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Malvankar S, Singh A, Ravi Kumar YS, Sahu S, Shah M, Murghai Y, Seervi M, Srivastava RK, Verma B. Modulation of various host cellular machinery during COVID-19 infection. Rev Med Virol 2023; 33:e2481. [PMID: 37758688 DOI: 10.1002/rmv.2481] [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: 11/29/2022] [Revised: 07/24/2023] [Accepted: 09/10/2023] [Indexed: 09/29/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) emerged in December 2019, causing a range of respiratory infections from mild to severe. This resulted in the ongoing global COVID-19 pandemic, which has had a significant impact on public health. The World Health Organization declared COVID-19 as a global pandemic in March 2020. Viruses are intracellular pathogens that rely on the host's machinery to establish a successful infection. They exploit the gene expression machinery of host cells to facilitate their own replication. Gaining a better understanding of gene expression modulation in SARS-CoV2 is crucial for designing and developing effective antiviral strategies. Efforts are currently underway to understand the molecular-level interaction between the host and the pathogen. In this review, we describe how SARS-CoV2 infection modulates gene expression by interfering with cellular processes, including transcription, post-transcription, translation, post-translation, epigenetic modifications as well as processing and degradation pathways. Additionally, we emphasise the therapeutic implications of these findings in the development of new therapies to treat SARS-CoV2 infection.
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Affiliation(s)
- Shivani Malvankar
- Department of Biotechnology, All India Institute of Medical Sciences, New Delhi, India
| | - Anjali Singh
- Department of Biotechnology, All India Institute of Medical Sciences, New Delhi, India
| | - Y S Ravi Kumar
- Department of Biotechnology, M. S. Ramaiah Institute of Technology, Bengaluru, India
| | - Swetangini Sahu
- Department of Biotechnology, All India Institute of Medical Sciences, New Delhi, India
| | - Megha Shah
- Department of Biotechnology, All India Institute of Medical Sciences, New Delhi, India
| | - Yamini Murghai
- Department of Biotechnology, All India Institute of Medical Sciences, New Delhi, India
| | - Mahendra Seervi
- Department of Biotechnology, All India Institute of Medical Sciences, New Delhi, India
| | - Rupesh K Srivastava
- Department of Biotechnology, All India Institute of Medical Sciences, New Delhi, India
| | - Bhupendra Verma
- Department of Biotechnology, All India Institute of Medical Sciences, New Delhi, India
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Prabowo NA, Megantara MA, Apriningsih H. The role of N-acetylcysteine in decreasing neutrophil-lymphocyte ratio in COVID-19 patients: A double-blind, randomized controlled trial. NARRA J 2023; 3:e121. [PMID: 38454976 PMCID: PMC10919724 DOI: 10.52225/narraj.v3i2.121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Accepted: 05/09/2023] [Indexed: 03/09/2024]
Abstract
N-acetylcysteine has antioxidant and anti-inflammatory activities that could potentially improve the clinical outcomes of coronavirus disease 2019 (COVID-19) patients. N-acetylcysteine potentially inhibits NLRP3 (NOD-, LRR- and pyrin domain-containing protein 3) inflammasome and results in control oxidative stress and cytokine release in COVID-19 patients. The aim of this study was to assess the effect of N-acetylcysteine in reducing the neutrophil-lymphocyte ratio (NLR) in COVID-19 patients. A randomized controlled clinical trial was conducted among severe and moderate COVID-19 patients. The treatment group received oral 1200 mg daily of N-acetylcysteine (three times a day) and the standard care for COVID-19, while the control group received standard care for COVID-19 and a placebo. The NLR was determined on the first day of admission and after the seventh day of treatment. A paired Student t-test was used to compare the NLR before and after treatment while independent Student t-test was used to compare the NLR between treatment and control groups. A total of 40 severe and moderate COVID-19 were enrolled, 20 people in each group, with a mean age was 44.68±13.24 years old. The mean NLR on the first day was 9.44 in the treatment group and 8.84 in the control group. After the seventh day, the mean NLR was 4.27 and 11.54 in the treatment group and control group, respectively. The mean changes of NLR (the pre-treatment compared to post-treatment) in the treatment and control group were reduced 4.05 and increased 3.34, respectively. The NLR in treatment group significantly decreased compared to the control group (p<0.001). In conclusion, N-acetylcysteine 1200 mg daily could reduce the NLR in severe and moderate COVID-19 patients.
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Affiliation(s)
- Nurhasan A. Prabowo
- Department of Internal Medicine, Faculty of Medicine, Universitas Sebelas Maret, Surakarta, Indonesia
- Department of Internal Medicine, Universitas Sebelas Maret Hospital, Kartasura, Indonesia
| | - Marcelino A. Megantara
- Department of Internal Medicine, Faculty of Medicine, Universitas Sebelas Maret, Surakarta, Indonesia
| | - Hendrastutik Apriningsih
- Department of Internal Medicine, Faculty of Medicine, Universitas Sebelas Maret, Surakarta, Indonesia
- Department of Internal Medicine, Universitas Sebelas Maret Hospital, Kartasura, Indonesia
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COVID-19 therapeutics: Clinical application of repurposed drugs and futuristic strategies for target-based drug discovery. Genes Dis 2023; 10:1402-1428. [PMCID: PMC10079314 DOI: 10.1016/j.gendis.2022.12.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 12/07/2022] [Accepted: 12/16/2022] [Indexed: 06/17/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) causes the complicated disease COVID-19. Clinicians are continuously facing huge problems in the treatment of patients, as COVID-19-specific drugs are not available hence the principle of drug repurposing serves as a one-and-only hope. Globally, the repurposing of many drugs is underway; few of them are already approved by the regulatory bodies for their clinical use and most of them are in different phases of clinical trials. Here in this review, our main aim is to discuss in detail the up-to-date information on the target-based pharmacological classification of repurposed drugs, the potential mechanism of actions, and the current clinical trial status of various drugs which are under repurposing since early 2020. At last, we briefly proposed the probable pharmacological and therapeutic drug targets that may be preferred as a futuristic drug discovery approach in the development of effective medicines.
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Cetinkaya A, Kaya SI, Ozkan SA. A Comprehensive Overview of Sensors Applications for the Diagnosis of SARS-CoV-2 and of Drugs Used in its Treatment. Crit Rev Anal Chem 2023:1-21. [PMID: 36877165 DOI: 10.1080/10408347.2023.2186693] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
Abstract
During the COVID-19 process, determination-based analytical chemistry studies have had a major place at every stage. Many analytical techniques have been used in both diagnostic studies and drug analysis. Among these, electrochemical sensors are frequently preferred due to their high sensitivity, selectivity, short analysis time, reliability, ease of sample preparation, and low use of organic solvents. For the determination of drugs used in the SARS-CoV-2, such as favipiravir, molnupiravir, ribavirin, etc., electrochemical (nano)sensors are widely used in both pharmaceutical and biological samples. Diagnosis is the most critical step in the management of the disease, and electrochemical sensor tools are widely preferred for this purpose. Diagnostic electrochemical sensor tools can be biosensor-, nano biosensor-, or MIP-based sensors and utilize a wide variety of analytes such as viral proteins, viral RNA, antibodies, etc. This review overviews the sensor applications in SARS-CoV-2 in terms of diagnosis and determination of drugs by evaluating the most recent studies in the literature. In this way, it is aimed to compile the developments so far by shedding light on the most recent studies and giving ideas to researchers for future studies.
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Affiliation(s)
- Ahmet Cetinkaya
- Faculty of Pharmacy, Department of Analytical Chemistry, Ankara University, Ankara, Türkiye
- Graduate School of Health Sciences, Ankara University, Ankara, Türkiye
| | - S Irem Kaya
- Gulhane Faculty of Pharmacy, Department of Analytical Chemistry, University of Health Sciences, Ankara, Türkiye
| | - Sibel A Ozkan
- Faculty of Pharmacy, Department of Analytical Chemistry, Ankara University, Ankara, Türkiye
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Elama HS, Zeid AM, Shalan SM, El-Shabrawy Y, Eid MI. Eco-friendly spectrophotometric methods for determination of remdesivir and favipiravir; the recently approved antivirals for COVID-19 treatment. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 287:122070. [PMID: 36403556 PMCID: PMC9650262 DOI: 10.1016/j.saa.2022.122070] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Revised: 10/25/2022] [Accepted: 10/30/2022] [Indexed: 05/17/2023]
Abstract
Remdesivir (REM) and Favipiravir (FAV) are recently approved antivirals prescribed in severely ill COVID-19 patients. Therefore, development of new, simple, rapid, sensitive, and selective methods for analysis of such drugs in their pharmaceutical formulations will be highly advantageous. Herein, we have developed different spectrophotometric methods for analysis of the studied analytes. Method I is based on direct spectrophotometric analysis of REM and FAV in ethanol at λmax 244 and 323 nm, respectively. For simultaneous quantitation of REM and FAV, methods II-V were followed. Method II is based on derivative spectrophotometry in which REM was determined in second-order derivative spectra at 248 nm (the zero-crossing wavelength for FAV), while FAV was measured in first-order derivative spectra at 337 nm (the zero-crossing point for REM). Method III is the dual-wavelength method in which spectral intensities were subtracted at 244-207 nm for REM and at 330-400 nm for FAV. Method IV is the ratio subtraction in which ratio spectra were obtained by a suitable divisor followed by subtraction of intensities at 272-340 nm and 335-222 nm for REM and FAV, respectively. Method V is the derivative ratio method in which the obtained ratio spectra in method IV were converted to first-order derivative and then REM and FAV were recorded at 280 and 340 nm, respectively. Calibration graphs were linear in the ranges of 1-10 µg/mL for REM through all methods and 1-20 µg/mL for FAV in methods I and II, and 2-20 µg/mL by the other methods. The evolved methods were applied to pharmaceutical dosage forms of REM and FAV. All the proposed methods were further applied to human plasma samples containing both drugs with acceptable mean recoveries.
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Affiliation(s)
- Heba Samir Elama
- Pharmaceutical Analytical Chemistry Department, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt.
| | - Abdallah M Zeid
- Pharmaceutical Analytical Chemistry Department, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Shereen Mahmoud Shalan
- Pharmaceutical Analytical Chemistry Department, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Yasser El-Shabrawy
- Pharmaceutical Analytical Chemistry Department, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Manal Ibrahim Eid
- Pharmaceutical Analytical Chemistry Department, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
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Frias-De-Diego A, Gilbertie JM, Scholle F, Dejarnette S, Crisci E. Effect of BIO-PLY TM, a Platelet-Rich Plasma Derived Biologic on PRRSV-2-Infected Macrophages. Viruses 2022; 14:v14122666. [PMID: 36560670 PMCID: PMC9783555 DOI: 10.3390/v14122666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 11/22/2022] [Accepted: 11/23/2022] [Indexed: 11/30/2022] Open
Abstract
Porcine Reproductive and Respiratory Syndrome (PRRS) is the one of the most devastating diseases impacting the swine industry worldwide. Control and prevention methods rely on biosafety measures and vaccination. As an RNA virus with a high rate of mutation, vaccines are only partially effective against circulating and newly emerging strains. To reduce the burden of this disease, research on alternative control methods is needed. Here, we assess the in vitro antiviral effect of a novel platelet-rich plasma-derived biologic termed BIO-PLYTM (for the BIOactive fraction of Platelet-rich plasma LYsate) from both swine and equine origin. Our results show that BIO-PLYTM significantly reduces the amount of PRRSV viral load determined by RT-qPCR and the number of infectious viral particles measured by TCID50 in infected porcine alveolar and parenchymal macrophages. This study also showed limited toxicity of BIO-PLYTM in vitro and aspects of its immunomodulatory capacity evaluating the regulation of reactive oxygen species and cytokines production in infected cells. Finally, this study presents promising data on the effect of BIO-PLYTM on other RNA viruses such as human A influenza viruses and coronavirus.
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Affiliation(s)
- Alba Frias-De-Diego
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27607, USA
| | - Jessica M. Gilbertie
- Department of Biomedical Affairs and Research, Edward Via College of Osteopathic Medicine, Blacksburg, VA 24060, USA
| | - Frank Scholle
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | - Sarah Dejarnette
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | - Elisa Crisci
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27607, USA
- Correspondence: ; Tel.: +1-919-513-6255
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Pal LR, Cheng K, Nair NU, Martin-Sancho L, Sinha S, Pu Y, Riva L, Yin X, Schischlik F, Lee JS, Chanda SK, Ruppin E. Synthetic lethality-based prediction of anti-SARS-CoV-2 targets. iScience 2022; 25:104311. [PMID: 35502318 PMCID: PMC9044693 DOI: 10.1016/j.isci.2022.104311] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 10/19/2021] [Accepted: 04/04/2022] [Indexed: 02/07/2023] Open
Abstract
Novel strategies are needed to identify drug targets and treatments for the COVID-19 pandemic. The altered gene expression of virus-infected host cells provides an opportunity to specifically inhibit viral propagation via targeting the synthetic lethal and synthetic dosage lethal (SL/SDL) partners of such altered host genes. Pursuing this disparate antiviral strategy, here we comprehensively analyzed multiple in vitro and in vivo bulk and single-cell RNA-sequencing datasets of SARS-CoV-2 infection to predict clinically relevant candidate antiviral targets that are SL/SDL with altered host genes. The predicted SL/SDL-based targets are highly enriched for infected cell inhibiting genes reported in four SARS-CoV-2 CRISPR-Cas9 genome-wide genetic screens. We further selected a focused subset of 26 genes that we experimentally tested in a targeted siRNA screen using human Caco-2 cells. Notably, as predicted, knocking down these targets reduced viral replication and cell viability only under the infected condition without harming noninfected healthy cells.
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Affiliation(s)
- Lipika R. Pal
- Cancer Data Science Laboratory (CDSL), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Kuoyuan Cheng
- Cancer Data Science Laboratory (CDSL), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA
| | - Nishanth Ulhas Nair
- Cancer Data Science Laboratory (CDSL), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Laura Martin-Sancho
- Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Sanju Sinha
- Cancer Data Science Laboratory (CDSL), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA
| | - Yuan Pu
- Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Laura Riva
- Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Xin Yin
- Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Fiorella Schischlik
- Cancer Data Science Laboratory (CDSL), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Joo Sang Lee
- Cancer Data Science Laboratory (CDSL), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA
- Samsung Medical Center, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
| | - Sumit K. Chanda
- Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Eytan Ruppin
- Cancer Data Science Laboratory (CDSL), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA
- Department of Computer Science, University of Maryland, College Park, MD, USA
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Second-Order Scattering Quenching in Fluorescence Spectra of Natural Humates as a Tracer of Formation Stable Supramolecular System for the Delivery of Poorly Soluble Antiviral Drugs on the Example of Mangiferin and Favipiravir. Pharmaceutics 2022; 14:pharmaceutics14040767. [PMID: 35456601 PMCID: PMC9030643 DOI: 10.3390/pharmaceutics14040767] [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: 02/26/2022] [Revised: 03/25/2022] [Accepted: 03/29/2022] [Indexed: 12/04/2022] Open
Abstract
In the present work, the methods of dynamic light scattering and fluorescence spectroscopy were applied to study the optical properties of aqueous dilutions of the humic substances complex (HC) as a potential drug delivery system. The supramolecular structures in the humate solution were characterized as monodisperse systems of the submicron range with a tendency to decrease in particle size with a decrease in the dry matter concentration. The slightly alkaline medium (8.3) of the studied aqueous dilutions of HC causes the absence of a pronounced fluorescence maximum in the region from 400 to 500 nm. However, the presence of an analytically significant, inversely proportional to the concentration second-order scattering (SOS) signal at 2λex = λem was shown. In the examples of the antiviral substances mangiferin and favipiravir, it was shown that the use of the humic complex as a drug carrier makes it possible to increase the solubility by several times and simultaneously obtain a system with a smaller particle size of the dispersed phase. It has been shown that HC can interact with mangiferin and favipiravir to form stable structures, which lead to a significant decrease in SOS intensities on HC SOS spectra. The scattering wavelengths, λex/λem, were registered at 350 nm/750 nm for mangiferin and 365 nm/730 nm for favipiravir, respectively. The increments of the scattering intensities (I0/I) turned out to be proportional to the concentration of antiviral components in a certain range of concentrations.
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Matos ADR, Caetano BC, de Almeida Filho JL, Martins JSCDC, de Oliveira MGP, Sousa TDC, Horta MAP, Siqueira MM, Fernandez JH. Identification of Hypericin as a Candidate Repurposed Therapeutic Agent for COVID-19 and Its Potential Anti-SARS-CoV-2 Activity. Front Microbiol 2022; 13:828984. [PMID: 35222340 PMCID: PMC8866965 DOI: 10.3389/fmicb.2022.828984] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Accepted: 01/13/2022] [Indexed: 12/12/2022] Open
Abstract
The COVID-19 pandemic has had an unprecedented impact on the global economy and public health. Its etiologic agent, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is highly transmissible, pathogenic and has a rapid global spread. Currently, the increase in the number of new confirmed cases has been slowed down due to the increase of vaccination in some regions of the world. Still, the rise of new variants has influenced the detection of additional waves of rising cases that some countries have experienced. Since the virus replication cycle is composed of many distinct stages, some viral proteins related to them, as the main-protease (Mpro) and RNA dependent RNA polymerase (RdRp), constitute individual potential antiviral targets. In this study, we challenged the mentioned enzymes against compounds pre-approved by health regulatory agencies in a virtual screening and later in Molecular Mechanics/Poisson–Bolzmann Surface Area (MM/PBSA) analysis. Our results showed that, among the identified potential drugs with anti-SARS-CoV-2 properties, Hypericin, an important component of the Hypericum perforatum that presents antiviral and antitumoral properties, binds with high affinity to viral Mpro and RdRp. Furthermore, we evaluated the activity of Hypericin anti-SARS-CoV-2 replication in an in vitro model of Vero-E6 infected cells. Therefore, we show that Hypericin inhibited viral replication in a dose dependent manner. Moreover, the cytotoxicity of the compound, in cultured cells, was evaluated, but no significant activity was found. Thus, the results observed in this study indicate that Hypericin is an excellent candidate for repurposing for the treatment of COVID-19, with possible inhibition of two important phases of virus maturation.
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Affiliation(s)
- Aline da Rocha Matos
- Laboratório de Virus Respiratórios e do Sarampo, Insituto Oswaldo Cruz, Fundação Oswaldo Cruz (LVRS-IOC-Fiocruz), Rio de Janeiro, Brazil
| | - Braulia Costa Caetano
- Laboratório de Virus Respiratórios e do Sarampo, Insituto Oswaldo Cruz, Fundação Oswaldo Cruz (LVRS-IOC-Fiocruz), Rio de Janeiro, Brazil
| | - João Luiz de Almeida Filho
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense (LQFPP-CBB-UENF), Campos dos Goytacazes, Brazil
| | | | | | - Thiago das Chagas Sousa
- Laboratório de Virus Respiratórios e do Sarampo, Insituto Oswaldo Cruz, Fundação Oswaldo Cruz (LVRS-IOC-Fiocruz), Rio de Janeiro, Brazil
| | - Marco Aurélio Pereira Horta
- Plataforma de Laboratórios de Biossegurança Nível 3, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (NB3-IOC-Fiocruz), Rio de Janeiro, Brazil
| | - Marilda Mendonça Siqueira
- Laboratório de Virus Respiratórios e do Sarampo, Insituto Oswaldo Cruz, Fundação Oswaldo Cruz (LVRS-IOC-Fiocruz), Rio de Janeiro, Brazil
| | - Jorge Hernandez Fernandez
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense (LQFPP-CBB-UENF), Campos dos Goytacazes, Brazil
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Negru PA, Radu AF, Vesa CM, Behl T, Abdel-Daim MM, Nechifor AC, Endres L, Stoicescu M, Pasca B, Tit DM, Bungau SG. Therapeutic dilemmas in addressing SARS-CoV-2 infection: Favipiravir versus Remdesivir. Biomed Pharmacother 2022; 147:112700. [PMID: 35131656 PMCID: PMC8813547 DOI: 10.1016/j.biopha.2022.112700] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 01/27/2022] [Accepted: 02/02/2022] [Indexed: 02/07/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) represents an unmet clinical need, due to a high mortality rate, rapid mutation rate in the virus, increased chances of reinfection, lack of effectiveness of repurposed drugs and economic damage. COVID-19 pandemic has created an urgent need for effective molecules. Clinically proven efficacy and safety profiles have made favipiravir (FVP) and remdesivir (RDV) promising therapeutic options for use against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Even though both are prodrug molecules with an antiviral role based on a similar mechanism of action, differences in pharmacological, pharmacokinetic and pharmacotoxicological mechanisms have been identified. The present study aims to provide a comprehensive comparative assessment of FVP and RDV against SARS-CoV-2 infections, by centralizing medical data provided by significant literature and authorized clinical trials, focusing on the importance of a better understanding of the interactions between drug molecules and infectious agents in order to improve the global management of COVID-19 patients and to reduce the risk of antiviral resistance.
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Affiliation(s)
- Paul Andrei Negru
- Doctoral School of Biological and Biomedical Sciences, University of Oradea, 410087 Oradea, Romania.
| | - Andrei-Flavius Radu
- Doctoral School of Biological and Biomedical Sciences, University of Oradea, 410087 Oradea, Romania.
| | - Cosmin Mihai Vesa
- Department of Preclinical Disciplines, Faculty of Medicine and Pharmacy, University of Oradea, 410073 Oradea, Romania.
| | - Tapan Behl
- Chitkara College of Pharmacy, Chitkara University, Punjab 140401, India.
| | - Mohamed M. Abdel-Daim
- Department of Pharmaceutical Sciences, Pharmacy Program, Batterjee Medical College, P.O. Box 6231, Jedah 21442, Saudi Arabia,Pharmacology Department, Faculty of Veterinary Medicine, Suez Canal University, Ismailia 41522, Egypt
| | - Aurelia Cristina Nechifor
- Analytical Chemistry and Environmental Engineering Department, Polytechnic University of Bucharest, 011061 Bucharest, Romania.
| | - Laura Endres
- Department of Psycho-Neuroscience and Recovery, Faculty of Medicine and Pharmacy, University of Oradea, 410073 Oradea, Romania.
| | - Manuela Stoicescu
- Department of Medical Disciplines, Faculty of Medicine and Pharmacy, University of Oradea, 410073 Oradea, Romania.
| | - Bianca Pasca
- Doctoral School of Biological and Biomedical Sciences, University of Oradea, 410087 Oradea, Romania.
| | - Delia Mirela Tit
- Doctoral School of Biological and Biomedical Sciences, University of Oradea, 410087 Oradea, Romania; Department of Pharmacy, Faculty of Medicine and Pharmacy, University of Oradea, 410028 Oradea, Romania.
| | - Simona Gabriela Bungau
- Doctoral School of Biological and Biomedical Sciences, University of Oradea, 410087 Oradea, Romania; Department of Pharmacy, Faculty of Medicine and Pharmacy, University of Oradea, 410028 Oradea, Romania.
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Insight into the Advances in Clinical Trials of SARS-CoV-2 Vaccines. THE CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY = JOURNAL CANADIEN DES MALADIES INFECTIEUSES ET DE LA MICROBIOLOGIE MEDICALE 2022; 2022:6913772. [PMID: 35186175 PMCID: PMC8850041 DOI: 10.1155/2022/6913772] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 01/17/2022] [Indexed: 12/22/2022]
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has thrown a challenge to the scientific community. Several interventions to stop or limit the spread of infection have failed, and every time the virus emerges, it becomes more contagious and more deadly. Vaccinating a significant proportion of the population is one of the established methods to achieve herd immunity. More than 100 COVID-19 vaccines have been designed and tested against the virus. The development of a new vaccine takes years of testing, but due to the pandemic, healthcare authorities have given emergency use authorization for a few vaccines. Among them are BioNTech and Moderna vaccines (mRNA based); ChAdOx1, Gam-COVID-Vac, Janssen vaccines (vector-based); CoronaVac, COVAXIN (virus inactivated); and EpiVacCorona vaccine (viral peptide). Mixtures of vaccines are also being tested to evaluate their efficacy against mutant strains of SARS-CoV-2. All these vaccines in clinical trials have shown robust production of neutralizing antibodies sufficient to prevent infection. Some of the vaccinated people reported serious complications. However, no definitive relationship could be established between vaccination administration and the occurrence of these complications. None of the COVID-19 vaccines approved to date have been found to be effective against all of the SARS-CoV-2 variants.
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12
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Beheshtirouy S, Khani E, Khiali S, Entezari-Maleki T. Investigational antiviral drugs for the treatment of COVID-19 patients. Arch Virol 2022; 167:751-805. [PMID: 35138438 DOI: 10.1007/s00705-022-05368-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 11/15/2021] [Indexed: 12/27/2022]
Abstract
In the current pandemic of coronavirus disease 2019 (COVID-19), antiviral drugs are at the center of attention because of their critical role against severe acute respiratory disease syndrome coronavirus 2 (SARS-CoV-2). In addition to designing new antivirals against SARS-COV-2, a drug repurposing strategy is a practical approach for treating COVID-19. A brief insight about antivirals would help clinicians to choose the best medication for the treatment of COVID-19. In this review, we discuss both novel and repurposed investigational antivirals, focusing on in vitro, in vivo, and clinical trial studies.
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Affiliation(s)
- Samineh Beheshtirouy
- Department of Clinical Pharmacy, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Elnaz Khani
- Department of Clinical Pharmacy, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Sajad Khiali
- Department of Clinical Pharmacy, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Taher Entezari-Maleki
- Department of Clinical Pharmacy, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran. .,Cardiovascular Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
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13
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Wang X, Luo J, Wen Z, Shuai L, Wang C, Zhong G, He X, Cao H, Liu R, Ge J, Hua R, Sun Z, Wang X, Wang J, Bu Z. Diltiazem inhibits SARS-CoV-2 cell attachment and internalization and decreases the viral infection in mouse lung. PLoS Pathog 2022; 18:e1010343. [PMID: 35176124 PMCID: PMC8890723 DOI: 10.1371/journal.ppat.1010343] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 03/02/2022] [Accepted: 02/05/2022] [Indexed: 12/20/2022] Open
Abstract
The continuous emergence of severe acute respiratory coronavirus 2 (SARS-CoV-2) variants and the increasing number of breakthrough infection cases among vaccinated people support the urgent need for research and development of antiviral drugs. Viral entry is an intriguing target for antiviral drug development. We found that diltiazem, a blocker of the L-type calcium channel Cav1.2 pore-forming subunit (Cav1.2 α1c) and an FDA-approved drug, inhibits the binding and internalization of SARS-CoV-2, and decreases SARS-CoV-2 infection in cells and mouse lung. Cav1.2 α1c interacts with SARS-CoV-2 spike protein and ACE2, and affects the attachment and internalization of SARS-CoV-2. Our finding suggests that diltiazem has potential as a drug against SARS-CoV-2 infection and that Cav1.2 α1c is a promising target for antiviral drug development for COVID-19. The emergence of variants of SARS-CoV-2 and the breakthrough infections that have occurred in recipients of approved SARS-CoV-2 vaccines raise doubts about the effectiveness of the vaccines and highlight the importance of antiviral drugs. An ideal drug to treat COVID-19 should be safe, affordable, and accessible. However, remdesivir remains the only authorized drug approved by the US FDA for emergency use, and it appears to have little effect on hospitalized COVID-19 patients. Therefore, identifying drugs to treat SARS-CoV-2 infections remains extremely important and urgent. In this study, we found that the calcium channel blocker diltiazem, which has been approved in the US since 1982 and is cheap and widely used in clinical practice for many indications, inhibits the binding and internalization of SARS-CoV-2, and decreases SARS-CoV-2 infection in cells and mouse lung. The L-type calcium channel Cav1.2 pore-forming subunit (Cav1.2 α1c), the main target of diltiazem, interacts and colocalizes with SARS-CoV-2 spike protein and ACE2, thereby affecting cell attachment and internalization of SARS-CoV-2. Our finding suggests that diltiazem could be candidate COVID-19 treatment and that Cav1.2 α1c may be a promising target for anti-SARS-CoV-2 drugs.
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Affiliation(s)
- Xinxin Wang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People’s Republic of China
| | - Jie Luo
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People’s Republic of China
| | - Zhiyuan Wen
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People’s Republic of China
| | - Lei Shuai
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People’s Republic of China
| | - Chong Wang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People’s Republic of China
| | - Gongxun Zhong
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People’s Republic of China
| | - Xijun He
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People’s Republic of China
| | - Huizhen Cao
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People’s Republic of China
| | - Renqiang Liu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People’s Republic of China
| | - Jinying Ge
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People’s Republic of China
| | - Ronghong Hua
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People’s Republic of China
| | - Ziruo Sun
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People’s Republic of China
| | - Xijun Wang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People’s Republic of China
| | - Jinliang Wang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People’s Republic of China
- * E-mail: (JW); (ZB)
| | - Zhigao Bu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People’s Republic of China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, P. R. China
- * E-mail: (JW); (ZB)
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14
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Jeong HJ, Min S, Kim S, Namgoong SK, Jeong K. Hyperpolarization study on remdesivir with its biological reaction monitoring via signal amplification by reversible exchange. RSC Adv 2022; 12:4377-4381. [PMID: 35425403 PMCID: PMC8981083 DOI: 10.1039/d2ra00062h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 01/20/2022] [Indexed: 12/22/2022] Open
Abstract
Our experiments indicate hyperpolarized proton signals in the entire structure of remdesivir are obtained due to a long-distance polarization transfer by para-hydrogen. SABRE-based biological real-time reaction monitoring, by using a protein enzyme under mild conditions is carried out. It represents the first successful para-hydrogen based hyperpolarization application in biological reaction monitoring. Hyperpolarized proton signals in the entire structure of remdesivir are obtained due to a long-distance polarization transfer by para-hydrogen. Biological real-time reaction monitoring, by using a protein enzyme under mild conditions is carried out.![]()
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Affiliation(s)
- Hye Jin Jeong
- Department of Physics and Chemistry, Korea Military Academy, Seoul 01805, South Korea
| | - Sein Min
- Department of Chemistry, Seoul Women's University, Seoul 01797, South Korea
| | - Sarah Kim
- Department of Chemistry, Seoul Women's University, Seoul 01797, South Korea
| | - Sung Keon Namgoong
- Department of Chemistry, Seoul Women's University, Seoul 01797, South Korea
| | - Keunhong Jeong
- Department of Physics and Chemistry, Korea Military Academy, Seoul 01805, South Korea
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15
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Serra A, Fratello M, Federico A, Ojha R, Provenzani R, Tasnadi E, Cattelani L, Del Giudice G, Kinaret PAS, Saarimäki LA, Pavel A, Kuivanen S, Cerullo V, Vapalahti O, Horvath P, Lieto AD, Yli-Kauhaluoma J, Balistreri G, Greco D. Computationally prioritized drugs inhibit SARS-CoV-2 infection and syncytia formation. Brief Bioinform 2021; 23:6484515. [PMID: 34962256 PMCID: PMC8769897 DOI: 10.1093/bib/bbab507] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 11/03/2021] [Accepted: 11/04/2021] [Indexed: 12/12/2022] Open
Abstract
The pharmacological arsenal against the COVID-19 pandemic is largely based on generic anti-inflammatory strategies or poorly scalable solutions. Moreover, as the ongoing vaccination campaign is rolling slower than wished, affordable and effective therapeutics are needed. To this end, there is increasing attention toward computational methods for drug repositioning and de novo drug design. Here, multiple data-driven computational approaches are systematically integrated to perform a virtual screening and prioritize candidate drugs for the treatment of COVID-19. From the list of prioritized drugs, a subset of representative candidates to test in human cells is selected. Two compounds, 7-hydroxystaurosporine and bafetinib, show synergistic antiviral effects in vitro and strongly inhibit viral-induced syncytia formation. Moreover, since existing drug repositioning methods provide limited usable information for de novo drug design, the relevant chemical substructures of the identified drugs are extracted to provide a chemical vocabulary that may help to design new effective drugs.
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Affiliation(s)
- Angela Serra
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.,BioMediTech Institute, Tampere University, Tampere, Finland.,Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Tampere, Finland
| | - Michele Fratello
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.,BioMediTech Institute, Tampere University, Tampere, Finland.,Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Tampere, Finland
| | - Antonio Federico
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.,BioMediTech Institute, Tampere University, Tampere, Finland.,Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Tampere, Finland
| | - Ravi Ojha
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Riccardo Provenzani
- Drug Research Program, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Ervin Tasnadi
- Synthetic and Systems Biology Unit, Biological Research Centre, Eotvos Lorand Research Network, Szeged, Hungary
| | - Luca Cattelani
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.,BioMediTech Institute, Tampere University, Tampere, Finland.,Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Tampere, Finland
| | - Giusy Del Giudice
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.,BioMediTech Institute, Tampere University, Tampere, Finland.,Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Tampere, Finland
| | - Pia A S Kinaret
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.,BioMediTech Institute, Tampere University, Tampere, Finland.,Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Tampere, Finland.,Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Laura A Saarimäki
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.,BioMediTech Institute, Tampere University, Tampere, Finland.,Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Tampere, Finland
| | - Alisa Pavel
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.,BioMediTech Institute, Tampere University, Tampere, Finland.,Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Tampere, Finland
| | - Suvi Kuivanen
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Vincenzo Cerullo
- Drug Research Program, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Olli Vapalahti
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland.,Department of Virology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Peter Horvath
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland.,Synthetic and Systems Biology Unit, Biological Research Centre, Eotvos Lorand Research Network, Szeged, Hungary
| | - Antonio Di Lieto
- Department of Forensic Psychiatry, Aarhus University, Aarhus, Denmark
| | - Jari Yli-Kauhaluoma
- Drug Research Program, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Giuseppe Balistreri
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,Queensland Brain Institute, The University of Queensland, Brisbane, Australia
| | - Dario Greco
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.,BioMediTech Institute, Tampere University, Tampere, Finland.,Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Tampere, Finland.,Institute of Biotechnology, University of Helsinki, Helsinki, Finland
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16
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Abstract
Background COVID-19 is an ongoing viral pandemic produced by SARS-CoV-2. In light of in vitro efficacy, several medications were repurposed for its management. During clinical use, many of these medications produced inconsistent results or had varying limitations. Objective The purpose of this literature review is to explain the variable efficacy or limitations of Lopinavir/Ritonavir, Remdesivir, Hydroxychloroquine, and Favipiravir in clinical settings. Method A study of the literature on the pharmacodynamics (PD), pharmacokinetics (PK), safety profile, and clinical trials through academic databases using relevant search terms. Results & discussion The efficacy of an antiviral drug against COVID-19 is associated with its ability to achieve therapeutic concentration in the lung and intestinal tissues. This efficacy depends on the PK properties, particularly protein binding, volume of distribution, and half-life. The PK and PD of the model drugs need to be integrated to predict their limitations. Conclusion Current antiviral drugs have varying pharmacological constraints that may associate with limited efficacy, especially in severe COVID-19 patients, or safety concerns.
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17
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Zou H, Yang Y, Dai H, Xiong Y, Wang JQ, Lin L, Chen ZS. Recent Updates in Experimental Research and Clinical Evaluation on Drugs for COVID-19 Treatment. Front Pharmacol 2021; 12:732403. [PMID: 34880750 PMCID: PMC8646041 DOI: 10.3389/fphar.2021.732403] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 10/13/2021] [Indexed: 12/17/2022] Open
Abstract
Since the outbreak of corona virus disease 2019 (COVID-19) in Wuhan (China) in December 2019, the epidemic has rapidly spread to many countries around the world, posing a huge threat to global public health. In response to the pandemic, a number of clinical studies have been initiated to evaluate the effect of various treatments against COVID-19, combining medical strategies and clinical trial data from around the globe. Herein, we summarize the clinical evaluation about the drugs mentioned in this review for COVID-19 treatment. This review discusses the recent data regarding the efficacy of various treatments in COVID-19 patients, to control and prevent the outbreak.
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Affiliation(s)
| | - Yuqi Yang
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, Queens, NY, United States
| | - Huiqiang Dai
- Cell Research Center, Shenzhen Bolun Institute of Biotechnology, Shenzhen, China
| | - Yunchuang Xiong
- Cell Research Center, Shenzhen Bolun Institute of Biotechnology, Shenzhen, China
| | - Jing-Quan Wang
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, Queens, NY, United States
| | - Lusheng Lin
- Cell Research Center, Shenzhen Bolun Institute of Biotechnology, Shenzhen, China
| | - Zhe-Sheng Chen
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, Queens, NY, United States
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18
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John L, Soujanya Y, Mahanta HJ, Narahari Sastry G. Chemoinformatics and Machine Learning Approaches for Identifying Antiviral Compounds. Mol Inform 2021; 41:e2100190. [PMID: 34811938 DOI: 10.1002/minf.202100190] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 10/15/2021] [Indexed: 11/06/2022]
Abstract
Current pandemics propelled research efforts in unprecedented fashion, primarily triggering computational efforts towards new vaccine and drug development as well as drug repurposing. There is an urgent need to design novel drugs with targeted biological activity and minimum adverse reactions that may be useful to manage viral outbreaks. Hence an attempt has been made to develop Machine Learning based predictive models that can be used to assess whether a compound has the potency to be antiviral or not. To this end, a set of 2358 antiviral compounds were compiled from the CAS COVID-19 antiviral SAR dataset whose activity was reported based on IC50 value. A total 1157 two-dimensional molecular descriptors were computed among which, the most highly correlated descriptors were selected using Tree-based, Correlation-based and Mutual information-based feature selection methods. Seven Machine Learning algorithms i. e., Random Forest, XGBoost, Support Vector Machine, KNN, Decision Tree, MLP Classifier and Logistic Regression were benchmarked. The best performance was achieved by the models developed using Random Forest and XGBoost algorithms in all the feature selection methods. The maximum predictive accuracy of both these models was 88 % with internal validation. Whereas, with an external dataset, a maximum accuracy of 93.10 % for XGBoost and 100 % for Random Forest based model was achievable. Furthermore, the study demonstrated scaffold analysis of the molecules as a pragmatic approach to explore the importance of structurally diverse compounds in data driven studies.
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Affiliation(s)
- Lijo John
- Centre for Molecular Modeling, CSIR-Indian Institute of Chemical Technology, Tarnaka, Hyderabad, 500 007, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, Uttar Pradesh, India
| | - Yarasi Soujanya
- Centre for Molecular Modeling, CSIR-Indian Institute of Chemical Technology, Tarnaka, Hyderabad, 500 007, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, Uttar Pradesh, India
| | - Hridoy Jyoti Mahanta
- Advanced Computation and Data Sciences Division, CSIR- North East Institute of Science and Technology, Jorhat, 785006, Assam, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, Uttar Pradesh, India
| | - G Narahari Sastry
- Advanced Computation and Data Sciences Division, CSIR- North East Institute of Science and Technology, Jorhat, 785006, Assam, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, Uttar Pradesh, India
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19
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Hasan MM, Ahmed M, Urmy SA. Efficacy of limited antiviral treatment, testing, hospitalization, and social distancing for COVID-19 pandemic. SENSORS INTERNATIONAL 2021; 2:100112. [PMID: 34766060 PMCID: PMC8234322 DOI: 10.1016/j.sintl.2021.100112] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 06/07/2021] [Accepted: 06/08/2021] [Indexed: 12/03/2022] Open
Abstract
The control measures of a pandemic must be cautiously evaluated, especially when resources are “limited”. A model of COVID-19 transmission dynamics is applied to assess the impact of antiviral treatment, testing, hospitalization, and social distancing. Under the assumption of “unlimited” resources, five control strategies involving social distancing, testing, hospitalization, and antiviral treatment are tested. Then these “optimal” policies are sought in the case of limited resources on behalf of a COVID-19 pandemic scenario. The amplitude of peak epidemics will often be minimized by executing strategies from the beginning of a pandemic, spreading the epidemics’ greatest impact over a longer time frame. Therefore, the timing and potency of control measures can reduce the pressure on the system during the top of the epidemic through the pandemic, decreasing the pressure on the healthcare infrastructure. In case of limited access to antiviral supplies, the role of testing, hospitalization, and social distancing strategies is emphasized in this study.
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Affiliation(s)
- Md Mehadi Hasan
- Department of Mathematics, Jagannath University, Dhaka, 1100, Bangladesh
| | - Mostak Ahmed
- Department of Mathematics, Jagannath University, Dhaka, 1100, Bangladesh
| | - Suraiya Akter Urmy
- Department of Mathematics, Jahangirnagar University, Dhaka, 1342, Bangladesh
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20
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A Patent Review on the Therapeutic Application of Monoclonal Antibodies in COVID-19. Int J Mol Sci 2021; 22:ijms222111953. [PMID: 34769383 PMCID: PMC8584575 DOI: 10.3390/ijms222111953] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 10/24/2021] [Accepted: 11/02/2021] [Indexed: 12/17/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) contains spike proteins that assist the virus in entering host cells. In the absence of a specific intervention, efforts are afoot throughout the world to find an effective treatment for SARS-CoV-2. Through innovative techniques, monoclonal antibodies (MAbs) are being designed and developed to block a particular pathway of SARS-CoV-2 infection. More than 100 patent applications describing the development of MAbs and their application against SARS-CoV-2 have been registered. Most of them target the receptor binding protein so that the interaction between virus and host cell can be prevented. A few monoclonal antibodies are also being patented for the diagnosis of SARS-CoV-2. Some of them, like Regeneron® have already received emergency use authorization. These protein molecules are currently preferred for high-risk patients such as those over 65 years old with compromised immunity and those with metabolic disorders such as obesity. Being highly specific in action, monoclonal antibodies offer one of the most appropriate interventions for both the prevention and treatment of SARS-CoV-2. Technological advancement has helped in producing highly efficacious MAbs. However, these agents are known to induce immunogenic and non-immunogenic reactions. More research and testing are required to establish the suitability of administering MAbs to all patients at risk of developing a severe illness. This patent study is focused on MAbs as a therapeutic option for treating COVID-19, as well as their invention, patenting information, and key characteristics.
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21
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Tolksdorf B, Nie C, Niemeyer D, Röhrs V, Berg J, Lauster D, Adler JM, Haag R, Trimpert J, Kaufer B, Drosten C, Kurreck J. Inhibition of SARS-CoV-2 Replication by a Small Interfering RNA Targeting the Leader Sequence. Viruses 2021; 13:v13102030. [PMID: 34696460 PMCID: PMC8539227 DOI: 10.3390/v13102030] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/04/2021] [Accepted: 10/06/2021] [Indexed: 12/16/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has infected almost 200 million people worldwide and led to approximately 4 million deaths as of August 2021. Despite successful vaccine development, treatment options are limited. A promising strategy to specifically target viral infections is to suppress viral replication through RNA interference (RNAi). Hence, we designed eight small interfering RNAs (siRNAs) targeting the highly conserved 5′-untranslated region (5′-UTR) of SARS-CoV-2. The most promising candidate identified in initial reporter assays, termed siCoV6, targets the leader sequence of the virus, which is present in the genomic as well as in all subgenomic RNAs. In assays with infectious SARS-CoV-2, it reduced replication by two orders of magnitude and prevented the development of a cytopathic effect. Moreover, it retained its activity against the SARS-CoV-2 alpha variant and has perfect homology against all sequences of the delta variant that were analyzed by bioinformatic means. Interestingly, the siRNA was even highly active in virus replication assays with the SARS-CoV-1 family member. This work thus identified a very potent siRNA with a broad activity against various SARS-CoV viruses that represents a promising candidate for the development of new treatment options.
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Affiliation(s)
- Beatrice Tolksdorf
- Applied Biochemistry, Institute of Biotechnology, Technische Universität Berlin, 10623 Berlin, Germany; (B.T.); (V.R.); (J.B.)
| | - Chuanxiong Nie
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany; (C.N.); (D.L.); (R.H.)
| | - Daniela Niemeyer
- German Centre for Infection Research (DZIF), Charitéplatz 1, 10117 Berlin, Germany; (D.N.); (C.D.)
- Institute of Virology, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Viola Röhrs
- Applied Biochemistry, Institute of Biotechnology, Technische Universität Berlin, 10623 Berlin, Germany; (B.T.); (V.R.); (J.B.)
| | - Johanna Berg
- Applied Biochemistry, Institute of Biotechnology, Technische Universität Berlin, 10623 Berlin, Germany; (B.T.); (V.R.); (J.B.)
| | - Daniel Lauster
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany; (C.N.); (D.L.); (R.H.)
| | - Julia M. Adler
- Department of Veterinary Medicine, Institute of Virology, Freie Universität Berlin, 14163 Berlin, Germany; (J.M.A.); (J.T.); (B.K.)
- Department of Infectious Diseases and Respiratory Medicine, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Rainer Haag
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany; (C.N.); (D.L.); (R.H.)
| | - Jakob Trimpert
- Department of Veterinary Medicine, Institute of Virology, Freie Universität Berlin, 14163 Berlin, Germany; (J.M.A.); (J.T.); (B.K.)
| | - Benedikt Kaufer
- Department of Veterinary Medicine, Institute of Virology, Freie Universität Berlin, 14163 Berlin, Germany; (J.M.A.); (J.T.); (B.K.)
| | - Christian Drosten
- German Centre for Infection Research (DZIF), Charitéplatz 1, 10117 Berlin, Germany; (D.N.); (C.D.)
- Institute of Virology, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Jens Kurreck
- Applied Biochemistry, Institute of Biotechnology, Technische Universität Berlin, 10623 Berlin, Germany; (B.T.); (V.R.); (J.B.)
- Correspondence: ; Tel.:+ 49-30-314-27581
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22
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In silico identification of SARS-CoV-2 cell entry inhibitors from selected natural antivirals. J Mol Graph Model 2021; 109:108038. [PMID: 34607208 PMCID: PMC8479391 DOI: 10.1016/j.jmgm.2021.108038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 09/15/2021] [Accepted: 09/22/2021] [Indexed: 01/18/2023]
Abstract
The aim of this study is to identify potential drug-like molecules against SARS-CoV-2 virus among the natural antiviral compounds published in the Encyclopedia of Traditional Chinese Medicine. To test inhibition capability of these compounds first, we docked them with Spike protein, angiotensin-converting enzyme 2 (ACE2) (PDB ID: 6M0J) and neuropilin 1 (NRP1) (PDB ID: 7JJC) receptors, and found significant docking scores with extra precision up to -11 kcal/mol. Then, their stability in the binding pockets were further evaluated with molecular dynamics simulation. Eight natural antiviral compounds were identified as potential inhibitors against SARS-CoV-2 cell entry after 200 ns molecular dynamics simulations. We found CMP-3, CMP-4, CMP-5, CMP-6 and CMP-8 are strong binders for the spike protein, CMP-1, CMP-2, CMP-4, CMP-5 and CMP-7 are strong binders for the neuropilin receptor, and CMP-5 is a strong binder for the ACE2. Quercetin derivatives (CMP-4, CMP-5, CMP-6 and CMP-7) were found highly stable in the active domain of NRP1, ACE2 and Spike protein. Especially, CMP-5 showed an inhibitory activity for all targets. These natural antivirals may be potential drug candidates for the prevention of SARS-CoV-2 infection.
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23
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Alghamdi S. Clinical characteristics and treatment outcomes of severe (ICU) COVID-19 patients in Saudi Arabia: A single centre study. Saudi Pharm J 2021; 29:1096-1101. [PMID: 34366685 PMCID: PMC8332927 DOI: 10.1016/j.jsps.2021.08.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 08/01/2021] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND There is limited information describing the presenting features and treatment outcomes of intensive care unit (ICU) patients with coronavirus disease 2019 (COVID-19) in Saudi Arabia. OBJECTIVE To investigates the clinical, epidemiological, laboratory, radiological, vital signs and treatment characteristics/outcomes of severe (ICU) COVID-19 patients in Albaha region, Saudi Arabia. METHODS A retrospective cohort study was conducted from 01 April 2020 to 31 August 2020 involving files review of 171 patients admitted to the ICU of a COVID-19 treatment centre as a result of severe symptoms. RESULTS Around a third of the ICU patients admitted were over 66 years of age, 59.6% males, 45% diabetics, 39% hypertensive, 25.7% smokers. Patients had symptoms such as 79% fever, 78% cough, 75% headache, 59% sore throat, 57% runny nose, and 75% cough. More than half of the patients had <90% oxygen saturation. Bilateral infiltration was present in about 43% of patients. 85.4% lymphopenia, and 70.8% D-dimer (>0.5 u/ml) were the most significant laboratory results. The median stay in the hospital ranged from 4 to 15.6 days, and the ICU time ranged from 4 to 12.7 days. Approximately 29% of patients received antiviral, antimalarial, and antibiotic treatment, while 27.5% of patients received antibiotics and antimalarial therapy alone. Incorporating hydroxychloroquine in treatment protocols did not improve patients' outcomes. CONCLUSIONS Older age and cardio-metabolic comorbidities increase the risks of sever COVID-19. Different treatment protocols fail to improve mortality rates and urgent efforts are required to prevent the disease and reduce its severity.
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Affiliation(s)
- Saleh Alghamdi
- Department of Clinical Pharmacy, Faculty of Clinical Pharmacy, Albaha University, Albaha, Saudi Arabia
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24
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Kumar S, Çalışkan DM, Janowski J, Faist A, Conrad BCG, Lange J, Ludwig S, Brunotte L. Beyond Vaccines: Clinical Status of Prospective COVID-19 Therapeutics. Front Immunol 2021; 12:752227. [PMID: 34659259 PMCID: PMC8519339 DOI: 10.3389/fimmu.2021.752227] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 09/14/2021] [Indexed: 12/15/2022] Open
Abstract
Since November 2019 the SARS-CoV-2 pandemic has caused nearly 200 million infection and more than 4 million deaths globally (Updated information from the World Health Organization, as on 2nd Aug 2021). Within only one year into the pandemic, several vaccines were designed and reached approval for the immunization of the world population. The remarkable protective effects of the manufactured vaccines are demonstrated in countries with high vaccination rates, such as Israel and UK. However, limited production capacities, poor distribution infrastructures and political hesitations still hamper the availability of vaccines in many countries. In addition, due to the emergency of SARS-CoV-2 variants with immune escape properties towards the vaccines the global numbers of new infections as well as patients developing severe COVID-19, remains high. New studies reported that about 8% of infected individuals develop long term symptoms with strong personal restrictions on private as well as professional level, which contributes to the long socioeconomic problems caused by this pandemic. Until today, emergency use-approved treatment options for COVID-19 are limited to the antiviral Remdesivir, a nucleoside analogue targeting the viral polymerase, the glucocorticosteroide Dexamethasone as well as neutralizing antibodies. The therapeutic benefits of these treatments are under ongoing debate and clinical studies assessing the efficiency of these treatments are still underway. To identify new therapeutic treatments for COVID-19, now and by the post-pandemic era, diverse experimental approaches are under scientific evaluation in companies and scientific research teams all over the world. To accelerate clinical translation of promising candidates, repurposing approaches of known approved drugs are specifically fostered but also novel technologies are being developed and are under investigation. This review summarizes the recent developments from the lab bench as well as the clinical status of emerging therapeutic candidates and discusses possible therapeutic entry points for the treatment strategies with regard to the biology of SARS-CoV-2 and the clinical course of COVID-19.
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Affiliation(s)
- Sriram Kumar
- Institute of Virology, University of Münster, Münster, Germany
- EvoPAD Research Training Group 2220, University of Münster, Münster, Germany
| | - Duygu Merve Çalışkan
- Institute of Virology, University of Münster, Münster, Germany
- EvoPAD Research Training Group 2220, University of Münster, Münster, Germany
| | - Josua Janowski
- Institute of Virology, University of Münster, Münster, Germany
- SP BioSciences Graduate Program, University of Münster, Münster, Germany
| | - Aileen Faist
- Institute of Virology, University of Münster, Münster, Germany
- CiM-IMPRS Graduate Program, University of Münster, Münster, Germany
| | | | - Julius Lange
- Institute of Virology, University of Münster, Münster, Germany
| | - Stephan Ludwig
- Institute of Virology, University of Münster, Münster, Germany
- EvoPAD Research Training Group 2220, University of Münster, Münster, Germany
- CiM-IMPRS Graduate Program, University of Münster, Münster, Germany
- Interdisciplinary Centre for Medical Research, University of Münster, Münster, Germany
| | - Linda Brunotte
- Institute of Virology, University of Münster, Münster, Germany
- Interdisciplinary Centre for Medical Research, University of Münster, Münster, Germany
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25
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Pal LR, Cheng K, Nair NU, Martin-Sancho L, Sinha S, Pu Y, Riva L, Yin X, Schischlik F, Lee JS, Chanda SK, Ruppin E. Synthetic lethality-based prediction of anti-SARS-CoV-2 targets. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.09.14.460408. [PMID: 34545363 PMCID: PMC8452092 DOI: 10.1101/2021.09.14.460408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Novel strategies are needed to identify drug targets and treatments for the COVID-19 pandemic. The altered gene expression of virus-infected host cells provides an opportunity to specifically inhibit viral propagation via targeting the synthetic lethal (SL) partners of such altered host genes. Pursuing this antiviral strategy, here we comprehensively analyzed multiple in vitro and in vivo bulk and single-cell RNA-sequencing datasets of SARS-CoV-2 infection to predict clinically relevant candidate antiviral targets that are SL with altered host genes. The predicted SL-based targets are highly enriched for infected cell inhibiting genes reported in four SARS-CoV-2 CRISPR-Cas9 genome-wide genetic screens. Integrating our predictions with the results of these screens, we further selected a focused subset of 26 genes that we experimentally tested in a targeted siRNA screen using human Caco-2 cells. Notably, as predicted, knocking down these targets reduced viral replication and cell viability only under the infected condition without harming non-infected cells. Our results are made publicly available, to facilitate their in vivo testing and further validation.
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Affiliation(s)
- Lipika R. Pal
- Cancer Data Science Laboratory (CDSL), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Kuoyuan Cheng
- Cancer Data Science Laboratory (CDSL), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA
| | - Nishanth Ulhas Nair
- Cancer Data Science Laboratory (CDSL), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Laura Martin-Sancho
- Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Sanju Sinha
- Cancer Data Science Laboratory (CDSL), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA
| | - Yuan Pu
- Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Laura Riva
- Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Xin Yin
- Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Fiorella Schischlik
- Cancer Data Science Laboratory (CDSL), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Joo Sang Lee
- Cancer Data Science Laboratory (CDSL), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA
- Samsung Medical Center, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
| | - Sumit K. Chanda
- Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Eytan Ruppin
- Cancer Data Science Laboratory (CDSL), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA
- Department of Computer Science, University of Maryland, College Park, MD, USA
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26
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Kaur H, Sarma P, Bhattacharyya A, Sharma S, Chhimpa N, Prajapat M, Prakash A, Kumar S, Singh A, Singh R, Avti P, Thota P, Medhi B. Efficacy and safety of dihydroorotate dehydrogenase (DHODH) inhibitors "leflunomide" and "teriflunomide" in Covid-19: A narrative review. Eur J Pharmacol 2021; 906:174233. [PMID: 34111397 PMCID: PMC8180448 DOI: 10.1016/j.ejphar.2021.174233] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 05/30/2021] [Accepted: 06/02/2021] [Indexed: 01/12/2023]
Abstract
Dihydroorotate dehydrogenase (DHODH) is rate-limiting enzyme in biosynthesis of pyrimidone which catalyzes the oxidation of dihydro-orotate to orotate. Orotate is utilized in the biosynthesis of uridine-monophosphate. DHODH inhibitors have shown promise as antiviral agent against Cytomegalovirus, Ebola, Influenza, Epstein Barr and Picornavirus. Anti-SARS-CoV-2 action of DHODH inhibitors are also coming up. In this review, we have reviewed the safety and efficacy of approved DHODH inhibitors (leflunomide and teriflunomide) against COVID-19. In target-centered in silico studies, leflunomide showed favorable binding to active site of MPro and spike: ACE2 interface. In artificial-intelligence/machine-learning based studies, leflunomide was among the top 50 ligands targeting spike: ACE2 interaction. Leflunomide is also found to interact with differentially regulated pathways [identified by KEGG (Kyoto Encyclopedia of Genes and Genomes) and reactome pathway analysis of host transcriptome data] in cogena based drug-repurposing studies. Based on GSEA (gene set enrichment analysis), leflunomide was found to target pathways enriched in COVID-19. In vitro, both leflunomide (EC50 41.49 ± 8.8 μmol/L) and teriflunomide (EC50 26 μmol/L) showed SARS-CoV-2 inhibition. In clinical studies, leflunomide showed significant benefit in terms of decreasing the duration of viral shredding, duration of hospital stay and severity of infection. However, no advantage was seen while combining leflunomide and IFN alpha-2a among patients with prolonged post symptomatic viral shredding. Common adverse effects of leflunomide were hyperlipidemia, leucopenia, neutropenia and liver-function alteration. Leflunomide/teriflunomide may serve as an agent of importance to achieve faster virological clearance in COVID-19, however, findings needs to be validated in bigger sized placebo controlled studies.
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Affiliation(s)
- Hardeep Kaur
- Department of Pharmacology, PGIMER, Chandigarh, India
| | - Phulen Sarma
- Department of Pharmacology, PGIMER, Chandigarh, India
| | | | | | | | | | - Ajay Prakash
- Department of Pharmacology, PGIMER, Chandigarh, India
| | - Subodh Kumar
- Department of Pharmacology, PGIMER, Chandigarh, India
| | | | - Rahul Singh
- Department of Pharmacology, PGIMER, Chandigarh, India
| | - Pramod Avti
- Department of Biophysics, PGIMER, Chandigarh, India
| | - Prasad Thota
- Department of Pharmacology, PGIMER, Chandigarh, India
| | - Bikash Medhi
- Department of Pharmacology, PGIMER, Chandigarh, India.
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Khaitov M, Nikonova A, Shilovskiy I, Kozhikhova K, Kofiadi I, Vishnyakova L, Nikolskii A, Gattinger P, Kovchina V, Barvinskaia E, Yumashev K, Smirnov V, Maerle A, Kozlov I, Shatilov A, Timofeeva A, Andreev S, Koloskova O, Kuznetsova N, Vasina D, Nikiforova M, Rybalkin S, Sergeev I, Trofimov D, Martynov A, Berzin I, Gushchin V, Kovalchuk A, Borisevich S, Valenta R, Khaitov R, Skvortsova V. Silencing of SARS-CoV-2 with modified siRNA-peptide dendrimer formulation. Allergy 2021; 76:2840-2854. [PMID: 33837568 PMCID: PMC8251148 DOI: 10.1111/all.14850] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 03/09/2021] [Accepted: 03/15/2021] [Indexed: 12/12/2022]
Abstract
Background First vaccines for prevention of Coronavirus disease 2019 (COVID‐19) are becoming available but there is a huge and unmet need for specific forms of treatment. In this study we aimed to evaluate the anti‐SARS‐CoV‐2 effect of siRNA both in vitro and in vivo. Methods To identify the most effective molecule out of a panel of 15 in silico designed siRNAs, an in vitro screening system based on vectors expressing SARS‐CoV‐2 genes fused with the firefly luciferase reporter gene and SARS‐CoV‐2‐infected cells was used. The most potent siRNA, siR‐7, was modified by Locked nucleic acids (LNAs) to obtain siR‐7‐EM with increased stability and was formulated with the peptide dendrimer KK‐46 for enhancing cellular uptake to allow topical application by inhalation of the final formulation – siR‐7‐EM/KK‐46. Using the Syrian Hamster model for SARS‐CoV‐2 infection the antiviral capacity of siR‐7‐EM/KK‐46 complex was evaluated. Results We identified the siRNA, siR‐7, targeting SARS‐CoV‐2 RNA‐dependent RNA polymerase (RdRp) as the most efficient siRNA inhibiting viral replication in vitro. Moreover, we showed that LNA‐modification and complexation with the designed peptide dendrimer enhanced the antiviral capacity of siR‐7 in vitro. We demonstrated significant reduction of virus titer and lung inflammation in animals exposed to inhalation of siR‐7‐EM/KK‐46 in vivo. Conclusions Thus, we developed a therapeutic strategy for COVID‐19 based on inhalation of a modified siRNA‐peptide dendrimer formulation. The developed medication is intended for inhalation treatment of COVID‐19 patients.
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Affiliation(s)
| | - Alexandra Nikonova
- NRC Institute of Immunology FMBA Moscow Russia
- Mechnikov Research Institute for Vaccines and Sera Moscow Russia
| | | | | | | | | | | | | | | | | | | | | | | | - Ivan Kozlov
- NRC Institute of Immunology FMBA Moscow Russia
| | | | | | | | | | - Nadezhda Kuznetsova
- Federal State Budget Institution “National Research Centre for Epidemiology and Microbiology named after Honorary Academician N. F.Gamaleya” of the Ministry of Health of the Russian Federation Moscow Russia
| | - Daria Vasina
- Federal State Budget Institution “National Research Centre for Epidemiology and Microbiology named after Honorary Academician N. F.Gamaleya” of the Ministry of Health of the Russian Federation Moscow Russia
| | - Maria Nikiforova
- Federal State Budget Institution “National Research Centre for Epidemiology and Microbiology named after Honorary Academician N. F.Gamaleya” of the Ministry of Health of the Russian Federation Moscow Russia
| | | | | | | | | | - Igor Berzin
- Federal Medico‐biological Agency of Russia (FMBA Russia) Moscow Russia
| | - Vladimir Gushchin
- Federal State Budget Institution “National Research Centre for Epidemiology and Microbiology named after Honorary Academician N. F.Gamaleya” of the Ministry of Health of the Russian Federation Moscow Russia
| | - Aleksey Kovalchuk
- 48 Central Research Institute of the Ministry of Defense of the Russian Federation Moscow Russia
| | - Sergei Borisevich
- 48 Central Research Institute of the Ministry of Defense of the Russian Federation Moscow Russia
| | - Rudolf Valenta
- NRC Institute of Immunology FMBA Moscow Russia
- Medical University of Vienna Vienna Austria
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28
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Repurposing the estrogen receptor modulator raloxifene to treat SARS-CoV-2 infection. Cell Death Differ 2021; 29:156-166. [PMID: 34404919 PMCID: PMC8370058 DOI: 10.1038/s41418-021-00844-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 07/09/2021] [Accepted: 07/25/2021] [Indexed: 12/15/2022] Open
Abstract
The ongoing coronavirus disease 2019 (COVID-19) pandemic caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) necessitates strategies to identify prophylactic and therapeutic drug candidates to enter rapid clinical development. This is particularly true, given the uncertainty about the endurance of the immune memory induced by both previous infections or vaccines, and given the fact that the eradication of SARS-CoV-2 might be challenging to reach, given the attack rate of the virus, which would require unusually high protection by a vaccine. Here, we show how raloxifene, a selective estrogen receptor modulator with anti-inflammatory and antiviral properties, emerges as an attractive candidate entering clinical trials to test its efficacy in early-stage treatment COVID-19 patients.
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29
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Saini M, Rana M, Bhatti K, Das R, Mehta DK, Chidurala RM. Clinical Efficacy of Remdesivir and Favipiravir in the Treatment of Covid-19 Patients: Scenario So Far. Curr Drug Res Rev 2021; 14:11-19. [PMID: 34365935 DOI: 10.2174/2589977513666210806122901] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 04/17/2021] [Accepted: 04/28/2021] [Indexed: 11/22/2022]
Abstract
The novel SARS-CoV-2 is a new disease that has caused severe destruction to human lives across the globe, including infection, mortality and financial crises, for which, scientific researchers have been directed towards the development of treatment and controlling measures against coronavirus. Currently, there has been no approved drug for the treatment of the disease, but several antiviral drugs have shown therapeutic effects from which, remdesivir and favipiravir are two such drugs. These drugs have shown some therapeutic potential in the treatment of COVID-19 by inhibiting viral enzyme RNA-dependent RNA polymerase. The purpose of this systematic review is to provide an overview of the effectiveness of these two drugs based on the clinical trials reported in current published data.
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Affiliation(s)
- Manisha Saini
- M.M. College of Pharmacy, Maharishi Markandeshwar (Deemed to be) University, Mullana, Ambala, HR. India
| | - Minakshi Rana
- M.M. College of Pharmacy, Maharishi Markandeshwar (Deemed to be) University, Mullana, Ambala, HR. India
| | - Karun Bhatti
- Department of Medicine, M.M. Institute of Medical Sciences and Research, Maharishi Markandeshwar (Deemed to be) University, Mullana, Ambala, HR. India
| | - Rina Das
- M.M. College of Pharmacy, Maharishi Markandeshwar (Deemed to be) University, Mullana, Ambala, HR. India
| | - Dinesh Kumar Mehta
- M.M. College of Pharmacy, Maharishi Markandeshwar (Deemed to be) University, Mullana, Ambala, HR. India
| | - Ram Mohan Chidurala
- Hospitalist, Department of Medicine, Medstar southern Maryland hospital,7503, Surratts Rd, Clinton, Maryland 20735. United States
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Mishra P, Nandi CK. Structural Decoding of a Small Molecular Inhibitor on the Binding of SARS-CoV-2 to the ACE 2 Receptor. J Phys Chem B 2021; 125:8395-8405. [PMID: 34297554 PMCID: PMC8340085 DOI: 10.1021/acs.jpcb.1c03294] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 07/08/2021] [Indexed: 01/21/2023]
Abstract
Inhibition of the interaction of the receptor-binding domain (RBD) of the spike protein and the human angiotensin-converting enzyme 2 (ACE 2) receptor is the most effective therapeutic formulation to restrict the contagious respiratory illness and multiple organ failure caused by the novel SARS-CoV-2 virus. Based on the structural decoding of the RBD of the spike protein, here we have generated a new set of small molecules that have strong inhibiting properties on the binding of the spike protein to ACE 2 receptors. These small-molecule inhibitors surprisingly show binding to the main protease, nucleoprotein, and RNA-dependent RNA polymerase, which are the other responsible factors for the viral infection. The newly designed molecules show better performance than several existing repurposed drugs. Conformational changes from closed to closed lock and open conformations of the SARS-CoV-2 binding to the ACE 2 receptor were observed in the presence of these small molecular inhibitors, suggesting their strong abilities to counteract the SARS-CoV-2 infection.
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Affiliation(s)
- Pushpendra
Mani Mishra
- School of Basic Sciences, Indian
Institute of Technology Mandi, Himachal Pradesh 175005, India
| | - Chayan Kanti Nandi
- School of Basic Sciences, Indian
Institute of Technology Mandi, Himachal Pradesh 175005, India
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31
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Lanes TC, Ribeiro MAL, Oliveira DSD, Junior MGDN, Garcia FR, Melo JMFDO, Tiguman GMB. Guías de práctica clínica para el tratamiento de la enfermedad por Covid-19 en Brasil: revisión sistemática. REVISTA CUIDARTE 2021. [DOI: 10.15649/cuidarte.2025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Introducción: La enfermedad por coronavirus (Covid-19) es una patología infecciosa que afecta al sistema respiratorio, la cual se originó en China y se extendió rápidamente por todo el mundo. Objetivo: Evaluar la calidad metodológica y la transparencia de las guías de práctica clínica brasileñas para el tratamiento de la enfermedad por coronavirus (Covid-19). Materiales y métodos: Se realizó una revisión sistemática en 2020 en las bases de datos Medline (vía PubMed), Embase, Scopus, LILACS, National Guideline Clearinghouse y Guidelines International Network, además de consultas en los sitios web del Ministerio de Salud de Brasil, Asociación Médicas Brasileña, Consejo Federal de Medicina, Consejo Federal de Enfermería y Consejo Federal de Fisioterapia. La evaluación de la calidad metodológica y la transparencia de las guías se realizó con el instrumento Appraisal of Guidelines for Research and Evaluation (AGREE), segunda versión realizada por cuatro autores. Resultados: Se encontraron 33 guías, de las que se incluyeron 14 en el análisis. Hubo una sola guía que obtuvo una puntuación superior al 60% en todos los dominios. Entre los seis dominios, se presentaron puntuaciones más altas en los siguientes tres dominios: alcance y objetivo, participación de las partes interesadas y claridad de la presentación. Discusión: A pesar de la fragilidad metodológica, los autores se interesaron por presentar las recomendaciones de forma clara y concisa a través de información clave y opciones terapéuticas que faciliten la toma de decisiones. Conclusión: Las guías de práctica clínica brasileñas mostraron tener una baja calidad metodológica, de las que solamente una guía fue recomendada y clasificada como de alta calidad y transparencia metodológica.
Como citar este artículo: Lanes, Taís Carpes; Ribeiro, Mariane Albuquerque Lima; Oliveira, Daianny Seoni de; Junior, Marcos Gabriel do Nascimento; Garcia, Filipe Reis; Melo, Jéssyca Maria França de Oliveira; Tiguman, Gustavo Magno Baldin. Diretrizes de prática clínica para o tratamento da Covid-19 no Brasil: uma revisão sistemática. Revista Cuidarte. 2021;12(2):e2025 http://dx.doi.org/10.15649/cuidarte.2025
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A Review on the Effectivity of the Current COVID-19 Drugs and Vaccines: Are They Really Working Against the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Variants? CURRENT CLINICAL MICROBIOLOGY REPORTS 2021; 8:186-193. [PMID: 34249605 PMCID: PMC8254629 DOI: 10.1007/s40588-021-00172-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/18/2021] [Indexed: 12/21/2022]
Abstract
Purpose of Review In order to eradicate the COVID-19 pandemic, scientists around the world have been working very hard for a year or more with the motto of designing effective drugs and vaccines against the severe acute respiratory coronavirus 2 (SARS-CoV-2). Along with the positive results with the antiviral drugs and a few commercialized vaccines, the unresponsiveness as well as some side effects of such therapies have also been noticed, possibly due to the emergence of the SARS-CoV-2 variants. Therefore, current review summarized the actual effectiveness of the antivirals and vaccines which are in current use for the treatment of the COVID-19 patients. Recent Findings So far, some drugs have been found with hopeful results among which remdesivir and arbidol are with momentous clinical progress. Besides drug designing, vaccine development has been a major effort whereby the mRNA-1273 (Moderna) and BNT162b2 (Pfizer-BioNTech) vaccines showed the required efficacy and have been approved by the US Food and Drug Administration (USFDA). Summary While a number of existing/repurposed/repositioned or new drugs and the currently used commercial vaccines against SARS-CoV-2 apparently seem to be effective against COVID-19 mitigation, the new variants of the virus as well as the recently increased cases raised the doubt about the usefulness of these agents. Current review figured out the efficacy of different drugs and vaccines in terms of their action potential against SARS-CoV-2 and further recommended some useful measures which may be useful for future remedies.
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Yedjou CG, Njiki S, Enow J, Ikome O, Latinwo L, Long R, Ngnepieba P, Alo RA, Tchounwou PB. Pharmacological Effects of Selected Medicinal Plants and Vitamins Against COVID-19. JOURNAL OF FOOD AND NUTRITION (FRISCO, TEX.) 2021; 7:202. [PMID: 34395868 PMCID: PMC8362927 DOI: 10.17303/jfn.2021.7.202] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The coronavirus disease 2019 (COVID-19) is caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). It is a serious disease that has caused multiple deaths in various countries in the world. Globally, as of May 23, 2021, the total confirmed cases of COVID-19 have reach 166,346,635 with a total of 3,449,117 deaths. Several recent scientific studies have shown that medicinal plants and vitamins can benefit and improve the health of COVID-19 patients. However, the benefits of medicinal plants and vitamins in the treatment of COVID-19 remain unproven. Therefore, the objective of this article is to expounds the benefits of using medicinal plants (Allium sativum, curcumin, Nigella sativa, Zingiber officitale) and vitamins (vitamin C and vitamin D) that possess the antiviral properties for the prevention and/or control of COVID-19. To reach our objective, we searched scientific databases of ongoing trials in the Centers for Disease Control and Prevention websites, PubMed Central, Medline databases, and Google Scholar websites. We also searched databases on World Health Organization International Clinical Trials Registry Platform to collect relevant papers. We found that all of the selected medicinal plants and vitamins possess antiviral activities, and their individual intake shows promise for the prevention and/or control of COVID-19. We conclude that, the selected medicinal plants and vitamins possess anti-viral properties that are more likely to prevent and/or disrupt the SARS-CoV-2 replication cycle, enhance the human immune system and promote good health.
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Affiliation(s)
- Clement G Yedjou
- Department of Biological Sciences, College of Science and Technology, Florida Agricultural and Mechanical University, 1610 S. Martin Luther King Blvd, Tallahassee, United States
| | - Sylvianne Njiki
- Department of Biology, College of Science, Engineering and Technology, Jackson State University, 1400 Lynch Street, Box 18750, Jackson, United States
| | - Juliet Enow
- Department of Behavioral and Environmental Health. School of Public Health, Jackson State University, 350 W. Woodrow Wilson Drive, Jackson, United States
| | - Otto Ikome
- Department of Biology, College of Science, Engineering and Technology, Jackson State University, 1400 Lynch Street, Box 18750, Jackson, United States
| | - Lekan Latinwo
- Department of Biological Sciences, College of Science and Technology, Florida Agricultural and Mechanical University, 1610 S. Martin Luther King Blvd, Tallahassee, United States
| | - Richard Long
- Department of Biological Sciences, College of Science and Technology, Florida Agricultural and Mechanical University, 1610 S. Martin Luther King Blvd, Tallahassee, United States
| | - Pierre Ngnepieba
- Department of Mathematics, College of Science and Technology, Florida Agricultural and Mechanical University, 1610 S. Martin Luther King Blvd, Tallahassee, United States
| | - Richard A Alo
- Department of Computer and Information Science, College of Science and Technology, Florida Agricultural & Mechanical University, 1610 S. Martin Luther King Blvd, Tallahassee, United States
| | - Paul B Tchounwou
- Department of Biology, College of Science, Engineering and Technology, Jackson State University, 1400 Lynch Street, Box 18750, Jackson, United States
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Md Nayeem S, Sohail EM, Srihari NV, Indira P, Srinivasa Reddy M. Target SARS-CoV-2: theoretical exploration on clinical suitability of certain drugs. J Biomol Struct Dyn 2021; 40:8905-8912. [PMID: 33988066 PMCID: PMC8127163 DOI: 10.1080/07391102.2021.1924262] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 04/11/2021] [Indexed: 12/14/2022]
Abstract
We propose a unique theoretical methodology because of the global high priority rating to search for the repurposed drugs that outfit clinical suitability to SARS-CoV-2. The approach is based on the exploration of structural analysis, computation of biothermodynamics, interactions and the prediction of entropy sign successively via molecular dynamics. We tested this methodology for Favipiravir/Dolutegravir drugs on the apo form of SARS-CoV-2 main protease. This theoretical exploration not only suggested the presence of strong interactions between (SARS-CoV-2 + Favipiravir/Dolutegravir) but also emphasized the clinical suitability of Favipiravir over Dolutegravir to treat SARS-CoV-2 main protease. The supremacy of Favipiravir over Doultegravir is well supported by the results of global clinical trials on SARS-CoV-2 infection. Thus, this work will pave the way for incremental advancement towards future design and development of more specific inhibitors to treat SARS-CoV-2 infection in humans.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sk. Md Nayeem
- Department of Physics, K.R.K. Govt. Degree College, Addanki, AP, India
| | | | - N. V. Srihari
- Department of Physics, K.R.K. Govt. Degree College, Addanki, AP, India
| | - P. Indira
- Department of Physics, K.R.K. Govt. Degree College, Addanki, AP, India
| | - M. Srinivasa Reddy
- Department of Chemistry, T.R.R. Govt. Degree College, Kandukur, AP, India
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35
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Ağagündüz D, Çelik MN, Çıtar Dazıroğlu ME, Capasso R. Emergent Drug and Nutrition Interactions in COVID-19: A Comprehensive Narrative Review. Nutrients 2021; 13:nu13051550. [PMID: 34064534 PMCID: PMC8147951 DOI: 10.3390/nu13051550] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/26/2021] [Accepted: 04/28/2021] [Indexed: 01/08/2023] Open
Abstract
Coronaviruses are a large family of viruses that are known to cause respiratory tract infections ranging from colds to more severe diseases, such as Middle East Respiratory Syndrome (MERS) and the Severe Acute Respiratory Syndrome (SARS). New Coronavirus Disease 2019 (COVID-19), which led to deaths as well as social and economic disruptions, is an ongoing worldwide pandemic caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Currently, there is no approved treatment for COVID-19. Hence, only supportive care has been approved by the World Health Organization (WHO) for now. Pharmacological agents used for the adjunctive treatment of COVID-19 following the current literature and clinical experiences include antiviral, anti-inflammatory, and anti-malaria drugs, and other traditional or untraditional treatments. However, it has been reported that the use of these drugs may have some negative effects and comorbidities. Moreover, the current data have indicated that the risk of drug-drug interactions may also be high in polypharmacy cases, especially in elderly people, some comorbidity situations, and intensive care unit (ICU) patients. It is highly possible that these situations can not only increase the risk of drug-drug interactions but also increase the risk of food/nutrition-drug interactions and affect the nutritional status. However, this issue has not yet been entirely discussed in the literature. In this review, current information on the possible mechanisms as well as pharmacokinetic and pharmacodynamic effects of some pharmacological agents used in the treatment of COVID-19 and/or their secondary interactions with nutrition were evaluated and some future directions were given.
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Affiliation(s)
- Duygu Ağagündüz
- Department of Nutrition and Dietetics, Faculty of Health Sciences, Gazi University, Emek, Ankara 06490, Turkey; (M.N.Ç.); (M.E.Ç.D.)
- Correspondence: (D.A.); (R.C.)
| | - Menşure Nur Çelik
- Department of Nutrition and Dietetics, Faculty of Health Sciences, Gazi University, Emek, Ankara 06490, Turkey; (M.N.Ç.); (M.E.Ç.D.)
| | - Merve Esra Çıtar Dazıroğlu
- Department of Nutrition and Dietetics, Faculty of Health Sciences, Gazi University, Emek, Ankara 06490, Turkey; (M.N.Ç.); (M.E.Ç.D.)
| | - Raffaele Capasso
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Naples, Italy
- Correspondence: (D.A.); (R.C.)
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Singh N, Villoutreix BO. Resources and computational strategies to advance small molecule SARS-CoV-2 discovery: Lessons from the pandemic and preparing for future health crises. Comput Struct Biotechnol J 2021; 19:2537-2548. [PMID: 33936562 PMCID: PMC8074526 DOI: 10.1016/j.csbj.2021.04.059] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 04/22/2021] [Accepted: 04/24/2021] [Indexed: 12/11/2022] Open
Abstract
There is an urgent need to identify new therapies that prevent SARS-CoV-2 infection and improve the outcome of COVID-19 patients. This pandemic has thus spurred intensive research in most scientific areas and in a short period of time, several vaccines have been developed. But, while the race to find vaccines for COVID-19 has dominated the headlines, other types of therapeutic agents are being developed. In this mini-review, we report several databases and online tools that could assist the discovery of anti-SARS-CoV-2 small chemical compounds and peptides. We then give examples of studies that combined in silico and in vitro screening, either for drug repositioning purposes or to search for novel bioactive compounds. Finally, we question the overall lack of discussion and plan observed in academic research in many countries during this crisis and suggest that there is room for improvement.
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Affiliation(s)
- Natesh Singh
- Université de Paris, Inserm UMR 1141 NeuroDiderot, Robert-Debré Hospital, 75019 Paris, France
| | - Bruno O. Villoutreix
- Université de Paris, Inserm UMR 1141 NeuroDiderot, Robert-Debré Hospital, 75019 Paris, France
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Kausar S, Said Khan F, Ishaq Mujeeb Ur Rehman M, Akram M, Riaz M, Rasool G, Hamid Khan A, Saleem I, Shamim S, Malik A. A review: Mechanism of action of antiviral drugs. Int J Immunopathol Pharmacol 2021; 35:20587384211002621. [PMID: 33726557 PMCID: PMC7975490 DOI: 10.1177/20587384211002621] [Citation(s) in RCA: 113] [Impact Index Per Article: 37.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Antiviral drugs are a class of medicines particularly used for the treatment of
viral infections. Drugs that combat viral infections are called antiviral drugs.
Viruses are among the major pathogenic agents that cause number of serious
diseases in humans, animals and plants. Viruses cause many diseases in humans,
from self resolving diseases to acute fatal diseases. Developing strategies for
the antiviral drugs are focused on two different approaches: Targeting the
viruses themselves or the host cell factors. Antiviral drugs that directly
target the viruses include the inhibitors of virus attachment, inhibitors of
virus entry, uncoating inhibitors, polymerase inhibitors, protease inhibitors,
inhibitors of nucleoside and nucleotide reverse transcriptase and the inhibitors
of integrase. The inhibitors of protease (ritonavir, atazanavir and darunavir),
viral DNA polymerase (acyclovir, tenofovir, valganciclovir and valacyclovir) and
of integrase (raltegravir) are listed among the Top 200 Drugs by sales during
2010s. Still no effective antiviral drugs are available for many viral
infections. Though, there are a couple of drugs for herpesviruses, many for
influenza and some new antiviral drugs for treating hepatitis C infection and
HIV. Action mechanism of antiviral drugs consists of its transformation to
triphosphate following the viral DNA synthesis inhibition. An analysis of the
action mechanism of known antiviral drugs concluded that they can increase the
cell’s resistance to a virus (interferons), suppress the virus adsorption in the
cell or its diffusion into the cell and its deproteinisation process in the cell
(amantadine) along with antimetabolites that causes the inhibition of nucleic
acids synthesis. This review will address currently used antiviral drugs,
mechanism of action and antiviral agents reported against COVID-19.
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Affiliation(s)
- Shamaila Kausar
- Institute of Molecular Biology and
Biotechnology, The University of Lahore, Lahore, Pakistan
| | - Fahad Said Khan
- Department of Eastern Medicine,
Government College University Faisalabad, Faisalabad, Pakistan
- Fahad Said khan, Department of Eastern
Medicine, Government College University Faisalabad, Faisalabad, Pakistan.
| | | | - Muhammad Akram
- Department of Eastern Medicine,
Government College University Faisalabad, Faisalabad, Pakistan
| | - Muhammad Riaz
- Department of Allied Health Sciences,
Sargodha Medical College, University of Sargodha, Sargodha, Pakistan
| | - Ghulam Rasool
- Department of Allied Health Sciences,
Sargodha Medical College, University of Sargodha, Sargodha, Pakistan
| | - Abdul Hamid Khan
- Department of Eastern Medicine,
University of Poonch, Rawalakot, Azad Jammu and Kashmir, Pakistan
| | - Iqra Saleem
- Department of Pharmacy, Faculty of
Medical and Health Sciences, University of Poonch, Rawalakot, Azad Jammu and
Kashmir, Pakistan
| | - Saba Shamim
- Institute of Molecular Biology and
Biotechnology, The University of Lahore, Lahore, Pakistan
| | - Arif Malik
- Institute of Molecular Biology and
Biotechnology, The University of Lahore, Lahore, Pakistan
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Gogoi M, Borkotoky M, Borchetia S, Chowdhury P, Mahanta S, Barooah AK. Black tea bioactives as inhibitors of multiple targets of SARS-CoV-2 (3CLpro, PLpro and RdRp): a virtual screening and molecular dynamic simulation study. J Biomol Struct Dyn 2021; 40:7143-7166. [PMID: 33715595 DOI: 10.1080/07391102.2021.1897679] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The global pandemic due to the novel Severe Acute Respiratory Syndrome Corona Virus 2 (SARS-CoV-2) has taken more than a million lives. Lack of definitive vaccine/drugs against this highly contagious virus has accelerated exploratory research on novel natural and synthetic inhibitors. Tea is a rich source of bioactives and known to have antiviral properties. In this study, an in silico strategy involving ADMET property screening, receptor-ligand docking and molecular dynamic (MD) simulation was employed to screen potential tea bio-active inhibitors against three selected targets (RdRp, 3CLpro and PLpro) of SARS-CoV-2. Among the 70 tea bioactives screened, theaflavin 3,3'-di-gallate (TF3), Procyanidin B2 and Theaflavin 3-gallate (TF2a) exhibited highest binding affinities towards RdRp, 3CLpro/Mpro and PLpro targets of SARS-CoV-2 with low docking scores of -14.92, -11.68 and -10.90 kcal/mol, respectively. All of them showed a substantial number of hydrogen bonds along with other interactions in and around the active sites. Interestingly, the top bioactives in our study showed higher binding affinities compared with known antiviral drugs. Further, the top protein-ligand complexes showed less conformational changes during binding when subjected to MD simulation for 100 nanoseconds. The MMPBSA results revealed that RdRp-TF3, 3CLpro-Procyanidin B2 and PLpro-TF2a complexes were stable with binding free energies of -93.59 ± 43.97, -139.78 ± 16.51 and -96.88 ± 25.39 kJ/mol, respectively. Our results suggest that theaflavin 3,3'-digallate, Theaflavin 3-gallate and Procyanidin B2 found in black tea have the potential to act as inhibitors for selected targets of SARS-CoV-2 and can be considered as drug candidates in future studies against COVID-19.
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Affiliation(s)
- Madhurjya Gogoi
- Department of Biotechnology, Tea Research Association, Tocklai Tea Research Institute, Jorhat, Assam, India
| | - Meghali Borkotoky
- Department of Biotechnology, Tea Research Association, Tocklai Tea Research Institute, Jorhat, Assam, India
| | - Sangeeta Borchetia
- Department of Biotechnology, Tea Research Association, Tocklai Tea Research Institute, Jorhat, Assam, India
| | - Pritom Chowdhury
- Department of Biotechnology, Tea Research Association, Tocklai Tea Research Institute, Jorhat, Assam, India
| | - Saurov Mahanta
- National Institute of Electronics and Information Technology, Guwahati, Assam, India
| | - Anoop Kumar Barooah
- Tea Research Association, Tocklai Tea Research Institute, Jorhat, Assam, India
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Sorouri F, Emamgholipour Z, Keykhaee M, Najafi A, Firoozpour L, Sabzevari O, Sharifzadeh M, Foroumadi A, Khoobi M. The situation of small molecules targeting key proteins to combat SARS-CoV-2: Synthesis, metabolic pathway, mechanism of action, and potential therapeutic applications. Mini Rev Med Chem 2021; 22:273-311. [PMID: 33687881 DOI: 10.2174/1389557521666210308144302] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 12/14/2020] [Accepted: 12/28/2020] [Indexed: 12/15/2022]
Abstract
Due to the global epidemic and high mortality of 2019 coronavirus disease (COVID-19), there is an immediate need to discover drugs that can help before a vaccine becomes available. Given that the process of producing new drugs is so long, the strategy of repurposing existing drugs is one of the promising options for the urgent treatment of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes COVID-19 disease. Although FDA has approved Remdesivir for the use in hospitalized adults and pediatric patients suffering from COVID-19, no fully effective and reliable drug has been yet identified worldwide to treat COVID-19 specifically. Thus, scientists are still trying to find antivirals specific to COVID-19. This work reviews the chemical structure, metabolic pathway, mechanism of action of existing drugs with potential therapeutic applications for COVID-19. Further, we summarized the molecular docking stimulation of the medications related to key protein targets. These already drugs could be developed for further clinical trials to supply suitable therapeutic options for patients suffering from COVID-19.
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Affiliation(s)
- Farzaneh Sorouri
- Department of Pharmaceutical Biomaterials, Faculty of Pharmacy, Tehran University of Medical Science, Tehran. Iran
| | - Zahra Emamgholipour
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Science, Tehran. Iran
| | - Maryam Keykhaee
- Department of Pharmaceutical Biomaterials, Faculty of Pharmacy, Tehran University of Medical Science, Tehran. Iran
| | - Alireza Najafi
- Department of Immunology, Faculty of Medicine, Iran University of Medical Sciences, Tehran. Iran
| | - Loghman Firoozpour
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Science, Tehran. Iran
| | - Omid Sabzevari
- Department of Toxicology and Pharmacology, Faculty of Pharmacy, Toxicology and Poisoning Research Centre, Tehran University of Medical Sciences, Tehran. Iran
| | - Mohammad Sharifzadeh
- Department of Toxicology and Pharmacology, Faculty of Pharmacy, Toxicology and Poisoning Research Centre, Tehran University of Medical Sciences, Tehran. Iran
| | - Alireza Foroumadi
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Science, Tehran. Iran
| | - Mehdi Khoobi
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Science, Tehran. Iran
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40
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Ferreras C, Pascual-Miguel B, Mestre-Durán C, Navarro-Zapata A, Clares-Villa L, Martín-Cortázar C, De Paz R, Marcos A, Vicario JL, Balas A, García-Sánchez F, Eguizabal C, Solano C, Mora-Rillo M, Soria B, Pérez-Martínez A. SARS-CoV-2-Specific Memory T Lymphocytes From COVID-19 Convalescent Donors: Identification, Biobanking, and Large-Scale Production for Adoptive Cell Therapy. Front Cell Dev Biol 2021; 9:620730. [PMID: 33718360 PMCID: PMC7947351 DOI: 10.3389/fcell.2021.620730] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 02/01/2021] [Indexed: 12/15/2022] Open
Abstract
Syndrome coronavirus 2 (SARS-CoV-2) pandemic is causing a second outbreak significantly delaying the hope for the virus’ complete eradication. In the absence of effective vaccines, we need effective treatments with low adverse effects that can treat hospitalized patients with COVID-19 disease. In this study, we determined the existence of SARS-CoV-2-specific T cells within CD45RA– memory T cells in the blood of convalescent donors. Memory T cells can respond quickly to infection and provide long-term immune protection to reduce the severity of COVID-19 symptoms. Also, CD45RA– memory T cells confer protection from other pathogens encountered by the donors throughout their life. It is of vital importance to resolve other secondary infections that usually develop in patients hospitalized with COVID-19. We found SARS-CoV-2-specific memory T cells in all of the CD45RA– subsets (CD3+, CD4+, and CD8+) and in the central memory and effector memory subpopulations. The procedure for obtaining these cells is feasible, easy to implement for small-scale manufacture, quick and cost-effective, involves minimal manipulation, and has no GMP requirements. This biobank of specific SARS-CoV-2 memory T cells would be immediately available “off-the-shelf” to treat moderate/severe cases of COVID-19, thereby increasing the therapeutic options available for these patients.
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Affiliation(s)
- C Ferreras
- Hospital La Paz Institute for Health Research, IdiPAZ, University Hospital La Paz, Madrid, Spain
| | - B Pascual-Miguel
- Hospital La Paz Institute for Health Research, IdiPAZ, University Hospital La Paz, Madrid, Spain
| | - C Mestre-Durán
- Hospital La Paz Institute for Health Research, IdiPAZ, University Hospital La Paz, Madrid, Spain
| | - A Navarro-Zapata
- Hospital La Paz Institute for Health Research, IdiPAZ, University Hospital La Paz, Madrid, Spain
| | - L Clares-Villa
- Hospital La Paz Institute for Health Research, IdiPAZ, University Hospital La Paz, Madrid, Spain
| | - C Martín-Cortázar
- Hospital La Paz Institute for Health Research, IdiPAZ, University Hospital La Paz, Madrid, Spain
| | - R De Paz
- Hematology Department, University Hospital La Paz, Madrid, Spain
| | - A Marcos
- Hematology Department, University Hospital La Paz, Madrid, Spain
| | - J L Vicario
- Histocompatibility, Centro de Transfusión de Madrid, Madrid, Spain
| | - A Balas
- Histocompatibility, Centro de Transfusión de Madrid, Madrid, Spain
| | - F García-Sánchez
- Histocompatibility, Centro de Transfusión de Madrid, Madrid, Spain
| | - C Eguizabal
- Research Unit, Basque Center for Blood Transfusion and Human Tissues, Osakidetza, Galdakao, Spain.,Cell Therapy, Stem Cells and Tissues Group, Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
| | - C Solano
- Hospital Clínico Universitario de Valencia/Instituto de Investigación Sanitaria INCLIVA, Universidad de Valencia, Valencia, Spain
| | - M Mora-Rillo
- Infectious Diseases Unit, Internal Medicine Department, Hospital La Paz Institute for Health Research, IdiPAZ, University Hospital La Paz, Madrid, Spain
| | - B Soria
- Instituto de Bioingeniería, Universidad Miguel Hernández de Elche, Alicante, Spain.,Instituto de Investigación Sanitaria Hospital General y Universitario de Alicante (ISABIAL), Alicante, Spain
| | - A Pérez-Martínez
- Hospital La Paz Institute for Health Research, IdiPAZ, University Hospital La Paz, Madrid, Spain.,Pediatric Hemato-Oncology Department, University Hospital La Paz, Madrid, Spain.,Faculty of Medicine, Universidad Autónoma de Madrid, Madrid, Spain
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41
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Varughese JK, Joseph Libin KL, Sindhu KS, Rosily AV, Abi TG. Investigation of the inhibitory activity of some dietary bioactive flavonoids against SARS-CoV-2 using molecular dynamics simulations and MM-PBSA calculations. J Biomol Struct Dyn 2021; 40:6755-6770. [PMID: 33618628 DOI: 10.1080/07391102.2021.1891139] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Eventhough the development of vaccine against COVID-19 pandemic is progressing in different part of the world a well-defined treatment plan is not yet developed. Therefore, we investigate the inhibitory activity of a group of dietary bioactive flavonoids against SARS-CoV-2 main protease (Mpro), which are identified as one of the potential targets in the drug discovery process of COVID-19. After the initial virtual screening of a number of bioactive flavonoids, the binding affinity of three compounds - Naringin, Naringenin and Amentoflavone - at the active site of Mpro was investigated through MD Simulations, MM-PBSA and DFT Binding Energy calculations. From the MD trajectory analysis, Amentoflavone and Naringin showed consistent protein-ligand interactions with the aminoacid residues of the active site domains of Mpro. The excellent inhibitory activity of Amentoflavone and Naringin was established from its MM-PBSA binding energy values of -190.50 and -129.87 kJ/mol respectively. The MET165 residue of Mpro is identified as one of the key residue which contributed significantly to MM-PBSA binding energy through hydrophobic interactions. Furthermore, the DFT binding energy values of Amentoflavone (-182.92 kJ/mol) and Naringin (-160.67 kJ/mol) in active site molecular clusters with hydrogen bonds confirmed their potential inhibitory activity. These compounds are of high interest because of their wide availability, low cost, no side effects, and long history of use. We can prevent the severity of this disease for home care patients using these effective dietary supplements. We are hopeful that our results have implications for the development of prophylaxis of COVID-19.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Jibin K Varughese
- Department of Chemistry, Sacred Heart College, Thevara, Kochi, Kerala, India
| | - K L Joseph Libin
- Department of Chemistry, Sacred Heart College, Thevara, Kochi, Kerala, India
| | - K S Sindhu
- Department of Chemistry, Morning Star Home Science College Angamaly, Kerala, India
| | - A V Rosily
- Department of Chemistry, Morning Star Home Science College Angamaly, Kerala, India
| | - T G Abi
- Department of Chemistry, Sacred Heart College, Thevara, Kochi, Kerala, India
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42
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Jang M, Park R, Park YI, Cha YE, Yamamoto A, Lee JI, Park J. EGCG, a green tea polyphenol, inhibits human coronavirus replication in vitro. Biochem Biophys Res Commun 2021; 547:23-28. [PMID: 33588235 PMCID: PMC7874949 DOI: 10.1016/j.bbrc.2021.02.016] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 02/04/2021] [Indexed: 01/27/2023]
Abstract
COVID-19 pandemic results in record high deaths in many countries. Although a vaccine for SARS-CoV-2 is now available, effective antiviral drugs to treat coronavirus diseases are not available yet. Recently, EGCG, a green tea polyphenol, was reported to inhibit SARS-CoV-2 3CL-protease, however the effect of EGCG on coronavirus replication is unknown. In this report, human coronavirus HCoV-OC43 (beta coronavirus) and HCoV-229E (alpha coronavirus) were used to examine the effect of EGCG on coronavirus. EGCG treatment decreases 3CL-protease activity of HCoV-OC43 and HCoV-229E. Moreover, EGCG treatment decreased HCoV-OC43-induced cytotoxicity. Finally, we found that EGCG treatment decreased the levels of coronavirus RNA and protein in infected cell media. These results indicate that EGCG inhibits coronavirus replication.
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Affiliation(s)
- Minsu Jang
- Division of Biological Science and Technology, Yonsei University, Wonju, Republic of Korea
| | - Rackhyun Park
- Division of Biological Science and Technology, Yonsei University, Wonju, Republic of Korea
| | - Yea-In Park
- Division of Biological Science and Technology, Yonsei University, Wonju, Republic of Korea
| | - Yeo-Eun Cha
- Division of Biological Science and Technology, Yonsei University, Wonju, Republic of Korea
| | - Ayane Yamamoto
- Division of Biological Science and Technology, Yonsei University, Wonju, Republic of Korea
| | - Jin I Lee
- Division of Biological Science and Technology, Yonsei University, Wonju, Republic of Korea
| | - Junsoo Park
- Division of Biological Science and Technology, Yonsei University, Wonju, Republic of Korea.
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43
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Abuin P, Anderson A, Ferramosca A, Hernandez-Vargas EA, Gonzalez AH. Dynamical characterization of antiviral effects in COVID-19. ANNUAL REVIEWS IN CONTROL 2021; 52:587-601. [PMID: 34093069 PMCID: PMC8162791 DOI: 10.1016/j.arcontrol.2021.05.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 04/21/2021] [Accepted: 05/01/2021] [Indexed: 05/02/2023]
Abstract
Mathematical models describing SARS-CoV-2 dynamics and the corresponding immune responses in patients with COVID-19 can be critical to evaluate possible clinical outcomes of antiviral treatments. In this work, based on the concept of virus spreadability in the host, antiviral effectiveness thresholds are determined to establish whether or not a treatment will be able to clear the infection. In addition, the virus dynamic in the host - including the time-to-peak and the final monotonically decreasing behavior - is characterized as a function of the time to treatment initiation. Simulation results, based on nine patient data, show the potential clinical benefits of a treatment classification according to patient critical parameters. This study is aimed at paving the way for the different antivirals being developed to tackle SARS-CoV-2.
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Affiliation(s)
- Pablo Abuin
- Institute of Technological Development for the Chemical Industry (INTEC), CONICET-UNL, Santa Fe, Argentina
| | - Alejandro Anderson
- Institute of Technological Development for the Chemical Industry (INTEC), CONICET-UNL, Santa Fe, Argentina
| | - Antonio Ferramosca
- Department of Management, Information and Production Engineering, University of Bergamo, Via Marconi 5, 24044, Dalmine (BG), Italy
| | | | - Alejandro H Gonzalez
- Institute of Technological Development for the Chemical Industry (INTEC), CONICET-UNL, Santa Fe, Argentina
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Khan N, Kumar N, Geiger JD. Possible therapeutic targets for SARS-CoV-2 infection and COVID-19. JOURNAL OF ALLERGY AND INFECTIOUS DISEASES 2021; 2:75-83. [PMID: 37564275 PMCID: PMC10414779 DOI: 10.46439/allergy.2.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/12/2023]
Abstract
SARS-CoV-2 infection causes COVID-19, which has emerged as a health emergency worldwide. SARS-CoV-2 infects cells by binding to ACE2 receptors and enters into the cytoplasm following its escape from endolysosomes. Once in the cytoplasm, the virus replicates and eventually causes various pathological conditions including acute respiratory distress syndrome (ARDS) that is caused by pro-inflammatory cytokine storms. Thus, endolysosomes and cytokine storms are important therapeutic targets to suppress SARS-CoV-2 infection and COVID-19. Here, we discuss therapeutic targets of SARS-CoV-2 infection and available drugs that could be helpful in the suppression of the SARS-CoV-2 infection and pathological condition COVID-19. The urgency of the COVID-19 pandemic precludes the development of new drugs and increased focus on drug repurposing might provide the quickest way to finding effective medicines.
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Affiliation(s)
- Nabab Khan
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, North Dakota 58203, USA
| | - Nirmal Kumar
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, North Dakota 58203, USA
| | - Jonathan D. Geiger
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, North Dakota 58203, USA
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Rehman MFU, Fariha C, Anwar A, Shahzad N, Ahmad M, Mukhtar S, Farhan Ul Haque M. Novel coronavirus disease (COVID-19) pandemic: A recent mini review. Comput Struct Biotechnol J 2020; 19:612-623. [PMID: 33398233 PMCID: PMC7773542 DOI: 10.1016/j.csbj.2020.12.033] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 12/21/2020] [Accepted: 12/23/2020] [Indexed: 02/06/2023] Open
Abstract
The COVID-19, caused by a novel coronavirus, was declared as a global pandemic by WHO more than five months ago, and we are still experiencing a state of global emergency. More than 74.30 million confirmed cases of the COVID-19 have been reported globally so far, with an average fatality rate of almost 3.0%. Seven different types of coronaviruses had been detected from humans; three of them have resulted in severe outbreaks, i.e., MERS-CoV, SARS-CoV, and SARS-CoV-2. Phylogenetic analysis of the genomes suggests that the possible occurrence of recombination between SARS-like-CoVs from pangolin and bat might have led to the origin of SARS-CoV-2 and the COVID-19 outbreak. Coronaviruses are positive-sense, single-stranded RNA viruses and harbour a genome (30 kb) consisting of two terminal untranslated regions and twelve putative functional open reading frames (ORFs), encoding for non-structural and structural proteins. There are sixteen putative non-structural proteins, including proteases, RNA-dependent RNA polymerase, helicase, other proteins involved in the transcription and replication of SARS-CoV-2, and four structural proteins, including spike protein (S), envelope (E), membrane (M), and nucleocapsid (N). SARS-CoV-2 infection, with a heavy viral load in the body, destroys the human lungs through cytokine storm, especially in elderly persons and people with immunosuppressed disorders. A number of drugs have been repurposed and employed, but still, no specific antiviral medicine has been approved by the FDA to treat this disease. This review provides a current status of the COVID-19, epidemiology, an overview of phylogeny, mode of action, diagnosis, and possible treatment methods and vaccines.
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Affiliation(s)
| | - Chaudhary Fariha
- School of Biological Sciences, University of the Punjab, Lahore 54000, Pakistan
| | - Aqsa Anwar
- School of Biological Sciences, University of the Punjab, Lahore 54000, Pakistan
| | - Naveed Shahzad
- School of Biological Sciences, University of the Punjab, Lahore 54000, Pakistan
| | - Munir Ahmad
- School of Biological Sciences, University of the Punjab, Lahore 54000, Pakistan
| | - Salma Mukhtar
- School of Biological Sciences, University of the Punjab, Lahore 54000, Pakistan
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Shahid M, Shahzad-Ul-Hussan S. Structural insights of key enzymes into therapeutic intervention against SARS-CoV-2. J Struct Biol 2020; 213:107690. [PMID: 33383190 PMCID: PMC7769706 DOI: 10.1016/j.jsb.2020.107690] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 12/03/2020] [Accepted: 12/23/2020] [Indexed: 01/18/2023]
Abstract
COVID-19 pandemic, caused by SARS-CoV-2, has drastically affected human health all over the world. After the emergence of the pandemic the major focus of efforts to attenuate the infection has been on repurposing the already approved drugs to treat COVID-19 adopting a fast-track strategy. However, to date a specific regimen to treat COVID-19 is not available. Over the last few months a substantial amount of data about the structures of various key proteins and their recognition partners involved in the SARS-CoV-2 pathogenesis has emerged. These studies have not only provided the molecular level descriptions ofthe viral pathogenesis but also laid the foundation for rational drug design and discovery. In this review, we have recapitulated the structural details of four key viral enzymes, RNA-dependent RNA polymerase, 3-chymotrypsin like protease, papain-like protease and helicase, and two host factors including angiotensin-converting enzyme 2 and transmembrane serine protease involved in the SARS-CoV-2 pathogenesis, and described the potential hotspots present on these structures which could be explored for therapeutic intervention. We have also discussed the significance of endoplasmic reticulum α-glucosidases as potential targets for anti-SARS-CoV-2 drug discovery.
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Affiliation(s)
- Munazza Shahid
- Department of Biology, SBA School of Science and Engineering, Lahore University of Management Sciences, Lahore 54792, Pakistan
| | - Syed Shahzad-Ul-Hussan
- Department of Biology, SBA School of Science and Engineering, Lahore University of Management Sciences, Lahore 54792, Pakistan.
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Syal K. Guidelines on newly identified limitations of diagnostic tools for COVID-19 and consequences. J Med Virol 2020; 93:1837-1842. [PMID: 33200414 PMCID: PMC7753543 DOI: 10.1002/jmv.26673] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 11/05/2020] [Accepted: 11/12/2020] [Indexed: 01/07/2023]
Abstract
Coronavirus disease 2019 (COVID-19) caused by coronavirus has spread worldwide and has become the deadliest pandemic of the 21st century. Such rapid spread is predominantly attributed to the poor diagnosis and its asymptomatic transmission. In the absence of treatment regime, timely diagnosis is the best available remedy that can restrict its spread. An early diagnosis of COVID-19 is critical for determining the line of treatment and preventing long term complications in the infected subject. Unfortunately, available rapid antigen and antibody kits are known to be erroneous whereas reverse transcription polymerase chain reaction based tests are expensive, viral load dependent and at times inconclusive. In current scenario, the false-negative results imposed a major risk to the individual patient care and also to the efforts for containing the spread at the population level, where as false positives are traumatic for families and can lead to improper treatment resulting in severe complications. In this article, the limitations of available diagnostic procedures have been elaborated and plausible combination approach has been advised.
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Affiliation(s)
- Kirtimaan Syal
- Department of Biological Sciences, BITS-Pilani, Telangana, India
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Yang Y, Zhao Y, Zhang F, Zhang L, Li L. COVID-19 in Elderly Adults: Clinical Features, Molecular Mechanisms, and Proposed Strategies. Aging Dis 2020; 11:1481-1495. [PMID: 33269102 PMCID: PMC7673861 DOI: 10.14336/ad.2020.0903] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Accepted: 09/03/2020] [Indexed: 12/15/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) is causing problems worldwide. Most people are susceptible to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), but elderly populations are more susceptible. Elevated susceptibility and death rates in elderly COVID-19 patients, especially those with age-related complications, are challenges for pandemic prevention and control. In this paper, we review the clinical features of elderly patients with COVID-19 and explore the related molecular mechanisms that are essential for the exploration of preventive and therapeutic strategies in the current pandemic. Furthermore, we analyze the feasibility of currently recommended potential novel methods against COVID-19 among elderly populations.
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Affiliation(s)
| | | | | | | | - Lanjuan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China.
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Jensen MP, George M, Gilroy D, Sofat R. Beyond dexamethasone, emerging immuno-thrombotic therapies for COVID-19. Br J Clin Pharmacol 2020; 87:845-857. [PMID: 32881064 DOI: 10.1111/bcp.14540] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 08/20/2020] [Accepted: 08/21/2020] [Indexed: 01/08/2023] Open
Abstract
Host immunity is required to clear SARS-CoV-2, and inability to clear the virus because of host or pathogen factors renders those infected at risk of poor outcomes. Estimates of those who are able to clear the virus with asymptomatic or paucisymptomatic COVID-19 remain unclear, and dependent on widespread testing. However, evidence is emerging that in severe cases, pathological mechanisms of hyperinflammation and coagulopathy ensue, the former supported by results from the RECOVERY trial demonstrating a reduction in mortality with dexamethasone in advanced COVID-19. It remains unclear whether these pathogenic pathways are secondary to a failure to clear the virus because of maladaptive immune responses or if these are sequential COVID-19 defining illnesses. Understanding the pathophysiological mechanisms underpinning these cascades is essential to formulating rationale therapeutic approaches beyond the use of dexamethasone. Here, we review the pathophysiology thought to underlie COVID-19 with clinical correlates and the current therapeutic approaches being investigated.
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Affiliation(s)
| | - Marc George
- Centre for Clinical Pharmacology and Therapeutics, UCL, London, UK
| | - Derek Gilroy
- Centre for Clinical Pharmacology and Therapeutics, UCL, London, UK
| | - Reecha Sofat
- Centre for Clinical Pharmacology and Therapeutics, UCL, London, UK.,Institute of Health Informatics, 222 Euston Road, London, UK
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