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Li S, Li H, Lian R, Xie J, Feng R. New perspective of small-molecule antiviral drugs development for RNA viruses. Virology 2024; 594:110042. [PMID: 38492519 DOI: 10.1016/j.virol.2024.110042] [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: 10/21/2023] [Revised: 02/20/2024] [Accepted: 03/01/2024] [Indexed: 03/18/2024]
Abstract
High variability and adaptability of RNA viruses allows them to spread between humans and animals, causing large-scale infectious diseases which seriously threat human and animal health and social development. At present, AIDS, viral hepatitis and other viral diseases with high incidence and low cure rate are still spreading around the world. The outbreaks of Ebola, Zika, dengue and in particular of the global pandemic of COVID-19 have presented serious challenges to the global public health system. The development of highly effective and broad-spectrum antiviral drugs is a substantial and urgent research subject to deal with the current RNA virus infection and the possible new viral infections in the future. In recent years, with the rapid development of modern disciplines such as artificial intelligence technology, bioinformatics, molecular biology, and structural biology, some new strategies and targets for antivirals development have emerged. Here we review the main strategies and new targets for developing small-molecule antiviral drugs against RNA viruses through the analysis of the new drug development progress against several highly pathogenic RNA viruses, to provide clues for development of future antivirals.
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Affiliation(s)
- Shasha Li
- College of Life Science and Engineering, Northwest Minzu University, Lanzhou, 730030, China; Key Laboratory of Biotechnology and Bioengineering of State Ethnic Affairs Commission, Biomedical Research Center, Northwest Minzu University, Lanzhou, 730030, China
| | - Huixia Li
- Key Laboratory of Biotechnology and Bioengineering of State Ethnic Affairs Commission, Biomedical Research Center, Northwest Minzu University, Lanzhou, 730030, China
| | - Ruiya Lian
- College of Life Science and Engineering, Northwest Minzu University, Lanzhou, 730030, China; Key Laboratory of Biotechnology and Bioengineering of State Ethnic Affairs Commission, Biomedical Research Center, Northwest Minzu University, Lanzhou, 730030, China
| | - Jingying Xie
- College of Life Science and Engineering, Northwest Minzu University, Lanzhou, 730030, China; Key Laboratory of Biotechnology and Bioengineering of State Ethnic Affairs Commission, Biomedical Research Center, Northwest Minzu University, Lanzhou, 730030, China
| | - Ruofei Feng
- Key Laboratory of Biotechnology and Bioengineering of State Ethnic Affairs Commission, Biomedical Research Center, Northwest Minzu University, Lanzhou, 730030, China.
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2
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Israr J, Alam S, Kumar A. Drug repurposing for respiratory infections. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024; 207:207-230. [PMID: 38942538 DOI: 10.1016/bs.pmbts.2024.03.033] [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: 06/30/2024]
Abstract
Respiratory infections such as Coronavirus disease 2019 are a substantial worldwide health challenge, frequently resulting in severe sickness and death, especially in susceptible groups. Conventional drug development for respiratory infections faces obstacles such as extended timescales, substantial expenses, and the rise of resistance to current treatments. Drug repurposing is a potential method that has evolved to quickly find and reuse existing medications for treating respiratory infections. Drug repurposing utilizes medications previously approved for different purposes, providing a cost-effective and time-efficient method to tackle pressing medical needs. This chapter summarizes current progress and obstacles in repurposing medications for respiratory infections, focusing on notable examples of repurposed pharmaceuticals and their probable modes of action. The text also explores the significance of computational approaches, high-throughput screening, and preclinical investigations in identifying potential candidates for repurposing. The text delves into the significance of regulatory factors, clinical trial structure, and actual data in confirming the effectiveness and safety of repurposed medications for respiratory infections. Drug repurposing is a valuable technique for quickly increasing the range of treatments for respiratory infections, leading to better patient outcomes and decreasing the worldwide disease burden.
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Affiliation(s)
- Juveriya Israr
- Institute of Biosciences and Technology, Shri Ramswaroop Memorial University, Barabanki, Uttar Pradesh, India; Department of Biotechnology, Era University, Lucknow, Uttar Pradesh, India
| | - Shabroz Alam
- Department of Biotechnology, Era University, Lucknow, Uttar Pradesh, India
| | - Ajay Kumar
- Department of Biotechnology, Faculty of Engineering and Technology, Rama University, Mandhana, Kanpur, Uttar Pradesh, India.
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3
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Hoseininezhad-Namin MS, Rahimpour E, Jouyban A. Favipiravir, remdesivir, and lopinavir: metabolites, degradation products and their analytical methods. Drug Metab Rev 2024; 56:127-144. [PMID: 38445647 DOI: 10.1080/03602532.2024.2326415] [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: 12/20/2023] [Accepted: 02/23/2024] [Indexed: 03/07/2024]
Abstract
Severe acute respiratory syndrome 2 (SARS-CoV-2) caused the emergence of the COVID-19 pandemic all over the world. Several studies have suggested that antiviral drugs such as favipiravir (FAV), remdesivir (RDV), and lopinavir (LPV) may potentially prevent the spread of the virus in the host cells and person-to-person transmission. Simultaneously with the widespread use of these drugs, their stability and action mechanism studies have also attracted the attention of many researchers. This review focuses on the action mechanism, metabolites and degradation products of these antiviral drugs (FAV, RDV and LPV) and demonstrates various methods for their quantification and discrimination in the different biological samples. Herein, the instrumental methods for analysis of the main form of drugs or their metabolite and degradation products are classified into two types: optical and chromatography methods which the last one in combination with various detectors provides a powerful method for routine and stability analyses. Some representative studies are reported in this review and the details of them are carefully explained. It is hoped that this review will be a good guideline study and provide a better understanding of these drugs from the aspects investigated in this study.
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Affiliation(s)
- Mir Saleh Hoseininezhad-Namin
- Pharmaceutical Analysis Research Center and Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Elaheh Rahimpour
- Pharmaceutical Analysis Research Center and Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Abolghasem Jouyban
- Pharmaceutical Analysis Research Center and Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
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4
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Oduro-Kwateng E, Soliman ME. DON/DRP-104 as potent serine protease inhibitors implicated in SARS-CoV-2 infection: Comparative binding modes with human TMPRSS2 and novel therapeutic approach. J Cell Biochem 2024. [PMID: 38284235 DOI: 10.1002/jcb.30528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 12/31/2023] [Accepted: 01/10/2024] [Indexed: 01/30/2024]
Abstract
Human transmembrane serine protease 2 (TMPRSS2) is an important member of the type 2 transmembrane serine protease (TTSP) family with significant therapeutic markings. The search for potent TMPRSS2 inhibitors against severe acute respiratory syndrome coronavirus 2 infection with favorable tissue specificity and off-site toxicity profiles remains limited. Therefore, probing the anti-TMPRSS2 potential of enhanced drug delivery systems, such as nanotechnology and prodrug systems, has become compelling. We report the first in silico study of TMPRSS2 against a prodrug, [isopropyl(S)-2-((S)-2-acetamido-3-(1H-indol-3-yl)-propanamido)-6-diazo-5-oxo-hexanoate] also known as DRP-104 synthesized from 6-Diazo-5-oxo-l-norleucine (DON). We performed comparative studies on DON and DRP-104 against a clinically potent TMPRSS2 inhibitor, nafamostat, and a standard serine protease inhibitor, 4-(2-Aminoethyl) benzenesulfonyl fluoride (AEBSF) against TMPRSS2 and found improved TMPRSS2 inhibition through synergistic binding of the S1/S1' subdomains. Both DON and DRP-104 had better thermodynamic profiles than AEBSF and nafamostat. DON was found to confer structural stability with strong positive correlated inter-residue motions, whereas DRP-104 was found to confer kinetic stability with restricted residue displacements and reduced loop flexibility. Interestingly, the Scavenger Receptor Cysteine-Rich (SRCR) domain of TMPRSS2 may be involved in its inhibition mechanics. Two previously unidentified loops, designated X (270-275) and Y (293-296) underwent minimal and major structural transitions, respectively. In addition, residues 273-277 consistently transitioned to a turn conformation in all ligated systems, whereas unique transitions were identified for other transitioning residue groups in each TMPRSS2-inhibitor complex. Intriguingly, while both DON and DRP-104 showed similar loop transition patterns, DRP-104 preserved loop structural integrity. As evident from our systematic comparative study using experimentally/clinically validated inhibitors, DRP-104 may serve as a potent and novel TMPRSS2 inhibitor and warrants further clinical investigation.
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Affiliation(s)
- Ernest Oduro-Kwateng
- School of Health Sciences, Molecular Bio-Computation and Drug Design Research Group, Westville Campus, University of KwaZulu Natal, Durban, South Africa
| | - Mahmoud E Soliman
- School of Health Sciences, Molecular Bio-Computation and Drug Design Research Group, Westville Campus, University of KwaZulu Natal, Durban, South Africa
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5
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Martínez-Arribas B, Annang F, Díaz-González R, Pérez-Moreno G, Martín J, Mackenzie TA, Castillo F, Reyes F, Genilloud O, Ruiz-Pérez LM, Vicente F, Ramos MC, González-Pacanowska D. Establishment of a screening platform based on human coronavirus OC43 for the identification of microbial natural products with antiviral activity. Microbiol Spectr 2024; 12:e0167923. [PMID: 38009959 PMCID: PMC10783114 DOI: 10.1128/spectrum.01679-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 10/24/2023] [Indexed: 11/29/2023] Open
Abstract
IMPORTANCE The COVID-19 pandemic has revealed the lack of effective treatments against betacoronaviruses and the urgent need for new broad-spectrum antivirals. Natural products are a valuable source of bioactive compounds with pharmaceutical potential that may lead to the discovery of new antiviral agents. Specifically, compared to conventional synthetic molecules, microbial natural extracts possess a unique and vast chemical diversity and are amenable to large-scale production. The implementation of a high-throughput screening platform using the betacoronavirus OC43 in a human cell line infection model has provided proof of concept of the approach and has allowed for the rapid and efficient evaluation of 1,280 microbial extracts. The identification of several active compounds validates the potential of the platform for the search for new compounds with antiviral capacity.
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Affiliation(s)
- Blanca Martínez-Arribas
- Instituto de Parasitología y Biomedicina López-Neyra, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Frederick Annang
- Fundación MEDINA, Parque Tecnológico de Ciencias de la Salud, Granada, Spain
| | - Rosario Díaz-González
- Instituto de Parasitología y Biomedicina López-Neyra, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Guiomar Pérez-Moreno
- Instituto de Parasitología y Biomedicina López-Neyra, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Jesús Martín
- Fundación MEDINA, Parque Tecnológico de Ciencias de la Salud, Granada, Spain
| | - Thomas A. Mackenzie
- Fundación MEDINA, Parque Tecnológico de Ciencias de la Salud, Granada, Spain
| | - Francisco Castillo
- Fundación MEDINA, Parque Tecnológico de Ciencias de la Salud, Granada, Spain
| | - Fernando Reyes
- Fundación MEDINA, Parque Tecnológico de Ciencias de la Salud, Granada, Spain
| | - Olga Genilloud
- Fundación MEDINA, Parque Tecnológico de Ciencias de la Salud, Granada, Spain
| | - Luis Miguel Ruiz-Pérez
- Instituto de Parasitología y Biomedicina López-Neyra, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Francisca Vicente
- Fundación MEDINA, Parque Tecnológico de Ciencias de la Salud, Granada, Spain
| | - María C. Ramos
- Fundación MEDINA, Parque Tecnológico de Ciencias de la Salud, Granada, Spain
| | - Dolores González-Pacanowska
- Instituto de Parasitología y Biomedicina López-Neyra, Consejo Superior de Investigaciones Científicas, Granada, Spain
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Mei M, Impagnatiello M, Jiao J, Reiser U, Tontsch-Grunt U, Zhang J, Nicklin P, Yu B, Wang Y, He Y, Tan X. An orally-available monovalent SMAC mimetic compound as a broad-spectrum antiviral. Protein Cell 2024; 15:69-75. [PMID: 37294910 PMCID: PMC10762662 DOI: 10.1093/procel/pwad033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 05/15/2023] [Indexed: 06/11/2023] Open
Affiliation(s)
- Miao Mei
- Tsinghua-Peking Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, MOE Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
- Chinese Institutes for Medical Research, Beijing 100069, China
| | | | - Jun Jiao
- Tsinghua-Peking Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, MOE Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
- Chinese Institutes for Medical Research, Beijing 100069, China
| | - Ulrich Reiser
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | | | - Ju Zhang
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Paul Nicklin
- Research Beyond Borders, Boehringer Ingelheim, Biberach an der Riss, Germany
| | - Bingke Yu
- Research Beyond Borders, Boehringer Ingelheim, Shanghai 200120, China
| | - Yu Wang
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Yuan He
- Research Beyond Borders, Boehringer Ingelheim, Shanghai 200120, China
| | - Xu Tan
- Tsinghua-Peking Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, MOE Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
- Chinese Institutes for Medical Research, Beijing 100069, China
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7
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Arman BY, Brun J, Hill ML, Zitzmann N, von Delft A. An Update on SARS-CoV-2 Clinical Trial Results-What We Can Learn for the Next Pandemic. Int J Mol Sci 2023; 25:354. [PMID: 38203525 PMCID: PMC10779148 DOI: 10.3390/ijms25010354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 12/21/2023] [Accepted: 12/24/2023] [Indexed: 01/12/2024] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has claimed over 7 million lives worldwide, providing a stark reminder of the importance of pandemic preparedness. Due to the lack of approved antiviral drugs effective against coronaviruses at the start of the pandemic, the world largely relied on repurposed efforts. Here, we summarise results from randomised controlled trials to date, as well as selected in vitro data of directly acting antivirals, host-targeting antivirals, and immunomodulatory drugs. Overall, repurposing efforts evaluating directly acting antivirals targeting other viral families were largely unsuccessful, whereas several immunomodulatory drugs led to clinical improvement in hospitalised patients with severe disease. In addition, accelerated drug discovery efforts during the pandemic progressed to multiple novel directly acting antivirals with clinical efficacy, including small molecule inhibitors and monoclonal antibodies. We argue that large-scale investment is required to prepare for future pandemics; both to develop an arsenal of broad-spectrum antivirals beyond coronaviruses and build worldwide clinical trial networks that can be rapidly utilised.
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Affiliation(s)
- Benediktus Yohan Arman
- Antiviral Drug Discovery Unit, Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK; (J.B.); (N.Z.)
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford OX1 3QU, UK
| | - Juliane Brun
- Antiviral Drug Discovery Unit, Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK; (J.B.); (N.Z.)
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford OX1 3QU, UK
| | - Michelle L. Hill
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK;
| | - Nicole Zitzmann
- Antiviral Drug Discovery Unit, Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK; (J.B.); (N.Z.)
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford OX1 3QU, UK
| | - Annette von Delft
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford OX1 3QU, UK
- Centre for Medicine Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
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8
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Arutyunova E, Belovodskiy A, Chen P, Khan MB, Joyce M, Saffran H, Lu J, Turner Z, Bai B, Lamer T, Young HS, Vederas J, Tyrrell DL, Lemieux MJ, Nieman JA. The Effect of Deuteration and Homologation of the Lactam Ring of Nirmatrelvir on Its Biochemical Properties and Oxidative Metabolism. ACS BIO & MED CHEM AU 2023; 3:528-541. [PMID: 38144257 PMCID: PMC10739250 DOI: 10.1021/acsbiomedchemau.3c00039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 09/26/2023] [Accepted: 09/27/2023] [Indexed: 12/26/2023]
Abstract
This study explores the relationship between structural alterations of nirmatrelvir, such as homologation and deuteration, and metabolic stability of newly synthesized derivatives. We developed a reliable synthetic protocol toward dideutero-nirmatrelvir and its homologated analogues with high isotopic incorporation. Deuteration of the primary metabolic site of nirmatrelvir provides a 3-fold improvement of its human microsomal stability but is accompanied by an increased metabolism rate at secondary sites. Homologation of the lactam ring allows the capping group modification to decrease and delocalize the molecule's lipophilicity, reducing the metabolic rate at secondary sites. The effect of deuteration was less pronounced for the 6-membered lactam than for its 5-membered analogue in human microsomes, but the trend is reversed in the case of mouse microsomes. X-ray data revealed that the homologation of the lactam ring favors the orientation of the drug's nitrile warhead for interaction with the catalytic sulfur of the SARS-CoV-2 Mpro, improving its binding. Comparable potency against SARS-CoV-2 Mpro from several variants of concern and selectivity over human cysteine proteases cathepsin B, L, and S was observed for the novel deuterated/homologated derivative and nirmatrelvir. Synthesized compounds displayed a large interspecies variability in hamster, rat, and human hepatocyte stability assays. Overall, we aimed to apply a rational approach in changing the physicochemical properties of the drug to refine its biochemical and biological parameters.
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Affiliation(s)
- Elena Arutyunova
- Department
of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
- Li
Ka Shing Institute of Virology, University
of Alberta, Edmonton, AB T6G 2E1, Canada
| | - Alexandr Belovodskiy
- Li Ka
Shing Applied Virology Institute, University
of Alberta, Edmonton, AB T6G 2E1, Canada
- Department
of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB T6G 2E1, Canada
| | - Pu Chen
- Department
of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
- Li
Ka Shing Institute of Virology, University
of Alberta, Edmonton, AB T6G 2E1, Canada
| | | | - Michael Joyce
- Li
Ka Shing Institute of Virology, University
of Alberta, Edmonton, AB T6G 2E1, Canada
- Department
of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB T6G 2E1, Canada
| | - Holly Saffran
- Li
Ka Shing Institute of Virology, University
of Alberta, Edmonton, AB T6G 2E1, Canada
- Department
of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB T6G 2E1, Canada
| | - Jimmy Lu
- Department
of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
- Li
Ka Shing Institute of Virology, University
of Alberta, Edmonton, AB T6G 2E1, Canada
| | - Zoe Turner
- Department
of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Bing Bai
- Li Ka
Shing Applied Virology Institute, University
of Alberta, Edmonton, AB T6G 2E1, Canada
- Department
of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB T6G 2E1, Canada
| | - Tess Lamer
- Department
of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Howard S. Young
- Department
of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - John
C. Vederas
- Department
of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - D. Lorne Tyrrell
- Li
Ka Shing Institute of Virology, University
of Alberta, Edmonton, AB T6G 2E1, Canada
- Li Ka
Shing Applied Virology Institute, University
of Alberta, Edmonton, AB T6G 2E1, Canada
- Department
of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB T6G 2E1, Canada
| | - M. Joanne Lemieux
- Department
of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
- Li
Ka Shing Institute of Virology, University
of Alberta, Edmonton, AB T6G 2E1, Canada
| | - James A. Nieman
- Li Ka
Shing Applied Virology Institute, University
of Alberta, Edmonton, AB T6G 2E1, Canada
- Department
of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB T6G 2E1, Canada
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Chai J, Zheng J, Tong Y, Chai F, Tian M. Construction of the molecularly imprinted adsorbent based on shaddock peel biochar sphere for highly sensitive detection of ribavirin in food and water resources. ENVIRONMENTAL RESEARCH 2023; 236:116756. [PMID: 37507037 DOI: 10.1016/j.envres.2023.116756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 07/24/2023] [Accepted: 07/26/2023] [Indexed: 07/30/2023]
Abstract
Ribavirin (RBV) that is not metabolically released into the environment can contaminate the environment and even make organisms resistant to it. Therefore, it is of great significance to establish a simple and effective method for adsorbing RBV in the environment. In this study, a novel biochar-based boronate affinity molecularly imprinted polymers (C@H@B-MIPs) were synthesized. This is the first time that shaddock peel biochar sphere was used as a carrier for specific recognition of RBV. The polymerization conditions were optimized and the binding properties of RBV were studied. Benefiting from the synergistic effect of boronate affinity and surface imprinting, the C@H@B-MIPs showed rapid equilibrium kinetics of 15 min, high adsorption capacity of 18.30 mg g-1, and excellent reusability for RBV. The linear range was 0.05-100 mg L-1, and the detection limit was 0.023 mg L-1. This method was triumphant applied to the selective adsorption of RBV in food and water resources with recovery rates of 81.4-97.7%. This study provides a practical platform for the manufacture of efficient biomass-based adsorbents.
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Affiliation(s)
- Jinyue Chai
- Key Laboratory of Photochemical Biomaterials and Energy Storage Materials, Heilongjiang Province, College of Chemistry and Chemical Engineering, Harbin Normal University, Harbin, 150025, PR China
| | - Junlei Zheng
- Key Laboratory of Photochemical Biomaterials and Energy Storage Materials, Heilongjiang Province, College of Chemistry and Chemical Engineering, Harbin Normal University, Harbin, 150025, PR China
| | - Yukui Tong
- Key Laboratory of Photochemical Biomaterials and Energy Storage Materials, Heilongjiang Province, College of Chemistry and Chemical Engineering, Harbin Normal University, Harbin, 150025, PR China
| | - Fang Chai
- Key Laboratory of Photochemical Biomaterials and Energy Storage Materials, Heilongjiang Province, College of Chemistry and Chemical Engineering, Harbin Normal University, Harbin, 150025, PR China.
| | - Miaomiao Tian
- Key Laboratory of Photochemical Biomaterials and Energy Storage Materials, Heilongjiang Province, College of Chemistry and Chemical Engineering, Harbin Normal University, Harbin, 150025, PR China.
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10
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Chen R, Bao J, Huang X, Chen Q, Huang M, Gao M, Yu F, Chen J, Zou W, Shi L, Chen X, Feng B, Wang R, Feng B, Zheng S, Yu F. Comparison of "hock-a-loogie" saliva versus nasopharyngeal and oropharyngeal swabs for detecting common respiratory pathogens. Heliyon 2023; 9:e20965. [PMID: 37867842 PMCID: PMC10587520 DOI: 10.1016/j.heliyon.2023.e20965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 10/10/2023] [Accepted: 10/12/2023] [Indexed: 10/24/2023] Open
Abstract
Self-collection of saliva samples has attracted considerable attention in recent years, particularly during the coronavirus disease 2019 pandemic. However, studies investigating the detection of other common respiratory pathogens in saliva samples are limited. In this study, nasopharyngeal swabs (NPS), oropharyngeal swabs (OPS), and "hock-a-loogie" saliva (HLS) were collected from 469 patients to detect 13 common respiratory pathogens. Overall positivity rates for NPS (66.1 %), HLS (63.5 %), and OPS (57.8 %) were statistically different (P = 0.028), with an overall concordance of 72.7 %. Additionally, detection rates for NPS (85.9 %) and HLS (83.2 %) for all pathogens were much higher than for OPS (73.3 %). Coronavirus and human rhinovirus were most frequently detected pathogens in NPS (P < 0.001). Mycoplasma pneumoniae was significantly more prevalent in the HLS group (P = 0.008). In conclusion, NPS was a reliable sample type for detecting common respiratory pathogens. HLS was more easily collected and can be used in emergencies or specific conditions. Mixed NPS/OPS and NPS/HLS specimens have the potential to improve detection rates, although OPS testing alone has a relatively high risk for missed detection.
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Affiliation(s)
- Renke Chen
- The First Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, China
| | - Jiaqi Bao
- Department of Laboratory Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Clinical In Vitro Diagnostic Techniques of Zhejiang Province, Hangzhou, China
- Institute of Laboratory Medicine, Zhejiang University, Hangzhou, China
| | - Xiaojuan Huang
- Department of Laboratory Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Qianna Chen
- Department of Laboratory Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Maowen Huang
- Center of Clinical Laboratory, Ningbo Beilun People's Hospital, Ningbo, China
| | - Min Gao
- Department of Clinical Laboratory, Huzhou Central Hospital, Affiliated Central Hospital Huzhou University, Huzhou, China
| | - Fanghao Yu
- Department of Clinical Laboratory, Yiwu Central Hospital, Yiwu, China
| | - Jiayao Chen
- Department of Clinical Laboratory, Zhoushan Hospital of Zhejiang Province, Zhoushan, China
| | - Weihua Zou
- Department of Clinical Laboratory, Huzhou Central Hospital, Affiliated Central Hospital Huzhou University, Huzhou, China
| | - Lumei Shi
- Center of Clinical Laboratory, Ningbo Beilun People's Hospital, Ningbo, China
| | - Xiao Chen
- Department of Laboratory Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Clinical In Vitro Diagnostic Techniques of Zhejiang Province, Hangzhou, China
- Institute of Laboratory Medicine, Zhejiang University, Hangzhou, China
| | - Bo Feng
- Department of Nephrology, Jiaxing Hospital of Traditional Chinese Medicine, Jiaxing, China
| | - Ruonan Wang
- Department of Laboratory Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Clinical In Vitro Diagnostic Techniques of Zhejiang Province, Hangzhou, China
- Institute of Laboratory Medicine, Zhejiang University, Hangzhou, China
| | - Baihuan Feng
- Department of Laboratory Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Clinical In Vitro Diagnostic Techniques of Zhejiang Province, Hangzhou, China
- Institute of Laboratory Medicine, Zhejiang University, Hangzhou, China
| | - Shufa Zheng
- Department of Laboratory Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Clinical In Vitro Diagnostic Techniques of Zhejiang Province, Hangzhou, China
- Institute of Laboratory Medicine, Zhejiang University, Hangzhou, China
| | - Fei Yu
- Department of Laboratory Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Clinical In Vitro Diagnostic Techniques of Zhejiang Province, Hangzhou, China
- Institute of Laboratory Medicine, Zhejiang University, Hangzhou, China
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11
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Awad AM, Hansen K, Del Rio D, Flores D, Barghash RF, Kakkola L, Julkunen I, Awad K. Insights into COVID-19: Perspectives on Drug Remedies and Host Cell Responses. Biomolecules 2023; 13:1452. [PMID: 37892134 PMCID: PMC10604481 DOI: 10.3390/biom13101452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 09/19/2023] [Accepted: 09/21/2023] [Indexed: 10/29/2023] Open
Abstract
In light of the COVID-19 global pandemic caused by SARS-CoV-2, ongoing research has centered on minimizing viral spread either by stopping viral entry or inhibiting viral replication. Repurposing antiviral drugs, typically nucleoside analogs, has proven successful at inhibiting virus replication. This review summarizes current information regarding coronavirus classification and characterization and presents the broad clinical consequences of SARS-CoV-2 activation of the angiotensin-converting enzyme 2 (ACE2) receptor expressed in different human cell types. It provides publicly available knowledge on the chemical nature of proposed therapeutics and their target biomolecules to assist in the identification of potentially new drugs for the treatment of SARS-CoV-2 infection.
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Affiliation(s)
- Ahmed M. Awad
- Department of Chemistry, California State University Channel Islands, Camarillo, CA 93012, USA
| | - Kamryn Hansen
- Department of Chemistry, California State University Channel Islands, Camarillo, CA 93012, USA
| | - Diana Del Rio
- Department of Chemistry, California State University Channel Islands, Camarillo, CA 93012, USA
| | - Derek Flores
- Department of Chemistry, California State University Channel Islands, Camarillo, CA 93012, USA
| | - Reham F. Barghash
- Institute of Chemical Industries Research, National Research Centre, Dokki, Cairo 12622, Egypt
| | - Laura Kakkola
- Institute of Biomedicine, Faculty of Medicine, University of Turku, 20014 Turku, Finland
| | - Ilkka Julkunen
- Institute of Biomedicine, Faculty of Medicine, University of Turku, 20014 Turku, Finland
- Clinical Microbiology, Turku University Hospital, 20521 Turku, Finland
| | - Kareem Awad
- Institute of Biomedicine, Faculty of Medicine, University of Turku, 20014 Turku, Finland
- Department of Therapeutic Chemistry, Institute of Pharmaceutical and Drug Industries Research, National Research Center, Dokki, Cairo 12622, Egypt
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12
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Pashameah RA, Soltane R, Sayed AM. Discovery of raffinose sulfate as a potential SARS CoV-2 inhibitor via blocking its binding with angiotensin converting enzyme 2. Int J Biol Macromol 2023; 248:125818. [PMID: 37473891 DOI: 10.1016/j.ijbiomac.2023.125818] [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: 04/14/2023] [Revised: 06/23/2023] [Accepted: 07/11/2023] [Indexed: 07/22/2023]
Abstract
The present study aimed to characterize the possible binding sites on the SARS CoV-2 RBD-ACE2 complex and to highlight sulfated oligosaccharides as potential anti-SARS CoV-2 via inducing RBD-ACE2 complex destabilization and dissociation. By combining pharmacophore-based and structural-based virtual screening approaches we were able to discover raffinose sulfate (RS) as a potential antiviral sulfated oligosaccharide against two SARS CoV-2 variants (i.e., wild type and Omicron) (IC50 = 4.45 ± 0.28 μM and 4.65 ± 0.32 μM, respectively). Upon MD simulation, RS was able to establish stable binding at the RBD-ACE2 interface inducing a rapid dissociation. Accordingly, and by using bio-layer interferometry (BLI) assays, RS was able to significantly weaken the affinity between RBD (of both variants) and ACE2. Additionally, we found that RS has a poor cellular permeability indicating that its interaction with the RBD-ACE2 complex may be the main mechanism by which it mediates its antiviral activity against SARS CoV-2. Despite its proposed interaction with the RBD-ACE2 complex, RS did not show any inhibitory activity against ACE2 catalytic activity. In light of these findings, the RS scaffold can be further developed into a novel anti-SARS CoV-2 drug with improved activity and tolerability in comparison with other sulfated polysaccharides e.g., heparin and heparan.
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Affiliation(s)
- Rami Adel Pashameah
- Department of Chemistry, Faculty of Applied Science, Umm Al-Qura University, Makkah 21955, Saudi Arabia.
| | - Raya Soltane
- Department of Basic Sciences, Adham University College, Umm Al-Qura University, Makkah 21955, Saudi Arabia.
| | - Ahmed M Sayed
- Department of Pharmacognosy, Faculty of Pharmacy, Nahda University, 62513 Beni-Suef, Egypt.
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13
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Hassan AHE, El-Sayed SM, Yamamoto M, Gohda J, Matsumoto T, Shirouzu M, Inoue JI, Kawaguchi Y, Mansour RMA, Anvari A, Farahat AA. In Silico and In Vitro Evaluation of Some Amidine Derivatives as Hit Compounds towards Development of Inhibitors against Coronavirus Diseases. Viruses 2023; 15:1171. [PMID: 37243257 PMCID: PMC10223987 DOI: 10.3390/v15051171] [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: 03/09/2023] [Revised: 05/04/2023] [Accepted: 05/12/2023] [Indexed: 05/28/2023] Open
Abstract
Coronaviruses, including SARS-CoV-2, SARS-CoV, MERS-CoV and influenza A virus, require the host proteases to mediate viral entry into cells. Rather than targeting the continuously mutating viral proteins, targeting the conserved host-based entry mechanism could offer advantages. Nafamostat and camostat were discovered as covalent inhibitors of TMPRSS2 protease involved in viral entry. To circumvent their limitations, a reversible inhibitor might be required. Considering nafamostat structure and using pentamidine as a starting point, a small set of structurally diverse rigid analogues were designed and evaluated in silico to guide selection of compounds to be prepared for biological evaluation. Based on the results of in silico study, six compounds were prepared and evaluated in vitro. At the enzyme level, compounds 10-12 triggered potential TMPRSS2 inhibition with low micromolar IC50 concentrations, but they were less effective in cellular assays. Meanwhile, compound 14 did not trigger potential TMPRSS2 inhibition at the enzyme level, but it showed potential cellular activity regarding inhibition of membrane fusion with a low micromolar IC50 value of 10.87 µM, suggesting its action could be mediated by another molecular target. Furthermore, in vitro evaluation showed that compound 14 inhibited pseudovirus entry as well as thrombin and factor Xa. Together, this study presents compound 14 as a hit compound that might serve as a starting point for developing potential viral entry inhibitors with possible application against coronaviruses.
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Affiliation(s)
- Ahmed H E Hassan
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Selwan M El-Sayed
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Mizuki Yamamoto
- Research Center for Asian Infectious Diseases, Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Jin Gohda
- Research Center for Asian Infectious Diseases, Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Takehisa Matsumoto
- Drug Discovery Structural Biology Platform Unit, RIKEN Center for Biosystems Dynamics Research, Kanagawa 230-0045, Japan
| | - Mikako Shirouzu
- Drug Discovery Structural Biology Platform Unit, RIKEN Center for Biosystems Dynamics Research, Kanagawa 230-0045, Japan
| | - Jun-Ichiro Inoue
- Infection and Advanced Research Center (UTOPIA), The University of Tokyo Pandemic Preparedness, Tokyo 108-8639, Japan
| | - Yasushi Kawaguchi
- Research Center for Asian Infectious Diseases, Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
- Division of Molecular Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Reem M A Mansour
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Abtin Anvari
- Master of Pharmaceutical Sciences Program, California Northstate University, 9700 W Taron Dr., Elk Grove, CA 95757, USA
| | - Abdelbasset A Farahat
- Master of Pharmaceutical Sciences Program, California Northstate University, 9700 W Taron Dr., Elk Grove, CA 95757, USA
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
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14
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Reddy KR, Sahni C, Sharma S. Antiviral Activity of Svarnvir-IV Tablet Assayed for Activity Against SARS-CoV-2 In Vitro. Cureus 2023; 15:e39421. [PMID: 37362483 PMCID: PMC10288389 DOI: 10.7759/cureus.39421] [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] [Accepted: 05/24/2023] [Indexed: 06/28/2023] Open
Abstract
The coronavirus disease (COVID-19), caused by the virus SARS-CoV-2, has become a global pandemic in a very short time span. While several vaccines have been developed in the last year, specific treatments for CoV infection are still being explored. Thus, the situation highlights the need to develop safe and efficacious antiviral therapeutics. Ayurvedic Rasayana therapy has been traditionally used in India for its holistic healing systems and proven history of empirical use. There is emerging evidence that Ayurvedic treatment methodologies and herbal medicines may be effective strategies in combating COVID-19. The present study is aimed at evaluating the antiviral and therapeutic activity of an Ayurvedic herbomineral formulation (Svarnvir-IV tablet, 450 mg) against the SARS-CoV-2 virus in vitro. A cell-based assay was conducted to evaluate the cytotoxicity of the Svarnvir-IV tablets (Aimil Pharmaceuticals, Delhi, India) for the determination of virucidal activity assessment (at 2 hours) and therapeutic activity assessment (at 1 hour, 2 hours, and 4 hours). When incubated with SARS-CoV-2 virus at 0.1 multiplicity of infection (MoI) for two hours, Svarnvir-IV tablet exhibited virucidal activity against SARS-CoV-2 with an EC50 value of 0.0058 mg/ml. It also exhibited therapeutic activity when treated with cells infected with the SARS-CoV-2 virus (0.1 MoI) for 1 hour, 2 hours and 4 hours post-infection, with an EC50 value of 0.094 mg/ml, 0.023 mg/ml, and 0.05 mg/ml, respectively. The original supporting data obtained from this study, along with existing Ayurvedic traditional information, has shown encouraging results.
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Affiliation(s)
- K Ramachandra Reddy
- Department of Rasa Shastra, Faculty of Ayurveda, Institute of Medical Sciences, Banaras Hindu University, Varanasi, IND
| | - Chetan Sahni
- Department of Anatomy, Institute of Medical Sciences, Banaras Hindu University, Varanasi, IND
| | - Sanchit Sharma
- Research and Development, Aimil Pharmaceuticals, Delhi, IND
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15
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Ershov PV, Yablokov EO, Mezentsev YV, Chuev GN, Fedotova MV, Kruchinin SE, Ivanov AS. SARS-COV-2 Coronavirus Papain-like Protease PLpro as an Antiviral Target for Inhibitors of Active Site and Protein-Protein Interactions. Biophysics (Nagoya-shi) 2023; 67:902-912. [PMID: 36883182 PMCID: PMC9984130 DOI: 10.1134/s0006350922060082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Revised: 08/09/2022] [Accepted: 08/12/2022] [Indexed: 03/06/2023] Open
Abstract
The papain-like protease PLpro of the SARS-CoV-2 coronavirus is a multifunctional enzyme that catalyzes the proteolytic processing of two viral polyproteins, pp1a and pp1ab. PLpro also cleaves peptide bonds between host cell proteins and ubiquitin (or ubiquitin-like proteins), which is associated with a violation of immune processes. Nine structures of the most effective inhibitors of the PLpro active center were prioritized according to the parameters of biochemical (IC 50) and cellular tests to assess the suppression of viral replication (EC 50) and cytotoxicity (CC 50). A literature search has shown that PLpro can interact with at least 60 potential protein partners in cells, 23 of which are targets for other viral proteins (human papillomavirus and Epstein-Barr virus). The analysis of protein-protein interactions showed that the proteins USP3, UBE2J1, RCHY1, and FAF2 involved in deubiquitinylation and ubiquitinylation processes contain the largest number of bonds with other proteins; the interaction of viral proteins with them can affect the architecture of the entire network of protein-protein interactions. Using the example of a spatial model of the PLpro/ubiquitin complex and a set of 154 naturally occurring compounds with known antiviral activity, 13 compounds (molecular masses in the range of 454-954 Da) were predicted as potential PLpro inhibitors. These compounds bind to the "hot" amino acid residues of the protease at the positions Gly163, Asp164, Arg166, Glu167, and Tyr264 involved in the interaction with ubiquitin. Thus, pharmacological effects on peripheral PLpro sites, which play important roles in binding protein substrates, may be an additional target-oriented antiviral strategy.
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Affiliation(s)
- P. V. Ershov
- Institute of Biomedical Chemistry, 119121 Moscow, Russia
| | - E. O. Yablokov
- Institute of Biomedical Chemistry, 119121 Moscow, Russia
| | | | - G. N. Chuev
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, 142290 Pushchino, Moscow oblast Russia
| | - M. V. Fedotova
- Krestov Institute of Solution Chemistry, Russian Academy of Sciences, 153045 Ivanovo, Russia
| | - S. E. Kruchinin
- Krestov Institute of Solution Chemistry, Russian Academy of Sciences, 153045 Ivanovo, Russia
| | - A. S. Ivanov
- Institute of Biomedical Chemistry, 119121 Moscow, Russia
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16
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Sayed AM, Ibrahim AH, Tajuddeen N, Seibel J, Bodem J, Geiger N, Striffler K, Bringmann G, Abdelmohsen UR. Korupensamine A, but not its atropisomer, korupensamine B, inhibits SARS-CoV-2 in vitro by targeting its main protease (M pro). Eur J Med Chem 2023; 251:115226. [PMID: 36893625 PMCID: PMC9972725 DOI: 10.1016/j.ejmech.2023.115226] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 02/07/2023] [Accepted: 02/20/2023] [Indexed: 03/06/2023]
Abstract
By combining docking and molecular dynamics simulations, we explored a library of 65 mostly axially chiral naphthylisoquinoline alkaloids and their analogues, with most different molecular architectures and structural analogues, for their activity against SARS-CoV-2. Although natural biaryls are often regarded without consideration of their axial chirality, they can bind to protein targets in an atroposelective manner. By combining docking results with steered molecular dynamics simulations, we identified one alkaloid, korupensamine A, that atropisomer-specifically inhibited the main protease (Mpro) activity of SARS-CoV-2 significantly in comparison to the reference covalent inhibitor GC376 (IC50 = 2.52 ± 0.14 and 0.88 ± 0.15 μM, respectively) and reduced viral growth by five orders of magnitude in vitro (EC50 = 4.23 ± 1.31 μM). To investigate the binding pathway and mode of interaction of korupensamine A within the active site of the protease, we utilized Gaussian accelerated molecular dynamics simulations, which reproduced the docking pose of korupensamine A inside the active site of the enzyme. The study presents naphthylisoquinoline alkaloids as a new class of potential anti-COVID-19 agents.
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Affiliation(s)
- Ahmed M Sayed
- Department of Pharmacognosy, Faculty of Pharmacy, Nahda University, Beni-Suef, 62513, Egypt
| | - Alyaa Hatem Ibrahim
- Department of Pharmacognosy, Faculty of Pharmacy, Sohag University, Sohag, 82524, Egypt
| | - Nasir Tajuddeen
- Department of Chemistry, Ahmadu Bello University, 15 Sokoto Road Samaru, Zaria, 810107, Nigeria
| | - Jürgen Seibel
- Institute of Organic Chemistry, University of Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Jochen Bodem
- Institute of Virology and Immunobiology, University of Würzburg, Versbacher Str. 7, 97078, Würzburg, Germany
| | - Nina Geiger
- Institute of Virology and Immunobiology, University of Würzburg, Versbacher Str. 7, 97078, Würzburg, Germany
| | - Kathrin Striffler
- Institute of Virology and Immunobiology, University of Würzburg, Versbacher Str. 7, 97078, Würzburg, Germany
| | - Gerhard Bringmann
- Institute of Organic Chemistry, University of Würzburg, Am Hubland, 97074, Würzburg, Germany.
| | - Usama Ramadan Abdelmohsen
- Department of Pharmacognosy, Faculty of Pharmacy, Minia University, Minia, 61519, Egypt; Department of Pharmacognosy, Faculty of Pharmacy, Deraya University, Universities Zone, New Minia City, 61111, Egypt.
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17
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Di Lorenzo P, Casella C, Marisei M, Sarno L, Aquino CI, Osuna E, Guida M, Niola M. A COVID Dilemma: How to Manage Pregnancies in Case of Severe Respiratory Failure? Healthcare (Basel) 2023; 11:healthcare11040486. [PMID: 36833020 PMCID: PMC9957288 DOI: 10.3390/healthcare11040486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 02/01/2023] [Accepted: 02/04/2023] [Indexed: 02/10/2023] Open
Abstract
To date, the impact of the COVID-19 pandemic on the world's health, economics and politics is still heavy, and efforts to mitigate virus transmission have caused remarkable disruption. From the early onset of the pandemic, generated by SARS-CoV-2 spread, the scientific community was aware of its impact on vulnerable individuals, including pregnant women. The purpose of this paper is to highlight scientific pitfalls and ethical dilemmas emerging from management of severe respiratory distress in pregnant women in order to add evidence to this topic through an ethical debate. In the here-presented paper, three cases of severe respiratory syndrome are analyzed. No specific therapeutic protocol was available to guide physicians in a cost-benefit balance, and unequivocal conduct was not a priori suggested from scientific evidence. However, vaccines' advent, viral variants lurking on the horizon and other possible pandemic challenges make it necessary to maximize the experience gained through these difficult years. Antenatal management of pregnancies complicated by COVID-19 infection with severe respiratory failure is still heterogeneous and ethical concerns must be pointed out.
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Affiliation(s)
- Pierpaolo Di Lorenzo
- Department of Advanced Biomedical Sciences, University of Naples Federico II, 80131 Naples, Italy
| | - Claudia Casella
- Department of Advanced Biomedical Sciences, University of Naples Federico II, 80131 Naples, Italy
| | - Mariagrazia Marisei
- Department of Advanced Biomedical Sciences, University of Naples Federico II, 80131 Naples, Italy
- Correspondence: ; Tel.: +39-0817464734
| | - Laura Sarno
- Department of Neuroscience and Reproductive and Odontostomatological Sciences, University of Naples Federico II, 80131 Naples, Italy
| | - Carmen Imma Aquino
- Department of Gynecology, Obstetrics University of Piemonte Orientale, Ospedale Maggiore della Carità, 28100 Novara, Italy
| | - Eduardo Osuna
- Department of Sociosanitary Sciences, University of Murcia, 30005 Murcia, Spain
| | - Maurizio Guida
- Department of Neuroscience and Reproductive and Odontostomatological Sciences, University of Naples Federico II, 80131 Naples, Italy
| | - Massimo Niola
- Department of Advanced Biomedical Sciences, University of Naples Federico II, 80131 Naples, Italy
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18
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Kullappan M, Mary U, Ambrose JM, Veeraraghavan VP, Surapaneni KM. Elucidating the role of N440K mutation in SARS-CoV-2 spike - ACE-2 binding affinity and COVID-19 severity by virtual screening, molecular docking and dynamics approach. J Biomol Struct Dyn 2023; 41:912-929. [PMID: 34904526 DOI: 10.1080/07391102.2021.2014973] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
COVID-19 has become a public health concern around the world. The frequency of N440K variant was higher during the second wave in South India. The mutation was observed in the Receptor Binding Domain region (RBD) of the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) spike (S) protein. The binding affinity of SARS-CoV-2-Angiotensin-Converting Enzyme-2 (ACE-2) plays a major role in the transmission and severity of the disease. To understand the binding affinity of the wild and mutant SARS-CoV-2 S with ACE2, molecular modeling studies were carried out. We discovered that the wild SARS-CoV-2 S RBD-ACE-2 complex has a high binding affinity and stability than that of the mutant. The N440K strain escapes from antibody neutralization, which might increase reinfection and decrease vaccine efficiency. To find a potential inhibitor against mutant N440K SARS-CoV-2, a virtual screening process was carried out and found ZINC169293961, ZINC409421825 and ZINC22060839 as the best binding energy compounds. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Malathi Kullappan
- Department of Research, Panimalar Medical College Hospital & Research Institute, Varadharajapuram, Poonamallee, Chennai, India
| | - Usha Mary
- Department of Chemistry, Panimalar Engineering College, Varadharajapuram, Poonamallee, Chennai, India
| | - Jenifer M Ambrose
- Department of Research, Panimalar Medical College Hospital & Research Institute, Varadharajapuram, Poonamallee, Chennai, India
| | - Vishnu Priya Veeraraghavan
- Department of Biochemistry, Saveetha Dental College, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Velappanchavadi, Chennai, Tamil Nadu, India
| | - Krishna Mohan Surapaneni
- Department of Research, Panimalar Medical College Hospital & Research Institute, Varadharajapuram, Poonamallee, Chennai, India.,Department of Biochemistry, Panimalar Medical College Hospital & Research Institute, Varadharajapuram, Poonamallee, Chennai, India.,Department of Molecular Virology, Clinical Skills & Simulation, Research, Panimalar Medical College Hospital & Research Institute, Varadharajapuram, Poonamallee, Chennai, India.,Department of Clinical Skills & Simulation, Panimalar Medical College Hospital & Research Institute, Varadharajapuram, Poonamallee, Chennai, India
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19
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Liu J, Ge C, Zha L, Lin L, Li R. Simple Nano-Luciferase-Based Assay for the Rapid and High-Throughput Detection of SARS-CoV-2 3C-Like Protease. Anal Chem 2023; 95:714-719. [PMID: 36576396 PMCID: PMC9843625 DOI: 10.1021/acs.analchem.2c02590] [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: 06/16/2022] [Accepted: 12/09/2022] [Indexed: 12/29/2022]
Abstract
In this study, we described an easy-to-perform nano-luciferase (nLuc) sensor for the rapid detection of 3-chymotrypsin-like protease (3CLpro) encoded by SARS-CoV-2. The technology is based on the cleavage reaction of recombinant-nLuc via 3CLpro. The nLuc-based assay is a general, one-step method and is naturally specific in detection. The stability, sensitivity, detection range, and response time are fully characterized. The application of 3CLpro detection in artificial and human saliva as well as antiviral drug screening demonstrates that the method can quantify 3CLpro with high sensitivity in one step. With its unique features, the nLuc-based assay may find broad applications in the auxiliary diagnosis of SARS-CoV-2, as well as other types of coronavirus infection.
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Affiliation(s)
- Jingxin Liu
- College
of Health Science and Environmental Engineering, Shenzhen Technology University, 3002 Lantian Road, Pingshan District, Shenzhen, Guangdong 518118, P. R. China
| | - Chenchen Ge
- College
of Health Science and Environmental Engineering, Shenzhen Technology University, 3002 Lantian Road, Pingshan District, Shenzhen, Guangdong 518118, P. R. China
| | - Ling Zha
- College
of Health Science and Environmental Engineering, Shenzhen Technology University, 3002 Lantian Road, Pingshan District, Shenzhen, Guangdong 518118, P. R. China
| | - Ligen Lin
- State
Key Laboratory of Quality Research in Chinese Medicine, Institute
of Chinese Medical Sciences, University
of Macau, Macao 999078, P. R. China
| | - Rongsong Li
- College
of Health Science and Environmental Engineering, Shenzhen Technology University, 3002 Lantian Road, Pingshan District, Shenzhen, Guangdong 518118, P. R. China
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20
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Naidu SAG, Mustafa G, Clemens RA, Naidu AS. Plant-Derived Natural Non-Nucleoside Analog Inhibitors (NNAIs) against RNA-Dependent RNA Polymerase Complex (nsp7/nsp8/nsp12) of SARS-CoV-2. J Diet Suppl 2023; 20:254-283. [PMID: 34850656 DOI: 10.1080/19390211.2021.2006387] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The emergence of fast-spreading SARS-CoV-2 mutants has sparked a new phase of COVID-19 pandemic. There is a dire necessity for antivirals targeting highly conserved genomic domains on SARS-CoV-2 that are less prone to mutation. The nsp12, also known as the RNA-dependent RNA-polymerase (RdRp), the core component of 'SARS-CoV-2 replication-transcription complex', is a potential well-conserved druggable antiviral target. Several FDA-approved RdRp 'nucleotide analog inhibitors (NAIs)' such as remdesivir, have been repurposed to treat COVID-19 infections. The NAIs target RdRp protein translation and competitively block the nucleotide insertion into the RNA chain, resulting in the inhibition of viral replication. However, the replication proofreading function of nsp14-ExoN could provide resistance to SARS-CoV-2 against many NAIs. Conversely, the 'non-nucleoside analog inhibitors (NNAIs)' bind to allosteric sites on viral polymerase surface, change the redox state; thereby, exert antiviral activity by altering interactions between the enzyme substrate and active core catalytic site of the RdRp. NNAIs neither require metabolic activation (unlike NAIs) nor compete with intracellular pool of nucleotide triphosphates (NTPs) for anti-RdRp activity. The NNAIs from phytonutrient origin are potential antiviral candidates compared to their synthetic counterparts. Several in-silico studies reported the antiviral spectrum of natural phytonutrient-NNAIs such as Suramin, Silibinin (flavonolignan), Theaflavin (tea polyphenol), Baicalein (5,6,7-trihydroxyflavone), Corilagin (gallotannin), Hesperidin (citrus bioflavonoid), Lycorine (pyrrolidine alkaloid), with superior redox characteristics (free binding energy, hydrogen-bonds, etc.) than antiviral drugs (i.e. remdesivir, favipiravir). These phytonutrient-NNAIs also exert anti-inflammatory, antioxidant, immunomodulatory and cardioprotective functions, with multifunctional therapeutic benefits in the clinical management of COVID-19.
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Affiliation(s)
| | - Ghulam Mustafa
- Department of Biochemistry, Government College University, Faisalabad, Pakistan
| | - Roger A Clemens
- Department of International Regulatory Science, University of Southern California School of Pharmacy, Los Angeles, CA, USA
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21
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Baron G, Borella S, della Vedova L, Vittorio S, Vistoli G, Carini M, Aldini G, Altomare A. An integrated metabolomic and proteomic approach for the identification of covalent inhibitors of the main protease (Mpro) of SARS-COV-2 from crude natural extracts. Talanta 2023; 252:123824. [PMID: 36027618 PMCID: PMC9371774 DOI: 10.1016/j.talanta.2022.123824] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/03/2022] [Accepted: 08/05/2022] [Indexed: 11/21/2022]
Abstract
Mpro represents one of the most promising drug targets for SARS-Cov-2, as it plays a crucial role in the maturation of viral polyproteins into functional proteins. HTS methods are currently used to screen Mpro inhibitors, and rely on searching chemical databases and compound libraries, meaning that they only consider previously structurally clarified and isolated molecules. A great advancement in the hit identification strategy would be to set-up an approach aimed at exploring un-deconvoluted mixtures of compounds such as plant extracts. Hence, the aim of the present study is to set-up an analytical platform able to fish-out bioactive molecules from complex natural matrices even where there is no knowledge on the constituents. The proposed approach begins with a metabolomic step aimed at annotating the MW of the matrix constituents. A further metabolomic step is based on identifying those natural electrophilic compounds able to form a Michael adduct with thiols, a peculiar chemical feature of many Mpro inhibitors that covalently bind the catalytic Cys145 in the active site, thus stabilizing the complex. A final step consists of incubating recombinant Mpro with natural extracts and identifying compounds adducted to the residues within the Mpro active site by bottom-up proteomic analysis (nano-LC-HRMS). Data analysis is based on two complementary strategies: (i) a targeted search applied by setting the adducted moieties identified as Michael acceptors of Cys as variable modifications; (ii) an untargeted approach aimed at identifying the whole range of adducted peptides containing Cys145 on the basis of the characteristic b and y fragment ions independent of the adduct. The method was set-up and then successfully tested to fish-out bioactive compounds from the crude extract of Scutellaria baicalensis, a Chinese plant containing the catechol-like flavonoid baicalin and its corresponding aglycone baicalein which are well-established inhibitors of Mpro. Molecular dynamics (MD) simulations were carried out in order to explore the binding mode of baicalin and baicalein, within the SARS-CoV-2 Mpro active site, allowing a better understanding of the role of the nucleophilic residues (i.e. His41, Cys145, His163 and His164) in the protein-ligand recognition process.
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22
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Zhang X, Yuan H, Yang Z, Hu X, Mahmmod YS, Zhu X, Zhao C, Zhai J, Zhang XX, Luo S, Wang XH, Xue M, Zheng C, Yuan ZG. SARS-CoV-2: An Updated Review Highlighting Its Evolution and Treatments. Vaccines (Basel) 2022; 10:2145. [PMID: 36560555 PMCID: PMC9780920 DOI: 10.3390/vaccines10122145] [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: 11/08/2022] [Revised: 12/07/2022] [Accepted: 12/08/2022] [Indexed: 12/23/2022] Open
Abstract
Since the SARS-CoV-2 outbreak, pharmaceutical companies and researchers worldwide have worked hard to develop vaccines and drugs to end the SARS-CoV-2 pandemic. The potential pathogen responsible for Coronavirus Disease 2019 (COVID-19), SARS-CoV-2, belongs to a novel lineage of beta coronaviruses in the subgenus arbovirus. Antiviral drugs, convalescent plasma, monoclonal antibodies, and vaccines are effective treatments for SARS-CoV-2 and are beneficial in preventing infection. Numerous studies have already been conducted using the genome sequence of SARS-CoV-2 in comparison with that of other SARS-like viruses, and numerous treatments/prevention measures are currently undergoing or have already undergone clinical trials. We summarize these studies in depth in the hopes of highlighting some key details that will help us to better understand the viral origin, epidemiology, and treatments of the virus.
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Affiliation(s)
- Xirui Zhang
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Hao Yuan
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Zipeng Yang
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Key Laboratory of Livestock Disease Prevention of Guangdong Province, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
| | - Xiaoyu Hu
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Yasser S. Mahmmod
- Infectious Diseases, Department of Animal Medicine, Faculty of Veterinary Medicine, Zagazig University, Zagazig 44511, Egypt
- Veterinary Sciences Division, Al Ain Men’s College, Higher Colleges of Technology, Abu Dhabi 17155, United Arab Emirates
| | - Xiaojing Zhu
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Cuiping Zhao
- The 80th Army Hospital of the Chinese people’s Liberation Army, Weifang 261021, China
| | - Jingbo Zhai
- Key Laboratory of Zoonose Prevention and Control at Universities of Inner Mongolia Autonomous Region, Medical College, Inner Mongolia Minzu University, Tongliao 028000, China
| | - Xiu-Xiang Zhang
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Shengjun Luo
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Key Laboratory of Livestock Disease Prevention of Guangdong Province, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
| | - Xiao-Hu Wang
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Key Laboratory of Livestock Disease Prevention of Guangdong Province, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
| | - Mengzhou Xue
- Department of Cerebrovascular Diseases, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou 450014, China
| | - Chunfu Zheng
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Key Laboratory of Livestock Disease Prevention of Guangdong Province, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Zi-Guo Yuan
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
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Niemann B, Puleo A, Stout C, Markel J, Boone BA. Biologic Functions of Hydroxychloroquine in Disease: From COVID-19 to Cancer. Pharmaceutics 2022; 14:pharmaceutics14122551. [PMID: 36559044 PMCID: PMC9787624 DOI: 10.3390/pharmaceutics14122551] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 11/05/2022] [Accepted: 11/10/2022] [Indexed: 11/23/2022] Open
Abstract
Chloroquine (CQ) and Hydroxychloroquine (HCQ), initially utilized in the treatment of malaria, have now developed a long list of applications. Despite their clinical relevance, their mechanisms of action are not clearly defined. Major pathways by which these agents are proposed to function include alkalinization of lysosomes and endosomes, downregulation of C-X-C chemokine receptor type 4 (CXCR4) expression, high-mobility group box 1 protein (HMGB1) inhibition, alteration of intracellular calcium, and prevention of thrombus formation. However, there is conflicting data present in the literature. This is likely the result of the complex overlapping pathways between these mechanisms of action that have not previously been highlighted. In fact, prior research has focused on very specific portions of particular pathways without describing these in the context of the extensive CQ/HCQ literature. This review summarizes the detailed data regarding CQ/HCQ's mechanisms of action while also providing insight into the overarching themes. Furthermore, this review provides clinical context to the application of these diverse drugs including their role in malaria, autoimmune disorders, cardiovascular disease, thrombus formation, malignancies, and viral infections.
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Affiliation(s)
- Britney Niemann
- Department of Surgery, West Virginia University, Morgantown, WV 26506, USA
- Correspondence: ; Tel.: +1-304-293-1254
| | - Amanda Puleo
- Department of Surgery, West Virginia University, Morgantown, WV 26506, USA
| | - Conley Stout
- Department of Surgery, West Virginia University, Morgantown, WV 26506, USA
| | - Justin Markel
- Department of Surgery, West Virginia University, Morgantown, WV 26506, USA
| | - Brian A. Boone
- Department of Surgery, West Virginia University, Morgantown, WV 26506, USA
- Department of Microbiology, Immunology and Cell Biology, West Virginia University, Morgantown, WV 26506, USA
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Gangadharan S, Ambrose JM, Rajajagadeesan A, Kullappan M, Patil S, Gandhamaneni SH, Veeraraghavan VP, Nakkella AK, Agarwal A, Jayaraman S, Surapaneni KM. Repurposing of potential antiviral drugs against RNA-dependent RNA polymerase of SARS-CoV-2 by computational approach. J Infect Public Health 2022; 15:1180-1191. [PMID: 36240528 PMCID: PMC9514006 DOI: 10.1016/j.jiph.2022.09.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 09/16/2022] [Accepted: 09/20/2022] [Indexed: 01/18/2023] Open
Abstract
The high incidences of COVID-19 cases are believed to be associated with high transmissibility rates, which emphasizes the need for the discovery of evidence-based antiviral therapies for curing the disease. The rationale of repurposing existing classes of antiviral small molecule therapeutics against SARS-CoV-2 infection has been expected to accelerate the tedious and expensive drug development process. While Remdesivir has been recently approved to be the first treatment option for specific groups of COVID-19 patients, combinatory therapy with potential antiviral drugs may be necessary to enhance the efficacy in different populations. Hence, a comprehensive list of investigational antimicrobial drug compounds such as Favipiravir, Fidaxomicin, Galidesivir, GC376, Ribavirin, Rifabutin, and Umifenovir were computationally evaluated in this study. We performed in silico docking and molecular dynamics simulation on the selected small molecules against RNA-dependent RNA polymerase, which is one of the key target proteins of SARS-CoV-2, using AutoDock and GROMACS. Interestingly, our results revealed that the macrocyclic antibiotic, Fidaxomicin, possesses the highest binding affinity with the lowest energy value of -8.97 kcal/mol binding to the same active sites of RdRp. GC376, Rifabutin, Umifenovir and Remdesivir were identified as the next best compounds. Therefore, the above-mentioned compounds could be considered good leads for further preclinical and clinical experimentations as potentially efficient antiviral inhibitors for combination therapies against SARS-CoV-2.
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Affiliation(s)
- Sivakumar Gangadharan
- Department of Chemistry, Panimalar Engineering College, Varadharajapuram, Poonamallee, Chennai 600123, Tamil Nadu, India.
| | - Jenifer Mallavarpu Ambrose
- Department of Research, Panimalar Medical College Hospital & Research Institute, Varadharajapuram, Chennai 600123, Tamil Nadu, India.
| | - Anusha Rajajagadeesan
- Department of Biochemistry, Panimalar Medical College Hospital & Research Institute, Varadharajapuram, Chennai 600123, Tamil Nadu, India.
| | - Malathi Kullappan
- Department of Research, Panimalar Medical College Hospital & Research Institute, Varadharajapuram, Chennai 600123, Tamil Nadu, India.
| | - Shankargouda Patil
- College of Dental Medicine, Roseman University of Health Sciences, South Jordan, UTAH-84095, USA; Centre of Molecular Medicine and Diagnostics ( COMManD), Saveetha Dental College & Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai 600077, India.
| | - Sri Harshini Gandhamaneni
- Department of General Medicine, Panimalar Medical College Hospital & Research Institute, Varadharajapuram, Chennai 600123, Tamil Nadu, India.
| | - Vishnu Priya Veeraraghavan
- Centre of Molecular Medicine and Diagnostics ( COMManD), Saveetha Dental College & Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai 600077, India.
| | - Aruna Kumari Nakkella
- Department of Engineering Chemistry, Dr B R Ambedkar University, Etcherla, Srikakulam 532410, Andhra Pradesh, India.
| | - Alok Agarwal
- Department of Chemistry, Chinmaya Degree College, BHEL, Haridwar 249403, Uttarakhand, India.
| | - Selvaraj Jayaraman
- Centre of Molecular Medicine and Diagnostics ( COMManD), Saveetha Dental College & Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai 600077, India.
| | - Krishna Mohan Surapaneni
- Departments of Biochemistry, Molecular Virology, Research, Clinical Skills & Simulation, Panimalar Medical College Hospital & Research Institute, Varadharajapuram, Poonamallee, Chennai 600123, Tamil Nadu, India.
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Xu XR, Zhang W, Wu XX, Yang HQ, Sun YT, Pu YT, Wang B, Peng W, Sun LH, Guo Q, Zhou S, Fang BJ. Analysis of mechanisms of Shenhuang Granule in treating severe COVID-19 based on network pharmacology and molecular docking. JOURNAL OF INTEGRATIVE MEDICINE 2022; 20:561-574. [PMID: 35934629 PMCID: PMC9328842 DOI: 10.1016/j.joim.2022.07.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 06/15/2022] [Indexed: 11/08/2022]
Abstract
OBJECTIVE Severe cases of coronavirus disease 2019 (COVID-19) are expected to have a worse prognosis than mild cases. Shenhuang Granule (SHG) has been shown to be a safe and effective treatment for severe COVID-19 in a previous randomized clinical trial, but the active chemical constituents and underlying mechanisms of action remain unknown. The goal of this study is to explore the chemical basis and mechanisms of SHG in the treatment of severe COVID-19, using network pharmacology. METHODS Ultra-performance liquid chromatography-quadrupole time-of-flight mass spectrometry was employed to screen chemical constituents of SHG. Putative therapeutic targets were predicted by searching traditional Chinese medicine system pharmacology database and analysis platform, SwissTargetPrediction, and Gene Expression Omnibus (GEO) databases. The target protein-protein interaction network and enrichment analysis were performed to investigate the hub genes and presumptive mechanisms. Molecular docking and molecular dynamics simulations were used to verify the stability and interaction between the key chemical constituents of SHG and COVID-19 protein targets. RESULTS Forty-five chemical constituents of SHG were identified along with 131 corresponding therapeutic targets, including hub genes such as HSP90AA1, MMP9, CXCL8, PTGS2, IFNG, DNMT1, TYMS, MDM2, HDAC3 and ABCB1. Functional enrichment analysis indicated that SHG mainly acted on the neuroactive ligand-receptor interaction, calcium signaling pathway and cAMP signaling pathway. Molecular docking showed that the key constituents had a good affinity with the severe acute respiratory syndrome coronavirus 2 protein targets. Molecular dynamics simulations indicated that ginsenoside Rg4 formed a stable protein-ligand complex with helicase. CONCLUSION Multiple components of SHG regulated multiple targets to inhibit virus invasion and cytokine storm through several signaling pathways; this provides a scientific basis for clinical applications and further experiments.
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Affiliation(s)
- Xiang-ru Xu
- Department of Emergency, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
| | - Wen Zhang
- Department of Emergency, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
| | - Xin-xin Wu
- Department of Emergency, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
| | - Hong-qiang Yang
- Department of Emergency, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
| | - Yu-ting Sun
- Department of Emergency, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
| | - Yu-ting Pu
- Department of Emergency, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
| | - Bei Wang
- Department of Emergency, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
| | - Wei Peng
- Department of Emergency, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
| | - Li-hua Sun
- Department of Emergency, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
| | - Quan Guo
- Department of Emergency, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
| | - Shuang Zhou
- Acupuncture and Massage College, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China.
| | - Bang-jiang Fang
- Department of Emergency, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China,Institute of Critical Care, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China,Corresponding authors at: Department of Emergency, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China (B.J. Fang)
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26
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Kasarla SS, Borse SP, Kumar Y, Sharma N, Dikshit M. In vitro effect of Withania somnifera, AYUSH-64, and remdesivir on the activity of CYP-450 enzymes: Implications for possible herb−drug interactions in the management of COVID-19. Front Pharmacol 2022; 13:973768. [PMID: 36313313 PMCID: PMC9597875 DOI: 10.3389/fphar.2022.973768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 08/29/2022] [Indexed: 11/22/2022] Open
Abstract
Ayurvedic medicines Withania somnifera Dunal (ashwagandha) and AYUSH-64 have been used for the prevention and management of COVID-19 in India. The present study explores the effect of Ashwagandha and AYUSH-64 on important human CYP enzymes (CYP3A4, CYP2C8, and CYP2D6) to assess their interaction with remdesivir, a drug used for COVID-19 management during the second wave. The study also implies possible herb−drug interactions as ashwagandha and AYUSH-64 are being used for managing various pathological conditions. Aqueous extracts of ashwagandha and AYUSH-64 were characterized using LC-MS/MS. A total of 11 and 24 phytoconstituents were identified putatively from ashwagandha and AYUSH-64 extracts, respectively. In addition, in silico studies revealed good ADME properties of most of the phytoconstituents of these herbal drugs and suggested that some of these might possess CYP-450 inhibitory activity. In vitro CYP-450 studies with human liver microsomes showed moderate inhibition of CYP3A4, 2C8, and 2D6 by remdesivir, while ashwagandha had no inhibitory effect alone or in combination with remdesivir. AYUSH-64 also exhibited a similar trend; however, a moderate inhibitory effect on CYP2C8 was noticed. Thus, ashwagandha seems to be safe to co-administer with the substrates of CYP3A4, CYP2C8, and CYP2D6. However, caution is warranted in prescribing AYUSH-64 along with CYP2C8 substrate drugs. Furthermore, preclinical and clinical PK studies would be helpful for their effective and safer use in the management of various ailments along with other drugs.
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Affiliation(s)
- Siva Swapna Kasarla
- Translational Health Science and Technology Institute (THSTI), Faridabad, India
- Spatial Metabolomics Group, Leibniz-Institut für Analytische Wissenschaften-ISAS-e V, Dortmund, Germany
| | - Swapnil P. Borse
- AYUSH - Center of Excellence (AYUSH-CoE), Center for Complementary and Integrative Health [CCIH], Interdisciplinary School of Health Sciences (ISHS), Savitribai Phule Pune University Pune (SPPU), Pune, India
- *Correspondence: Swapnil P. Borse, ; Yashwant Kumar, ; Madhu Dikshit,
| | - Yashwant Kumar
- Translational Health Science and Technology Institute (THSTI), Faridabad, India
- *Correspondence: Swapnil P. Borse, ; Yashwant Kumar, ; Madhu Dikshit,
| | - Neha Sharma
- Translational Health Science and Technology Institute (THSTI), Faridabad, India
- Department of Pharmaceutical Analysis, Delhi Pharmaceutical Science and Research University, Pushp Vihar, New Delhi, India
| | - Madhu Dikshit
- Translational Health Science and Technology Institute (THSTI), Faridabad, India
- CSIR- Central Drug Research Institute, Lucknow, Uttar Pradesh, India
- *Correspondence: Swapnil P. Borse, ; Yashwant Kumar, ; Madhu Dikshit,
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27
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Zhang F, Wang Z, Vijver MG, Peijnenburg WJGM. Theoretical investigation on the interactions of microplastics with a SARS-CoV-2 RNA fragment and their potential impacts on viral transport and exposure. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 842:156812. [PMID: 35738381 PMCID: PMC9212631 DOI: 10.1016/j.scitotenv.2022.156812] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 06/08/2022] [Accepted: 06/15/2022] [Indexed: 02/08/2023]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes the coronavirus disease-19 (COVID-19) pandemic spread across the world and remains difficult to control. Environmental pollution and habitat conditions do facilitate SARS-CoV-2 transmission as well as increase the risk of exposure to SARS-CoV-2. The coexistence of microplastics (MPs) with SARS-CoV-2 affects the viral behavior in the indoor and outdoor environment, and it is essential to study the interactions between MPs and SARS-CoV-2 because they both are ubiquitously present in our environment. To determine the mechanisms underlying the impact of MPs on SARS-CoV-2, we used molecular dynamic simulations to investigate the molecular interactions between five MPs and a SARS-CoV-2 RNA fragment at temperatures ranging from 223 to 310 K in vacuum and in water. We furthermore compared the interactions of MPs and SARS-CoV-2 RNA fragment to the performance of SARS-CoV-1 and Hepatitis B virus (HBV) RNA fragments in interacting with the MPs. The interaction affinity between the MPs and the SARS-CoV-2 RNA fragment was found to be greater than the affinity between the MPs and the SARS-CoV-1 or HBV RNA fragments, independent of the environmental media, temperature, and type of MPs. The mechanisms of the interaction between the MPs and the SARS-CoV-2 RNA fragment involved electrostatic and hydrophobic processes, and the interaction affinity was associated with the inherent structural parameters (i.e., molecular volume, polar surface area, and molecular topological index) of the MPs monomers. Although the evidence on the infectious potential of SARS-CoV-2 RNA is not fully understood, humans are exposed to MPs via their lungs, and the strong interaction with the gene materials of SARS-CoV-2 likely affects the exposure of humans to SARS-CoV-2.
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Affiliation(s)
- Fan Zhang
- Institute of Environmental Sciences (CML), Leiden University, Leiden 2300 RA, the Netherlands
| | - Zhuang Wang
- School of Environmental Science and Engineering, Collaborative Innovation Center of Atmospheric Environment and Equipment Technology, Jiangsu Key Laboratory of Atmospheric Environment Monitoring and Pollution Control, Nanjing University of Information Science and Technology, Nanjing 210044, PR China
| | - Martina G Vijver
- Institute of Environmental Sciences (CML), Leiden University, Leiden 2300 RA, the Netherlands
| | - Willie J G M Peijnenburg
- Institute of Environmental Sciences (CML), Leiden University, Leiden 2300 RA, the Netherlands; Centre for Safety of Substances and Products, National Institute of Public Health and the Environment (RIVM), Bilthoven 3720 BA, the Netherlands.
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Bafna K, Cioffi CL, Krug RM, Montelione GT. Structural similarities between SARS-CoV2 3CL pro and other viral proteases suggest potential lead molecules for developing broad spectrum antivirals. Front Chem 2022; 10:948553. [PMID: 36353143 PMCID: PMC9638714 DOI: 10.3389/fchem.2022.948553] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 08/08/2022] [Indexed: 09/01/2023] Open
Abstract
Considering the significant impact of the recent COVID-19 outbreak, development of broad-spectrum antivirals is a high priority goal to prevent future global pandemics. Antiviral development processes generally emphasize targeting a specific protein from a particular virus. However, some antiviral agents developed for specific viral protein targets may exhibit broad spectrum antiviral activity, or at least provide useful lead molecules for broad spectrum drug development. There is significant potential for repurposing a wide range of existing viral protease inhibitors to inhibit the SARS-CoV2 3C-like protease (3CLpro). If effective even as relatively weak inhibitors of 3CLpro, these molecules can provide a diverse and novel set of scaffolds for new drug discovery campaigns. In this study, we compared the sequence- and structure-based similarity of SARS-CoV2 3CLpro with proteases from other viruses, and identified 22 proteases with similar active-site structures. This structural similarity, characterized by secondary-structure topology diagrams, is evolutionarily divergent within taxonomically related viruses, but appears to result from evolutionary convergence of protease enzymes between virus families. Inhibitors of these proteases that are structurally similar to the SARS-CoV2 3CLpro protease were identified and assessed as potential inhibitors of SARS-CoV2 3CLpro protease by virtual docking. Several of these molecules have docking scores that are significantly better than known SARS-CoV2 3CLpro inhibitors, suggesting that these molecules are also potential inhibitors of the SARS-CoV2 3CLpro protease. Some have been previously reported to inhibit SARS-CoV2 3CLpro. The results also suggest that established inhibitors of SARS-CoV2 3CLpro may be considered as potential inhibitors of other viral 3C-like proteases.
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Affiliation(s)
- Khushboo Bafna
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY, United States
- Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, NY, United States
| | - Christopher L. Cioffi
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY, United States
| | - Robert M. Krug
- Department of Molecular Biosciences, John Ring LaMontagne Center for Infectious Disease, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, United States
| | - Gaetano T. Montelione
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY, United States
- Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, NY, United States
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Nagpal D, Nagpal S, Kaushik D, Kathuria H. Current clinical status of new COVID-19 vaccines and immunotherapy. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:70772-70807. [PMID: 36063274 PMCID: PMC9442597 DOI: 10.1007/s11356-022-22661-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 08/18/2022] [Indexed: 04/15/2023]
Abstract
COVID-19, caused by SARS-CoV-2, is a positive-strand RNA belonging to Coronaviridae family, along with MERS and SARS. Since its first report in 2019 in Wuhan, China, it has affected over 530 million people and led to 6.3 million deaths worldwide until June 2022. Despite eleven vaccines being used worldwide already, new variants are of concern. Therefore, the governing bodies are re-evaluating the strategies for achieving universal vaccination. Initially, the WHO expected that vaccines showing around 50-80% efficacy would develop in 1-2 years. However, US-FDA announced emergency approval of the two m-RNA vaccines within 11 months of vaccine development, which enabled early vaccination for healthcare workers in many countries. Later, in January 2021, 63 vaccine candidates were under human clinical trials and 172 under preclinical development. Currently, the number of such clinical studies is still increasing. In this review, we have summarized the updates on the clinical status of the COVID-19 and the available treatments. Additionally, COVID-19 had created negative impacts on world's economy; affected agriculture, industries, and tourism service sectors; and majorly affected low-income countries. The review discusses the clinical outcomes, latest statistics, socio-economic impacts of pandemic and treatment approaches against SARS-CoV-2, and strategies against the new variant of concern. The review will help understand the current status of vaccines and other therapies while also providing insights about upcoming vaccines and therapies for COVID-19 management.
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Affiliation(s)
- Diksha Nagpal
- Department of Pharmaceutical Sciences, Maharshi Dayanand University, Rohtak, Haryana 124001 India
| | - Shakti Nagpal
- Department of Pharmacy, National University of Singapore, Singapore, 117543 Republic of Singapore
| | - Deepak Kaushik
- Department of Pharmaceutical Sciences, Maharshi Dayanand University, Rohtak, Haryana 124001 India
| | - Himanshu Kathuria
- Department of Pharmacy, National University of Singapore, Singapore, 117543 Republic of Singapore
- Nusmetics Pte Ltd, Makerspace, i4 building, 3 Research Link, Singapore, 117602 Republic of Singapore
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Novel Drug Design for Treatment of COVID-19: A Systematic Review of Preclinical Studies. CANADIAN JOURNAL OF INFECTIOUS DISEASES AND MEDICAL MICROBIOLOGY 2022; 2022:2044282. [PMID: 36199815 PMCID: PMC9527439 DOI: 10.1155/2022/2044282] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 05/23/2022] [Accepted: 08/03/2022] [Indexed: 11/27/2022]
Abstract
Background Since the beginning of the novel coronavirus (SARS-CoV-2) disease outbreak, there has been an increasing interest in discovering potential therapeutic agents for this disease. In this regard, we conducted a systematic review through an overview of drug development (in silico, in vitro, and in vivo) for treating COVID-19. Methods A systematic search was carried out in major databases including PubMed, Web of Science, Scopus, EMBASE, and Google Scholar from December 2019 to March 2021. A combination of the following terms was used: coronavirus, COVID-19, SARS-CoV-2, drug design, drug development, In silico, In vitro, and In vivo. A narrative synthesis was performed as a qualitative method for the data synthesis of each outcome measure. Results A total of 2168 articles were identified through searching databases. Finally, 315 studies (266 in silico, 34 in vitro, and 15 in vivo) were included. In studies with in silico approach, 98 article study repurposed drug and 91 studies evaluated herbal medicine on COVID-19. Among 260 drugs repurposed by the computational method, the best results were observed with saquinavir (n = 9), ritonavir (n = 8), and lopinavir (n = 6). Main protease (n = 154) following spike glycoprotein (n = 62) and other nonstructural protein of virus (n = 45) was among the most studied targets. Doxycycline, chlorpromazine, azithromycin, heparin, bepridil, and glycyrrhizic acid showed both in silico and in vitro inhibitory effects against SARS-CoV-2. Conclusion The preclinical studies of novel drug design for COVID-19 focused on main protease and spike glycoprotein as targets for antiviral development. From evaluated structures, saquinavir, ritonavir, eucalyptus, Tinospora cordifolia, aloe, green tea, curcumin, pyrazole, and triazole derivatives in in silico studies and doxycycline, chlorpromazine, and heparin from in vitro and human monoclonal antibodies from in vivo studies showed promised results regarding efficacy. It seems that due to the nature of COVID-19 disease, finding some drugs with multitarget antiviral actions and anti-inflammatory potential is valuable and some herbal medicines have this potential.
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Taha Z, Arulanandam R, Maznyi G, Godbout E, Carter-Timofte ME, Kurmasheva N, Reinert LS, Chen A, Crupi MJ, Boulton S, Laroche G, Phan A, Rezaei R, Alluqmani N, Jirovec A, Acal A, Brown EE, Singaravelu R, Petryk J, Idorn M, Potts KG, Todesco H, John C, Mahoney DJ, Ilkow CS, Giguère P, Alain T, Côté M, Paludan SR, Olagnier D, Bell JC, Azad T, Diallo JS. Identification of FDA-approved bifonazole as a SARS-CoV-2 blocking agent following a bioreporter drug screen. Mol Ther 2022; 30:2998-3016. [PMID: 35526097 PMCID: PMC9075979 DOI: 10.1016/j.ymthe.2022.04.025] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 04/25/2022] [Accepted: 04/29/2022] [Indexed: 02/01/2023] Open
Abstract
We established a split nanoluciferase complementation assay to rapidly screen for inhibitors that interfere with binding of the receptor binding domain (RBD) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike glycoprotein with its target receptor, angiotensin-converting enzyme 2 (ACE2). After a screen of 1,200 US Food and Drug Administration (FDA)-approved compounds, we identified bifonazole, an imidazole-based antifungal agent, as a competitive inhibitor of RBD-ACE2 binding. Mechanistically, bifonazole binds ACE2 around residue K353, which prevents association with the RBD, affecting entry and replication of spike-pseudotyped viruses as well as native SARS-CoV-2 and its variants of concern (VOCs). Intranasal administration of bifonazole reduces lethality in K18-hACE2 mice challenged with vesicular stomatitis virus (VSV)-spike by 40%, with a similar benefit after live SARS-CoV-2 challenge. Our screen identified an antiviral agent that is effective against SARS-CoV-2 and VOCs such as Omicron that employ the same receptor to infect cells and therefore has high potential to be repurposed to control, treat, or prevent coronavirus disease 2019 (COVID-19).
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Affiliation(s)
- Zaid Taha
- Centre for Cancer Therapeutics, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada,Department of Biochemistry, Microbiology, and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Rozanne Arulanandam
- Centre for Cancer Therapeutics, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada
| | - Glib Maznyi
- Centre for Cancer Therapeutics, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada
| | - Elena Godbout
- Centre for Cancer Therapeutics, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada
| | | | - Naziia Kurmasheva
- Department of Biomedicine, Aarhus University, 8000 Aarhus C, Denmark
| | - Line S. Reinert
- Department of Biomedicine, Aarhus University, 8000 Aarhus C, Denmark
| | - Andrew Chen
- Centre for Cancer Therapeutics, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada
| | - Mathieu J.F. Crupi
- Centre for Cancer Therapeutics, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada
| | - Stephen Boulton
- Centre for Cancer Therapeutics, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada
| | - Geneviève Laroche
- Department of Biochemistry, Microbiology, and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Alexandra Phan
- Department of Biochemistry, Microbiology, and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Reza Rezaei
- Centre for Cancer Therapeutics, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada,Department of Biochemistry, Microbiology, and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Nouf Alluqmani
- Centre for Cancer Therapeutics, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada,Department of Biochemistry, Microbiology, and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Anna Jirovec
- Centre for Cancer Therapeutics, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada,Department of Biochemistry, Microbiology, and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Alexandra Acal
- Centre for Cancer Therapeutics, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada
| | - Emily E.F. Brown
- Centre for Cancer Therapeutics, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada
| | - Ragunath Singaravelu
- Centre for Cancer Therapeutics, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada
| | - Julia Petryk
- Centre for Cancer Therapeutics, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada
| | - Manja Idorn
- Department of Biomedicine, Aarhus University, 8000 Aarhus C, Denmark
| | - Kyle G. Potts
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada,Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, AB T2N 4N1, Canada,Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Hayley Todesco
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada,Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, AB T2N 4N1, Canada,Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Cini John
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada,Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, AB T2N 4N1, Canada,Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Douglas J. Mahoney
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada,Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, AB T2N 4N1, Canada,Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Carolina S. Ilkow
- Centre for Cancer Therapeutics, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada,Department of Biochemistry, Microbiology, and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Patrick Giguère
- Department of Biochemistry, Microbiology, and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Tommy Alain
- Department of Biochemistry, Microbiology, and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada,Children’s Hospital of Eastern Ontario Research Institute, Ottawa, ON K1H 8L1, Canada
| | - Marceline Côté
- Department of Biochemistry, Microbiology, and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Søren R. Paludan
- Department of Biomedicine, Aarhus University, 8000 Aarhus C, Denmark
| | - David Olagnier
- Department of Biomedicine, Aarhus University, 8000 Aarhus C, Denmark
| | - John C. Bell
- Centre for Cancer Therapeutics, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada,Department of Biochemistry, Microbiology, and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Taha Azad
- Centre for Cancer Therapeutics, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada
| | - Jean-Simon Diallo
- Centre for Cancer Therapeutics, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada; Department of Biochemistry, Microbiology, and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada.
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Siniavin AE, Novikov MS, Gushchin VA, Terechov AA, Ivanov IA, Paramonova MP, Gureeva ES, Russu LI, Kuznetsova NA, Shidlovskaya EV, Luyksaar SI, Vasina DV, Zolotov SA, Zigangirova NA, Logunov DY, Gintsburg AL. Antiviral Activity of N 1,N 3-Disubstituted Uracil Derivatives against SARS-CoV-2 Variants of Concern. Int J Mol Sci 2022; 23:ijms231710171. [PMID: 36077564 PMCID: PMC9456261 DOI: 10.3390/ijms231710171] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 08/24/2022] [Accepted: 08/25/2022] [Indexed: 11/16/2022] Open
Abstract
Despite the widespread use of the COVID-19 vaccines, the search for effective antiviral drugs for the treatment of patients infected with SARS-CoV-2 is still relevant. Genetic variability leads to the continued circulation of new variants of concern (VOC). There is a significant decrease in the effectiveness of antibody-based therapy, which raises concerns about the development of new antiviral drugs with a high spectrum of activity against VOCs. We synthesized new analogs of uracil derivatives where uracil was substituted at the N1 and N3 positions. Antiviral activity was studied in Vero E6 cells against VOC, including currently widely circulating SARS-CoV-2 Omicron. All synthesized compounds of the panel showed a wide antiviral effect. In addition, we determined that these compounds inhibit the activity of recombinant SARS-CoV-2 RdRp. Our study suggests that these non-nucleoside uracil-based analogs may be of future use as a treatment for patients infected with circulating SARS-CoV-2 variants.
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Affiliation(s)
- Andrei E. Siniavin
- N.F. Gamaleya National Research Center for Epidemiology and Microbiology, Ivanovsky Institute of Virology, Ministry of Health of the Russian Federation, 123098 Moscow, Russia
- Department of Molecular Neuroimmune Signalling, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Correspondence: (A.E.S.); (V.A.G.)
| | - Mikhail S. Novikov
- Department of Pharmaceutical & Toxicological Chemistry, Volgograd State Medical University, 400131 Volgograd, Russia
| | - Vladimir A. Gushchin
- N.F. Gamaleya National Research Center for Epidemiology and Microbiology, Ivanovsky Institute of Virology, Ministry of Health of the Russian Federation, 123098 Moscow, Russia
- Department of Virology, Lomonosov Moscow State University, 119991 Moscow, Russia
- Correspondence: (A.E.S.); (V.A.G.)
| | - Alexander A. Terechov
- N.F. Gamaleya National Research Center for Epidemiology and Microbiology, Ivanovsky Institute of Virology, Ministry of Health of the Russian Federation, 123098 Moscow, Russia
| | - Igor A. Ivanov
- N.F. Gamaleya National Research Center for Epidemiology and Microbiology, Ivanovsky Institute of Virology, Ministry of Health of the Russian Federation, 123098 Moscow, Russia
- Department of Molecular Neuroimmune Signalling, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Maria P. Paramonova
- Department of Pharmaceutical & Toxicological Chemistry, Volgograd State Medical University, 400131 Volgograd, Russia
| | - Elena S. Gureeva
- Department of Pharmaceutical & Toxicological Chemistry, Volgograd State Medical University, 400131 Volgograd, Russia
| | - Leonid I. Russu
- N.F. Gamaleya National Research Center for Epidemiology and Microbiology, Ivanovsky Institute of Virology, Ministry of Health of the Russian Federation, 123098 Moscow, Russia
| | - Nadezhda A. Kuznetsova
- N.F. Gamaleya National Research Center for Epidemiology and Microbiology, Ivanovsky Institute of Virology, Ministry of Health of the Russian Federation, 123098 Moscow, Russia
| | - Elena V. Shidlovskaya
- N.F. Gamaleya National Research Center for Epidemiology and Microbiology, Ivanovsky Institute of Virology, Ministry of Health of the Russian Federation, 123098 Moscow, Russia
| | - Sergei I. Luyksaar
- N.F. Gamaleya National Research Center for Epidemiology and Microbiology, Ivanovsky Institute of Virology, Ministry of Health of the Russian Federation, 123098 Moscow, Russia
| | - Daria V. Vasina
- N.F. Gamaleya National Research Center for Epidemiology and Microbiology, Ivanovsky Institute of Virology, Ministry of Health of the Russian Federation, 123098 Moscow, Russia
| | - Sergei A. Zolotov
- N.F. Gamaleya National Research Center for Epidemiology and Microbiology, Ivanovsky Institute of Virology, Ministry of Health of the Russian Federation, 123098 Moscow, Russia
| | - Nailya A. Zigangirova
- N.F. Gamaleya National Research Center for Epidemiology and Microbiology, Ivanovsky Institute of Virology, Ministry of Health of the Russian Federation, 123098 Moscow, Russia
| | - Denis Y. Logunov
- N.F. Gamaleya National Research Center for Epidemiology and Microbiology, Ivanovsky Institute of Virology, Ministry of Health of the Russian Federation, 123098 Moscow, Russia
| | - Alexander L. Gintsburg
- N.F. Gamaleya National Research Center for Epidemiology and Microbiology, Ivanovsky Institute of Virology, Ministry of Health of the Russian Federation, 123098 Moscow, Russia
- Department of Infectiology and Virology, Federal State Autonomous Educational Institution of Higher Education I M Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), 119435 Moscow, Russia
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Giannopoulos GI. Fullerene Derivatives for Drug Delivery against COVID-19: A Molecular Dynamics Investigation of Dendro[60]fullerene as Nanocarrier of Molnupiravir. NANOMATERIALS (BASEL, SWITZERLAND) 2022; 12:nano12152711. [PMID: 35957142 PMCID: PMC9370322 DOI: 10.3390/nano12152711] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 07/30/2022] [Accepted: 08/05/2022] [Indexed: 05/27/2023]
Abstract
In this paper, a theoretical investigation is made regarding the possibility of using a water-soluble derivative of C60 as a drug delivery agent for treating Coronavirus disease 2019 (COVID-19). Molnupiravir is chosen as the transporting pharmaceutical compound since it has already proved to be very helpful in saving lives in case of hospitalization. According to the proposed formulation, a carboxyfullerene known as dendro[60]fullerene is externally connected with two molnupiravir molecules. Two properly formed nitrogen single bonds (N-N) are used as linkers between the dendro[60]fullerene and the two molnupiravir molecules to create the final form of the C60 derivate/molnupiravir conjugate. The energetics of the developed molecular system and its interaction with water and n-octanol are extensively studied via classical molecular dynamics (MD) using the COMPASS II force field. To study the interactions with water and n-octanol, an appropriate periodic amorphous unit cell is created that contains a single C60 derivative/molnupiravir system surrounded by numerous solvent molecules and simulated via MD in room conditions. In addition, the corresponding solvation-free energies of the investigated drug delivery system are computed and set in contrast with the corresponding properties of the water-soluble dendro[60]fullerene, to test its solubility capabilities.
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Affiliation(s)
- Georgios I Giannopoulos
- Department of Mechanical Engineering, University of Peloponnese, 1 Megalou Alexandrou Street, GR-26334 Patras, Greece
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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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Current Therapeutics for COVID-19, What We Know about the Molecular Mechanism and Efficacy of Treatments for This Novel Virus. Int J Mol Sci 2022; 23:ijms23147702. [PMID: 35887042 PMCID: PMC9319826 DOI: 10.3390/ijms23147702] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 07/06/2022] [Accepted: 07/10/2022] [Indexed: 12/15/2022] Open
Abstract
Severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) has caused significant morbidity and mortality worldwide. Though previous coronaviruses have caused substantial epidemics in recent years, effective therapies remained limited at the start of the Coronavirus disease 19 (COVID-19) pandemic. The emergence and rapid spread throughout the globe of the novel SARS-CoV-2 virus necessitated a rapid development of therapeutics. Given the multitude of therapies that have emerged over the last two years and the evolution of data surrounding the efficacy of these therapies, we aim to provide an update on the major clinical trials that influenced clinical utilization of various COVID-19 therapeutics. This review focuses on currently used therapies in the United States and discusses the molecular mechanisms by which these therapies target the SARS-CoV-2 virus or the COVID-19 disease process. PubMed and EMBASE were used to find trials assessing the efficacy of various COVID-19 therapies. The keywords SARS-CoV-2, COVID-19, and the names of the various therapies included in this review were searched in different combinations to find large-scale randomized controlled trials performed since the onset of the COVID-19 pandemic. Multiple therapeutic options are currently approved for the treatment of SARS-CoV-2 and prevention of severe disease in high-risk individuals in both in the inpatient and outpatient settings. In severe disease, a combination of antiviral and immunomodulatory treatments is currently recommended for treatment. Additionally, anti-viral agents have shown promise in preventing severe disease and hospitalization for those in the outpatient setting. More recently, current therapeutic approaches are directed toward early treatment with monoclonal antibodies directed against the SARS-CoV-2 virus. Despite this, no treatment to date serves as a definitive cure and vaccines against the SARS-CoV-2 virus remain our best defense to prevent further morbidity and mortality.
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Eskandarzade N, Ghorbani A, Samarfard S, Diaz J, Guzzi PH, Fariborzi N, Tahmasebi A, Izadpanah K. Network for network concept offers new insights into host- SARS-CoV-2 protein interactions and potential novel targets for developing antiviral drugs. Comput Biol Med 2022; 146:105575. [PMID: 35533462 PMCID: PMC9055686 DOI: 10.1016/j.compbiomed.2022.105575] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 04/16/2022] [Accepted: 04/27/2022] [Indexed: 01/08/2023]
Abstract
SARS-CoV-2, the causal agent of COVID-19, is primarily a pulmonary virus that can directly or indirectly infect several organs. Despite many studies carried out during the current COVID-19 pandemic, some pathological features of SARS-CoV-2 have remained unclear. It has been recently attempted to address the current knowledge gaps on the viral pathogenicity and pathological mechanisms via cellular-level tropism of SARS-CoV-2 using human proteomics, visualization of virus-host protein-protein interactions (PPIs), and enrichment analysis of experimental results. The synergistic use of models and methods that rely on graph theory has enabled the visualization and analysis of the molecular context of virus/host PPIs. We review current knowledge on the SARS-COV-2/host interactome cascade involved in the viral pathogenicity through the graph theory concept and highlight the hub proteins in the intra-viral network that create a subnet with a small number of host central proteins, leading to cell disintegration and infectivity. Then we discuss the putative principle of the "gene-for-gene and "network for network" concepts as platforms for future directions toward designing efficient anti-viral therapies.
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Affiliation(s)
- Neda Eskandarzade
- Department of Basic Sciences, School of Veterinary Medicine, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Abozar Ghorbani
- Nuclear Agriculture Research School, Nuclear Science and Technology Research Institute (NSTRI), Karaj, Iran,Corresponding author
| | - Samira Samarfard
- Berrimah Veterinary Laboratory, Department of Primary Industry and Resources, Berrimah, NT, 0828, Australia
| | - Jose Diaz
- Laboratorio de Dinámica de Redes Genéticas, Centro de Investigación en Dinámica Celular, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
| | - Pietro H. Guzzi
- Department of Medical and Surgical Sciences, Laboratory of Bioinformatics Unit, Italy
| | - Niloofar Fariborzi
- Department of Medical Entomology and Vector Control, School of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Ahmad Tahmasebi
- Institute of Biotechnology, College of Agriculture, Shiraz University, Shiraz, Iran
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Metalloproteinase-Dependent and TMPRSS2-Independent Cell Surface Entry Pathway of SARS-CoV-2 Requires the Furin Cleavage Site and the S2 Domain of Spike Protein. mBio 2022; 13:e0051922. [PMID: 35708281 PMCID: PMC9426510 DOI: 10.1128/mbio.00519-22] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The ongoing global vaccination program to prevent SARS-CoV-2 infection, the causative agent of COVID-19, has had significant success. However, recently, virus variants that can evade the immunity in a host achieved through vaccination have emerged. Consequently, new therapeutic agents that can efficiently prevent infection from these new variants, and hence COVID-19 spread, are urgently required. To achieve this, extensive characterization of virus-host cell interactions to identify effective therapeutic targets is warranted. Here, we report a cell surface entry pathway of SARS-CoV-2 that exists in a cell type-dependent manner and is TMPRSS2 independent but sensitive to various broad-spectrum metalloproteinase inhibitors such as marimastat and prinomastat. Experiments with selective metalloproteinase inhibitors and gene-specific small interfering RNAS (siRNAs) revealed that a disintegrin and metalloproteinase 10 (ADAM10) is partially involved in the metalloproteinase pathway. Consistent with our finding that the pathway is unique to SARS-CoV-2 among highly pathogenic human coronaviruses, both the furin cleavage motif in the S1/S2 boundary and the S2 domain of SARS-CoV-2 spike protein are essential for metalloproteinase-dependent entry. In contrast, the two elements of SARS-CoV-2 independently contributed to TMPRSS2-dependent S2 priming. The metalloproteinase pathway is involved in SARS-CoV-2-induced syncytium formation and cytopathicity, leading us to theorize that it is also involved in the rapid spread of SARS-CoV-2 and the pathogenesis of COVID-19. Thus, targeting the metalloproteinase pathway in addition to the TMPRSS2 and endosomal pathways could be an effective strategy by which to cure COVID-19 in the future. IMPORTANCE To develop effective therapeutics against COVID-19, it is necessary to elucidate in detail the infection mechanism of the causative agent, SARS-CoV-2. SARS-CoV-2 binds to the cell surface receptor ACE2 via the spike protein, and then the spike protein is cleaved by host proteases to enable entry. Here, we found that the metalloproteinase-mediated pathway is important for SARS-CoV-2 infection in addition to the TMPRSS2-mediated pathway and the endosomal pathway. The metalloproteinase-mediated pathway requires both the prior cleavage of spike into two domains and a specific sequence in the second domain, S2, conditions met by SARS-CoV-2 but lacking in the related human coronavirus SARS-CoV. Besides the contribution of metalloproteinases to SARS-CoV-2 infection, inhibition of metalloproteinases was important in preventing cell death, which may cause organ damage. Our study provides new insights into the complex pathogenesis unique to COVID-19 and relevant to the development of effective therapies.
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Debnath SK, Debnath M, Srivastava R, Omri A. Drugs repurposing for SARS-CoV-2: new insight of COVID-19 druggability. Expert Rev Anti Infect Ther 2022; 20:1187-1204. [PMID: 35615888 DOI: 10.1080/14787210.2022.2082944] [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: 12/15/2022]
Abstract
INTRODUCTION The ongoing epidemic of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) creates a massive panic worldwide due to the absence of effective medicines. Developing a new drug or vaccine is time-consuming to pass safety and efficacy testing. Therefore, repurposing drugs have been introduced to treat COVID-19 until effective drugs are developed. AREA COVERED A detailed search of repurposing drugs against SARS-CoV-2 was carried out using the PubMed database, focusing on articles published 2020 years onward. A different class of drugs has been described in this article to target hosts and viruses. Based on the previous pandemic experience of SARS-CoV and MERS, several antiviral and antimalarial drugs are discussed here. This review covers the failure of some repurposed drugs that showed promising activity in the earlier CoV-pandemic but were found ineffective against SARS-CoV-2. All these discussions demand a successful drug development strategy for screening and identifying an effective drug for better management of COVID-19. The drug development strategies described here will serve a new scope of research for academicians and researchers. EXPERT OPINION Repurposed drugs have been used since COVID-19 to eradicate disease propagation. Drugs found effective for MERS and SARS may not be effective against SARS-CoV-2. Drug libraries and artificial intelligence are helpful tools to screen and identify different molecules targeting viruses or hosts.
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Affiliation(s)
- Sujit Kumar Debnath
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Monalisha Debnath
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Rohit Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Abdelwahab Omri
- Department of Chemistry and Biochemistry, The Novel Drug & Vaccine Delivery Systems Facility, Laurentian University, Sudbury, Canada
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Antiviral Drug Discovery for the Treatment of COVID-19 Infections. Viruses 2022; 14:v14050961. [PMID: 35632703 PMCID: PMC9143071 DOI: 10.3390/v14050961] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 04/28/2022] [Accepted: 04/29/2022] [Indexed: 02/04/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a recently emerged human coronavirus. COVID-19 vaccines have proven to be successful in protecting the vaccinated from infection, reducing the severity of disease, and deterring the transmission of infection. However, COVID-19 vaccination faces many challenges, such as the decline in vaccine-induced immunity over time, and the decrease in potency against some SARS-CoV-2 variants including the recently emerged Omicron variant, resulting in breakthrough infections. The challenges that COVID-19 vaccination is facing highlight the importance of the discovery of antivirals to serve as another means to tackle the pandemic. To date, neutralizing antibodies that block viral entry by targeting the viral spike protein make up the largest class of antivirals that has received US FDA emergency use authorization (EUA) for COVID-19 treatment. In addition to the spike protein, other key targets for the discovery of direct-acting antivirals include viral enzymes that are essential for SARS-CoV-2 replication, such as RNA-dependent RNA polymerase and proteases, as judged by US FDA approval for remdesivir, and EUA for Paxlovid (nirmatrelvir + ritonavir) for treating COVID-19 infections. This review presents an overview of the current status and future direction of antiviral drug discovery for treating SARS-CoV-2 infections, covering important antiviral targets such as the viral spike protein, non-structural protein (nsp) 3 papain-like protease, nsp5 main protease, and the nsp12/nsp7/nsp8 RNA-dependent RNA polymerase complex.
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Ćavar Zeljković S, Schadich E, Džubák P, Hajdúch M, Tarkowski P. Antiviral Activity of Selected Lamiaceae Essential Oils and Their Monoterpenes Against SARS-Cov-2. Front Pharmacol 2022; 13:893634. [PMID: 35586050 PMCID: PMC9108200 DOI: 10.3389/fphar.2022.893634] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 04/14/2022] [Indexed: 12/24/2022] Open
Abstract
This study presents the very first report on the in vitro antiviral activity of selected essential oils of Lamiaceae plant species and their monoterpenes against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Nineteen essential oils were obtained by hydrodistillation of dried plant material, and their monoterpene profiles were determined. In addition, the exact concentrations of each monoterpene that were found at a significant level were defined. Both essential oils and their monoterpene components were tested for cytotoxic and antiviral activity against SARS-CoV-2 in infected Vero 76 cells. The results showed that the essential oils of four Mentha species, i.e., M. aquatica L. cv. Veronica, M. pulegium L., M. microphylla K.Koch, and M. x villosa Huds., but also Micromeria thymifolia (Scop.) Fritsch and Ziziphora clinopodioides Lam., and five different monoterpenes, i.e., carvacrol, carvone, 1,8-cineol, menthofuran, and pulegone, inhibited the SARS-CoV-2 replication in the infected cells. However, the antiviral activity varied both among essential oils and monoterpenes. Carvone and carvacrol exhibited moderate antiviral activity with IC50 concentrations of 80.23 ± 6.07 μM and 86.55 ± 12.73 μM, respectively, while the other monoterpenes were less active (IC50 > 100.00 μM). Structure-activity relations of related monoterpenes showed that the presence of keto and hydroxyl groups is associated with the activity of carvone and carvacrol, respectively. Furthermore, the carvone-rich essential oil of M. x villosa had the greatest activity among all active essential oils (IC50 127.00 ± 4.63 ppm) while the other active oils exhibited mild (140 ppm < IC50 < 200 ppm) to weak antiviral activity (IC50 > 200 ppm). Both essential oils and monoterpenes showed limited or no cytotoxicity against Vero 76 cells. Hierarchical cluster analysis showed that the differences in the antiviral activity of essential oils were directly attributed to the antiviral efficacies of their particular single monoterpenes. The findings presented here on the novel antiviral property of plant essential oils and monoterpenes might be used in the development of different measures against SARS-CoV-2.
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Affiliation(s)
- Sanja Ćavar Zeljković
- Centre of the Region Haná for Biotechnological and Agricultural Research, Department of Genetic Resources for Vegetables, Medicinal and Special Plants, Crop Research Institute, Olomouc, Czechia
- Centre of Region Haná for Biotechnological and Agricultural Research, Czech Advanced Technology and Research Institute, Palacky University, Olomouc, Czechia
- *Correspondence: Sanja Ćavar Zeljković, ,
| | - Ermin Schadich
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czechia
| | - Petr Džubák
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czechia
- Institute of Molecular and Translational Medicine, Czech Advanced Technology and Research Institute, Palacky University, Olomouc, Czechia
| | - Marián Hajdúch
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czechia
- Institute of Molecular and Translational Medicine, Czech Advanced Technology and Research Institute, Palacky University, Olomouc, Czechia
| | - Petr Tarkowski
- Centre of the Region Haná for Biotechnological and Agricultural Research, Department of Genetic Resources for Vegetables, Medicinal and Special Plants, Crop Research Institute, Olomouc, Czechia
- Centre of Region Haná for Biotechnological and Agricultural Research, Czech Advanced Technology and Research Institute, Palacky University, Olomouc, Czechia
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Jovanoski N, Kuznik A, Becker U, Hussein M, Briggs A. Cost-effectiveness of casirivimab/imdevimab in patients with COVID-19 in the ambulatory setting. J Manag Care Spec Pharm 2022; 28:555-565. [PMID: 35238626 DOI: 10.18553/jmcp.2022.21469] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
BACKGROUND: Most patients infected with SARS-CoV-2, resulting in COVID-19, have only mild symptoms that can be managed in an ambulatory setting. However, a significant number of patients develop a more severe form of the disease and require hospital care, with the risk of long-term sequelae or death. Casirivimab/imdevimab is a combination of 2 recombinant human monoclonal antibodies that has been shown to significantly reduce the risk of hospitalization or death in patients with mild to moderate COVID-19 in the ambulatory setting. OBJECTIVE: To establish the cost-effectiveness of casirivimab/imdevimab in ambulatory individuals with COVID-19. METHODS: A cost-effectiveness model was constructed to simulate the natural history of COVID-19 in ambulatory patients and to identify those patients for whom casirivimab/imdevimab may be a cost-effective treatment from a US payer perspective. Patients enter the model in the ambulatory health state and can receive either active treatment with casirivimab/imdevimab or usual care. Patients can either recover from the infection or be hospitalized, from where they can recover from infection or die. Following this acute phase, patients enter a Markov model to estimate lifetime quality-adjusted life years. The model uses the risk of hospitalization in both the active treatment and usual care cohorts, and age- and sex-specific risk of mortality. Other model inputs include hospitalization costs and health-related utilities in the ambulatory acute treatment phase, the hospitalized setting, and the post-acute phase. Accounting for the heterogeneity of risk by age and comorbidities, results are presented separately for various combinations of baseline age and usual care risk in a 7 × 9 matrix. Outcomes related to "long COVID" are assessed in scenario analyses. RESULTS: In the base case, at a willingness-to-pay threshold of $100,000, treatment with casirivimab/imdevimab was found to be cost-effective in most patients, including those older than 40 years of age with a baseline hospitalization risk greater than or equal to 2% and patients aged 20 years with a baseline risk of hospitalization greater than or equal to 4%, whereas for hospitalization risk greater than or equal to 10%, casirivimab/imdevimab is dominant. Casirivimab/imdevimab was not cost-effective in patients aged 20 years with a 3% or lower risk of hospitalization or in patients aged 30 years with a 2% risk. CONCLUSIONS: This economic analysis found that casirivimab/imdevimab is a cost-effective treatment for most ambulatory patients with COVID-19. DISCLOSURES: N. Jovanoski and U. Becker are employees of F Hoffman-La Roche Ltd.; A. Kuznik and M. Hussein are employees of Regeneron Pharmaceuticals Inc. and hold stock and stock options; A. Briggs has provided consultancy to F Hoffman-La Roche Ltd. and has received consultancy fees from Merck and Co., Inc., GlaxoSmithKline plc., and Novartis. This study was funded by Regeneron Pharmaceuticals, Inc.
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Affiliation(s)
| | | | | | | | - Andrew Briggs
- London School of Hygiene & Tropical Medicine, London, UK
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Niemeyer BF, Benam KH. Untapping host-targeting cross-protective efficacy of anticoagulants against SARS-CoV-2. Pharmacol Ther 2022; 233:108027. [PMID: 34718070 PMCID: PMC8552695 DOI: 10.1016/j.pharmthera.2021.108027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 10/13/2021] [Accepted: 10/25/2021] [Indexed: 02/07/2023]
Abstract
Responding quickly to emerging respiratory viruses, such as SARS-CoV-2 the causative agent of coronavirus disease 2019 (COVID-19) pandemic, is essential to stop uncontrolled spread of these pathogens and mitigate their socio-economic impact globally. This can be achieved through drug repurposing, which tackles inherent time- and resource-consuming processes associated with conventional drug discovery and development. In this review, we examine key preclinical and clinical therapeutic and prophylactic approaches that have been applied for treatment of SARS-CoV-2 infection. We break these strategies down into virus- versus host-targeting and discuss their reported efficacy, advantages, and disadvantages. Importantly, we highlight emerging evidence on application of host serine protease-inhibiting anticoagulants, such as nafamostat mesylate, as a potentially powerful therapy to inhibit virus activation and offer cross-protection against multiple strains of coronavirus, lower inflammatory response independent of its antiviral effect, and modulate clotting problems seen in COVID-19 pneumonia.
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Affiliation(s)
- Brian F Niemeyer
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Kambez H Benam
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA; Department of Bioengineering, University of Pittsburgh, Pittsburgh, PA 15219, USA; Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA 15213, USA.
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The impact of a rub and rinse regimen on removal of human coronaviruses from contemporary contact lens materials. Cont Lens Anterior Eye 2022; 45:101719. [PMID: 35643848 PMCID: PMC9124925 DOI: 10.1016/j.clae.2022.101719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 04/12/2022] [Accepted: 05/15/2022] [Indexed: 11/20/2022]
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Drug Repurposing for COVID-19: A Review and a Novel Strategy to Identify New Targets and Potential Drug Candidates. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27092723. [PMID: 35566073 PMCID: PMC9099573 DOI: 10.3390/molecules27092723] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/14/2022] [Accepted: 04/21/2022] [Indexed: 02/01/2023]
Abstract
In December 2019, the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19) was first identified in the province of Wuhan, China. Since then, there have been over 400 million confirmed cases and 5.8 million deaths by COVID-19 reported worldwide. The urgent need for therapies against SARS-CoV-2 led researchers to use drug repurposing approaches. This strategy allows the reduction in risks, time, and costs associated with drug development. In many cases, a repurposed drug can enter directly to preclinical testing and clinical trials, thus accelerating the whole drug discovery process. In this work, we will give a general overview of the main developments in COVID-19 treatment, focusing on the contribution of the drug repurposing paradigm to find effective drugs against this disease. Finally, we will present our findings using a new drug repurposing strategy that identified 11 compounds that may be potentially effective against COVID-19. To our knowledge, seven of these drugs have never been tested against SARS-CoV-2 and are potential candidates for in vitro and in vivo studies to evaluate their effectiveness in COVID-19 treatment.
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Sukmarini L. Antiviral Peptides (AVPs) of Marine Origin as Propitious Therapeutic Drug Candidates for the Treatment of Human Viruses. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27092619. [PMID: 35565968 PMCID: PMC9101517 DOI: 10.3390/molecules27092619] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 04/03/2022] [Accepted: 04/18/2022] [Indexed: 12/13/2022]
Abstract
The marine environment presents a favorable avenue for potential therapeutic agents as a reservoir of new bioactive natural products. Due to their numerous potential pharmacological effects, marine-derived natural products—particularly marine peptides—have gained considerable attention. These peptides have shown a broad spectrum of biological functions, such as antimicrobial, antiviral, cytotoxic, immunomodulatory, and analgesic effects. The emergence of new virus strains and viral resistance leads to continuing efforts to develop more effective antiviral drugs. Interestingly, antimicrobial peptides (AMPs) that possess antiviral properties and are alternatively regarded as antiviral peptides (AVPs) demonstrate vast potential as alternative peptide-based drug candidates available for viral infection treatments. Hence, AVPs obtained from various marine organisms have been evaluated. This brief review features recent updates of marine-derived AVPs from 2011 to 2021. Moreover, the biosynthesis of this class of compounds and their possible mechanisms of action are also discussed. Selected peptides from various marine organisms possessing antiviral activities against important human viruses—such as human immunodeficiency viruses, herpes simplex viruses, influenza viruses, hepatitis C virus, and coronaviruses—are highlighted herein.
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Affiliation(s)
- Linda Sukmarini
- Research Center for Applied Microbiology, National Research and Innovation Agency (BRIN), Jl. Raya Bogor Km. 46, Cibinong 16911, West Java, Indonesia
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Antiviral Activity of Contemporary Contact Lens Care Solutions against Two Human Seasonal Coronavirus Strains. Pathogens 2022; 11:pathogens11040472. [PMID: 35456147 PMCID: PMC9026382 DOI: 10.3390/pathogens11040472] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 04/04/2022] [Accepted: 04/12/2022] [Indexed: 02/04/2023] Open
Abstract
Background: Given that reports have suggested SARS-CoV-2 can be transmitted via conjunctiva, the ability of contact lens (CL) care products to reduce the infectiousness of two seasonal human coronavirus (HCoV) (HCoV-229E and HCoV-OC43) surrogates for SARS-CoV-2 was investigated. Methods: Biotrue and Boston Simplus (Bausch&Lomb), OPTI-FREE Puremoist and Clear Care (Alcon), and cleadew and cleadew GP (Ophtecs) were tested. Their ability to inactivate HCoV was evaluated using contact times of 4 and 6 h as well as 1% and 10% of virus inoculum. Results: Non-oxidative systems (Biotrue, Boston Simplus, and OPTI-FREE) did not exhibit a significant log10 reduction compared to controls for the two viral strains for either incubation time (all p > 0.05) when 10% tests were performed. For the 1% test, while Boston Simplus and OPTI-FREE exhibited a significant log10 reduction of both HCoV-229E (after 6 h) and HCoV-OC43 (after either 4 or 6 h incubation), those products showed less than 1 log10 reduction of the two infectious viruses. Oxidative systems based on hydrogen peroxide or povidone-iodine showed a significant log10 reduction compared with the controls for both HCoV-229E and HCoV-OC43 in all tested conditions (all p < 0.01). Clear Care led to virus inactivation to below the limit of quantification for tests performed with 1% of inoculum after 6 h incubation, while cleadew and cleadew GP led to inactivation of the two viruses to below the limit of quantification in all tested conditions. Conclusion: Oxidative CL disinfection systems showed significant virucidal activity against HCoV-229E and HCoV-OC43, while non-oxidative systems showed minimal ability to inactivate the HCoV species examined.
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Recent Advances in Influenza, HIV and SARS-CoV-2 Infection Prevention and Drug Treatment—The Need for Precision Medicine. CHEMISTRY 2022. [DOI: 10.3390/chemistry4020019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Viruses, and in particular, RNA viruses, dominate the WHO’s current list of ten global health threats. Of these, we review the widespread and most common HIV, influenza virus, and SARS-CoV-2 infections, as well as their possible prevention by vaccination and treatments by pharmacotherapeutic approaches. Beyond the vaccination, we discuss the virus-targeting and host-targeting drugs approved in the last five years, in the case of SARS-CoV-2 in the last one year, as well as new drug candidates and lead molecules that have been published in the same periods. We share our views on vaccination and pharmacotherapy, their mutually reinforcing strategic significance in combating pandemics, and the pros and cons of host and virus-targeted drug therapy. The COVID-19 pandemic has provided evidence of our limited armamentarium to fight emerging viral diseases. Novel broad-spectrum vaccines as well as drugs that could even be applied as prophylactic treatments or in early phases of the viremia, possibly through oral administration, are needed in all three areas. To meet these needs, the use of multi-data-based precision medicine in the practice and innovation of vaccination and drug therapy is inevitable.
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Fedeli P, Scendoni R, Cingolani M, Corrales Compagnucci M, Cirocchi R, Cannovo N. Informed Consent and Protection of Personal Data in Genetic Research on COVID-19. Healthcare (Basel) 2022; 10:healthcare10020349. [PMID: 35206963 PMCID: PMC8871888 DOI: 10.3390/healthcare10020349] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 01/17/2022] [Accepted: 02/09/2022] [Indexed: 11/16/2022] Open
Abstract
The particular characteristics of COVID-19 demand the careful biomedical study of samples from patients who have shown different symptomatology, in order to understand the genetic foundations of its phenotypic expression. Research on genetic material from COVID-19 patients is indispensable for understanding the biological bases for its varied clinical manifestations. The issue of “informed consent” constitutes the crux of the problem in regulating research biobanks, because it concerns the relationship between the person and the parts separated from the body. There are several consensus models that can be adopted, varying from quite restricted models of specific informed consent to forms that allow very broad authorization (open consent). Our current understanding of COVID-19 is incomplete. Thus, we cannot plan, with precision, the research to be conducted on biological samples that have been, or will be, collected from patients infected by the novel coronavirus. Therefore, we suggest utilizing the “participation pact” between researchers and donors, based on a new form of participation in research, which offers a choice based on the principles of solidarity and reciprocity, which represent the communication of “values”. In the last part of this paper, the general data protection regulation concerning the matter is discussed. The treatment of personal data must be performed with explicit goals, and donors must be provided with a clear, transparent explanation of the methods, goals and time of storage. The data must not be provided to unauthorized subjects. In conclusion, open informed consent forms will be necessary for research on individual patients and on populations.
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Affiliation(s)
| | - Roberto Scendoni
- Department of Law, University of Macerata, 62100 Macerata, Italy;
| | - Mariano Cingolani
- Department of Law, University of Macerata, 62100 Macerata, Italy;
- Correspondence:
| | - Marcelo Corrales Compagnucci
- Centre for Advanced Studies on Biomedical Innovation Law (CeBIL), Faculty of Law, University of Copenhagen, Karen Blixens Plads 16, DK-2300 Copenhagen, Denmark;
| | - Roberto Cirocchi
- Department of Surgical and Biomedical Sciences, University of Perugia, 06132 Perugia, Italy;
| | - Nunzia Cannovo
- Ethic Committee, University of Naples, 80138 Napoli, Italy;
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Santos SDS, Torres M, Galeano D, Sánchez MDM, Cernuzzi L, Paccanaro A. Machine learning and network medicine approaches for drug repositioning for COVID-19. PATTERNS (NEW YORK, N.Y.) 2022; 3:100396. [PMID: 34778851 PMCID: PMC8576113 DOI: 10.1016/j.patter.2021.100396] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 06/21/2021] [Accepted: 11/01/2021] [Indexed: 12/13/2022]
Abstract
We present two machine learning approaches for drug repurposing. While we have developed them for COVID-19, they are disease-agnostic. The two methodologies are complementary, targeting SARS-CoV-2 and host factors, respectively. Our first approach consists of a matrix factorization algorithm to rank broad-spectrum antivirals. Our second approach, based on network medicine, uses graph kernels to rank drugs according to the perturbation they induce on a subnetwork of the human interactome that is crucial for SARS-CoV-2 infection/replication. Our experiments show that our top predicted broad-spectrum antivirals include drugs indicated for compassionate use in COVID-19 patients; and that the ranking obtained by our kernel-based approach aligns with experimental data. Finally, we present the COVID-19 repositioning explorer (CoREx), an interactive online tool to explore the interplay between drugs and SARS-CoV-2 host proteins in the context of biological networks, protein function, drug clinical use, and Connectivity Map. CoREx is freely available at: https://paccanarolab.org/corex/.
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Affiliation(s)
- Suzana de Siqueira Santos
- Escola de Matemática Aplicada, Fundação Getulio Vargas, Rio de Janeiro 22250-900, Brazil
- COVID-19 International Research Team
| | - Mateo Torres
- Escola de Matemática Aplicada, Fundação Getulio Vargas, Rio de Janeiro 22250-900, Brazil
- COVID-19 International Research Team
| | - Diego Galeano
- Escola de Matemática Aplicada, Fundação Getulio Vargas, Rio de Janeiro 22250-900, Brazil
- Facultad de Ingenieria, Universidad Nacional de Asunción, Luque 110948, Paraguay
- COVID-19 International Research Team
| | | | - Luca Cernuzzi
- Universidad Católica “Nuestra Señora de la Asunción”, Asunción C.C. 1683, Paraguay
| | - Alberto Paccanaro
- Escola de Matemática Aplicada, Fundação Getulio Vargas, Rio de Janeiro 22250-900, Brazil
- Department of Computer Science, Centre for Systems and Synthetic Biology, Royal Holloway, University of London, Egham Hill, Egham TW20 0EX, UK
- COVID-19 International Research Team
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In Silico Screening of Potential Phytocompounds from Several Herbs against SARS-CoV-2 Indian Delta Variant B.1.617.2 to Inhibit the Spike Glycoprotein Trimer. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12020665] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
In October 2020, the SARS-CoV-2 B.1.617 lineage was discovered in India. It has since become a prominent variant in several Indian regions and 156 countries, including the United States of America. The lineage B.1.617.2 is termed the delta variant, harboring diverse spike mutations in the N-terminal domain (NTD) and the receptor-binding domain (RBD), which may heighten its immune evasion potentiality and cause it to be more transmissible than other variants. As a result, it has sparked substantial scientific investigation into the development of effective vaccinations and anti-viral drugs. Several efforts have been made to examine ancient medicinal herbs known for their health benefits and immune-boosting action against SARS-CoV-2, including repurposing existing FDA-approved anti-viral drugs. No efficient anti-viral drugs are available against the SARS-CoV-2 Indian delta variant B.1.617.2. In this study, efforts were made to shed light on the potential of 603 phytocompounds from 22 plant species to inhibit the Indian delta variant B.1.617.2. We also compared these compounds with the standard drug ceftriaxone, which was already suggested as a beneficial drug in COVID-19 treatment; these compounds were compared with other FDA-approved drugs: remdesivir, chloroquine, hydroxy-chloroquine, lopinavir, and ritonavir. From the analysis, the identified phytocompounds acteoside (−7.3 kcal/mol) and verbascoside (−7.1 kcal/mol), from the plants Clerodendrum serratum and Houttuynia cordata, evidenced a strong inhibitory effect against the mutated NTD (MT-NTD). In addition, the phytocompounds kanzonol V (−6.8 kcal/mol), progeldanamycin (−6.4 kcal/mol), and rhodoxanthin (−7.5 kcal/mol), from the plant Houttuynia cordata, manifested significant prohibition against RBD. Nevertheless, the standard drug, ceftriaxone, signals less inhibitory effect against MT-NTD and RBD with binding affinities of −6.3 kcal/mol and −6.5 kcal/mol, respectively. In this study, we also emphasized the pharmacological properties of the plants, which contain the screened phytocompounds. Our research could be used as a lead for future drug design to develop anti-viral drugs, as well as for preening the Siddha formulation to control the Indian delta variant B.1.617.2 and other future SARS-CoV-2 variants.
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