scientific communities in search of proper therapeutic options, the termination of this breakneck outbreak of COVID-19 has still not been made possible. Therefore, this review highlights the diverse molecular events induced by a viral infection, such as autophagy, unfolded protein response (UPR), and inflammasome, illustrating the intracellular cascades regulating viral replication inside the host cell. The SARS-CoV-2-mediated endoplasmic reticulum stress and apoptosis are also emphasized in the review. Additionally, host's immune response associated with SARS-CoV-2 infection, as well as the genetic and epigenetic changes, have been demonstrated, which altogether impart a better understanding of its epidemiology. Considering the drawbacks of available diagnostics and medications, herein we have presented the most sensitive nano-based biosensors for the rapid detection of viral components. Moreover, conceptualizing the viral-induced molecular changes inside its target cells, nano-based antiviral systems have also been proposed in this review.
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Affiliation(s)
- Sushmita Patra
- Department of Biotechnology, North Orissa University, Baripada, India
| | | | - Ganesh Kumar Maurya
- Zoology Section, Mahila Mahavidyalaya, Banaras Hindu University, Varanasi, India
| | - Bijayananda Panigrahi
- School of Biotechnology, Kalinga Institute of Industrial Technology, Bhubaneswar, India
| | - Swati Kumari
- School of Biotechnology, Kalinga Institute of Industrial Technology, Bhubaneswar, India
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155
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Molecular docking analysis of selected phytochemicals against SARS-CoV-2 M pro receptor. ACTA ACUST UNITED AC 2020; 33:766-781. [PMID: 33100613 PMCID: PMC7567421 DOI: 10.1007/s42535-020-00162-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 09/04/2020] [Accepted: 09/11/2020] [Indexed: 02/07/2023]
Abstract
Presently world is on a war with the novel coronavirus and with no immediate treatments available the scourge caused by the SARS-CoV-2 is increasing day by day. A lot of researches are going on for the potential drug candidate that could help the healthcare system in this fight. Plants are a natural data bank of bioactive compounds. Many phytochemicals are being studied for various ailments including cancer, bacterial and viral infections, etc. The present study aims to screen 38 bioactive compounds from 5 selected plants viz., Azadirachta indica, Curcuma longa, Zingiber officinale, Ocimum basilicum and Panax ginseng against SARS-CoV-2. Lipinski’s rule was taken as the foundation for initial screening. Shortlisted compounds were subjected to molecular docking study with Mpro receptor present in SARS-CoV-2. The study identified that gedunin, epoxyazadiradione, nimbin and ginsenosides have potential to inhibit Mpro activity and their binding energies are − 9.51 kcal/mol, − 8.47 kcal/mol, − 8.66 kcal/mol and − 9.63 kcal/mol respectively. Based on bioavailability radar studies gedunin and epoxyazadiradione are the two most potent compounds which are used for molecular dynamics simulation studies. Molecular dynamics studies showed that gedunin is more potent than epoxyazadiradione. To find the effectiveness and to propose the exact mechanism, in-vitro studies can be further performed on gedunin.
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156
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Metallodrug ranitidine bismuth citrate suppresses SARS-CoV-2 replication and relieves virus-associated pneumonia in Syrian hamsters. Nat Microbiol 2020; 5:1439-1448. [PMID: 33028965 DOI: 10.1038/s41564-020-00802-x] [Citation(s) in RCA: 123] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 09/21/2020] [Indexed: 12/15/2022]
Abstract
SARS-CoV-2 is causing a pandemic of COVID-19, with high infectivity and significant mortality1. Currently, therapeutic options for COVID-19 are limited. Historically, metal compounds have found use as antimicrobial agents, but their antiviral activities have rarely been explored. Here, we test a set of metallodrugs and related compounds, and identify ranitidine bismuth citrate, a commonly used drug for the treatment of Helicobacter pylori infection, as a potent anti-SARS-CoV-2 agent, both in vitro and in vivo. Ranitidine bismuth citrate exhibited low cytotoxicity and protected SARS-CoV-2-infected cells with a high selectivity index of 975. Importantly, ranitidine bismuth citrate suppressed SARS-CoV-2 replication, leading to decreased viral loads in both upper and lower respiratory tracts, and relieved virus-associated pneumonia in a golden Syrian hamster model. In vitro studies showed that ranitidine bismuth citrate and its related compounds exhibited inhibition towards both the ATPase (IC50 = 0.69 µM) and DNA-unwinding (IC50 = 0.70 µM) activities of the SARS-CoV-2 helicase via an irreversible displacement of zinc(II) ions from the enzyme by bismuth(III) ions. Our findings highlight viral helicase as a druggable target and the clinical potential of bismuth(III) drugs or other metallodrugs for the treatment of SARS-CoV-2 infection.
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157
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Senger MR, Evangelista TCS, Dantas RF, Santana MVDS, Gonçalves LCS, de Souza Neto LR, Ferreira SB, Silva-Junior FP. COVID-19: molecular targets, drug repurposing and new avenues for drug discovery. Mem Inst Oswaldo Cruz 2020; 115:e200254. [PMID: 33027420 PMCID: PMC7534958 DOI: 10.1590/0074-02760200254] [Citation(s) in RCA: 20] [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: 05/22/2020] [Accepted: 09/01/2020] [Indexed: 01/18/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a highly contagious infection that may break the healthcare system of several countries. Here, we aimed at presenting a critical view of ongoing drug repurposing efforts for COVID-19 as well as discussing opportunities for development of new treatments based on current knowledge of the mechanism of infection and potential targets within. Finally, we also discuss patent protection issues, cost effectiveness and scalability of synthetic routes for some of the most studied repurposing candidates since these are key aspects to meet global demand for COVID-19 treatment.
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Affiliation(s)
- Mario Roberto Senger
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório
de Bioquímica Experimental e Computacional de Fármacos, Rio de Janeiro, RJ,
Brasil
| | - Tereza Cristina Santos Evangelista
- Universidade Federal do Rio de Janeiro, Instituto de Química,
Laboratório de Síntese Orgânica e Prospecção Biológica, Rio de Janeiro, RJ,
Brasil
| | - Rafael Ferreira Dantas
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório
de Bioquímica Experimental e Computacional de Fármacos, Rio de Janeiro, RJ,
Brasil
| | - Marcos Vinicius da Silva Santana
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório
de Bioquímica Experimental e Computacional de Fármacos, Rio de Janeiro, RJ,
Brasil
| | - Luiz Carlos Saramago Gonçalves
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório
de Bioquímica Experimental e Computacional de Fármacos, Rio de Janeiro, RJ,
Brasil
| | - Lauro Ribeiro de Souza Neto
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório
de Bioquímica Experimental e Computacional de Fármacos, Rio de Janeiro, RJ,
Brasil
| | - Sabrina Baptista Ferreira
- Universidade Federal do Rio de Janeiro, Instituto de Química,
Laboratório de Síntese Orgânica e Prospecção Biológica, Rio de Janeiro, RJ,
Brasil
| | - Floriano Paes Silva-Junior
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório
de Bioquímica Experimental e Computacional de Fármacos, Rio de Janeiro, RJ,
Brasil
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158
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Jaiswal G, Kumar V. In-silico design of a potential inhibitor of SARS-CoV-2 S protein. PLoS One 2020; 15:e0240004. [PMID: 33002032 PMCID: PMC7529220 DOI: 10.1371/journal.pone.0240004] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 09/18/2020] [Indexed: 12/25/2022] Open
Abstract
The SARS-CoV-2 virus has caused a pandemic and is public health emergency of international concern. As of now, no registered therapies are available for treatment of coronavirus infection. The viral infection depends on the attachment of spike (S) glycoprotein to human cell receptor angiotensin-converting enzyme 2 (ACE2). We have designed a protein inhibitor (ΔABP-D25Y) targeting S protein using computational approach. The inhibitor consists of two α helical peptides homologues to protease domain (PD) of ACE2. Docking studies and molecular dynamic simulation revealed that the inhibitor binds exclusively at the ACE2 binding site of S protein. The computed binding affinity of the inhibitor is higher than the ACE2 and thus will likely out compete ACE2 for binding to S protein. Hence, the proposed inhibitor ΔABP-D25Y could be a potential blocker of S protein and receptor binding domain (RBD) attachment.
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Affiliation(s)
- Grijesh Jaiswal
- Amity Institute of Molecular Medicine and Stem Cell Research (AIMMSCR), Amity University, Noida Uttar Pradesh, India
| | - Veerendra Kumar
- Amity Institute of Molecular Medicine and Stem Cell Research (AIMMSCR), Amity University, Noida Uttar Pradesh, India
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159
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Hosseini FS, Amanlou M. Anti-HCV and anti-malaria agent, potential candidates to repurpose for coronavirus infection: Virtual screening, molecular docking, and molecular dynamics simulation study. Life Sci 2020; 258:118205. [PMID: 32777300 PMCID: PMC7413873 DOI: 10.1016/j.lfs.2020.118205] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 07/24/2020] [Accepted: 08/01/2020] [Indexed: 01/25/2023]
Abstract
AIMS Coronavirus disease 2019 (COVID-19) has appeared in Wuhan, China but the fast transmission has led to its widespread prevalence in various countries, which has made it a global concern. Another concern is the lack of definitive treatment for this disease. The researchers tried different treatment options which are not specific. The current study aims to identify potential small molecule inhibitors against the main protease protein of SARS-CoV-2 by the computational approach. MAIN METHODS In this study, a virtual screening procedure employing docking of the two different datasets from the ZINC database, including 1615 FDA approved drugs and 4266 world approved drugs were used to identify new potential small molecule inhibitors for the newly released crystal structure of main protease protein of SARS-CoV-2. In the following to validate the docking result, molecular dynamics simulations were applied on selected ligands to identify the behavior and stability of them in the binding pocket of the main protease in 150 nanoseconds (ns). Furthermore, binding energy using the MMPBSA approach was also calculated. KEY FINDINGS The result indicates that simeprevir (Hepatitis C virus NS3/4A protease inhibitor) and pyronaridine (antimalarial agent) could fit well to the binding pocket of the main protease and because of some other beneficial features including broad-spectrum antiviral properties and ADME profile, they might be a promising drug candidate for repurposing to the treatment of COVID-19. SIGNIFICANCE Simeprevir and pyronaridine were selected by the combination of virtual screening and molecular dynamics simulation approaches as a potential candidate for treatment of COVID-19.
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Affiliation(s)
- Faezeh Sadat Hosseini
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Massoud Amanlou
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran; Experimental Medicine Research Center, Tehran University of Medical Sciences, Tehran, Iran.
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160
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Khatoon F, Prasad K, Kumar V. Neurological manifestations of COVID-19: available evidences and a new paradigm. J Neurovirol 2020; 26:619-630. [PMID: 32839951 PMCID: PMC7444681 DOI: 10.1007/s13365-020-00895-4] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 07/17/2020] [Accepted: 08/14/2020] [Indexed: 01/01/2023]
Abstract
The recent pandemic outbreak of coronavirus is pathogenic and a highly transmittable viral infection caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV2). In this time of ongoing pandemic, many emerging reports suggested that the SARS-CoV-2 has inimical effects on neurological functions, and even causes serious neurological damage. The neurological symptoms associated with COVID-19 include headache, dizziness, depression, anosmia, encephalitis, stroke, epileptic seizures, and Guillain-Barre syndrome along with many others. The involvement of the CNS may be related with poor prognosis and disease worsening. Here, we review the evidence of nervous system involvement and currently known neurological manifestations in COVID-19 infections caused by SARS-CoV-2. We prioritize the 332 human targets of SARS-CoV-2 according to their association with brain-related disease and identified 73 candidate genes. We prioritize these 73 genes according to their spatio-temporal expression in the different regions of brain and also through evolutionary intolerance analysis. The prioritized genes could be considered potential indicators of COVID-19-associated neurological symptoms and thus act as a possible therapeutic target for the prevention and treatment of CNS manifestations associated with COVID-19 patients.
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Affiliation(s)
- Fatima Khatoon
- Amity Institute of Neuropsychology & Neurosciences, Amity University, Noida, Uttar Pradesh, 201303, India
| | - Kartikay Prasad
- Amity Institute of Neuropsychology & Neurosciences, Amity University, Noida, Uttar Pradesh, 201303, India
| | - Vijay Kumar
- Amity Institute of Neuropsychology & Neurosciences, Amity University, Noida, Uttar Pradesh, 201303, India.
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161
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Baby K, Maity S, Mehta CH, Suresh A, Nayak UY, Nayak Y. Targeting SARS-CoV-2 RNA-dependent RNA polymerase: An in silico drug repurposing for COVID-19. F1000Res 2020; 9:1166. [PMID: 33204411 PMCID: PMC7610171 DOI: 10.12688/f1000research.26359.1] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/15/2020] [Indexed: 01/18/2023] Open
Abstract
Background: The coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), took more lives than combined epidemics of SARS, MERS, H1N1, and Ebola. Currently, the prevention and control of spread are the goals in COVID-19 management as there are no specific drugs to cure or vaccines available for prevention. Hence, the drug repurposing was explored by many research groups, and many target proteins have been examined. The major protease (M pro), and RNA-dependent RNA polymerase (RdRp) are two target proteins in SARS-CoV-2 that have been validated and extensively studied for drug development in COVID-19. The RdRp shares a high degree of homology between those of two previously known coronaviruses, SARS-CoV and MERS-CoV. Methods: In this study, the FDA approved library of drugs were docked against the active site of RdRp using Schrodinger's computer-aided drug discovery tools for in silico drug-repurposing. Results: We have shortlisted 14 drugs from the Standard Precision docking and interaction-wise study of drug-binding with the active site on the enzyme. These drugs are antibiotics, NSAIDs, hypolipidemic, coagulant, thrombolytic, and anti-allergics. In molecular dynamics simulations, pitavastatin, ridogrel and rosoxacin displayed superior binding with the active site through ARG555 and divalent magnesium. Conclusion: Pitavastatin, ridogrel and rosoxacin can be further optimized in preclinical and clinical studies to determine their possible role in COVID-19 treatment.
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Affiliation(s)
- Krishnaprasad Baby
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Swastika Maity
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Chetan H. Mehta
- Department of Pharmaceutics, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Akhil Suresh
- Department of Pharmaceutics, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Usha Y. Nayak
- Department of Pharmaceutics, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Yogendra Nayak
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
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162
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Rehman HM, Mirza MU, Ahmad MA, Saleem M, Froeyen M, Ahmad S, Gul R, Alghamdi HA, Aslam MS, Sajjad M, Bhinder MA. A Putative Prophylactic Solution for COVID-19: Development of Novel Multiepitope Vaccine Candidate against SARS-COV-2 by Comprehensive Immunoinformatic and Molecular Modelling Approach. BIOLOGY 2020; 9:E296. [PMID: 32962156 PMCID: PMC7563440 DOI: 10.3390/biology9090296] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 09/04/2020] [Accepted: 09/05/2020] [Indexed: 12/13/2022]
Abstract
The outbreak of 2019-novel coronavirus (SARS-CoV-2) that causes severe respiratory infection (COVID-19) has spread in China, and the World Health Organization has declared it a pandemic. However, no approved drug or vaccines are available, and treatment is mainly supportive and through a few repurposed drugs. The urgency of the situation requires the development of SARS-CoV-2-based vaccines. Immunoinformatic and molecular modelling are time-efficient methods that are generally used to accelerate the discovery and design of the candidate peptides for vaccine development. In recent years, the use of multiepitope vaccines has proved to be a promising immunization strategy against viruses and pathogens, thus inducing more comprehensive protective immunity. The current study demonstrated a comprehensive in silico strategy to design stable multiepitope vaccine construct (MVC) from B-cell and T-cell epitopes of essential SARS-CoV-2 proteins with the help of adjuvants and linkers. The integrated molecular dynamics simulations analysis revealed the stability of MVC and its interaction with human Toll-like receptors (TLRs), which trigger an innate and adaptive immune response. Later, the in silico cloning in a known pET28a vector system also estimated the possibility of MVC expression in Escherichia coli. Despite that this study lacks validation of this vaccine construct in terms of its efficacy, the current integrated strategy encompasses the initial multiple epitope vaccine design concepts. After validation, this MVC can be present as a better prophylactic solution against COVID-19.
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Affiliation(s)
- Hafiz Muzzammel Rehman
- Institute of Biochemistry and Biotechnology, University of the Punjab, Lahore 54590, Punjab, Pakistan; (H.M.R.); (M.S.A.)
- Department of Human Genetics and Molecular Biology, University of Health Sciences, Lahore 54590, Punjab, Pakistan; (M.A.A.); (M.A.B.)
| | - Muhammad Usman Mirza
- Department of Pharmaceutical and Pharmacological Sciences, Rega Institute for Medical Research, Medicinal Chemistry, University of Leuven, B-3000 Leuven, Belgium; (M.U.M.); (M.F.)
| | - Mian Azhar Ahmad
- Department of Human Genetics and Molecular Biology, University of Health Sciences, Lahore 54590, Punjab, Pakistan; (M.A.A.); (M.A.B.)
- Department of Health, Government of the Punjab, Lahore 54590, Punjab, Pakistan
| | - Mahjabeen Saleem
- Institute of Biochemistry and Biotechnology, University of the Punjab, Lahore 54590, Punjab, Pakistan; (H.M.R.); (M.S.A.)
| | - Matheus Froeyen
- Department of Pharmaceutical and Pharmacological Sciences, Rega Institute for Medical Research, Medicinal Chemistry, University of Leuven, B-3000 Leuven, Belgium; (M.U.M.); (M.F.)
| | - Sarfraz Ahmad
- Drug Design and Development Research Group (DDDRG), Department of Chemistry, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia;
| | - Roquyya Gul
- Faculty of Life Sciences, Gulab Devi Educational Complex, Lahore 54590, Punjab, Pakistan;
| | - Huda Ahmed Alghamdi
- Department of Biology, College of Sciences, King Khalid University, Abha 61413, Saudi Arabia;
| | - Muhammad Shahbaz Aslam
- Institute of Biochemistry and Biotechnology, University of the Punjab, Lahore 54590, Punjab, Pakistan; (H.M.R.); (M.S.A.)
| | - Muhammad Sajjad
- School of Biological Sciences, University of the Punjab, Quaid e Azam Campus, Lahore 54590, Punjab, Pakistan;
| | - Munir Ahmad Bhinder
- Department of Human Genetics and Molecular Biology, University of Health Sciences, Lahore 54590, Punjab, Pakistan; (M.A.A.); (M.A.B.)
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Panossian A, Brendler T. The Role of Adaptogens in Prophylaxis and Treatment of Viral Respiratory Infections. Pharmaceuticals (Basel) 2020; 13:E236. [PMID: 32911682 PMCID: PMC7558817 DOI: 10.3390/ph13090236] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 09/01/2020] [Accepted: 09/03/2020] [Indexed: 02/07/2023] Open
Abstract
The aim of our review is to demonstrate the potential of herbal preparations, specifically adaptogens for prevention and treatment of respiratory infections, as well as convalescence, specifically through supporting a challenged immune system, increasing resistance to viral infection, inhibiting severe inflammatory progression, and driving effective recovery. The evidence from pre-clinical and clinical studies with Andrographis paniculata, Eleutherococcus senticosus, Glycyrrhiza spp., Panax spp., Rhodiola rosea, Schisandra chinensis, Withania somnifera, their combination products and melatonin suggests that adaptogens can be useful in prophylaxis and treatment of viral infections at all stages of progression of inflammation as well as in aiding recovery of the organism by (i) modulating innate and adaptive immunity, (ii) anti-inflammatory activity, (iii) detoxification and repair of oxidative stress-induced damage in compromised cells, (iv) direct antiviral effects of inhibiting viral docking or replication, and (v) improving quality of life during convalescence.
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Affiliation(s)
- Alexander Panossian
- Phytomed AB, Vaxtorp, 31275 Halland, Sweden
- EuropharmaUSA, Green Bay, WI 54311, USA
| | - Thomas Brendler
- Department of Botany and Plant Biotechnology, University of Johannesburg, Johannesburg 2000, South Africa;
- Traditional Medicinals Inc., Rohnert Park, CA 94928, USA
- Plantaphile, Collingswood, NJ 08108, USA
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164
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Exploring the SARS-CoV-2 Proteome in the Search of Potential Inhibitors via Structure-Based Pharmacophore Modeling/Docking Approach. COMPUTATION 2020. [DOI: 10.3390/computation8030077] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
To date, SARS-CoV-2 infectious disease, named COVID-19 by the World Health Organization (WHO) in February 2020, has caused millions of infections and hundreds of thousands of deaths. Despite the scientific community efforts, there are currently no approved therapies for treating this coronavirus infection. The process of new drug development is expensive and time-consuming, so that drug repurposing may be the ideal solution to fight the pandemic. In this paper, we selected the proteins encoded by SARS-CoV-2 and using homology modeling we identified the high-quality model of proteins. A structure-based pharmacophore modeling study was performed to identify the pharmacophore features for each target. The pharmacophore models were then used to perform a virtual screening against the DrugBank library (investigational, approved and experimental drugs). Potential inhibitors were identified for each target using XP docking and induced fit docking. MM-GBSA was also performed to better prioritize potential inhibitors. This study will provide new important comprehension of the crucial binding hot spots usable for further studies on COVID-19. Our results can be used to guide supervised virtual screening of large commercially available libraries.
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165
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Villas-Boas GR, Rescia VC, Paes MM, Lavorato SN, de Magalhães-Filho MF, Cunha MS, Simões RDC, de Lacerda RB, de Freitas-Júnior RS, Ramos BHDS, Mapeli AM, Henriques MDST, de Freitas WR, Lopes LAF, Oliveira LGR, da Silva JG, Silva-Filho SE, da Silveira APS, Leão KV, Matos MMDS, Fernandes JS, Cuman RKN, Silva-Comar FMDS, Comar JF, Brasileiro LDA, dos Santos JN, Oesterreich SA. The New Coronavirus (SARS-CoV-2): A Comprehensive Review on Immunity and the Application of Bioinformatics and Molecular Modeling to the Discovery of Potential Anti-SARS-CoV-2 Agents. Molecules 2020; 25:E4086. [PMID: 32906733 PMCID: PMC7571161 DOI: 10.3390/molecules25184086] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 09/03/2020] [Accepted: 09/04/2020] [Indexed: 02/07/2023] Open
Abstract
On March 11, 2020, the World Health Organization (WHO) officially declared the outbreak caused by the new coronavirus (SARS-CoV-2) a pandemic. The rapid spread of the disease surprised the scientific and medical community. Based on the latest reports, news, and scientific articles published, there is no doubt that the coronavirus has overloaded health systems globally. Practical actions against the recent emergence and rapid expansion of the SARS-CoV-2 require the development and use of tools for discovering new molecular anti-SARS-CoV-2 targets. Thus, this review presents bioinformatics and molecular modeling strategies that aim to assist in the discovery of potential anti-SARS-CoV-2 agents. Besides, we reviewed the relationship between SARS-CoV-2 and innate immunity, since understanding the structures involved in this infection can contribute to the development of new therapeutic targets. Bioinformatics is a technology that assists researchers in coping with diseases by investigating genetic sequencing and seeking structural models of potential molecular targets present in SARS-CoV2. The details provided in this review provide future points of consideration in the field of virology and medical sciences that will contribute to clarifying potential therapeutic targets for anti-SARS-CoV-2 and for understanding the molecular mechanisms responsible for the pathogenesis and virulence of SARS-CoV-2.
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Affiliation(s)
- Gustavo R. Villas-Boas
- Research Group on Development of Pharmaceutical Products (P&DProFar), Center for Biological and Health Sciences, Federal University of Western Bahia, Rua Bertioga, 892, Morada Nobre II, Barreiras CEP 47810-059, BA, Brazil; (V.C.R.); (M.M.P.); (S.N.L.); (M.F.d.M.-F.); (M.S.C.); (R.d.C.S.)
| | - Vanessa C. Rescia
- Research Group on Development of Pharmaceutical Products (P&DProFar), Center for Biological and Health Sciences, Federal University of Western Bahia, Rua Bertioga, 892, Morada Nobre II, Barreiras CEP 47810-059, BA, Brazil; (V.C.R.); (M.M.P.); (S.N.L.); (M.F.d.M.-F.); (M.S.C.); (R.d.C.S.)
| | - Marina M. Paes
- Research Group on Development of Pharmaceutical Products (P&DProFar), Center for Biological and Health Sciences, Federal University of Western Bahia, Rua Bertioga, 892, Morada Nobre II, Barreiras CEP 47810-059, BA, Brazil; (V.C.R.); (M.M.P.); (S.N.L.); (M.F.d.M.-F.); (M.S.C.); (R.d.C.S.)
| | - Stefânia N. Lavorato
- Research Group on Development of Pharmaceutical Products (P&DProFar), Center for Biological and Health Sciences, Federal University of Western Bahia, Rua Bertioga, 892, Morada Nobre II, Barreiras CEP 47810-059, BA, Brazil; (V.C.R.); (M.M.P.); (S.N.L.); (M.F.d.M.-F.); (M.S.C.); (R.d.C.S.)
| | - Manoel F. de Magalhães-Filho
- Research Group on Development of Pharmaceutical Products (P&DProFar), Center for Biological and Health Sciences, Federal University of Western Bahia, Rua Bertioga, 892, Morada Nobre II, Barreiras CEP 47810-059, BA, Brazil; (V.C.R.); (M.M.P.); (S.N.L.); (M.F.d.M.-F.); (M.S.C.); (R.d.C.S.)
| | - Mila S. Cunha
- Research Group on Development of Pharmaceutical Products (P&DProFar), Center for Biological and Health Sciences, Federal University of Western Bahia, Rua Bertioga, 892, Morada Nobre II, Barreiras CEP 47810-059, BA, Brazil; (V.C.R.); (M.M.P.); (S.N.L.); (M.F.d.M.-F.); (M.S.C.); (R.d.C.S.)
| | - Rafael da C. Simões
- Research Group on Development of Pharmaceutical Products (P&DProFar), Center for Biological and Health Sciences, Federal University of Western Bahia, Rua Bertioga, 892, Morada Nobre II, Barreiras CEP 47810-059, BA, Brazil; (V.C.R.); (M.M.P.); (S.N.L.); (M.F.d.M.-F.); (M.S.C.); (R.d.C.S.)
| | - Roseli B. de Lacerda
- Department of Pharmacology of the Biological Sciences Center, Federal University of Paraná, Jardim das Américas, Caixa. postal 19031, Curitiba CEP 81531-990, PR, Brazil;
| | - Renilson S. de Freitas-Júnior
- Clinical Health is Life-Integrated Health Center, Rua dos Andrades, 99, Barreirinhas, Barreiras CEP 47810-689, BA, Brazil;
| | - Bruno H. da S. Ramos
- Institute of the Spine and Pain Clinic, Rua Dr. Renato Gonçalves, 108, Renato Gonçalves, Barreiras CEP 47806-021, BA, Brazil;
| | - Ana M. Mapeli
- Research Group on Biomolecules and Catalyze, Center for Biological and Health Sciences, Federal University of Western Bahia, Rua Bertioga, 892, Morada Nobre II, Barreiras CEP 47810-059, BA, Brazil;
| | - Matheus da S. T. Henriques
- Laboratory of Pharmacology of Toxins (LabTox), Graduate Program in Pharmacology and Medicinal Chemistry (PPGFQM), Institute of Biomedical Sciences (ICB) Federal University of Rio de Janeiro (UFRJ), Avenida Carlos Chagas Filho, 373, Cidade Universitária, Rio de Janeiro CEP 21941-590, RJ, Brazil;
| | - William R. de Freitas
- Research Group on Biodiversity and Health (BIOSA), Center for Training in Health Sciences, Federal University of Southern Bahia, Praça Joana Angélica, 58, São José, Teixeira de Freitas, Teixeira de Freitas CEP 45988-058, Brazil;
| | - Luiz A. F. Lopes
- University Hospital of the Federal University of Grande Dourados (HU-UFGD), Federal University of Grande Dourados, Rua Ivo Alves da Rocha, 558, Altos do Indaiá, Dourados CEP 79823-501, MS, Brazil;
| | - Luiz G. R. Oliveira
- Nucleus of Studies on Infectious Agents and Vectors (Naive), Federal University of Western Bahia, Rua Bertioga, 892, Morada Nobre II, Barreiras CEP 47810-059, BA, Brazil;
| | - Jonatas G. da Silva
- Federal University of Western Bahia, Rua Bertioga, 892, Morada Nobre II, Barreiras CEP 47810-059, BA, Brazil; (J.G.d.S.); (K.V.L.); (J.S.F.)
| | - Saulo E. Silva-Filho
- Pharmaceutical Sciences, Food and Nutrition College, Federal University of Mato Grosso do Sul, Avenida Costa e Silva, s/nº, Bairro Universitário, Campo Grande CEP 79070-900, MS, Brazil;
| | - Ana P. S. da Silveira
- Faculty of Biological and Health Sciences, University Center Unigran Capital, Rua Balbina de Matos, 2121, Jd. University, Dourados CEP 79.824-900, MS, Brazil;
| | - Katyuscya V. Leão
- Federal University of Western Bahia, Rua Bertioga, 892, Morada Nobre II, Barreiras CEP 47810-059, BA, Brazil; (J.G.d.S.); (K.V.L.); (J.S.F.)
| | - Maria M. de S. Matos
- Health Sciences at ABC Health University Center, Avenida Príncipe de Gales, 667, Bairro Princípe de Gales, Santo André CEP 09060-870, SP, Brazil;
| | - Jamille S. Fernandes
- Federal University of Western Bahia, Rua Bertioga, 892, Morada Nobre II, Barreiras CEP 47810-059, BA, Brazil; (J.G.d.S.); (K.V.L.); (J.S.F.)
| | - Roberto K. N. Cuman
- Department of Pharmacology and Therapeutics, State University of Maringá, Avenida Colombo, nº 5790, Jardim Universitário, Maringá CEP 87020-900, PR, Brazil; (R.K.N.C.); (F.M.d.S.S.-C.)
| | - Francielli M. de S. Silva-Comar
- Department of Pharmacology and Therapeutics, State University of Maringá, Avenida Colombo, nº 5790, Jardim Universitário, Maringá CEP 87020-900, PR, Brazil; (R.K.N.C.); (F.M.d.S.S.-C.)
| | - Jurandir F. Comar
- Department of Biochemistry, State University of Maringá, Avenida Colombo, nº 5790, Jardim Universitário, Maringá CEP 87020-900, PR, Brazil;
| | - Luana do A. Brasileiro
- Nacional Cancer Institute (INCA), Rua Visconde de Santa Isabel, 274, Rio de Janeiro CEP 20560-121, RJ, Brazil;
| | | | - Silvia A. Oesterreich
- Faculty of Health Sciences, Federal University of Grande Dourados, Dourados Rodovia Dourados, Itahum Km 12, Cidade Universitaria, Caixa postal 364, Dourados CEP 79804-970, Mato Grosso do Sul, Brazil;
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166
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Mirza MU, Saadabadi A, Vanmeert M, Salo-Ahen OMH, Abdullah I, Claes S, De Jonghe S, Schols D, Ahmad S, Froeyen M. Discovery of HIV entry inhibitors via a hybrid CXCR4 and CCR5 receptor pharmacophore-based virtual screening approach. Eur J Pharm Sci 2020; 155:105537. [PMID: 32890663 PMCID: PMC7467125 DOI: 10.1016/j.ejps.2020.105537] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 08/10/2020] [Accepted: 08/30/2020] [Indexed: 12/30/2022]
Abstract
Chemokine receptors are key regulators of cell migration in terms of immunity and inflammation. Among these, CCR5 and CXCR4 play pivotal roles in cancer metastasis and HIV-1 transmission and infection. They act as essential co-receptors for HIV and furnish a route to the cell entry. In particular, inhibition of either CCR5 or CXCR4 leads very often the virus to shift to a more virulent dual-tropic strain. Therefore, dual receptor inhibition might improve the therapeutic strategies against HIV. In this study, we aimed to discover selective CCR5, CXCR4, and dual CCR5/CXCR4 antagonists using both receptor- and ligand-based computational methods. We employed this approach to fully incorporate the interaction attributes of the binding pocket together with molecular dynamics (MD) simulations and binding free energy calculations. The best hits were evaluated for their anti-HIV-1 activity against CXCR4- and CCR5-specific NL4.3 and BaL strains. Moreover, the Ca2+ mobilization assay was used to evaluate their antagonistic activity. From the 27 tested compounds, three were identified as inhibitors: compounds 27 (CCR5), 6 (CXCR4) and 3 (dual) with IC50 values ranging from 10.64 to 64.56 μM. The binding mode analysis suggests that the active compounds form a salt bridge with the glutamates and π-stacking interactions with the aromatic side chains binding site residues of the respective co-receptor. The presented hierarchical virtual screening approach provides essential aspects in identifying potential antagonists in terms of selectivity against a specific co-receptor. The compounds having multiple heterocyclic nitrogen atoms proved to be relatively more specific towards CXCR4 inhibition as compared to CCR5. The identified compounds serve as a starting point for further development of HIV entry inhibitors through synthesis and quantitative structure-activity relationship studies.
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Affiliation(s)
- Muhammad Usman Mirza
- Medicinal Chemistry, Department of Pharmaceutical and Pharmacological Sciences, Rega Institute for Medical Research, KU Leuven, B-3000 Leuven, Belgium
| | - Atefeh Saadabadi
- Pharmaceutical Sciences Laboratory, Faculty of Science and Engineering, Pharmacy, Åbo Akademi University, FI-20520 Turku, Finland; Structural Bioinformatics Laboratory, Faculty of Science and Engineering, Biochemistry, Åbo Akademi University, FI-20520 Turku, Finland
| | - Michiel Vanmeert
- Medicinal Chemistry, Department of Pharmaceutical and Pharmacological Sciences, Rega Institute for Medical Research, KU Leuven, B-3000 Leuven, Belgium
| | - Outi M H Salo-Ahen
- Pharmaceutical Sciences Laboratory, Faculty of Science and Engineering, Pharmacy, Åbo Akademi University, FI-20520 Turku, Finland; Structural Bioinformatics Laboratory, Faculty of Science and Engineering, Biochemistry, Åbo Akademi University, FI-20520 Turku, Finland
| | - Iskandar Abdullah
- Department of Chemistry, Faculty of Sciences, University Malaya, Kuala Lumpur 59100, Malaysia
| | - Sandra Claes
- Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, B-3000 Leuven, Belgium
| | - Steven De Jonghe
- Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, B-3000 Leuven, Belgium
| | - Dominique Schols
- Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, B-3000 Leuven, Belgium
| | - Sarfraz Ahmad
- Department of Chemistry, Faculty of Sciences, University Malaya, Kuala Lumpur 59100, Malaysia
| | - Matheus Froeyen
- Medicinal Chemistry, Department of Pharmaceutical and Pharmacological Sciences, Rega Institute for Medical Research, KU Leuven, B-3000 Leuven, Belgium.
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167
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Ghosh R, Chakraborty A, Biswas A, Chowdhuri S. Identification of polyphenols from Broussonetia papyrifera as SARS CoV-2 main protease inhibitors using in silico docking and molecular dynamics simulation approaches. J Biomol Struct Dyn 2020; 39:6747-6760. [PMID: 32762411 PMCID: PMC7484588 DOI: 10.1080/07391102.2020.1802347] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The current COVID-19 pandemic is caused by SARS CoV-2. To date, ∼463,000 people died
worldwide due to this disease. Several attempts have been taken in search of effective
drugs to control the spread of SARS CoV-2 infection. The main protease (Mpro) from SARS
CoV-2 plays a vital role in viral replication and thus serves as an important drug target.
This Mpro shares a high degree of sequence similarity (>96%) with the same protease
from SARS CoV-1 and MERS. It was already reported that Broussonetia
papyrifera polyphenols efficiently inhibit the catalytic activity of SARS CoV-1
and MERS Mpro. But whether these polyphenols exhibit any inhibitory effect on SARS CoV-2
Mpro is far from clear. To understand this fact, here we have adopted computational
approaches. Polyphenols having proper drug-likeness properties and two repurposed drugs
(lopinavir and darunavir; having binding affinity −7.3 to −7.4 kcal/mol) were docked
against SARS CoV-2 Mpro to study their binding properties. Only six polyphenols
(broussochalcone A, papyriflavonol A, 3'-(3-methylbut-2-enyl)-3',4',7-trihydroxyflavane,
broussoflavan A, kazinol F and kazinol J) had interaction with both the
catalytic residues (His41 and Cys145) of Mpro and exhibited good binding affinity (−7.6 to
−8.2 kcal/mol). Molecular dynamic simulations (100 ns) revealed that all Mpro-polyphenol
complexes are more stable, conformationally less fluctuated; slightly less compact and
marginally expanded than Mpro-darunavir/lopinavir complex. Even the number of
intermolecular H-bond and MM-GBSA analysis suggested that these six polyphenols are more
potent Mpro inhibitors than the two repurposed drugs (lopinavir and darunavir) and may
serve as promising anti-COVID-19 drugs. Communicated by Ramaswamy H. Sarma
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Affiliation(s)
- Rajesh Ghosh
- School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, India
| | - Ayon Chakraborty
- School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, India
| | - Ashis Biswas
- School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, India
| | - Snehasis Chowdhuri
- School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, India
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168
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Abstract
The current global pandemic COVID-19 caused by the SARS-CoV-2 virus has already inflicted insurmountable damage both to the human lives and global economy. There is an immediate need for identification of effective drugs to contain the disastrous virus outbreak. Global efforts are already underway at a war footing to identify the best drug combination to address the disease. In this review, an attempt has been made to understand the SARS-CoV-2 life cycle, and based on this information potential druggable targets against SARS-CoV-2 are summarized. Also, the strategies for ongoing and future drug discovery against the SARS-CoV-2 virus are outlined. Given the urgency to find a definitive cure, ongoing drug repurposing efforts being carried out by various organizations are also described. The unprecedented crisis requires extraordinary efforts from the scientific community to effectively address the issue and prevent further loss of human lives and health.
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Affiliation(s)
- Ambrish Saxena
- Indian Institute of Technology Tirupati, Tirupati, India
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169
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Asghari A, Naseri M, Safari H, Saboory E, Parsamanesh N. The Novel Insight of SARS-CoV-2 Molecular Biology and Pathogenesis and Therapeutic Options. DNA Cell Biol 2020; 39:1741-1753. [PMID: 32716648 DOI: 10.1089/dna.2020.5703] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
On December 31, 2019, a novel coronavirus, being the third highly infective CoV and named as coronavirus disease 2019 (COVID-19) in the city of Wuhan, was announced by the World Health Organization. COVID-19 has a 2% mortality rate, is known as the third extremely infective CoV infection, and has a mortality rate less than MERS-CoV and SARS-CoV. The CoV family comprises a chief number of positive single-stranded ss (+) RNA viruses that are recognized in mammals. The 2019-nCoV patients showed that the angiotensin-converting enzyme II (ACE2) was the same for SARS-CoV. Structural proteins have an essential role in virus released and budding to various host cells. Notably, evidence indicated human-to-human transmission, along with several exported patients of virus infection worldwide. Nowadays, no licensed antivirals drugs or vaccines for being utilized against these coronavirus infections are recognized. There is an urgent requirement for an extensive research of CoV infections to disclose the route of extension, pathogenesis, and diagnosis and then to recognize the therapeutic targets to facilitate disease control and surveillance. In this article, we present an overview of the common biological criteria of CoVs and explain pathogenesis with a focus on the therapeutic approach to suggest potential goals for treating and monitoring this emerging zoonotic disease.
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Affiliation(s)
- Arghavan Asghari
- Student Research Committee and Birjand University of Medical Sciences, Birjand, Iran
| | - Mohsen Naseri
- Cellular and Molecular Research Center, Birjand University of Medical Sciences, Birjand, Iran
| | - Hamidreza Safari
- Department of Immunology, Torbat Jam Faculty of Medical Sciences, Torbat Jam, Iran
| | - Ehsan Saboory
- Zanjan Metabolic Diseases Research Center, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Negin Parsamanesh
- Zanjan Metabolic Diseases Research Center, Zanjan University of Medical Sciences, Zanjan, Iran
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170
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Rowaiye AB, Onuh OA, Oli AN, Okpalefe OA, Oni S, Nwankwo EJ. The pandemic COVID-19: a tale of viremia, cellular oxidation and immune dysfunction. Pan Afr Med J 2020; 36:188. [PMID: 32952832 PMCID: PMC7467617 DOI: 10.11604/pamj.2020.36.188.23476] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 05/27/2020] [Indexed: 02/06/2023] Open
Abstract
COVID-19, caused by SARS-CoV-2 is a tester of the immune system. While it spares the healthy, it brings severe morbidity and in a few cases, mortality to its victims. This article aims at critically reviewing the key virulence factors of COVID-19 which are the viremia, cellular oxidation and immune dysfunction. The averse economic effect of certain disease control measures such as national lock-downs and social distancing, though beneficial, makes them unsustainable. Worse still is the fact that wild animals and domestic pets are carriers of SARS-CoV-2 suggesting that the disease would take longer than expected to be eradicated globally. A better understanding of the pathological dynamics of COVID-19 would help the general populace to prepare for possible infection by the invisible enemy. While the world prospects for vaccines and therapeutic agents against the SARS-CoV-2, clinicians should also seek to modulate the immune system for optimum performance. Immunoprophylactic and immunomodulatory strategies are recommended for the different strata of stakeholders combating the pandemic with the hope that morbidities and mortalities associated with COVID-19 would be drastically reduced.
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Affiliation(s)
- Adekunle Babajide Rowaiye
- Department of Medical Biotechnology, National Biotechnology Development Agency, Abuja, Nigeria.,Department of Pharmaceutical Microbiology and Biotechnology, Faculty of Pharm Scs, Nnamdi Azikiwe University, Awka, Nigeria
| | - Olukemi Adejoke Onuh
- Department of Medical Biotechnology, National Biotechnology Development Agency, Abuja, Nigeria
| | - Angus Nnamdi Oli
- Department of Pharmaceutical Microbiology and Biotechnology, Faculty of Pharm Scs, Nnamdi Azikiwe University, Awka, Nigeria
| | | | - Solomon Oni
- Bioresources Development Centre, Isanlu, National Biotechnology Development Agency, Abuja, Nigeria
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171
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Estrada E. COVID-19 and SARS-CoV-2. Modeling the present, looking at the future. PHYSICS REPORTS 2020; 869:1-51. [PMID: 32834430 PMCID: PMC7386394 DOI: 10.1016/j.physrep.2020.07.005] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 07/27/2020] [Indexed: 05/21/2023]
Abstract
Since December 2019 the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has produced an outbreak of pulmonary disease which has soon become a global pandemic, known as COronaVIrus Disease-19 (COVID-19). The new coronavirus shares about 82% of its genome with the one which produced the 2003 outbreak (SARS CoV-1). Both coronaviruses also share the same cellular receptor, which is the angiotensin-converting enzyme 2 (ACE2) one. In spite of these similarities, the new coronavirus has expanded more widely, more faster and more lethally than the previous one. Many researchers across the disciplines have used diverse modeling tools to analyze the impact of this pandemic at global and local scales. This includes a wide range of approaches - deterministic, data-driven, stochastic, agent-based, and their combinations - to forecast the progression of the epidemic as well as the effects of non-pharmaceutical interventions to stop or mitigate its impact on the world population. The physical complexities of modern society need to be captured by these models. This includes the many ways of social contacts - (multiplex) social contact networks, (multilayers) transport systems, metapopulations, etc. - that may act as a framework for the virus propagation. But modeling not only plays a fundamental role in analyzing and forecasting epidemiological variables, but it also plays an important role in helping to find cures for the disease and in preventing contagion by means of new vaccines. The necessity for answering swiftly and effectively the questions: could existing drugs work against SARS CoV-2? and can new vaccines be developed in time? demands the use of physical modeling of proteins, protein-inhibitors interactions, virtual screening of drugs against virus targets, predicting immunogenicity of small peptides, modeling vaccinomics and vaccine design, to mention just a few. Here, we review these three main areas of modeling research against SARS CoV-2 and COVID-19: (1) epidemiology; (2) drug repurposing; and (3) vaccine design. Therefore, we compile the most relevant existing literature about modeling strategies against the virus to help modelers to navigate this fast-growing literature. We also keep an eye on future outbreaks, where the modelers can find the most relevant strategies used in an emergency situation as the current one to help in fighting future pandemics.
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Affiliation(s)
- Ernesto Estrada
- Instituto Universitario de Matemáticas y Aplicaciones, Universidad de Zaragoza, 50009 Zaragoza, Spain
- ARAID Foundation, Government of Aragón, 50018 Zaragoza, Spain
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Fawad M, Mubarik S, Malik SS, Hao Y, Yu C, Ren J. Trend Dynamics of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Transmission in 16 Cities of Hubei Province, China. Clin Epidemiol 2020; 12:699-709. [PMID: 32669878 PMCID: PMC7337437 DOI: 10.2147/clep.s254806] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 06/11/2020] [Indexed: 12/13/2022] Open
Abstract
Objective A severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was detected by researchers from a patient in Wuhan, Hubei province, China, in December 2019, and broke out in January 2020. Then, the pandemic was detected in countries around the world. Therefore, precise estimates of its current and future trends are highly required for future policy implications. Methods We retrieved data from the Health Commission of Hubei, China. Logistic-S curve model was used to estimate the current and future trends of SARS-CoV-2-infected cases among 16 cities of Hubei, China from Jan-11 to Feb-24, 2020. Results Out of 64,287 confirmed cases of SARS-CoV-2 infection in Hubei, higher percentage of cases were in Wuhan and Xiaogan. The highest death percentage was found in Wuhan and Qianjiang. A significant percentage of cures were found in Enshi Prefecture and Huanggang, while Wuhan showed the lowest percentage of cures. Rising trends in infected cases were observed throughout the study period, particularly in Wuhan, and a higher trend was observed after 12-Feb. Gradual decline trend of SARS-CoV-2 cases was observed during Feb-25 to Mar-15 in Hubei Province. Future forecast showed that the average number of SARS-CoV-2-infected cases might be decreased or stable in Hubei in the coming 20 days. Conclusion The public must take precautionary measures in order to control and prevent disease spread and avoid extra travelling.
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Affiliation(s)
- Muhammad Fawad
- Henan Academy of Big Data, Zhengzhou University, Zhengzhou 450052, People's Republic of China.,School of Mathematics and Statistics, Zhengzhou University, Zhengzhou 450001, People's Republic of China
| | - Sumaira Mubarik
- Department of Epidemiology and Biostatistics, School of Health Sciences, Wuhan University, Wuhan, Hubei 430071, People's Republic of China
| | | | - Yangyang Hao
- School of Mathematics and Statistics, Zhengzhou University, Zhengzhou 450001, People's Republic of China
| | - Chuanhua Yu
- Department of Epidemiology and Biostatistics, School of Health Sciences, Wuhan University, Wuhan, Hubei 430071, People's Republic of China
| | - Jingli Ren
- Henan Academy of Big Data, Zhengzhou University, Zhengzhou 450052, People's Republic of China
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173
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Iftikhar H, Ali HN, Farooq S, Naveed H, Shahzad-Ul-Hussan S. Identification of potential inhibitors of three key enzymes of SARS-CoV2 using computational approach. Comput Biol Med 2020; 122:103848. [PMID: 32658735 PMCID: PMC7282781 DOI: 10.1016/j.compbiomed.2020.103848] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 06/04/2020] [Accepted: 06/04/2020] [Indexed: 12/18/2022]
Abstract
The recent outbreak of coronavirus disease-19 (COVID-19) continues to drastically affect healthcare throughout the world. To date, no approved treatment regimen or vaccine is available to effectively attenuate or prevent the infection. Therefore, collective and multidisciplinary efforts are needed to identify new therapeutics or to explore effectiveness of existing drugs and drug-like small molecules against SARS-CoV-2 for lead identification and repurposing prospects. This study addresses the identification of small molecules that specifically bind to any of the three essential proteins (RdRp, 3CL-protease and helicase) of SARS-CoV-2. By applying computational approaches we screened a library of 4574 compounds also containing FDA-approved drugs against these viral proteins. Shortlisted hits from initial screening were subjected to iterative docking with the respective proteins. Ranking score on the basis of binding energy, clustering score, shape complementarity and functional significance of the binding pocket was applied to identify the binding compounds. Finally, to minimize chances of false positives, we performed docking of the identified molecules with 100 irrelevant proteins of diverse classes thereby ruling out the non-specific binding. Three FDA-approved drugs showed binding to 3CL-protease either at the catalytic pocket or at an allosteric site related to functionally important dimer formation. A drug-like molecule showed binding to RdRp in its catalytic pocket blocking the key catalytic residues. Two other drug-like molecules showed specific interactions with helicase at a key domain involved in catalysis. This study provides lead drugs or drug-like molecules for further in vitro and clinical investigation for drug repurposing and new drug development prospects.
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Affiliation(s)
- Hafsa Iftikhar
- Department of Biology, Syed Babar Ali School of Science and Engineering, Lahore University of Management Sciences, Lahore, Pakistan
| | - Hafiza Nayyer Ali
- Department of Biology, Syed Babar Ali School of Science and Engineering, Lahore University of Management Sciences, Lahore, Pakistan
| | - Sadia Farooq
- Department of Computer Science, National University of Computer & Emerging Sciences, Islamabad, Pakistan
| | - Hammad Naveed
- Department of Computer Science, National University of Computer & Emerging Sciences, Islamabad, Pakistan.
| | - Syed Shahzad-Ul-Hussan
- Department of Biology, Syed Babar Ali School of Science and Engineering, Lahore University of Management Sciences, Lahore, Pakistan.
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174
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Ortega JT, Serrano ML, Jastrzebska B. Class A G Protein-Coupled Receptor Antagonist Famotidine as a Therapeutic Alternative Against SARS-CoV2: An In Silico Analysis. Biomolecules 2020; 10:E954. [PMID: 32599963 PMCID: PMC7355875 DOI: 10.3390/biom10060954] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 06/08/2020] [Accepted: 06/22/2020] [Indexed: 12/11/2022] Open
Abstract
The pandemic associated with Severe Acute Respiratory Syndrome Coronavirus type 2 (SARS-CoV2) and its disease named COVID-19 challenged the scientific community to discover effective therapeutic solutions in a short period. Repurposing existing drugs is one viable approach that emphasizes speed during these urgent times. Famotidine, a class A G protein-coupled receptor antagonist used for the treatment of gastroesophageal reflux was recently identified in an in silico screening. Additionally, a recent retrospective clinical report showed that the treatment with famotidine provided a good outcome in patients infected with SARS-CoV2. A clinical trial testing effectiveness of famotidine in combination with hydroxychloroquine is currently ongoing in the United States (US). In the 1990s, famotidine was described as an antiviral agent against human immunodeficiency virus (HIV). Interestingly, some HIV protease inhibitors are presently being used against SARS-CoV2. However, it is not clear if famotidine could be effective against SARS-CoV2. Thus, by using a computational analysis, we aimed to examine if the antiviral effect of famotidine could be related to the inhibition of proteases involved in the virus replication. Our results showed that famotidine could interact within the catalytic site of the three proteases associated with SARS-CoV2 replication. However, weak binding affinity of famotidine to these proteases suggests that a successful famotidine therapy could likely be achieved only in combination with other antiviral drugs. Finally, analysis of famotidine's pharmacokinetic parameters indicated that its effect against SARS-CoV2 infection could be reached only upon intravenous administration. This work will contribute to the pharmacological knowledge of famotidine as an antiviral agent against SARS-CoV2.
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Affiliation(s)
- Joseph T. Ortega
- Department of Pharmacology, Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Maria Luisa Serrano
- Unidad de Química Medicinal, Facultad de Farmacia, Universidad Central de Venezuela, Caracas 1041-A, Venezuela;
| | - Beata Jastrzebska
- Department of Pharmacology, Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
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175
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Ghaebi M, Osali A, Valizadeh H, Roshangar L, Ahmadi M. Vaccine development and therapeutic design for 2019-nCoV/SARS-CoV-2: Challenges and chances. J Cell Physiol 2020; 235:9098-9109. [PMID: 32557648 PMCID: PMC7323389 DOI: 10.1002/jcp.29771] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 04/28/2020] [Indexed: 12/11/2022]
Abstract
The ongoing outbreak of the recently emerged 2019 novel coronavirus (nCoV), which has seriously threatened global health security, is caused by severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) with high morbidity and mortality. Despite the burden of the disease worldwide, still, no licensed vaccine or any specific drug against 2019‐nCoV is available. Data from several countries show that few repurposed drugs using existing antiviral drugs have not (so far) been satisfactory and more recently were proven to be even highly toxic. These findings underline an urgent need for preventative and therapeutic interventions designed to target specific aspects of 2019‐nCoV. Again the major factor in this urgency is that the process of data acquisition by physical experiment is time‐consuming and expensive to obtain. Scientific simulations and more in‐depth data analysis permit to validate or refute drug repurposing opportunities predicted via target similarity profiling to speed up the development of a new more effective anti‐2019‐nCoV therapy especially where in vitro and/or in vivo data are not yet available. In addition, several research programs are being developed, aiming at the exploration of vaccines to prevent and treat the 2019‐nCoV. Computational‐based technology has given us the tools to explore and identify potentially effective drug and/or vaccine candidates which can effectively shorten the time and reduce the operating cost. The aim of the present review is to address the available information on molecular determinants in disease pathobiology modules and define the computational approaches employed in systematic drug repositioning and vaccine development settings for SARS‐CoV‐2.
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Affiliation(s)
- Mahnaz Ghaebi
- Department of Immunology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.,Students Research Center Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Abdolreza Osali
- Department of Immunology, School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Hamed Valizadeh
- Tuberculosis and Lung Disease Research Center of Tabriz University of Medical Sciences, Tabriz, Iran
| | - Leila Roshangar
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Majid Ahmadi
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
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176
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Habtemariam S, Nabavi SF, Banach M, Berindan-Neagoe I, Sarkar K, Sil PC, Nabavi SM. Should We Try SARS-CoV-2 Helicase Inhibitors for COVID-19 Therapy? Arch Med Res 2020; 51:733-735. [PMID: 32536457 PMCID: PMC7261434 DOI: 10.1016/j.arcmed.2020.05.024] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 05/28/2020] [Indexed: 12/31/2022]
Abstract
The discovery of new drugs for treating the new coronavirus (SARS-CoV-2) or repurposing those already in use for other viral infections is possible through understanding of the viral replication cycle and pathogenicity. This article highlights the advantage of targeting one of the non-structural proteins, helicase (nsp13), over other SARS-CoV-2 proteins. Highlighting the experience gained from targeting Nsp13 in similar coronaviruses (SARS-CoV and MERS) and known inhibitors, the article calls for research on helicase inhibitors as potential COVID-19 therapy.
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Affiliation(s)
- Solomon Habtemariam
- Pharmacognosy Research Laboratories and Herbal Analysis Services, University of Greenwich, Central Avenue, Chatham-Maritime, UK
| | - Seyed Fazel Nabavi
- Applied Biotechnology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran; Division of Translational Medicine, Baqiyatallah Hospital, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Maciej Banach
- Department of Hypertension, Medical University of Lodz, Poland; Polish Mothers Memorial Hospital Research Institute, Lodz, Poland
| | - Ioana Berindan-Neagoe
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania; Department of Functional Genomics and Experimental Pathology, The Oncology Institute "Prof. Dr. Ion Chiricuta", Cluj-Napoca, Romania; MEDFUTURE-Research Center for Advanced Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Kasturi Sarkar
- Department of Microbiology, St. Xavier's College, Kolkata, India
| | - Parames C Sil
- Department of Molecular Medicine, Bose Institute, Kolkata, India
| | - Seyed Mohammad Nabavi
- Applied Biotechnology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran; Division of Translational Medicine, Baqiyatallah Hospital, Baqiyatallah University of Medical Sciences, Tehran, Iran.
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177
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Gimeno A, Mestres-Truyol J, Ojeda-Montes MJ, Macip G, Saldivar-Espinoza B, Cereto-Massagué A, Pujadas G, Garcia-Vallvé S. Prediction of Novel Inhibitors of the Main Protease (M-pro) of SARS-CoV-2 through Consensus Docking and Drug Reposition. Int J Mol Sci 2020; 21:E3793. [PMID: 32471205 PMCID: PMC7312484 DOI: 10.3390/ijms21113793] [Citation(s) in RCA: 89] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 05/16/2020] [Accepted: 05/22/2020] [Indexed: 12/22/2022] Open
Abstract
Since the outbreak of the COVID-19 pandemic in December 2019 and its rapid spread worldwide, the scientific community has been under pressure to react and make progress in the development of an effective treatment against the virus responsible for the disease. Here, we implement an original virtual screening (VS) protocol for repositioning approved drugs in order to predict which of them could inhibit the main protease of the virus (M-pro), a key target for antiviral drugs given its essential role in the virus' replication. Two different libraries of approved drugs were docked against the structure of M-pro using Glide, FRED and AutoDock Vina, and only the equivalent high affinity binding modes predicted simultaneously by the three docking programs were considered to correspond to bioactive poses. In this way, we took advantage of the three sampling algorithms to generate hypothetic binding modes without relying on a single scoring function to rank the results. Seven possible SARS-CoV-2 M-pro inhibitors were predicted using this approach: Perampanel, Carprofen, Celecoxib, Alprazolam, Trovafloxacin, Sarafloxacin and ethyl biscoumacetate. Carprofen and Celecoxib have been selected by the COVID Moonshot initiative for in vitro testing; they show 3.97 and 11.90% M-pro inhibition at 50 µM, respectively.
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Affiliation(s)
- Aleix Gimeno
- Departament de Bioquímica i Biotecnologia, Research group in Cheminformatics & Nutrition, Campus de Sescelades, Universitat Rovira i Virgili, 43007 Tarragona, Catalonia, Spain; (A.G.); (J.M.-T.); (G.M.); (B.S.-E.); (A.C.-M.)
| | - Júlia Mestres-Truyol
- Departament de Bioquímica i Biotecnologia, Research group in Cheminformatics & Nutrition, Campus de Sescelades, Universitat Rovira i Virgili, 43007 Tarragona, Catalonia, Spain; (A.G.); (J.M.-T.); (G.M.); (B.S.-E.); (A.C.-M.)
| | - María José Ojeda-Montes
- Escoles Universitàries Gimbernat i Tomàs Cerdà, 08174 Sant Cugat del Vallès, Barcelona, Catalonia, Spain;
| | - Guillem Macip
- Departament de Bioquímica i Biotecnologia, Research group in Cheminformatics & Nutrition, Campus de Sescelades, Universitat Rovira i Virgili, 43007 Tarragona, Catalonia, Spain; (A.G.); (J.M.-T.); (G.M.); (B.S.-E.); (A.C.-M.)
| | - Bryan Saldivar-Espinoza
- Departament de Bioquímica i Biotecnologia, Research group in Cheminformatics & Nutrition, Campus de Sescelades, Universitat Rovira i Virgili, 43007 Tarragona, Catalonia, Spain; (A.G.); (J.M.-T.); (G.M.); (B.S.-E.); (A.C.-M.)
| | - Adrià Cereto-Massagué
- Departament de Bioquímica i Biotecnologia, Research group in Cheminformatics & Nutrition, Campus de Sescelades, Universitat Rovira i Virgili, 43007 Tarragona, Catalonia, Spain; (A.G.); (J.M.-T.); (G.M.); (B.S.-E.); (A.C.-M.)
| | - Gerard Pujadas
- Departament de Bioquímica i Biotecnologia, Research group in Cheminformatics & Nutrition, Campus de Sescelades, Universitat Rovira i Virgili, 43007 Tarragona, Catalonia, Spain; (A.G.); (J.M.-T.); (G.M.); (B.S.-E.); (A.C.-M.)
- EURECAT, TECNIO, CEICS, Avinguda Universitat 1, 43204 Reus Catalonia, Spain
| | - Santiago Garcia-Vallvé
- Departament de Bioquímica i Biotecnologia, Research group in Cheminformatics & Nutrition, Campus de Sescelades, Universitat Rovira i Virgili, 43007 Tarragona, Catalonia, Spain; (A.G.); (J.M.-T.); (G.M.); (B.S.-E.); (A.C.-M.)
- EURECAT, TECNIO, CEICS, Avinguda Universitat 1, 43204 Reus Catalonia, Spain
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178
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Awadasseid A, Wu Y, Tanaka Y, Zhang W. Initial success in the identification and management of the coronavirus disease 2019 (COVID-19) indicates human-to-human transmission in Wuhan, China. Int J Biol Sci 2020; 16:1846-1860. [PMID: 32398954 PMCID: PMC7211182 DOI: 10.7150/ijbs.45018] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 03/19/2020] [Indexed: 12/15/2022] Open
Abstract
Coronavirus (CoV) has been one of the major pandemic threats to human health in the last two decades. The human coronavirus was first identified in 1960s. CoVs 229E, NL63, OC43, HKU1, SARS-CoV, and MERS-CoV have caused numerous disasters or human deaths worldwide. Recently, an outbreak of the previously unknown deadly CoV disease 2019 (COVID-19) caused by Severe Acute Respiratory Syndrome CoV 2 (SARS-CoV-2, early named 2019-nCoV) occurred in Wuhan, China, and it had caused 81238 cases of confirmed infection, including 3250 deaths until March 19, 2020. Its risks and pandemic potential have brought global consideration. We summarized epidemiology, virological characteristics, clinical symptoms, diagnostic methods, clinical treatments, and prevention methods for COVID-19 to present a reference for the future wave of probable CoV outbreaks.
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Affiliation(s)
- Annoor Awadasseid
- Lab of Chemical Biology and Molecular Drug Design, College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, 310014, China
- Center for Natural Products Research, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, PR China
| | - Yanling Wu
- Lab of Molecular Immunology, Virus Inspection Department, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, 310051, China
| | - Yoshimasa Tanaka
- Center for Medical Innovation, Nagasaki University, 1-7-1 Sakamoto, Nagasaki 852-8588, Japan
| | - Wen Zhang
- Lab of Chemical Biology and Molecular Drug Design, College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, 310014, China
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