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Shahid M, Alaofi AL, Ahmad Ansari M, Fayaz Ahmad S, Alsuwayeh S, Taha E, Raish M. Utilizing sinapic acid as an inhibitory antiviral agent against MERS-CoV PLpro. Saudi Pharm J 2024; 32:101986. [PMID: 38487020 PMCID: PMC10937238 DOI: 10.1016/j.jsps.2024.101986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 02/05/2024] [Indexed: 03/17/2024] Open
Abstract
Concerns about the social and economic collapse, high mortality rates, and stress on the healthcare system are developing due to the coronavirus onslaught in the form of various species and their variants. In the recent past, infections brought on by coronaviruses severe acute respiratory syndrome coronaviruses (SARS-CoV and SARS-CoV-2) as well as middle east respiratory syndrome coronavirus (MERS-CoV) have been reported. There is a severe lack of medications to treat various coronavirus types including MERS-CoV which is hazard to public health due to its ability for pandemic spread by human-to-human transmission. Here, we utilized sinapic acid (SA) against papain-like protease (PLpro), a crucial enzyme involved in MERS-CoV replication, because phytomedicine derived from nature has less well-known negative effects. The thermal shift assay (TSA) was used in the current study to determine whether the drug interact with the recombinant MERS-CoV PLpro. Also, inhibition assay was conducted as the hydrolysis of fluorogenic peptide from the Z-RLRGG-AMC-peptide bond in the presence of SA to determine the level of inhibition of the MERS-CoV PLpro. To study the structural binding efficiency Autodock Vina was used to dock SA to the MERS-CoV PLpro and results were analyzed using PyMOL and Maestro Schrödinger programs. Our results show a convincing interaction between SA and the MERS protease, as SA reduced MERS-CoV PLpro in a dose-dependent way IC50 values of 68.58 μM (of SA). The TSA showed SA raised temperature of melting to 54.61 °C near IC50 and at approximately 2X IC50 concentration (111.5 μM) the Tm for SA + MERS-CoV PLpro was 59.72 °C. SA was docked to MERS-CoV PLpro to identify the binding site. SA bound to the blocking loop (BL2) region of MERS-CoV PLpro interacts with F268, E272, V275, and P249 residues of MERS-CoV PLpro. The effectiveness of protease inhibitors against MERS-CoV has been established and SA is already known for broad range biological activity including antiviral properties; it can be a suitable candidate for anti-MERS-CoV treatment.
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Affiliation(s)
- Mudassar Shahid
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Ahmed L. Alaofi
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Mushtaq Ahmad Ansari
- Department of Phamacology and Toxicology, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia
| | - Sheikh Fayaz Ahmad
- Department of Phamacology and Toxicology, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia
| | - Saleh Alsuwayeh
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Ehab Taha
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Mohammad Raish
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
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2
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Deng M, Zhang C, Yan W, Chen L, He B, Li Y. Development of Fluorescence-Based Assays for Key Viral Proteins in the SARS-CoV-2 Infection Process and Lifecycle. Int J Mol Sci 2024; 25:2850. [PMID: 38474097 DOI: 10.3390/ijms25052850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 02/09/2024] [Accepted: 02/25/2024] [Indexed: 03/14/2024] Open
Abstract
Since the appearance of SARS-CoV-2 in 2019, the ensuing COVID-19 (Corona Virus Disease 2019) pandemic has posed a significant threat to the global public health system, human health, life, and economic well-being. Researchers worldwide have devoted considerable efforts to curb its spread and development. The latest studies have identified five viral proteins, spike protein (Spike), viral main protease (3CLpro), papain-like protease (PLpro), RNA-dependent RNA polymerase (RdRp), and viral helicase (Helicase), which play crucial roles in the invasion of SARS-CoV-2 into the human body and its lifecycle. The development of novel anti-SARS-CoV-2 drugs targeting these five viral proteins holds immense promise. Therefore, the development of efficient, high-throughput screening methodologies specifically designed for these viral proteins is of utmost importance. Currently, a plethora of screening techniques exists, with fluorescence-based assays emerging as predominant contenders. In this review, we elucidate the foundational principles and methodologies underpinning fluorescence-based screening approaches directed at these pivotal viral targets, hoping to guide researchers in the judicious selection and refinement of screening strategies, thereby facilitating the discovery and development of lead compounds for anti-SARS-CoV-2 pharmaceuticals.
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Affiliation(s)
- Mingzhenlong Deng
- State Key Laboratory of Functions and Applications of Medicinal Plants, Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Provincial Key Laboratory of Pharmaceutics, School of Pharmacy, Guizhou Medical University, Guiyang 550004, China
| | - Chuang Zhang
- State Key Laboratory of Functions and Applications of Medicinal Plants, Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Provincial Key Laboratory of Pharmaceutics, School of Pharmacy, Guizhou Medical University, Guiyang 550004, China
| | - Wanli Yan
- State Key Laboratory of Functions and Applications of Medicinal Plants, Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Provincial Key Laboratory of Pharmaceutics, School of Pharmacy, Guizhou Medical University, Guiyang 550004, China
| | - Lei Chen
- State Key Laboratory of Functions and Applications of Medicinal Plants, Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Provincial Key Laboratory of Pharmaceutics, School of Pharmacy, Guizhou Medical University, Guiyang 550004, China
| | - Bin He
- State Key Laboratory of Functions and Applications of Medicinal Plants, Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Provincial Key Laboratory of Pharmaceutics, School of Pharmacy, Guizhou Medical University, Guiyang 550004, China
| | - Yan Li
- School of Basic Medical Science, Guizhou Medical University, Guiyang 550004, China
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Moghadasi SA, Moraes SN, Harris RS. Cellular Assays for Dynamic Quantification of Deubiquitinase Activity and Inhibition. J Mol Biol 2023; 435:168316. [PMID: 37858708 DOI: 10.1016/j.jmb.2023.168316] [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: 08/03/2023] [Revised: 10/12/2023] [Accepted: 10/12/2023] [Indexed: 10/21/2023]
Abstract
Deubiquitinases (DUBs) are proteolytic enzymes that catalyze the removal of ubiquitin from protein substrates. The critical role of DUBs in regulating protein ubiquitination makes them attractive drug targets in oncology, neurodegenerative disease, and antiviral development. Biochemical assays for quantifying DUB activity have enabled characterization of substrate preferences and discovery of small molecule inhibitors. However, assessing the efficacy of these inhibitors in cellular contexts to support clinical drug development has been limited by a lack of tractable cell-based assays. To address this gap, we developed a two-color flow cytometry-based assay that allows for sensitive quantification of DUB activity and inhibition in living cells. The utility of this system was demonstrated by quantifying the potency of GRL0617 against the viral DUB SARS-CoV-2 PLpro, identifying potential GRL0617 resistance mutations, and performing structure-function analysis of the vOTU domain from the recently emerged Yezo virus. In addition, the system was optimized for cellular DUBs by modifying a GFP-targeting nanobody to recruit USP7 and USP28 to benchmark a panel of reported inhibitors and assess inhibition kinetics. Together, these results demonstrate the utility of these assays for studying DUB biology in a cellular context with potential to aid in inhibitor discovery and development.
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Affiliation(s)
- Seyed Arad Moghadasi
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA
| | - Sofia N Moraes
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA
| | - Reuben S Harris
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA; Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, TX 78229, USA.
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4
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Leonard RA, Rao VN, Bartlett A, Froggatt HM, Luftig MA, Heaton BE, Heaton NS. A low-background, fluorescent assay to evaluate inhibitors of diverse viral proteases. J Virol 2023; 97:e0059723. [PMID: 37578235 PMCID: PMC10506478 DOI: 10.1128/jvi.00597-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 06/11/2023] [Indexed: 08/15/2023] Open
Abstract
Multiple coronaviruses (CoVs) can cause respiratory diseases in humans. While prophylactic vaccines designed to prevent infection are available for severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), incomplete vaccine efficacy, vaccine hesitancy, and the threat of other pathogenic CoVs for which vaccines do not exist have highlighted the need for effective antiviral therapies. While antiviral compounds targeting the viral polymerase and protease are already in clinical use, their sensitivity to potential resistance mutations as well as their breadth against the full range of human and preemergent CoVs remain incompletely defined. To begin to fill that gap in knowledge, we report here the development of an improved, noninfectious, cell-based fluorescent assay with high sensitivity and low background that reports on the activity of viral proteases, which are key drug targets. We demonstrate that the assay is compatible with not only the SARS-CoV-2 Mpro protein but also orthologues from a range of human and nonhuman CoVs as well as clinically reported SARS-CoV-2 drug-resistant Mpro variants. We then use this assay to define the breadth of activity of two clinically used protease inhibitors, nirmatrelvir and ensitrelvir. Continued use of this assay will help define the strengths and limitations of current therapies and may also facilitate the development of next-generation protease inhibitors that are broadly active against both currently circulating and preemergent CoVs. IMPORTANCE Coronaviruses (CoVs) are important human pathogens with the ability to cause global pandemics. Working in concert with vaccines, antivirals specifically limit viral disease in people who are actively infected. Antiviral compounds that target CoV proteases are already in clinical use; their efficacy against variant proteases and preemergent zoonotic CoVs, however, remains incompletely defined. Here, we report an improved, noninfectious, and highly sensitive fluorescent method of defining the sensitivity of CoV proteases to small molecule inhibitors. We use this approach to assay the activity of current antiviral therapies against clinically reported SARS-CoV-2 protease mutants and a panel of highly diverse CoV proteases. Additionally, we show this system is adaptable to other structurally nonrelated viral proteases. In the future, this assay can be used to not only better define the strengths and limitations of current therapies but also help develop new, broadly acting inhibitors that more broadly target viral families.
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Affiliation(s)
- Rebecca A. Leonard
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Vishwas N. Rao
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
- Medical Scientist Training Program, Duke University School of Medicine, Durham, North Carolina, USA
| | - Alexandria Bartlett
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Heather M. Froggatt
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Micah A. Luftig
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
- Duke Center for Virology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Brook E. Heaton
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Nicholas S. Heaton
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
- Duke Center for Virology, Duke University School of Medicine, Durham, North Carolina, USA
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA
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Chang J, Kim J, Hong S, Jeong K, Kim S, Lee W. Protocol for in vitro fluorescence assay of papain-like protease and cell-based immunofluorescence assay of coronavirus infection. STAR Protoc 2023; 4:102295. [PMID: 37167057 PMCID: PMC10123355 DOI: 10.1016/j.xpro.2023.102295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/21/2023] [Accepted: 04/19/2023] [Indexed: 05/13/2023] Open
Abstract
Here, we describe detailed steps to constitute an in vitro assay for monitoring papain-like protease of coronavirus and a cell-based immunofluorescence infection assay. These assays can be adapted for high-throughput screening to determine the efficacy of novel protease inhibitors of coronaviruses and other viruses. In addition, cell-based immunofluorescence infection assay can be used to visually analyze antiviral efficacy of any novel compounds. For complete details on the use and execution of this protocol, please refer to Jeong et al. (2022).1.
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Affiliation(s)
- JuOae Chang
- Department of Pharmacy, School of Pharmacy, Sungkyunkwan University, Suwon-si, Gyeonggi-do 16419, South Korea
| | - Jinhee Kim
- Zoonotic Virus Laboratory, Institut Pasteur Korea, Seongnam-si, Gyeonggi-do 13488, South Korea
| | - Subin Hong
- Department of Pharmacy, School of Pharmacy, Sungkyunkwan University, Suwon-si, Gyeonggi-do 16419, South Korea
| | - Kwiwan Jeong
- Gyeonggido Business and Science Accelerator, Suwon-si, Gyeonggi-do 16229, South Korea
| | - Seungtaek Kim
- Zoonotic Virus Laboratory, Institut Pasteur Korea, Seongnam-si, Gyeonggi-do 13488, South Korea.
| | - Wonsik Lee
- Department of Pharmacy, School of Pharmacy, Sungkyunkwan University, Suwon-si, Gyeonggi-do 16419, South Korea.
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Zhang J, Jiang Y, Wu C, Zhou D, Gong J, Zhao T, Jin Z. Development of FRET and Stress Granule Dual-Based System to Screen for Viral 3C Protease Inhibitors. Molecules 2023; 28:molecules28073020. [PMID: 37049786 PMCID: PMC10096049 DOI: 10.3390/molecules28073020] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 03/20/2023] [Accepted: 03/27/2023] [Indexed: 03/31/2023] Open
Abstract
3C proteases (3Cpros) of picornaviruses and 3C-like proteases (3CLpros) of coronaviruses and caliciviruses represent a group of structurally and functionally related viral proteases that play pleiotropic roles in supporting the viral life cycle and subverting host antiviral responses. The design and screening for 3C/3CLpro inhibitors may contribute to the development broad-spectrum antiviral therapeutics against viral diseases related to these three families. However, current screening strategies cannot simultaneously assess a compound’s cytotoxicity and its impact on enzymatic activity and protease-mediated physiological processes. The viral induction of stress granules (SGs) in host cells acts as an important antiviral stress response by blocking viral translation and stimulating the host immune response. Most of these viruses have evolved 3C/3CLpro-mediated cleavage of SG core protein G3BP1 to counteract SG formation and disrupt the host defense. Yet, there are no SG-based strategies screening for 3C/3CLpro inhibitors. Here, we developed a fluorescence resonance energy transfer (FRET) and SG dual-based system to screen for 3C/3CLpro inhibitors in living cells. We took advantage of FRET to evaluate the protease activity of poliovirus (PV) 3Cpro and live-monitor cellular SG dynamics to cross-verify its effect on the host antiviral response. Our drug screen uncovered a novel role of Telaprevir and Trifluridine as inhibitors of PV 3Cpro. Moreover, Telaprevir and Trifluridine also modulated 3Cpro-mediated physiological processes, including the cleavage of host proteins, inhibition of the innate immune response, and consequent facilitation of viral replication. Taken together, the FRET and SG dual-based system exhibits a promising potential in the screening for inhibitors of viral proteases that cleave G3BP1.
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Kandeel M. An overview of the recent progress in Middle East Respiratory Syndrome Coronavirus (MERS-CoV) drug discovery. Expert Opin Drug Discov 2023; 18:385-400. [PMID: 36971501 DOI: 10.1080/17460441.2023.2192921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Abstract
INTRODUCTION The Middle East respiratory syndrome coronavirus (MERS-CoV) has remained a public health concern since it first emerged in 2012. Although many potential treatments for MERS-CoV have been developed and tested, none have had complete success in stopping the spread of this deadly disease. MERS-CoV replication comprises attachment, entry, fusion and replication steps. Targeting these events may lead to the creation of medications that effectively treat MERS-CoV infection. AREAS COVERED This review updates the research on the development of inhibitors of MERS-CoV. The main topics are MERS-CoV‒related proteins and host cell proteins that are involved in viral protein activation and infection. EXPERT OPINION Research on discovering drugs that can inhibit MERS-CoV started at a slow pace, and although efforts have steadily increased, clinical trials for new drugs specifically targeting MERS-CoV have not been extensive enough. The explosion in efforts to find new medications for the SARS-CoV-2 virus indirectly enhanced the volume of data on MERS-CoV inhibition by including MERS-CoV in drug assays. The appearance of COVID-19 completely transformed the data available on MERS-CoV inhibition. Despite the fact that new infected cases are constantly being diagnosed, there are currently no approved vaccines for or inhibitors of MERS-CoV.
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Meshkini F, Moradi A, Hosseinkhani S. Upregulation of RIPK1 implicates in HEK 293T cell death upon transient transfection of A53T-α-synuclein. Int J Biol Macromol 2023; 230:123216. [PMID: 36634793 DOI: 10.1016/j.ijbiomac.2023.123216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 01/04/2023] [Accepted: 01/07/2023] [Indexed: 01/11/2023]
Abstract
BACKGROUND Alpha-synuclein (α-SN) is the central protein in synucleinopathies including Parkinson's disease. Nevertheless, the molecular mechanisms through which α-SN leads to neuronal death remain unclear. METHODS To elucidate the relationship between α-SN and apoptosis, some indicators of the intrinsic and extrinsic apoptotic cell death were assessed in normal and a stable HEK293T cell line expressing firefly luciferase after transfection with the wild-type (WT) and A53T mutant α-SN. RESULTS Opposite to WT-α-SN, overexpression of A53T-α-SN resulted in enhanced expression of almost two fold for RIPK1 (93.0 %), FADD (45 %), Caspase-8, and Casp-9 activity (52.0 %) in measured time. Transfection of both WT-α-SN and A53T-α-SN showed an increase in the Casp-3/Procasp-3 ratio (WT: 60.5 %; A53T: 41.0 %), Casp-3 activity (WT: 65.0 %; A53T: 20.5 %), and a decrease in luciferase activity (WT: 50 %; A53T: 34.8 %). Overexpression of A53T-α-SN brought about with more cell death percentage compared to WT-α-SN within 36 h. No significant alteration in cytochrome c and reactive oxygen species release into cytosol were observed for both WT-α-SN and A53T-α-SN. CONCLUSION Altogether, these findings highlight the link between disease related mutants of α-SN (like A53T-α-SN) in triggering of RIPK1-dependent extrinsic apoptotic pathway in cell death during neurodegeneration.
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Affiliation(s)
- Fatemeh Meshkini
- Department of Biochemistry, School of Medicine, Shahid Sadoughi University of Medical Sciences and Health Services, Yazd, Iran
| | - Ali Moradi
- Department of Biochemistry, School of Medicine, Shahid Sadoughi University of Medical Sciences and Health Services, Yazd, Iran
| | - Saman Hosseinkhani
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.
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Ali Dahhas M, M Alkahtani H, Malik A, Almehizia AA, Bakheit AH, Akber Ansar S, AlAbdulkarim AS, S Alrasheed L, Alsenaidy MA. Screening and identification of potential MERS-CoV papain-like protease (PLpro) inhibitors; Steady-state kinetic and Molecular dynamic studies. Saudi Pharm J 2023; 31:228-244. [PMID: 36540698 PMCID: PMC9756750 DOI: 10.1016/j.jsps.2022.12.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/11/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022] Open
Abstract
MERS-CoV belongs to the coronavirus group. Recent years have seen a rash of coronavirus epidemics. In June 2012, MERS-CoV was discovered in the Kingdom of Saudi Arabia, with 2,591 MERSA cases confirmed by lab tests by the end of August 2022 and 894 deaths at a case-fatality ratio (CFR) of 34.5% documented worldwide. Saudi Arabia reported the majority of these cases, with 2,184 cases and 813 deaths (CFR: 37.2%), necessitating a thorough understanding of the molecular machinery of MERS-CoV. To develop antiviral medicines, illustrative investigation of the protein in coronavirus subunits are required to increase our understanding of the subject. In this study, recombinant expression and purification of MERS-CoV (PLpro), a primary goal for the development of 22 new inhibitors, were completed using a high throughput screening methodology that employed fragment-based libraries in conjunction with structure-based virtual screening. Compounds 2, 7, and 20, showed significant biological activity. Moreover, a docking analysis revealed that the three compounds had favorable binding mood and binding free energy. Molecular dynamic simulation demonstrated the stability of compound 2 (2-((Benzimidazol-2-yl) thio)-1-arylethan-1-ones) the strongest inhibitory activity against the PLpro enzyme. In addition, disubstitutions at the meta and para locations are the only substitutions that may boost the inhibitory action against PLpro. Compound 2 was chosen as a MERS-CoV PLpro inhibitor after passing absorption, distribution, metabolism, and excretion studies; however, further investigations are required.
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Key Words
- 3CLpro, 3-Chymotrypsin -like Protease
- ADMET, Absorption, distribution, metabolism, excretion and toxicity
- CFR, Case fatality rate
- DTT, Dithiothreitol
- Drug Design
- Drug Discovery
- E. coli, Escherichia coli
- EDTA, Ethylenediaminetetraacetic acid
- HCoV-, Human Coronavirus
- HIA, Human intestinal absorption
- His-tag, Histidine tag
- IPTG, Isopropyl b-D-1-thiogalactopyranoside
- Inhibitors
- Kan, Kanamicyn
- LB, Luria–Bertani
- MD, Molecular dynamic
- MERS-CoV PLpro Inhibitors
- MOE, Molecular Operating Environment
- MPLpro, MERS papain-like protease
- Molecular Docking
- Molecular dynamic simulation
- Ni-NTA, Nickel-nitrilotri
- Nonstructural proteins
- PLIF, Protein- ligand interaction fingerprint
- Papain-like protease
- Protease
- RMSD, Root Mean Square Deviation
- RMSF, Root Mean Square Fluctuation
- pp1a, Polyprotein 1a
- pp1b, Polyprotein 1b
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Affiliation(s)
- Mohammed Ali Dahhas
- Department of Pharmaceutics, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia
| | - Hamad M Alkahtani
- Department of Pharmaceutical Chemistry, Department Chairman, P.O. Box 2457, Riyadh 11451, Saudi Arabia
| | - Ajamaluddin Malik
- Department of Biochemistry, College of Science, King Saud University. King Saud University, PO Box 2455, Riyadh 11451, Saudi Arabia
| | | | - Ahmed H Bakheit
- Department of Pharmaceutical Chemistry, Department Chairman, P.O. Box 2457, Riyadh 11451, Saudi Arabia
| | - Siddique Akber Ansar
- Department of Pharmaceutical Chemistry, Department Chairman, P.O. Box 2457, Riyadh 11451, Saudi Arabia
| | - Abdullah S AlAbdulkarim
- Department of Pharmaceutics, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia
| | - Lamees S Alrasheed
- Department of Pharmaceutical Chemistry, Department Chairman, P.O. Box 2457, Riyadh 11451, Saudi Arabia
| | - Mohammad A Alsenaidy
- Department of Pharmaceutics, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia
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Sasaki M, Tabata K, Kishimoto M, Itakura Y, Kobayashi H, Ariizumi T, Uemura K, Toba S, Kusakabe S, Maruyama Y, Iida S, Nakajima N, Suzuki T, Yoshida S, Nobori H, Sanaki T, Kato T, Shishido T, Hall WW, Orba Y, Sato A, Sawa H. S-217622, a SARS-CoV-2 main protease inhibitor, decreases viral load and ameliorates COVID-19 severity in hamsters. Sci Transl Med 2023; 15:eabq4064. [PMID: 36327352 PMCID: PMC9765455 DOI: 10.1126/scitranslmed.abq4064] [Citation(s) in RCA: 33] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
In parallel with vaccination, oral antiviral agents are highly anticipated to act as countermeasures for the treatment of the coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Oral antiviral medication demands not only high antiviral activity but also target specificity, favorable oral bioavailability, and high metabolic stability. Although a large number of compounds have been identified as potential inhibitors of SARS-CoV-2 infection in vitro, few have proven to be effective in vivo. Here, we show that oral administration of S-217622 (ensitrelvir), an inhibitor of SARS-CoV-2 main protease (Mpro; also known as 3C-like protease), decreases viral load and ameliorates disease severity in SARS-CoV-2-infected hamsters. S-217622 inhibited viral proliferation at low nanomolar to submicromolar concentrations in cells. Oral administration of S-217622 demonstrated favorable pharmacokinetic properties and accelerated recovery from acute SARS-CoV-2 infection in hamster recipients. Moreover, S-217622 exerted antiviral activity against SARS-CoV-2 variants of concern, including the highly pathogenic Delta variant and the recently emerged Omicron BA.5 and BA.2.75 variants. Overall, our study provides evidence that S-217622, an antiviral agent that is under evaluation in a phase 3 clinical trial (clinical trial registration no. jRCT2031210350), has remarkable antiviral potency and efficacy against SARS-CoV-2 and is a prospective oral therapeutic option for COVID-19.
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Affiliation(s)
- Michihito Sasaki
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, 001-220, Japan.,Corresponding author. (M.S.); (H.S.)
| | - Koshiro Tabata
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, 001-220, Japan
| | - Mai Kishimoto
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, 001-220, Japan
| | - Yukari Itakura
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, 001-220, Japan
| | - Hiroko Kobayashi
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, 001-220, Japan
| | - Takuma Ariizumi
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, 001-220, Japan
| | - Kentaro Uemura
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, 001-220, Japan.,Shionogi & Co., Ltd., Osaka 561-0825, Japan.,Laboratory of Biomolecular Science, Faculty of Pharmaceutical Science, Hokkaido University, Sapporo, 060-0812, Japan
| | - Shinsuke Toba
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, 001-220, Japan.,Shionogi & Co., Ltd., Osaka 561-0825, Japan
| | - Shinji Kusakabe
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, 001-220, Japan.,Shionogi & Co., Ltd., Osaka 561-0825, Japan
| | - Yuki Maruyama
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, 001-220, Japan.,Shionogi & Co., Ltd., Osaka 561-0825, Japan
| | - Shun Iida
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan
| | - Noriko Nakajima
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan
| | - Tadaki Suzuki
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan
| | | | | | | | | | | | - William W. Hall
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, 001-0020, Japan.,National Virus Reference Laboratory, School of Medicine, University College of Dublin, 4, Ireland.,Global Virus Network, Baltimore, MD, 21201, USA
| | - Yasuko Orba
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, 001-220, Japan.,International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, 001-0020, Japan
| | - Akihiko Sato
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, 001-220, Japan.,Shionogi & Co., Ltd., Osaka 561-0825, Japan.,Institute for Vaccine Research and Development (IVReD), Hokkaido University, Sapporo, 001-0021, Japan
| | - Hirofumi Sawa
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, 001-220, Japan.,International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, 001-0020, Japan.,Global Virus Network, Baltimore, MD, 21201, USA.,Institute for Vaccine Research and Development (IVReD), Hokkaido University, Sapporo, 001-0021, Japan.,One Health Research Center, Hokkaido University, Sapporo, 001-0020, Japan.,Corresponding author. (M.S.); (H.S.)
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11
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Liu J, Ge C, Zha L, Lin L, Li R. Simple Nano-Luciferase-Based Assay for the Rapid and High-Throughput Detection of SARS-CoV-2 3C-Like Protease. Anal Chem 2023; 95:714-719. [PMID: 36576396 PMCID: PMC9843625 DOI: 10.1021/acs.analchem.2c02590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 12/09/2022] [Indexed: 12/29/2022]
Abstract
In this study, we described an easy-to-perform nano-luciferase (nLuc) sensor for the rapid detection of 3-chymotrypsin-like protease (3CLpro) encoded by SARS-CoV-2. The technology is based on the cleavage reaction of recombinant-nLuc via 3CLpro. The nLuc-based assay is a general, one-step method and is naturally specific in detection. The stability, sensitivity, detection range, and response time are fully characterized. The application of 3CLpro detection in artificial and human saliva as well as antiviral drug screening demonstrates that the method can quantify 3CLpro with high sensitivity in one step. With its unique features, the nLuc-based assay may find broad applications in the auxiliary diagnosis of SARS-CoV-2, as well as other types of coronavirus infection.
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Affiliation(s)
- Jingxin Liu
- College
of Health Science and Environmental Engineering, Shenzhen Technology University, 3002 Lantian Road, Pingshan District, Shenzhen, Guangdong 518118, P. R. China
| | - Chenchen Ge
- College
of Health Science and Environmental Engineering, Shenzhen Technology University, 3002 Lantian Road, Pingshan District, Shenzhen, Guangdong 518118, P. R. China
| | - Ling Zha
- College
of Health Science and Environmental Engineering, Shenzhen Technology University, 3002 Lantian Road, Pingshan District, Shenzhen, Guangdong 518118, P. R. China
| | - Ligen Lin
- State
Key Laboratory of Quality Research in Chinese Medicine, Institute
of Chinese Medical Sciences, University
of Macau, Macao 999078, P. R. China
| | - Rongsong Li
- College
of Health Science and Environmental Engineering, Shenzhen Technology University, 3002 Lantian Road, Pingshan District, Shenzhen, Guangdong 518118, P. R. China
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12
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Geethakumari AM, Ahmed WS, Rasool S, Fatima A, Nasir Uddin SM, Aouida M, Biswas KH. A genetically encoded BRET-based SARS-CoV-2 M pro protease activity sensor. Commun Chem 2022; 5:117. [PMID: 36187754 PMCID: PMC9516532 DOI: 10.1038/s42004-022-00731-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 09/07/2022] [Indexed: 01/27/2023] Open
Abstract
The main protease, Mpro, is critical for SARS-CoV-2 replication and an appealing target for designing anti-SARS-CoV-2 agents. Therefore, there is a demand for the development of improved sensors to monitor its activity. Here, we report a pair of genetically encoded, bioluminescence resonance energy transfer (BRET)-based sensors for detecting Mpro proteolytic activity in live cells as well as in vitro. The sensors were generated by sandwiching peptides containing the Mpro N-terminal autocleavage sites, either AVLQSGFR (short) or KTSAVLQSGFRKME (long), in between the mNeonGreen and NanoLuc proteins. Co-expression of the sensors with Mpro in live cells resulted in their cleavage while mutation of the critical C145 residue (C145A) in Mpro completely abrogated their cleavage. Additionally, the sensors recapitulated the inhibition of Mpro by the well-characterized pharmacological agent GC376. Further, in vitro assays with the BRET-based Mpro sensors revealed a molecular crowding-mediated increase in the rate of Mpro activity and a decrease in the inhibitory potential of GC376. The sensors developed here will find direct utility in studies related to drug discovery targeting the SARS-CoV-2 Mpro and functional genomics application to determine the effect of sequence variation in Mpro.
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Affiliation(s)
- Anupriya M. Geethakumari
- Division of Biological and Biomedical Sciences, College of Health & Life Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, 34110 Qatar
| | - Wesam S. Ahmed
- Division of Biological and Biomedical Sciences, College of Health & Life Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, 34110 Qatar
| | - Saad Rasool
- Division of Genomics and Precision Medicine, College of Health & Life Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, 34110 Qatar
| | - Asma Fatima
- Division of Biological and Biomedical Sciences, College of Health & Life Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, 34110 Qatar
| | - S. M. Nasir Uddin
- Division of Biological and Biomedical Sciences, College of Health & Life Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, 34110 Qatar
| | - Mustapha Aouida
- Division of Biological and Biomedical Sciences, College of Health & Life Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, 34110 Qatar
| | - Kabir H. Biswas
- Division of Biological and Biomedical Sciences, College of Health & Life Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, 34110 Qatar
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13
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Hou N, Peng C, Zhang L, Zhu Y, Hu Q. BRET-Based Self-Cleaving Biosensors for SARS-CoV-2 3CLpro Inhibitor Discovery. Microbiol Spectr 2022; 10:e0255921. [PMID: 35758897 PMCID: PMC9430692 DOI: 10.1128/spectrum.02559-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 05/28/2022] [Indexed: 12/02/2022] Open
Abstract
The 3C-like protease (3CLpro) of SARS-CoV-2 is an attractive drug target for developing antivirals against SARS-CoV-2. A few small molecule inhibitors of 3CLpro are in clinical trials for COVID-19 treatments, and more inhibitors are under development. One limiting factor for 3CLpro inhibitors development is that the cellular activities of such inhibitors should be evaluated in Biosafety Level 3 (BSL-3) laboratories. Here, we design DNA-coded biosensors that can be used in BSL-2 laboratories to set up cell-based assays for 3CLpro inhibitor discovery. The biosensors were constructed by linking a green fluorescent protein (GFP2) to the N-terminus and a Renilla luciferase (RLuc8) to the C-terminus of SARS-CoV-2 3CLpro, with the linkers derived from the cleavage sequences of 3CLpro. After overexpression of the biosensors in human embryonic kidney (HEK) 293T cells, 3CLpro can be released from GFP2 and RLuc by self-cleavage, resulting in a decrease of the bioluminescence resonance energy transfer (BRET) signal. Using one of these biosensors, pBRET-10, we evaluated the cellular activities of several 3CLpro inhibitors. These inhibitors restored the BRET signal by blocking the proteolysis of pBRET-10, and their relative activities measured using pBRET-10 were consistent with their previously reported anti-SARS-CoV-2 activities. We conclude that the biosensor pBRET-10 is a useful tool for SARS-CoV-2 3CLpro inhibitor discovery. IMPORTANCE The virus proteases 3CLpro are validated drug targets for developing antivirals to treat coronavirus diseases, such as COVID-19. However, the development of 3CLpro inhibitors relies heavily on BSL-3 laboratories. Here, we report a series of BRET-based self-cleaving biosensors that can be used to set up cell-based assays to evaluate the cell permeability and cellular activity of SARS-CoV-2 3CLpro inhibitors in BSL-2 laboratories. The cell-based assay is suitable for high-throughput screening for 3CLpro inhibitors because of the simplicity and good reproducibility of our biosensors. The design strategy can also be used to design biosensors for other viral proteases for which the activation processes involve the self-cleavage of polyproteins.
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Affiliation(s)
- Ningke Hou
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University; Center for Infectious Disease Research, Westlake Laboratory of Life Sciences and Biomedicine; and Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Chen Peng
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University; Center for Infectious Disease Research, Westlake Laboratory of Life Sciences and Biomedicine; and Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Lijing Zhang
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University; Center for Infectious Disease Research, Westlake Laboratory of Life Sciences and Biomedicine; and Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Yuyao Zhu
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University; Center for Infectious Disease Research, Westlake Laboratory of Life Sciences and Biomedicine; and Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Qi Hu
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University; Center for Infectious Disease Research, Westlake Laboratory of Life Sciences and Biomedicine; and Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
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14
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Expression, purification, and biophysical characterization of recombinant MERS-CoV main (M pro) protease. Int J Biol Macromol 2022; 209:984-990. [PMID: 35452699 PMCID: PMC9017057 DOI: 10.1016/j.ijbiomac.2022.04.077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 04/04/2022] [Accepted: 04/11/2022] [Indexed: 11/21/2022]
Abstract
MERS-CoV main protease (Mpro) is essential for the maturation of the coronavirus; therefore, considered a potential drug target. Detailed conformational information is essential to developing antiviral therapeutics. However, the conformation of MERS-CoV Mpro under different conditions is poorly characterized. In this study, MERS-CoV Mpro was recombinantly produced in E.coli and characterized its structural stability with respect to changes in pH and temperatures. The intrinsic and extrinsic fluorescence measurements revealed that MERS-CoV Mpro tertiary structure was exposed to the polar environment due to the unfolding of the tertiary structure. However, the secondary structure of MERS-CoV Mpro was gained at low pH because of charge-charge repulsion. Furthermore, differential scanning fluorometry studies of Mpro showed a single thermal transition at all pHs except at pH 2.0; no transitions were observed. The data from the spectroscopic studies suggest that the MERS-CoV Mpro forms a molten globule-like state at pH 2.0. Insilico studies showed that the covid-19 Mpro shows 96.08% and 50.65% similarity to that of SARS-CoV Mpro and MERS-CoV Mpro, respectively. This study provides a basic understanding of the thermodynamic and structural properties of MERS-CoV Mpro.
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15
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Komissarov A, Karaseva M, Roschina M, Kostrov S, Demidyuk I. The SARS-CoV-2 main protease doesn't induce cell death in human cells in vitro. PLoS One 2022; 17:e0266015. [PMID: 35609027 PMCID: PMC9129031 DOI: 10.1371/journal.pone.0266015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 03/11/2022] [Indexed: 11/19/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of coronavirus disease 2019 (COVID-19) which has extremely rapidly spread worldwide. In order to develop the effective antiviral therapies, it is required to understand the molecular mechanisms of the SARS-CoV-2 pathogenesis. The main protease, or 3C-like protease (3CLpro), plays the essential role in the coronavirus replication that makes the enzyme a promising therapeutic target. Viral enzymes are known to be multifunctional. Particularly, 3CLpro of SARS-CoV was shown to induce apoptosis in addition to its main function. In the present study we analyzed the cytotoxicity of active SARS-CoV-2 3CLpro and its inactivated form upon their individual expression in four human cell lines. For this purpose, we constructed a protein biosensor which allows to detect the proteolytic activity of SARS-CoV-2 3CLpro and confirmed the expression of the active protease in all cell lines used. We studied viability and morphology of the cells and found that both active and inactivated enzyme variants induce no cell death in contrast to the homologous 3CL protease of SARS-CoV. These results indicate that SARS-CoV-2 3CLpro is unlikely contribute to the cytopathic effect observed during viral infection directly.
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Affiliation(s)
- Alexey Komissarov
- Institute of Molecular Genetics of National Research Centre Kurchatov Institute, Moscow, Russian Federation
| | - Maria Karaseva
- Institute of Molecular Genetics of National Research Centre Kurchatov Institute, Moscow, Russian Federation
| | - Marina Roschina
- Institute of Molecular Genetics of National Research Centre Kurchatov Institute, Moscow, Russian Federation
| | - Sergey Kostrov
- Institute of Molecular Genetics of National Research Centre Kurchatov Institute, Moscow, Russian Federation
| | - Ilya Demidyuk
- Institute of Molecular Genetics of National Research Centre Kurchatov Institute, Moscow, Russian Federation
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16
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Kumari R, Kumar V, Dhankhar P, Dalal V. Promising antivirals for PLpro of SARS-CoV-2 using virtual screening, molecular docking, dynamics, and MMPBSA. J Biomol Struct Dyn 2022:1-17. [PMID: 35510600 DOI: 10.1080/07391102.2022.2071340] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The recent pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection (COVID-19) is a viral respiratory disease that has been spread all over the globe. Therefore, it is an urgent requirement to identify and develop drugs for this contagious infection. The papain-like protease (PLpro) of SARS-CoV-2 performs critical functions in virus replication and immune evasion, making it an enticing therapeutic target. SARS-CoV-2 and SARS-CoV PLpro proteases have significant similarities, and an inhibitor discovered for SARS-CoV PLpro is an exciting first step toward therapeutic development. Here, a set of antiviral molecules were screened at the catalytic and S-binding allosteric sites of papain-like protease (PLpro). Molecular docking results suggested that five molecules (44560613, 136277567, S5652, SC75741, and S3833) had good binding affinities at both sites of PLpro. Molecular dynamics analysis like root mean square deviation (RMSD), root mean square fluctuation (RMSF), radius of gyration (Rg), solvent accessible surface area (SASA), and hydrogen bond results showed that identified molecules with PLpro tend to form stable PLpro-inhibitor(s) complexes. Molecular Mechanics/Position-Boltzmann Surface Area (MMPBSA) analysis confirmed that antiviral molecules bound PLpro complex had lower energy (-184.72 ± 7.81 to -215.67 ± 6.73 kJ/mol) complexes. Noticeably, computational approaches revealed promising antivirals candidates for PLpro, which may be further tested by biochemical and cell-based assays to assess their potential for SARS-CoV-2.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Reena Kumari
- Department of Mathematics and Statistics, Swami Vivekanand Subharti University, Meerut, India
| | - Viney Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, India
| | - Poonam Dhankhar
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA, USA
| | - Vikram Dalal
- Department of Anesthesiology, Washington University in St. Louis, St. Louis MO, USA
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17
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Entesari M, Zamani M, Heidarizadeh M, Moradi R, Khakdan F, Rafiei F. An Insight Into Detection Pathways/Biosensors of Highly Infectious Coronaviruses. Mol Biotechnol 2022; 64:339-354. [PMID: 34655396 PMCID: PMC8520350 DOI: 10.1007/s12033-021-00417-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 10/07/2021] [Indexed: 01/12/2023]
Abstract
The outbreak of COVID-19 pandemic and its consequences have inflicted a substantial damage on the world. In this study, it was attempted to review the recent coronaviruses appeared among the human being and their epidemic/pandemic spread throughout the world. Currently, there is an inevitable need for the establishment of a quick and easily available biosensor for tracing COVID-19 in all countries. It has been known that the incubation time of COVID-19 lasts about 14 days and 25% of the infected individuals are asymptomatic. To improve the ability to determine SARS-CoV-2 precisely and reduce the risk of eliciting false-negative results produced by mutating nature of coronaviruses, many researchers have established a real-time reverse transcriptase-polymerase chain reaction (RT-PCR) assay using mismatch-tolerant molecular beacons as multiplex real-time RT-PCR to distinguish between pathogenic and non-pathogenic strains of coronaviruses. The possible mechanisms and pathways for the detection of coronaviruses by biosensors have been reviewed in this study.
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Affiliation(s)
- Mehrnaz Entesari
- Department of Genetic Engineering and Molecular Genetics, Zanjan University, Zanjan, Iran
| | - Mina Zamani
- Department of Biology, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Mohammad Heidarizadeh
- Department of Biotechnology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Rasoul Moradi
- Department of Chemical Engineering, School of Engineering & Applied Science, Khazar University, Baku, Azerbaijan
| | | | - Fariba Rafiei
- Department of Agronomy & Plant Breeding, Collage of Agriculture & Natural Resources, University of Tehran, Karaj, Iran
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18
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Chen K, Krischuns T, Varga L, Harigua-Souiai E, Paisant S, Zettor A, Chiaravalli J, Delpal A, Courtney D, O'Brien A, Baker S, Decroly E, Isel C, Agou F, Jacob Y, Blondel A, Naffakh N. A highly sensitive cell-based luciferase assay for high-throughput automated screening of SARS-CoV-2 nsp5/3CLpro inhibitors. Antiviral Res 2022; 201:105272. [PMID: 35278581 PMCID: PMC8906008 DOI: 10.1016/j.antiviral.2022.105272] [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: 10/13/2021] [Revised: 02/19/2022] [Accepted: 02/23/2022] [Indexed: 12/15/2022]
Abstract
Effective drugs against SARS-CoV-2 are urgently needed to treat severe cases of infection and for prophylactic use. The main viral protease (nsp5 or 3CLpro) represents an attractive and possibly broad-spectrum target for drug development as it is essential to the virus life cycle and highly conserved among betacoronaviruses. Sensitive and efficient high-throughput screening methods are key for drug discovery. Here we report the development of a gain-of-signal, highly sensitive cell-based luciferase assay to monitor SARS-CoV-2 nsp5 activity and show that it is suitable for the screening of compounds in a 384-well format. A benefit of miniaturisation and automation is that screening can be performed in parallel on a wild-type and a catalytically inactive nsp5, which improves the selectivity of the assay. We performed molecular docking-based screening on a set of 14,468 compounds from an in-house chemical database, selected 359 candidate nsp5 inhibitors and tested them experimentally. We identified two molecules which show anti-nsp5 activity, both in our cell-based assay and in vitro on purified nsp5 protein, and inhibit SARS-CoV-2 replication in A549-ACE2 cells with EC50 values in the 4–8 μM range. The here described high-throughput-compatible assay will allow the screening of large-scale compound libraries for SARS-CoV-2 nsp5 inhibitors. Moreover, we provide evidence that this assay can be adapted to other coronaviruses and viruses which rely on a viral protease.
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19
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Gerber PP, Duncan LM, Greenwood EJD, Marelli S, Naamati A, Teixeira-Silva A, Crozier TWM, Gabaev I, Zhan JR, Mulroney TE, Horner EC, Doffinger R, Willis AE, Thaventhiran JED, Protasio AV, Matheson NJ. A protease-activatable luminescent biosensor and reporter cell line for authentic SARS-CoV-2 infection. PLoS Pathog 2022; 18:e1010265. [PMID: 35143592 PMCID: PMC8865646 DOI: 10.1371/journal.ppat.1010265] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Revised: 02/23/2022] [Accepted: 01/11/2022] [Indexed: 12/13/2022] Open
Abstract
Efforts to define serological correlates of protection against COVID-19 have been hampered by the lack of a simple, scalable, standardised assay for SARS-CoV-2 infection and antibody neutralisation. Plaque assays remain the gold standard, but are impractical for high-throughput screening. In this study, we show that expression of viral proteases may be used to quantitate infected cells. Our assays exploit the cleavage of specific oligopeptide linkers, leading to the activation of cell-based optical biosensors. First, we characterise these biosensors using recombinant SARS-CoV-2 proteases. Next, we confirm their ability to detect viral protease expression during replication of authentic virus. Finally, we generate reporter cells stably expressing an optimised luciferase-based biosensor, enabling viral infection to be measured within 24 h in a 96- or 384-well plate format, including variants of concern. We have therefore developed a luminescent SARS-CoV-2 reporter cell line, and demonstrated its utility for the relative quantitation of infectious virus and titration of neutralising antibodies.
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Affiliation(s)
- Pehuén Pereyra Gerber
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
- Cambridge Institute for Therapeutic Immunology and Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, United Kingdom
| | - Lidia M. Duncan
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
- Cambridge Institute for Therapeutic Immunology and Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, United Kingdom
| | - Edward JD Greenwood
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
- Cambridge Institute for Therapeutic Immunology and Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, United Kingdom
| | - Sara Marelli
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
- Cambridge Institute for Therapeutic Immunology and Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, United Kingdom
| | - Adi Naamati
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
- Cambridge Institute for Therapeutic Immunology and Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, United Kingdom
| | - Ana Teixeira-Silva
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
- Cambridge Institute for Therapeutic Immunology and Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, United Kingdom
| | - Thomas WM Crozier
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
- Cambridge Institute for Therapeutic Immunology and Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, United Kingdom
| | - Ildar Gabaev
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
- Cambridge Institute for Therapeutic Immunology and Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, United Kingdom
| | - Jun R. Zhan
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
- Cambridge Institute for Therapeutic Immunology and Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, United Kingdom
| | | | - Emily C. Horner
- MRC Toxicology Unit, University of Cambridge, Cambridge, United Kingdom
| | - Rainer Doffinger
- Department of Clinical Biochemistry and Immunology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Anne E. Willis
- MRC Toxicology Unit, University of Cambridge, Cambridge, United Kingdom
| | - James ED Thaventhiran
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
- MRC Toxicology Unit, University of Cambridge, Cambridge, United Kingdom
| | - Anna V. Protasio
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Nicholas J. Matheson
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
- Cambridge Institute for Therapeutic Immunology and Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge, United Kingdom
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20
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Hajizadeh M, Moosavi-Movahedi Z, Sheibani N, Moosavi-Movahedi AA. An outlook on suicide enzyme inhibition and drug design. JOURNAL OF THE IRANIAN CHEMICAL SOCIETY 2022; 19. [PMCID: PMC8501922 DOI: 10.1007/s13738-021-02416-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/10/2023]
Abstract
There have been recent renewed interests in the importance of suicide enzyme inhibition. The principal objective of this review is to investigate all types of suicide inhibitions for natural enzymes, artificial biocatalysts as well as therapeutic potential of enzyme suicide inhibition. It is discussed the suicide inhibition beneficial in drug design and treatments and non-beneficial achievements for some industrial enzymes such as HRP peroxidase enzyme. The design of biomimetic artificial enzymes explained to prevent inhibition by protecting the active site via environmental conditions. Suicide enzyme inhibition development can be the key mechanism against sever diseases such as SARS. In this report, suicide enzyme inactivation classes are classified based on target enzyme groups via their substrates.
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Affiliation(s)
- Mina Hajizadeh
- Institute of Biochemistry and Biophysics (IBB), The University of Tehran, Tehran, Iran
| | | | - Nader Sheibani
- Department of Ophthalmology and Visual Sciences, Cell and Regenerative Biology, and Biomedical Engineering, University of Wisconsin School of Medicine and Public Health, Madison, WI USA
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21
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Chen KY, Krischuns T, Ortega Varga L, Harigua-Souiai E, Paisant S, Zettor A, Chiaravalli J, Courtney D, O’Brien A, Baker SC, Isel C, Agou F, Jacob Y, Blondel A, Naffakh N. A highly sensitive cell-based luciferase assay for high-throughput automated screening of SARS-CoV-2 nsp5/3CLpro inhibitors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.12.18.473303. [PMID: 34981051 PMCID: PMC8722588 DOI: 10.1101/2021.12.18.473303] [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: 12/15/2022]
Abstract
Effective drugs against SARS-CoV-2 are urgently needed to treat severe cases of infection and for prophylactic use. The main viral protease (nsp5 or 3CLpro) represents an attractive and possibly broad-spectrum target for drug development as it is essential to the virus life cycle and highly conserved among betacoronaviruses. Sensitive and efficient high-throughput screening methods are key for drug discovery. Here we report the development of a gain-of-signal, highly sensitive cell-based luciferase assay to monitor SARS-CoV-2 nsp5 activity and show that it is suitable for high-throughput screening of compounds in a 384-well format. A benefit of miniaturisation and automation is that screening can be performed in parallel on a wild-type and a catalytically inactive nsp5, which improves the selectivity of the assay. We performed molecular docking-based screening on a set of 14,468 compounds from an in-house chemical database, selected 359 candidate nsp5 inhibitors and tested them experimentally. We identified four molecules, including the broad-spectrum antiviral merimepodib/VX-497, which show anti-nsp5 activity and inhibit SARS-CoV-2 replication in A549-ACE2 cells with IC 50 values in the 4-21 µM range. The here described assay will allow the screening of large-scale compound libraries for SARS-CoV-2 nsp5 inhibitors. Moreover, we provide evidence that this assay can be adapted to other coronaviruses and viruses which rely on a viral protease.
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Affiliation(s)
- KY Chen
- RNA Biology and Influenza Virus Unit, Institut Pasteur, CNRS UMR3569, Université de Paris, Paris, France
| | - T Krischuns
- RNA Biology and Influenza Virus Unit, Institut Pasteur, CNRS UMR3569, Université de Paris, Paris, France
| | - L Ortega Varga
- Structural Bioinformatics Unit, Institut Pasteur, Université de Paris, Paris, France
| | - E Harigua-Souiai
- Laboratory of Molecular Epidemiology and Experimental Pathology – LR16IPT04, Institut Pasteur de Tunis, Université de Tunis El Manar, Tunis, Tunisia
| | - S Paisant
- RNA Biology and Influenza Virus Unit, Institut Pasteur, CNRS UMR3569, Université de Paris, Paris, France
| | - A Zettor
- Chemogenomic and Biological Screening Platform, Institut Pasteur, Université de Paris, Paris, France
| | - J Chiaravalli
- Chemogenomic and Biological Screening Platform, Institut Pasteur, Université de Paris, Paris, France
| | - D Courtney
- RNA Biology and Influenza Virus Unit, Institut Pasteur, CNRS UMR3569, Université de Paris, Paris, France
| | - A O’Brien
- Department of Microbiology and Immunology, Loyola University Chicago, Stritch School of Medicine, Maywood, IL, USA
| | - SC Baker
- Department of Microbiology and Immunology, Loyola University Chicago, Stritch School of Medicine, Maywood, IL, USA
| | - C Isel
- RNA Biology and Influenza Virus Unit, Institut Pasteur, CNRS UMR3569, Université de Paris, Paris, France
| | - F Agou
- Chemogenomic and Biological Screening Platform, Institut Pasteur, Université de Paris, Paris, France
| | - Y Jacob
- Molecular Genetics of RNA Viruses, Institut Pasteur, CNRS UMR3569, Université de Paris, Paris, France
| | - A Blondel
- Structural Bioinformatics Unit, Institut Pasteur, Université de Paris, Paris, France
| | - N Naffakh
- RNA Biology and Influenza Virus Unit, Institut Pasteur, CNRS UMR3569, Université de Paris, Paris, France
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22
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Azad T, Janse van Rensburg HJ, Morgan J, Rezaei R, Crupi MJF, Chen R, Ghahremani M, Jamalkhah M, Forbes N, Ilkow C, Bell JC. Luciferase-Based Biosensors in the Era of the COVID-19 Pandemic. ACS NANOSCIENCE AU 2021; 1:15-37. [PMID: 37579261 PMCID: PMC8370122 DOI: 10.1021/acsnanoscienceau.1c00009] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Luciferase-based biosensors have a wide range of applications and assay formats, including their relatively recent use in the study of viruses. Split luciferase, bioluminescence resonance energy transfer, circularly permuted luciferase, cyclic luciferase, and dual luciferase systems have all been used to interrogate the structure and function of prominent viruses infecting humans, animals, and plants. The utility of these assays is demonstrated by numerous studies which have not only successfully characterized interactions between viral and host cell proteins but that have also used these systems to identify viral inhibitors. In the present COVID-19 pandemic, luciferase-based biosensors are already playing a critical role in the study of the culprit virus SARS-CoV-2 as well as in the development of serological assays and drug development via high-throughput screening. In this review paper, we provide a summary of existing luciferase-based biosensors and their applications in virology.
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Affiliation(s)
- Taha Azad
- Centre
for Innovative Cancer Research, Ottawa Hospital
Research Institute, Ottawa K1H 8L6, Canada
- Department
of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa K1H 8M5, Canada
| | | | - Jessica Morgan
- Centre
for Innovative Cancer Research, Ottawa Hospital
Research Institute, Ottawa K1H 8L6, Canada
- Department
of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa K1H 8M5, Canada
| | - Reza Rezaei
- Centre
for Innovative Cancer Research, Ottawa Hospital
Research Institute, Ottawa K1H 8L6, Canada
- Department
of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa K1H 8M5, Canada
| | - Mathieu J. F. Crupi
- Centre
for Innovative Cancer Research, Ottawa Hospital
Research Institute, Ottawa K1H 8L6, Canada
- Department
of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa K1H 8M5, Canada
| | - Rui Chen
- Centre
for Innovative Cancer Research, Ottawa Hospital
Research Institute, Ottawa K1H 8L6, Canada
- Department
of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa K1H 8M5, Canada
| | - Mina Ghahremani
- Canada
Department of Biology, University of Ottawa, Ottawa K1N 6N5, Canada
| | - Monire Jamalkhah
- Centre
for Innovative Cancer Research, Ottawa Hospital
Research Institute, Ottawa K1H 8L6, Canada
- Department
of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa K1H 8M5, Canada
| | - Nicole Forbes
- Centre
for Communicable Diseases and Infection Control, Public Health Agency of Canada, Ottawa K2E 1B6, Canada
| | - Carolina Ilkow
- Centre
for Innovative Cancer Research, Ottawa Hospital
Research Institute, Ottawa K1H 8L6, Canada
- Department
of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa K1H 8M5, Canada
| | - John C. Bell
- Centre
for Innovative Cancer Research, Ottawa Hospital
Research Institute, Ottawa K1H 8L6, Canada
- Department
of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa K1H 8M5, Canada
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23
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Franko N, Teixeira AP, Xue S, Charpin-El Hamri G, Fussenegger M. Design of modular autoproteolytic gene switches responsive to anti-coronavirus drug candidates. Nat Commun 2021; 12:6786. [PMID: 34811361 PMCID: PMC8609006 DOI: 10.1038/s41467-021-27072-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 10/20/2021] [Indexed: 11/28/2022] Open
Abstract
The main (Mpro) and papain-like (PLpro) proteases encoded by SARS-CoV-2 are essential to process viral polyproteins into functional units, thus representing key targets for anti-viral drug development. There is a need for an efficient inhibitor screening system that can identify drug candidates in a cellular context. Here we describe modular, tunable autoproteolytic gene switches (TAGS) relying on synthetic transcription factors that self-inactivate, unless in the presence of coronavirus protease inhibitors, consequently activating transgene expression. TAGS rapidly report the impact of drug candidates on Mpro and PLpro activities with a high signal-to-noise response and a sensitivity matching concentration ranges inhibiting viral replication. The modularity of the TAGS enabled the study of other Coronaviridae proteases, characterization of mutations and multiplexing of gene switches in human cells. Mice implanted with Mpro or PLpro TAGS-engineered cells enabled analysis of the activity and bioavailability of protease inhibitors in vivo in a virus-free setting.
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Affiliation(s)
- Nik Franko
- ETH Zurich, Department of Biosystems Science and Engineering, Mattenstrasse 26, CH-4058, Basel, Switzerland
| | - Ana Palma Teixeira
- ETH Zurich, Department of Biosystems Science and Engineering, Mattenstrasse 26, CH-4058, Basel, Switzerland
| | - Shuai Xue
- ETH Zurich, Department of Biosystems Science and Engineering, Mattenstrasse 26, CH-4058, Basel, Switzerland
| | - Ghislaine Charpin-El Hamri
- Département Génie Biologique, Institut Universitaire de Technologie, Université Claude Bernard Lyon 1, F-69622, Villeurbanne, Cedex, France
| | - Martin Fussenegger
- ETH Zurich, Department of Biosystems Science and Engineering, Mattenstrasse 26, CH-4058, Basel, Switzerland.
- University of Basel, Faculty of Life Science, Basel, Switzerland.
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24
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Sharma A, Mishra RK, Goud KY, Mohamed MA, Kummari S, Tiwari S, Li Z, Narayan R, Stanciu LA, Marty JL. Optical Biosensors for Diagnostics of Infectious Viral Disease: A Recent Update. Diagnostics (Basel) 2021; 11:2083. [PMID: 34829430 PMCID: PMC8625106 DOI: 10.3390/diagnostics11112083] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 10/26/2021] [Accepted: 11/05/2021] [Indexed: 12/15/2022] Open
Abstract
The design and development of biosensors, analytical devices used to detect various analytes in different matrices, has emerged. Biosensors indicate a biorecognition element with a physicochemical analyzer or detector, i.e., a transducer. In the present scenario, various types of biosensors have been deployed in healthcare and clinical research, for instance, biosensors for blood glucose monitoring. Pathogenic microbes are contributing mediators of numerous infectious diseases that are becoming extremely serious worldwide. The recent outbreak of COVID-19 is one of the most recent examples of such communal and deadly diseases. In efforts to work towards the efficacious treatment of pathogenic viral contagions, a fast and precise detection method is of the utmost importance in biomedical and healthcare sectors for early diagnostics and timely countermeasures. Among various available sensor systems, optical biosensors offer easy-to-use, fast, portable, handy, multiplexed, direct, real-time, and inexpensive diagnosis with the added advantages of specificity and sensitivity. Many progressive concepts and extremely multidisciplinary approaches, including microelectronics, microelectromechanical systems (MEMSs), nanotechnologies, molecular biology, and biotechnology with chemistry, are used to operate optical biosensors. A portable and handheld optical biosensing device would provide fast and reliable results for the identification and quantitation of pathogenic virus particles in each sample. In the modern day, the integration of intelligent nanomaterials in the developed devices provides much more sensitive and highly advanced sensors that may produce the results in no time and eventually help clinicians and doctors enormously. This review accentuates the existing challenges engaged in converting laboratory research to real-world device applications and optical diagnostics methods for virus infections. The review's background and progress are expected to be insightful to the researchers in the sensor field and facilitate the design and fabrication of optical sensors for life-threatening viruses with broader applicability to any desired pathogens.
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Affiliation(s)
- Atul Sharma
- Department of Pharmaceutical Chemistry, SGT College of Pharmacy, SGT University, Budhera, Gurugram 122505, Haryana, India
| | - Rupesh Kumar Mishra
- Bindley Bio-Science Center, Lab 222, 1203 W. State St., Purdue University, West Lafayette, IN 47907, USA
- School of Materials Engineering, Purdue University, 701 West Stadium Avenue, West Lafayette, IN 47907, USA
| | - K Yugender Goud
- Department of NanoEngineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Mona A Mohamed
- Pharmaceutical Chemistry Department, National Organization for Drug Control and Research (NODCAR), Egyptian Drug Authority, Giza 99999, Egypt
| | - Shekher Kummari
- Department of Chemistry, National Institute of Technology, Warangal 506004, Telangana, India
| | - Swapnil Tiwari
- School of Studies in Chemistry, Pt. Ravishankar Shukla University, Raipur 492010, Chattisgarh, India
| | - Zhanhong Li
- School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, 516 Jungong Road, Yangpu District, Shanghai 200093, China
| | - Roger Narayan
- Department of Materials Science and Engineering, NC State University, Raleigh, NC 27695, USA
- Joint Department of Biomedical Engineering, North Carolina State University, Raleigh, NC 27695, USA
| | - Lia A Stanciu
- School of Materials Engineering, Purdue University, 701 West Stadium Avenue, West Lafayette, IN 47907, USA
| | - Jean Louis Marty
- BAE-LBBM Laboratory, University of Perpignan via Domitia, 52 Avenue Paul Alduy, CEDEX 9, 66860 Perpignan, France
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25
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Mathieu C, Touret F, Jacquemin C, Janin YL, Nougairède A, Brailly M, Mazelier M, Décimo D, Vasseur V, Hans A, Valle-Casuso JC, de Lamballerie X, Horvat B, André P, Si-Tahar M, Lotteau V, Vidalain PO. A Bioluminescent 3CL Pro Activity Assay to Monitor SARS-CoV-2 Replication and Identify Inhibitors. Viruses 2021; 13:1814. [PMID: 34578395 PMCID: PMC8473059 DOI: 10.3390/v13091814] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 09/04/2021] [Accepted: 09/06/2021] [Indexed: 02/07/2023] Open
Abstract
Our therapeutic arsenal against viruses is very limited and the current pandemic of SARS-CoV-2 highlights the critical need for effective antivirals against emerging coronaviruses. Cellular assays allowing a precise quantification of viral replication in high-throughput experimental settings are essential to the screening of chemical libraries and the selection of best antiviral chemical structures. To develop a reporting system for SARS-CoV-2 infection, we generated cell lines expressing a firefly luciferase maintained in an inactive form by a consensus cleavage site for the viral protease 3CLPro of coronaviruses, so that the luminescent biosensor is turned on upon 3CLPro expression or SARS-CoV-2 infection. This cellular assay was used to screen a metabolism-oriented library of 492 compounds to identify metabolic vulnerabilities of coronaviruses for developing innovative therapeutic strategies. In agreement with recent reports, inhibitors of pyrimidine biosynthesis were found to prevent SARS-CoV-2 replication. Among the top hits, we also identified the NADPH oxidase (NOX) inhibitor Setanaxib. The anti-SARS-CoV-2 activity of Setanaxib was further confirmed using ACE2-expressing human pulmonary cells Beas2B as well as human primary nasal epithelial cells. Altogether, these results validate our cell-based functional assay and the interest of screening libraries of different origins to identify inhibitors of SARS-CoV-2 for drug repurposing or development.
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Affiliation(s)
- Cyrille Mathieu
- CIRI, Centre International de Recherche en Infectiologie, Team Immunobiology of the Viral Infections, Univ Lyon, Institut National de la Santé et de la Recherche Médicale (Inserm), U1111, Centre National de la Recherche Scientifique (CNRS), UMR5308, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, 69007 Lyon, France; (C.M.); (M.B.); (M.M.); (D.D.); (B.H.)
| | - Franck Touret
- Unité des Virus Emergents (UVE), Aix Marseille Univ, Institut de Recherche pour le Développement (IRD) 190, Institut National de la Santé et de la Recherche Médicale (Inserm) U1207, IHU Méditerranée Infection, 13005 Marseille, France; (F.T.); (A.N.); (X.d.L.)
| | - Clémence Jacquemin
- CIRI, Centre International de Recherche en Infectiologie, Team Viral Infection, Metabolism and Immunity, Univ Lyon, Institut National de la Santé et de la Recherche Médicale (Inserm), U1111, Centre National de la Recherche Scientifique (CNRS), UMR5308, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, 69007 Lyon, France; (C.J.); (P.A.)
| | - Yves L. Janin
- Unité de Chimie et Biocatalyse, Institut Pasteur, Centre National de la Recherche Scientifique (CNRS), UMR 3523, 28 rue du Dr. Roux, CEDEX 15, 75724 Paris, France;
| | - Antoine Nougairède
- Unité des Virus Emergents (UVE), Aix Marseille Univ, Institut de Recherche pour le Développement (IRD) 190, Institut National de la Santé et de la Recherche Médicale (Inserm) U1207, IHU Méditerranée Infection, 13005 Marseille, France; (F.T.); (A.N.); (X.d.L.)
| | - Manon Brailly
- CIRI, Centre International de Recherche en Infectiologie, Team Immunobiology of the Viral Infections, Univ Lyon, Institut National de la Santé et de la Recherche Médicale (Inserm), U1111, Centre National de la Recherche Scientifique (CNRS), UMR5308, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, 69007 Lyon, France; (C.M.); (M.B.); (M.M.); (D.D.); (B.H.)
| | - Magalie Mazelier
- CIRI, Centre International de Recherche en Infectiologie, Team Immunobiology of the Viral Infections, Univ Lyon, Institut National de la Santé et de la Recherche Médicale (Inserm), U1111, Centre National de la Recherche Scientifique (CNRS), UMR5308, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, 69007 Lyon, France; (C.M.); (M.B.); (M.M.); (D.D.); (B.H.)
| | - Didier Décimo
- CIRI, Centre International de Recherche en Infectiologie, Team Immunobiology of the Viral Infections, Univ Lyon, Institut National de la Santé et de la Recherche Médicale (Inserm), U1111, Centre National de la Recherche Scientifique (CNRS), UMR5308, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, 69007 Lyon, France; (C.M.); (M.B.); (M.M.); (D.D.); (B.H.)
| | - Virginie Vasseur
- Centre d’Etude des Pathologies Respiratoires (CEPR), Institut National de la Santé et de la Recherche Médicale (Inserm), U1100, Faculty of Medecine, University of Tours, 37000 Tours, France; (V.V.); (M.S.-T.)
| | - Aymeric Hans
- Laboratoire de Santé Animale, Site de Normandie de l’Agence nationale de sécurité sanitaire de l’alimentation, de l’environnement et du travail (ANSES), Physiopathologie et épidémiologie des maladies équines (PhEED) Unit, 14430 Goustranville, France; (A.H.); (J.-C.V.-C.)
| | - José-Carlos Valle-Casuso
- Laboratoire de Santé Animale, Site de Normandie de l’Agence nationale de sécurité sanitaire de l’alimentation, de l’environnement et du travail (ANSES), Physiopathologie et épidémiologie des maladies équines (PhEED) Unit, 14430 Goustranville, France; (A.H.); (J.-C.V.-C.)
| | - Xavier de Lamballerie
- Unité des Virus Emergents (UVE), Aix Marseille Univ, Institut de Recherche pour le Développement (IRD) 190, Institut National de la Santé et de la Recherche Médicale (Inserm) U1207, IHU Méditerranée Infection, 13005 Marseille, France; (F.T.); (A.N.); (X.d.L.)
| | - Branka Horvat
- CIRI, Centre International de Recherche en Infectiologie, Team Immunobiology of the Viral Infections, Univ Lyon, Institut National de la Santé et de la Recherche Médicale (Inserm), U1111, Centre National de la Recherche Scientifique (CNRS), UMR5308, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, 69007 Lyon, France; (C.M.); (M.B.); (M.M.); (D.D.); (B.H.)
| | - Patrice André
- CIRI, Centre International de Recherche en Infectiologie, Team Viral Infection, Metabolism and Immunity, Univ Lyon, Institut National de la Santé et de la Recherche Médicale (Inserm), U1111, Centre National de la Recherche Scientifique (CNRS), UMR5308, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, 69007 Lyon, France; (C.J.); (P.A.)
| | - Mustapha Si-Tahar
- Centre d’Etude des Pathologies Respiratoires (CEPR), Institut National de la Santé et de la Recherche Médicale (Inserm), U1100, Faculty of Medecine, University of Tours, 37000 Tours, France; (V.V.); (M.S.-T.)
| | - Vincent Lotteau
- CIRI, Centre International de Recherche en Infectiologie, Team Viral Infection, Metabolism and Immunity, Univ Lyon, Institut National de la Santé et de la Recherche Médicale (Inserm), U1111, Centre National de la Recherche Scientifique (CNRS), UMR5308, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, 69007 Lyon, France; (C.J.); (P.A.)
| | - Pierre-Olivier Vidalain
- CIRI, Centre International de Recherche en Infectiologie, Team Viral Infection, Metabolism and Immunity, Univ Lyon, Institut National de la Santé et de la Recherche Médicale (Inserm), U1111, Centre National de la Recherche Scientifique (CNRS), UMR5308, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, 69007 Lyon, France; (C.J.); (P.A.)
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26
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YUSUF AJ, ABDULLAHI MI, MUSA AM, ABUBAKAR H, AMALI AM, NASIR AH. Potential inhibitors of SARS CoV-2 from Neocarya macrophylla: Chemoinformatic and Molecular modeling studies against three key targets. Turk J Pharm Sci 2021; 19:202-212. [DOI: 10.4274/tjps.galenos.2021.57527] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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27
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Akinlalu AO, Chamundi A, Yakumbur DT, Afolayan FID, Duru IA, Arowosegbe MA, Enejoh OA. Repurposing FDA-approved drugs against multiple proteins of SARS-CoV-2: An in silico study. SCIENTIFIC AFRICAN 2021; 13:e00845. [PMID: 34308004 PMCID: PMC8272888 DOI: 10.1016/j.sciaf.2021.e00845] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 05/28/2021] [Accepted: 07/05/2021] [Indexed: 01/10/2023] Open
Abstract
The current crisis of the COVID-19 pandemic around the world has been devastating as many lives have been lost to the novel SARS CoV-2 virus. Thus, there is an urgent need for the right therapeutic drug to curb the disease. However, there is time constraint in drug development, hence the need for drug repurposing approach, a relatively fast and less expensive alternative. In this study, 1,100 Food and Drug Administration (FDA) approved drugs were obtained from DrugBank and trimmed to 791 ligands based on illicitness, withdrawal from the market, being chemical agents rather than drugs, being investigational drugs and having molecular weight greater than 500 (Kg/mol). The ligands were docked against six drug targets of the novel SARS CoV-2 - 3-chymotrypsin-like protease (3CLpro), Angiotensin-converting enzyme (ACE2), ADP ribose phosphatase of NSP3 (NSP3), NSP9 RNA binding protein (NSP9), RNA dependent RNA polymerase (RdRp) and Replicase Polyprotein 1a (RP1a). UCSF Chimera, PyRx and Discovery Studio, were used to prepare the proteins, dock the ligands and visualize the complexes, respectively. Remdesivir, Lopinavir and Hydroxychloroquine were used as reference drugs. Pharmacokinetic properties of the ligands were obtained using AdmetSAR. The binding energies of the standard drugs ranged from -5.4 to -8.7 kcal/mol while over 400 of the ligands screened showed binding energy lower than -5.4 kcal/mol. Out of the 791 number of compounds docked, 10, 91, 132, 92, 54 and 96 compounds showed lower binding energies than all the controls against 3CLPro, ACE2, NSP3, NSP9, RP1a and RdRp, respectively. Ligands that bound all target proteins, and showed the lowest binding energies with good ADMET properties and particularly showed the lowest binding against ACE2 are ethynodiol diacetate (-15.6 kcal/mol), methylnaltrexone (-15.5 kcal/mol), ketazolam (-14.5 kcal/mol) and naloxone (-13.6 kcal/mol). Further investigations are recommended for ethynodiol diacetate, methylnaltrexone, ketazolam and naloxone through preclinical and clinical studies to ascertain their effectiveness.
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Affiliation(s)
| | - Annapoorna Chamundi
- Department of Bioinformatics, Sri Krishna College of Arts and Science, Coimbatore, Tamilnadu, India
| | - Donald Terseer Yakumbur
- World Bank Africa Center of Excellence, Center for Food Technology and Research, Benue State University, Makurdi, Nigeria
| | | | - Ijeoma Akunna Duru
- Department of Chemistry, Federal University of Technology Owerri, Nigeria
| | | | - Ojochenemi Aladi Enejoh
- Genetics, Genomics and Bioinformatics Department, National Biotechnology Development Agency, Abuja, Nigeria
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28
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Inhibitors of Coronavirus 3CL Proteases Protect Cells from Protease-Mediated Cytotoxicity. J Virol 2021; 95:e0237420. [PMID: 33910954 DOI: 10.1128/jvi.02374-20] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
We describe a mammalian cell-based assay to identify coronavirus 3CL protease (3CLpro) inhibitors. This assay is based on rescuing protease-mediated cytotoxicity and does not require live virus. By enabling the facile testing of compounds across a range of 15 distantly related coronavirus 3CLpro enzymes, we identified compounds with broad 3CLpro-inhibitory activity. We also adapted the assay for use in compound screening and in doing so uncovered additional severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) 3CLpro inhibitors. We observed strong concordance between data emerging from this assay and those obtained from live-virus testing. The reported approach democratizes the testing of 3CLpro inhibitors by developing a simplified method for identifying coronavirus 3CLpro inhibitors that can be used by the majority of laboratories, rather than the few with extensive biosafety infrastructure. We identified two lead compounds, GC376 and compound 4, with broad activity against all 3CL proteases tested, including 3CLpro enzymes from understudied zoonotic coronaviruses. IMPORTANCE Multiple coronavirus pandemics have occurred over the last 2 decades. This has highlighted a need to be proactive in the development of therapeutics that can be readily deployed in the case of future coronavirus pandemics. We developed and validated a simplified cell-based assay for the identification of chemical inhibitors of 3CL proteases encoded by a wide range of coronaviruses. This assay is reporter free, does not require specialized biocontainment, and is optimized for performance in high-throughput screening. By testing reported 3CL protease inhibitors against a large collection of 3CL proteases with variable sequence similarity, we identified compounds with broad activity against 3CL proteases and uncovered structural insights into features that contribute to their broad activity. Furthermore, we demonstrated that this assay is suitable for identifying chemical inhibitors of proteases from families other than 3CL proteases.
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29
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Allam AE, Amen Y, Ashour A, Assaf HK, Hassan HA, Abdel-Rahman IM, Sayed AM, Shimizu K. In silico study of natural compounds from sesame against COVID-19 by targeting M pro, PL pro and RdRp. RSC Adv 2021; 11:22398-22408. [PMID: 35480825 PMCID: PMC9034212 DOI: 10.1039/d1ra03937g] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 05/31/2021] [Indexed: 01/18/2023] Open
Abstract
Natural products and traditional medicine products with known safety profiles are a promising source for the discovery of new drug leads. Natural products as sesame were reported to exhibit potential to protect from COVID-19 disease. In our study, the total methanolic extract of Sesamum indicum L. seeds (sesame) were led to isolation of seven known compounds, five lignan; sesamin 1, sesamolin 2, pinoresinol 3, hydroxymatairesinol 6, spicatolignan 7, together with two simple phenolic compounds; ferulic acid 4 and vanillic acid 5. All isolated compounds were evaluated in silico against three important SARS-CoV-2 protein targets; main protease (Mpro), papain-like protease (PLpro) and RNA-dependent RNA polymerase (RdRp) which possessed crucial role in replication and proliferation of the virus inside the human cell. The results revealed that compound 6 has the high affinity against the three main proteins, specially towards the SARS-CoV-2 Mpro that exceeded the currently used SARS-CoV-2 Mpro inhibitor darunavir as well as, exhibiting a similar binding energy at SARS CoV-2 PLpro when compared with the co-crystallized ligand. This activity continued to include the RdRp as it displayed a comparable docking score with remdesivir. Inferiorly, compounds 1 and 2 showed also similar triple inhibitory effect against the three main proteins while compound 7 exhibited a dual inhibitory effect against SARS CoV-2 PLPro and RdRp. Further molecular dynamic simulation experiments were performed to validate these docking experiments and to calculate their binding free energies (ΔGs). Compounds 1, 2, 3, 6, and 7 showed comparable binding stability inside the active site of each enzyme with ΔG values ranged from -4.9 to -8.8 kcal mol-1. All the compounds were investigated for their ADME and drug likeness properties, which showed acceptable ADME properties and obeying Lipinski's rule of five parameters. It can be concluded that the isolated compounds from sesame lignans could be an alternative source for the development of new natural leads against COVID-19.
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Affiliation(s)
- Ahmed E Allam
- Department of Pharmacognosy, Faculty of Pharmacy, Al-Azhar University Assiut 71524 Egypt
| | - Yhiya Amen
- Department of Pharmacognosy, Faculty of Pharmacy, Mansoura University Mansoura 35516 Egypt
| | - Ahmed Ashour
- Department of Pharmacognosy, Faculty of Pharmacy, Mansoura University Mansoura 35516 Egypt
| | - Hamdy K Assaf
- Department of Pharmacognosy, Faculty of Pharmacy, Al-Azhar University Assiut 71524 Egypt
| | - Heba Ali Hassan
- Department of Pharmacognosy, Faculty of Pharmacy, Deraya University, Universities Zone New Minia City 61111 Egypt
| | - Islam M Abdel-Rahman
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Deraya University New-Minia 61111 Egypt
| | - Ahmed M Sayed
- Department of Pharmacognosy, Faculty of Pharmacy, Nahda University Beni-Suef 62513 Egypt
| | - Kuniyoshi Shimizu
- Department of Agro-Environmental Sciences, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University Fukuoka Japan 819-0395
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Alamri MA, Tahir Ul Qamar M, Afzal O, Alabbas AB, Riadi Y, Alqahtani SM. Discovery of anti-MERS-CoV small covalent inhibitors through pharmacophore modeling, covalent docking and molecular dynamics simulation. J Mol Liq 2021; 330:115699. [PMID: 33867606 PMCID: PMC8040153 DOI: 10.1016/j.molliq.2021.115699] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 02/13/2021] [Accepted: 02/16/2021] [Indexed: 02/07/2023]
Abstract
Middle east respiratory syndrome coronavirus (MERS-CoV) is a fatal pathogen that poses a serious health risk worldwide and especially in the middle east countries. Targeting the MERS-CoV 3-chymotrypsin-like cysteine protease (3CLpro) with small covalent inhibitors is a significant approach to inhibit replication of the virus. The present work includes generating a pharmacophore model based on the X-ray crystal structures of MERS-CoV 3CLpro in complex with two covalently bound inhibitors. In silico screening of covalent chemical database having 31,642 compounds led to the identification of 378 compounds that fulfils the pharmacophore queries. Lipinski rules of five were then applied to select only compounds with the best physiochemical properties for orally bioavailable drugs. 260 compounds were obtained and subjected to covalent docking-based virtual screening to determine their binding energy scores. The top three candidate compounds, which were shown to adapt similar binding modes as the reported covalent ligands were selected. The mechanism and stability of binding of these compounds were confirmed by 100 ns molecular dynamic simulation followed by MM/PBSA binding free energy calculation. The identified compounds can facilitate the rational design of novel covalent inhibitors of MERS-CoV 3CLpro enzyme as anti-MERS CoV drugs.
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Affiliation(s)
- Mubarak A Alamri
- Department of Pharmaceutical Chemistry, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
| | | | - Obaid Afzal
- Department of Pharmaceutical Chemistry, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
| | - Alhumaidi B Alabbas
- Department of Pharmaceutical Chemistry, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
| | - Yassine Riadi
- Department of Pharmaceutical Chemistry, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
| | - Safar M Alqahtani
- Department of Pharmaceutical Chemistry, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
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Mobed A, Sepehri Shafigh E. Biosensors promising bio-device for pandemic screening "COVID-19". Microchem J 2021; 164:106094. [PMID: 33623173 PMCID: PMC7892310 DOI: 10.1016/j.microc.2021.106094] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Revised: 02/14/2021] [Accepted: 02/15/2021] [Indexed: 01/12/2023]
Abstract
Undoubtedly, the coronavirus pandemic is one of the most influential events not only in medicine but also in the economic field in the world. Rapid transmission and high mortality rates, as well as prolonged and asymptomatic communal periods, are the most important reasons for the global panic due to coronavirus. Since coronavirus treatment and specific vaccines are not yet available, early detection of the virus is critical. A rapid and accurate diagnosis can play a crucial role in the treatment and control of the COVID 19 disease. Serological, ELISA, and molecular-based tests, including PCR and RT-PCR, are among the most important routine methods for detecting coronaviruses. False-positive/negative results, low sensitivity and specificity, and the need for advanced equipment are among the disadvantages and problems of routine methods. To eliminate the drawbacks of routine methods, new technologies are being developed. Biosensors are one of the most important ones. This paper is a summary of the up-to-date states of innovative bio-sensing tools for the ultrasensitive detection of coronaviruses (COVID 19) with encouraging uses for future challenges in disease diagnosis.
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Affiliation(s)
- Ahmad Mobed
- Aging Research Institute, Faculty of Medicine, Tabriz University of Medical Sciences, Iran,Physical Medicine and Rehabilitation Research Center, Tabriz University of Medical Sciences, Tabriz, Iran,Corresponding author at: Aging Research Institute, Faculty of Medicine, Tabriz University of Medical Sciences, Iran
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Kumar SU, Priya NM, Nithya SR, Kannan P, Jain N, Kumar DT, Magesh R, Younes S, Zayed H, Doss CGP. A review of novel coronavirus disease (COVID-19): based on genomic structure, phylogeny, current shreds of evidence, candidate vaccines, and drug repurposing. 3 Biotech 2021; 11:198. [PMID: 33816047 PMCID: PMC8003899 DOI: 10.1007/s13205-021-02749-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 03/16/2021] [Indexed: 12/15/2022] Open
Abstract
Coronavirus disease (COVID-19) pandemic is instigated by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). As of March 13, 2021, more than 118.9 million cases were infected with COVID-19 worldwide. SARS-CoV-2 is a positive-sense single-stranded RNA beta-CoV. Most COVID-19 infected individuals recover within 1-3 weeks. Nevertheless, approximately 5% of patients develop acute respiratory distress syndrome and other systemic complications, leading to death. Structural genetic analyses of SARS-CoV-2 have shown genomic resemblances but a low evolutionary correlation to SARS-CoV-1 responsible for the 2002-2004 outbreak. The S glycoprotein is critical for cell adhesion and the entrance of the virus into the host. The process of cell entry uses the cellular receptor named angiotensin-converting enzyme 2. Recent evidence proposed that the CD147 as a SARS-CoV-2's potential receptor. The viral genome is mainly held by two non-structural proteins (NSPs), ORF1a and ORF1ab, along with structural proteins. Although NSPs are conserved among the βCoVs, mutations in NSP2 and NSP3 may play critical roles in transmitting the virus and cell tropism. To date, no specific/targeted anti-viral treatments exist. Notably, more than 50 COVID-19 candidate vaccines in clinical trials, and a few being administered. Preventive precautions are the primary strategy to limit the viral load transmission and spread, emphasizing the urgent need for developing significant drug targets and vaccines against COVID-19. This review provides a cumulative overview of the genomic structure, transmission, phylogeny of SARS-CoV-2 from Indian clusters, treatment options, updated discoveries, and future standpoints for COVID-19. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-02749-0.
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Affiliation(s)
- S. Udhaya Kumar
- Department of Integrative Biology, School of BioSciences and Technology, Vellore Institute of Technology, Tamil Nadu, Vellore, 632 014 India
| | - N. Madhana Priya
- Department of Biotechnology, Sri Ramachandra Institute of Higher Education and Research (DU), Tamil Nadu, Porur, Chennai, 600116 India
| | - S. R. Nithya
- Department of Biotechnology, Sri Ramachandra Institute of Higher Education and Research (DU), Tamil Nadu, Porur, Chennai, 600116 India
| | - Priyanka Kannan
- Department of Biotechnology, Sri Ramachandra Institute of Higher Education and Research (DU), Tamil Nadu, Porur, Chennai, 600116 India
| | - Nikita Jain
- Department of Integrative Biology, School of BioSciences and Technology, Vellore Institute of Technology, Tamil Nadu, Vellore, 632 014 India
| | - D. Thirumal Kumar
- Department of Integrative Biology, School of BioSciences and Technology, Vellore Institute of Technology, Tamil Nadu, Vellore, 632 014 India
- Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences, Chennai, 602105 India
| | - R. Magesh
- Department of Biotechnology, Sri Ramachandra Institute of Higher Education and Research (DU), Tamil Nadu, Porur, Chennai, 600116 India
| | - Salma Younes
- Department of Biomedical Sciences, College of Health and Sciences, QU Health, Qatar University, Doha, Qatar
| | - Hatem Zayed
- Department of Biomedical Sciences, College of Health and Sciences, QU Health, Qatar University, Doha, Qatar
| | - C. George Priya Doss
- Department of Integrative Biology, School of BioSciences and Technology, Vellore Institute of Technology, Tamil Nadu, Vellore, 632 014 India
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Almasi F, Mohammadipanah F. Hypothetical targets and plausible drugs of coronavirus infection caused by SARS-CoV-2. Transbound Emerg Dis 2021; 68:318-332. [PMID: 32662203 PMCID: PMC7405402 DOI: 10.1111/tbed.13734] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 07/09/2020] [Accepted: 07/09/2020] [Indexed: 12/21/2022]
Abstract
The world is confronting a dire situation due to the recent pandemic of the novel coronavirus disease (SARS-CoV-2) with the mortality rate passed over 470,000. Attaining efficient drugs evolve in parallel to the understanding of the SARS-CoV-2 pathogenesis. The current drugs in the pipeline and some plausible drugs are overviewed in this paper. Although different types of anti-viral targets are applicable for SARS-CoV-2 drug screenings, the more promising targets can be considered as 3C-like main protease (3Cl protease) and RNA polymerase. The remdesivir could be considered the closest bifunctional drug to the provisional clinical administration for SARS-CoV-2. The known molecular targets of the SARS-CoV-2 include fourteen targets, while four molecules of angiotensin-converting enzyme 2 (ACE2), cathepsin L, 3Cl protease and RNA-dependent RNA polymerase (RdRp) are suggested as more promising potential targets. Accordingly, dual-acting drugs as an encouraging solution in drug discovery are suggested. Emphasizing the potential route of SARS-CoV-2 infection and virus entry-related factors like integrins, cathepsin and ACE2 seems valuable. The potential molecular targets of each phase of the SARS-CoV-2 life cycle are discussed and highlighted in this paper. Much progress in understanding the SARS-CoV-2 and molecular details of its life cycle followed by the identification of new therapeutic targets are needed to lead us to an efficient approach in anti-SARS-CoV-2 drug discovery.
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Affiliation(s)
- Faezeh Almasi
- Pharmaceutical Biotechnology LabDepartment of Microbial BiotechnologySchool of Biology and Center of Excellence in Phylogeny of Living OrganismsCollege of ScienceUniversity of TehranTehranIran
| | - Fatemeh Mohammadipanah
- Pharmaceutical Biotechnology LabDepartment of Microbial BiotechnologySchool of Biology and Center of Excellence in Phylogeny of Living OrganismsCollege of ScienceUniversity of TehranTehranIran
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Patel B, Sharma S, Nair N, Majeed J, Goyal RK, Dhobi M. Therapeutic opportunities of edible antiviral plants for COVID-19. Mol Cell Biochem 2021; 476:2345-2364. [PMID: 33587232 PMCID: PMC7882868 DOI: 10.1007/s11010-021-04084-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 01/25/2021] [Indexed: 01/05/2023]
Abstract
The pandemic of Serious Acute Respiratory Syndrome Corona Virus-2 (SARS-CoV-2) that produces corona virus disease (COVID-19) has challenged the entire mankind by rapidly spreading globally in 210 countries affecting over 25 million people and about 1 million deaths worldwide. It continues to spread, afflicting the health system globally. So far there is no remedy for the ailment and the available antiviral regimens have been unsatisfactory for the clinical outcomes and the mode of treatment has been mainly supportive for the prevention of COVID-19-induced morbidity and mortality. From the time immortal the traditional plant-based ethno-medicines have provided the leads for the treatment of infectious diseases. Phytopharmaceuticals have provided potential and less toxic antiviral drugs as compared to conventional modern therapeutics which are associated with severe toxicities. The ethnopharmacological knowledge about plants has provided food supplements and nutraceuticals as a promise for prevention and treatment of the current pandemic. In this review article, we have attempted to comprehend the information about the edible medicinal plant materials with potential antiviral activity specifically against RNA virus which additionally possess property to improve immunity along with external and internal respiration and exhibit anti-inflammatory properties for the prevention and treatment of the disease. This will open an arena for the development of novel nutraceutical herbal formulations as an alternative therapy that can be used for the prevention and treatment of COVID-19.
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Affiliation(s)
- Bhoomika Patel
- Institute of Pharmacy, Nirma University, Ahmedabad, Gujarat, 382481, India
| | - Supriya Sharma
- Delhi Pharmaceutical Sciences and Research University, New Delhi, 110017, India
| | - Nisha Nair
- Delhi Pharmaceutical Sciences and Research University, New Delhi, 110017, India
| | - Jaseela Majeed
- Delhi Pharmaceutical Sciences and Research University, New Delhi, 110017, India
| | - Ramesh K Goyal
- Delhi Pharmaceutical Sciences and Research University, New Delhi, 110017, India
| | - Mahaveer Dhobi
- Delhi Pharmaceutical Sciences and Research University, New Delhi, 110017, India.
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Roe MK, Junod NA, Young AR, Beachboard DC, Stobart CC. Targeting novel structural and functional features of coronavirus protease nsp5 (3CL pro, M pro) in the age of COVID-19. J Gen Virol 2021; 102. [PMID: 33507143 PMCID: PMC8515871 DOI: 10.1099/jgv.0.001558] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Coronavirus protease nsp5 (Mpro, 3CLpro) remains a primary target for coronavirus therapeutics due to its indispensable and conserved role in the proteolytic processing of the viral replicase polyproteins. In this review, we discuss the diversity of known coronaviruses, the role of nsp5 in coronavirus biology, and the structure and function of this protease across the diversity of known coronaviruses, and evaluate past and present efforts to develop inhibitors to the nsp5 protease with a particular emphasis on new and mostly unexplored potential targets of inhibition. With the recent emergence of pandemic SARS-CoV-2, this review provides novel and potentially innovative strategies and directions to develop effective therapeutics against the coronavirus protease nsp5.
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Affiliation(s)
- Molly K Roe
- Department of Biological Sciences, Butler University, Indianapolis, IN, USA
| | - Nathan A Junod
- Department of Biological Sciences, Butler University, Indianapolis, IN, USA
| | - Audrey R Young
- Department of Biological Sciences, Butler University, Indianapolis, IN, USA
| | - Dia C Beachboard
- Department of Biology, DeSales University, Center Valley, PA, USA
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Elucidating the tunability of binding behavior for the MERS-CoV macro domain with NAD metabolites. Commun Biol 2021; 4:123. [PMID: 33504944 PMCID: PMC7840908 DOI: 10.1038/s42003-020-01633-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 12/16/2020] [Indexed: 12/30/2022] Open
Abstract
The macro domain is an ADP-ribose (ADPR) binding module, which is considered to act as a sensor to recognize nicotinamide adenine dinucleotide (NAD) metabolites, including poly ADPR (PAR) and other small molecules. The recognition of macro domains with various ligands is important for a variety of biological functions involved in NAD metabolism, including DNA repair, chromatin remodeling, maintenance of genomic stability, and response to viral infection. Nevertheless, how the macro domain binds to moieties with such structural obstacles using a simple cleft remains a puzzle. We systematically investigated the Middle East respiratory syndrome-coronavirus (MERS-CoV) macro domain for its ligand selectivity and binding properties by structural and biophysical approaches. Of interest, NAD, which is considered not to interact with macro domains, was co-crystallized with the MERS-CoV macro domain. Further studies at physiological temperature revealed that NAD has similar binding ability with ADPR because of the accommodation of the thermal-tunable binding pocket. This study provides the biochemical and structural bases of the detailed ligand-binding mode of the MERS-CoV macro domain. In addition, our observation of enhanced binding affinity of the MERS-CoV macro domain to NAD at physiological temperature highlights the need for further study to reveal the biological functions. Meng-Hsuan Lin et al. investigate MERS-CoV macro domain binding selectivity with NAD and NAD metabolites under various conditions. At physiological temperature, NAD is observed to have enhanced binding affinity to the MERS-CoV macro domain, shedding light on a new possible role of the MERS-CoV macro domain in viral replication.
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O'Brien A, Chen DY, Hackbart M, Close BJ, O'Brien TE, Saeed M, Baker SC. Detecting SARS-CoV-2 3CLpro expression and activity using a polyclonal antiserum and a luciferase-based biosensor. Virology 2021; 556:73-78. [PMID: 33548599 PMCID: PMC7837110 DOI: 10.1016/j.virol.2021.01.010] [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: 10/19/2020] [Revised: 01/18/2021] [Accepted: 01/18/2021] [Indexed: 02/07/2023]
Abstract
The need to stem the current outbreak of SARS-CoV-2 responsible for COVID-19 is driving the search for inhibitors that will block coronavirus replication and pathogenesis. The coronavirus 3C-like protease (3CLpro) encoded in the replicase polyprotein is an attractive target for antiviral drug development because protease activity is required for generating a functional replication complex. Reagents that can be used to screen for protease inhibitors and for identifying the replicase products of SARS-CoV-2 are urgently needed. Here we describe a luminescence-based biosensor assay for evaluating small molecule inhibitors of SARS-CoV-2 3CLpro/main protease. We also document that a polyclonal rabbit antiserum developed against SARS-CoV 3CLpro cross reacts with the highly conserved 3CLpro of SARS-CoV-2. These reagents will facilitate the pre-clinical evaluation of SARS-CoV-2 protease inhibitors.
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Affiliation(s)
- Amornrat O'Brien
- Department of Microbiology and Immunology, Loyola University Chicago, Stritch School of Medicine, Maywood, IL, USA
| | - Da-Yuan Chen
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA; National Emerging Infectious Diseases Laboratories, Boston University, MA, USA
| | - Matthew Hackbart
- Department of Microbiology and Immunology, Loyola University Chicago, Stritch School of Medicine, Maywood, IL, USA
| | - Brianna J Close
- National Emerging Infectious Diseases Laboratories, Boston University, MA, USA; Department of Microbiology, Boston University School of Medicine, Boston, MA, USA
| | - Timothy E O'Brien
- Department of Mathematics and Statistics, Loyola University Chicago, Chicago, IL, USA
| | - Mohsan Saeed
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA; National Emerging Infectious Diseases Laboratories, Boston University, MA, USA.
| | - Susan C Baker
- Department of Microbiology and Immunology, Loyola University Chicago, Stritch School of Medicine, Maywood, IL, USA.
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Rabaan AA, Al-Ahmed SH, Sah R, Alqumber MA, Haque S, Patel SK, Pathak M, Tiwari R, Yatoo MI, Haq AU, Bilal M, Dhama K, Rodriguez-Morales AJ. MERS-CoV: epidemiology, molecular dynamics, therapeutics, and future challenges. Ann Clin Microbiol Antimicrob 2021; 20:8. [PMID: 33461573 PMCID: PMC7812981 DOI: 10.1186/s12941-020-00414-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 12/22/2020] [Indexed: 02/07/2023] Open
Abstract
The Severe Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has gained research attention worldwide, given the current pandemic. Nevertheless, a previous zoonotic and highly pathogenic coronavirus, the Middle East Respiratory Syndrome coronavirus (MERS-CoV), is still causing concern, especially in Saudi Arabia and neighbour countries. The MERS-CoV has been reported from respiratory samples in more than 27 countries, and around 2500 cases have been reported with an approximate fatality rate of 35%. After its emergence in 2012 intermittent, sporadic cases, nosocomial infections and many community clusters of MERS continued to occur in many countries. Human-to-human transmission resulted in the large outbreaks in Saudi Arabia. The inherent genetic variability among various clads of the MERS-CoV might have probably paved the events of cross-species transmission along with changes in the inter-species and intra-species tropism. The current review is drafted using an extensive review of literature on various databases, selecting of publications irrespective of favouring or opposing, assessing the merit of study, the abstraction of data and analysing data. The genome of MERS-CoV contains around thirty thousand nucleotides having seven predicted open reading frames. Spike (S), envelope (E), membrane (M), and nucleocapsid (N) proteins are the four main structural proteins. The surface located spike protein (S) of betacoronaviruses has been established to be one of the significant factors in their zoonotic transmission through virus-receptor recognition mediation and subsequent initiation of viral infection. Three regions in Saudi Arabia (KSA), Eastern Province, Riyadh and Makkah were affected severely. The epidemic progression had been the highest in 2014 in Makkah and Riyadh and Eastern Province in 2013. With a lurking epidemic scare, there is a crucial need for effective therapeutic and immunological remedies constructed on sound molecular investigations.
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Affiliation(s)
- Ali A Rabaan
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, Dhahran, Saudi Arabia
| | - Shamsah H Al-Ahmed
- Specialty Paediatric Medicine, Qatif Central Hospital, Qatif, Saudi Arabia
| | - Ranjit Sah
- Tribhuvan University Institute of Medicine, Kathmandu, Nepal
| | - Mohammed A Alqumber
- Laboratory Medicine Department, Faculty of Applied Medical Sciences, Albaha University, Albaha, Saudi Arabia
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing & Allied Health Sciences, Jazan University, Jazan, Saudi Arabia
| | - Shailesh Kumar Patel
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, 243 122, India
| | - Mamta Pathak
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, 243 122, India
| | - Ruchi Tiwari
- Department of Veterinary Microbiology and Immunology, College of Veterinary Sciences, UP Pandit Deen Dayal Upadhayay Pashu Chikitsa Vigyan Vishwavidyalay Evum Go-Anusandhan Sansthan (DUVASU), Mathura, 281001, India
| | - Mohd Iqbal Yatoo
- Division of Veterinary Clinical Complex, Faculty of Veterinary Sciences and Animal Husbandry, Sher-E-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shuhama, Alusteng Srinagar, Shalimar, Srinagar, Jammu and Kashmir, 190006, India
| | - Abrar Ul Haq
- Division of Clinical Veterinary Medicine Ethics & Jurisprudence, Faculty of Veterinary Sciences and Animal Husbandry, Sher E Kashmir University of Agricultural Sciences and Technology, Kashmir, Shuhama, Srinagar, 190006, India
| | - Muhammad Bilal
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, 223003, China
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, 243 122, India.
| | - Alfonso J Rodriguez-Morales
- Public Health and Infection Research Group, Faculty of Health Sciences, Universidad Tecnologica de Pereira, Pereira, Colombia. .,Grupo de Investigación Biomedicina, Faculty of Medicine, Fundación Universitaria Autónoma de las Americas, Pereira, Risaralda, Colombia. .,School of Medicine, Universidad Privada Franz Tamayo (UNIFRANZ), Cochabamba, Bolivia.
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Abstract
The pandemic causing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has globally infected more than 50 million people and ∼1.2 million have succumbed to this deadly pathogen. With the vaccine trials still in clinical phases, mitigation of Coronavirus Disease 2019 (COVID-19) relies primarily on robust virus detection methods and subsequent quarantine measures. Hence, the importance of rapid, affordable and reproducible virus testing will serve the need to identify and treat infected subjects in a timely manner. Based on the type of diagnostic assay, the primary targets are viral genome (RNA) and encoded proteins. Currently, COVID-19 detection is performed using various molecular platforms as well as serodiagnostics that exhibit approximately 71% sensitivity. These methods encounter several limitations including sensitivity, specificity, availability of skilled expertise and instrument access. Saliva-based COVID-19 diagnostics are emerging as a superior alternative to nasal swabs because of the ease of sample collection, no interaction during sampling, and high viral titers during early stages of infection. In addition, SARS-CoV-2 is detected in the environment as aerosols associated with suspended particulate matter. Designing virus detection strategies in diverse samples will allow timely monitoring of virus spread in humans and its persistence in the environment. With the passage of time, advanced technologies are overcoming limitations associated with detection. Enhanced sensitivity and specificity of next-generation diagnostics are key features enabling improved prognostic care. In this comprehensive review, we analyze currently adopted advanced technologies and their concurrent use in the development of diagnostics for SARS-CoV-2 detection.
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Affiliation(s)
- Manali Datta
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, Rajasthan, India
| | - Desh Deepak Singh
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, Rajasthan, India
| | - Afsar R Naqvi
- Department of Periodontics, College of Dentistry, University of Illinois at Chicago, Chicago, IL, USA
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Drug Repurposing: Dipeptidyl Peptidase IV (DPP4) Inhibitors as Potential Agents to Treat SARS-CoV-2 (2019-nCoV) Infection. Pharmaceuticals (Basel) 2021; 14:ph14010044. [PMID: 33430081 PMCID: PMC7827924 DOI: 10.3390/ph14010044] [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: 12/20/2020] [Revised: 01/02/2021] [Accepted: 01/06/2021] [Indexed: 12/15/2022] Open
Abstract
The current outbreak of severe acute respiratory distress syndrome (SARS) or nCOVID-19 pandemic, caused by the coronavirus-2 (CoV-2), continues to wreak havoc globally. As novel vaccines are being discovered and developed, small molecule drugs still constitute a viable treatment option for SARS-CoV-2 infections due to their advantages such as superior patient compliance for oral therapies, reduced manufacturing costs and ease of large scale distribution due to better stability and storage profiles. Discovering new drugs for SARS-CoV-2 infections is a time consuming and expensive proposition. In this regard, drug repurposing is an appealing approach which can provide rapid access to therapeutics with proven record of safety and efficacy. We investigated the drug repurposing potential of a library of dipeptidyl peptidase 4 (DPP4) inhibitors which are currently marketed for type-2 diabetes as treatment option for SARS-CoV-2 infections. These computational studies led to the identification of three marketed DPP4 inhibitors; gemigliptin, linagliptin and evogliptin as potential inhibitors of SARS-CoV-2 Mpro viral cysteine protease. In addition, our computational modeling shows that these drugs have the potential to inhibit other viral cysteine proteases from the beta coronavirus family, including the SAR-CoV Mpro and MERS-CoV CLpro suggesting their potential to be repurposed as broad-spectrum antiviral agents.
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Çetin G, Klafack S, Studencka-Turski M, Krüger E, Ebstein F. The Ubiquitin-Proteasome System in Immune Cells. Biomolecules 2021; 11:biom11010060. [PMID: 33466553 PMCID: PMC7824874 DOI: 10.3390/biom11010060] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 12/16/2020] [Accepted: 12/22/2020] [Indexed: 12/11/2022] Open
Abstract
The ubiquitin–proteasome system (UPS) is the major intracellular and non-lysosomal protein degradation system. Thanks to its unique capacity of eliminating old, damaged, misfolded, and/or regulatory proteins in a highly specific manner, the UPS is virtually involved in almost all aspects of eukaryotic life. The critical importance of the UPS is particularly visible in immune cells which undergo a rapid and profound functional remodelling upon pathogen recognition. Innate and/or adaptive immune activation is indeed characterized by a number of substantial changes impacting various cellular processes including protein homeostasis, signal transduction, cell proliferation, and antigen processing which are all tightly regulated by the UPS. In this review, we summarize and discuss recent progress in our understanding of the molecular mechanisms by which the UPS contributes to the generation of an adequate immune response. In this regard, we also discuss the consequences of UPS dysfunction and its role in the pathogenesis of recently described immune disorders including cancer and auto-inflammatory diseases.
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Littler DR, MacLachlan BJ, Watson GM, Vivian JP, Gully BS. A pocket guide on how to structure SARS-CoV-2 drugs and therapies. Biochem Soc Trans 2020; 48:2625-2641. [PMID: 33258925 PMCID: PMC7752054 DOI: 10.1042/bst20200396] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 10/27/2020] [Accepted: 10/29/2020] [Indexed: 01/18/2023]
Abstract
The race to identify a successful treatment for COVID19 will be defined by fundamental research into the replication cycle of the SARS-CoV-2 virus. This has identified five distinct stages from which numerous vaccination and clinical trials have emerged alongside an innumerable number of drug discovery studies currently in development for disease intervention. Informing every step of the viral replication cycle has been an unprecedented 'call-to-arms' by the global structural biology community. Of the 20 main SARS-CoV-2 proteins, 13 have been resolved structurally for SARS-CoV-2 with most having a related SARS-CoV and MERS-CoV structural homologue totalling some 300 structures currently available in public repositories. Herein, we review the contribution of structural studies to our understanding of the virus and their role in structure-based development of therapeutics.
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Affiliation(s)
- Dene R. Littler
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
- Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, VIC, Australia
| | - Bruce J. MacLachlan
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
- Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, VIC, Australia
| | - Gabrielle M. Watson
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
- Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, VIC, Australia
| | - Julian P. Vivian
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
- Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, VIC, Australia
| | - Benjamin S. Gully
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
- Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, VIC, Australia
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Jo S, Kim S, Shin DH, Kim MS. Inhibition of SARS-CoV 3CL protease by flavonoids. J Enzyme Inhib Med Chem 2020; 35:145-151. [PMID: 31724441 PMCID: PMC6882434 DOI: 10.1080/14756366.2019.1690480] [Citation(s) in RCA: 412] [Impact Index Per Article: 103.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 10/27/2019] [Accepted: 10/29/2019] [Indexed: 11/24/2022] Open
Abstract
There were severe panics caused by Severe Acute Respiratory Syndrome (SARS) and Middle-East Respiratory Syndrome-Coronavirus. Therefore, researches targeting these viruses have been required. Coronaviruses (CoVs) have been rising targets of some flavonoids. The antiviral activity of some flavonoids against CoVs is presumed directly caused by inhibiting 3C-like protease (3CLpro). Here, we applied a flavonoid library to systematically probe inhibitory compounds against SARS-CoV 3CLpro. Herbacetin, rhoifolin and pectolinarin were found to efficiently block the enzymatic activity of SARS-CoV 3CLpro. The interaction of the three flavonoids was confirmed using a tryptophan-based fluorescence method, too. An induced-fit docking analysis indicated that S1, S2 and S3' sites are involved in binding with flavonoids. The comparison with previous studies showed that Triton X-100 played a critical role in objecting false positive or overestimated inhibitory activity of flavonoids. With the systematic analysis, the three flavonoids are suggested to be templates to design functionally improved inhibitors.
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Affiliation(s)
- Seri Jo
- College of Pharmacy and Graduates School of Pharmaceutical Sciences, Ewha W. University, Seoul, Republic of Korea
| | - Suwon Kim
- College of Pharmacy and Graduates School of Pharmaceutical Sciences, Ewha W. University, Seoul, Republic of Korea
| | - Dong Hae Shin
- College of Pharmacy and Graduates School of Pharmaceutical Sciences, Ewha W. University, Seoul, Republic of Korea
| | - Mi-Sun Kim
- College of Pharmacy and Graduates School of Pharmaceutical Sciences, Ewha W. University, Seoul, Republic of Korea
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Yadav M, Dhagat S, Eswari JS. Emerging strategies on in silico drug development against COVID-19: challenges and opportunities. Eur J Pharm Sci 2020; 155:105522. [PMID: 32827661 PMCID: PMC7438372 DOI: 10.1016/j.ejps.2020.105522] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 08/14/2020] [Accepted: 08/18/2020] [Indexed: 12/22/2022]
Abstract
The importance of coronaviruses as human pathogen has been highlighted by the recent outbreak of SARS-CoV-2 leading to the search of suitable drugs to overcome respiratory infections caused by the virus. Due to the lack of specific drugs against coronavirus, the existing antiviral and antimalarial drugs are currently being administered to the patients infected with SARS-CoV-2. The scientists are also considering repurposing of some of the existing drugs as a suitable option in search of effective drugs against coronavirus till the establishment of a potent drug and/or vaccine. Computer-aided drug discovery provides a promising attempt to enable scientists to develop new and target specific drugs to combat any disease. The discovery of novel targets for COVID-19 using computer-aided drug discovery tools requires knowledge of the structure of coronavirus and various target proteins present in the virus. Targeting viral proteins will make the drug specific against the virus, thereby, increasing the chances of viral mortality. Hence, this review provides the structure of SARS-CoV-2 virus along with the important viral components involved in causing infection. It also focuses on the role of various target proteins in disease, the mechanism by which currently administered drugs act against the virus and the repurposing of few drugs. The gap arising from the absence of specific drugs is addressed by proposing potential antiviral drug targets which might provide insights into structure-based drug development against SARS-CoV-2.
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Affiliation(s)
- Manisha Yadav
- Department of Biotechnology, National Institute of Technology Raipur, C.G., 492010, India
| | - Swasti Dhagat
- Department of Biotechnology, National Institute of Technology Raipur, C.G., 492010, India
| | - J Satya Eswari
- Department of Biotechnology, National Institute of Technology Raipur, C.G., 492010, India.
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Alhalaili B, Popescu IN, Kamoun O, Alzubi F, Alawadhia S, Vidu R. Nanobiosensors for the Detection of Novel Coronavirus 2019-nCoV and Other Pandemic/Epidemic Respiratory Viruses: A Review. SENSORS (BASEL, SWITZERLAND) 2020; 20:E6591. [PMID: 33218097 PMCID: PMC7698809 DOI: 10.3390/s20226591] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 11/10/2020] [Accepted: 11/11/2020] [Indexed: 02/08/2023]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic is considered a public health emergency of international concern. The 2019 novel coronavirus (2019-nCoV) or severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that caused this pandemic has spread rapidly to over 200 countries, and has drastically affected public health and the economies of states at unprecedented levels. In this context, efforts around the world are focusing on solving this problem in several directions of research, by: (i) exploring the origin and evolution of the phylogeny of the SARS-CoV-2 viral genome; (ii) developing nanobiosensors that could be highly effective in detecting the new coronavirus; (iii) finding effective treatments for COVID-19; and (iv) working on vaccine development. In this paper, an overview of the progress made in the development of nanobiosensors for the detection of human coronaviruses (SARS-CoV, SARS-CoV-2, and Middle East respiratory syndrome coronavirus (MERS-CoV) is presented, along with specific techniques for modifying the surface of nanobiosensors. The newest detection methods of the influenza virus responsible for acute respiratory syndrome were compared with conventional methods, highlighting the newest trends in diagnostics, applications, and challenges of SARS-CoV-2 (COVID-19 causative virus) nanobiosensors.
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Affiliation(s)
- Badriyah Alhalaili
- Nanotechnology and Advanced Materials Program, Kuwait Institute for Scientific Research, P.O. Box 24885, Safat 13109, Kuwait; (B.A.); (F.A.); (S.A.)
| | - Ileana Nicoleta Popescu
- Faculty of Materials Engineering and Mechanics, Valahia University of Targoviste, 13 Aleea Sinaia Street, 130004 Targoviste, Romania
| | - Olfa Kamoun
- Physics of Semiconductor Devices Unit, Faculty of Sciences of Tunis, Tunis El Manar University, Tunis 1068, Tunisia;
| | - Feras Alzubi
- Nanotechnology and Advanced Materials Program, Kuwait Institute for Scientific Research, P.O. Box 24885, Safat 13109, Kuwait; (B.A.); (F.A.); (S.A.)
| | - Sami Alawadhia
- Nanotechnology and Advanced Materials Program, Kuwait Institute for Scientific Research, P.O. Box 24885, Safat 13109, Kuwait; (B.A.); (F.A.); (S.A.)
| | - Ruxandra Vidu
- Faculty of Materials Science and Engineering, University Politehnica of Bucharest, 060042 Bucharest, Romania
- Department of Electrical and Computer Engineering, University of California Davis, Davis, CA 95616, USA
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Orooji Y, Sohrabi H, Hemmat N, Oroojalian F, Baradaran B, Mokhtarzadeh A, Mohaghegh M, Karimi-Maleh H. An Overview on SARS-CoV-2 (COVID-19) and Other Human Coronaviruses and Their Detection Capability via Amplification Assay, Chemical Sensing, Biosensing, Immunosensing, and Clinical Assays. NANO-MICRO LETTERS 2020; 13:18. [PMID: 33163530 PMCID: PMC7604542 DOI: 10.1007/s40820-020-00533-y] [Citation(s) in RCA: 111] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 09/06/2020] [Indexed: 05/03/2023]
Abstract
A novel coronavirus of zoonotic origin (SARS-CoV-2) has recently been recognized in patients with acute respiratory disease. COVID-19 causative agent is structurally and genetically similar to SARS and bat SARS-like coronaviruses. The drastic increase in the number of coronavirus and its genome sequence have given us an unprecedented opportunity to perform bioinformatics and genomics analysis on this class of viruses. Clinical tests like PCR and ELISA for rapid detection of this virus are urgently needed for early identification of infected patients. However, these techniques are expensive and not readily available for point-of-care (POC) applications. Currently, lack of any rapid, available, and reliable POC detection method gives rise to the progression of COVID-19 as a horrible global problem. To solve the negative features of clinical investigation, we provide a brief introduction of the general features of coronaviruses and describe various amplification assays, sensing, biosensing, immunosensing, and aptasensing for the determination of various groups of coronaviruses applied as a template for the detection of SARS-CoV-2. All sensing and biosensing techniques developed for the determination of various classes of coronaviruses are useful to recognize the newly immerged coronavirus, i.e., SARS-CoV-2. Also, the introduction of sensing and biosensing methods sheds light on the way of designing a proper screening system to detect the virus at the early stage of infection to tranquilize the speed and vastity of spreading. Among other approaches investigated among molecular approaches and PCR or recognition of viral diseases, LAMP-based methods and LFAs are of great importance for their numerous benefits, which can be helpful to design a universal platform for detection of future emerging pathogenic viruses.
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Affiliation(s)
- Yasin Orooji
- College of Materials Science and Engineering, Nanjing Forestry University, Nanjing, 210037 People’s Republic of China
- Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, Nanjing Forestry University, Nanjing, 210037 People’s Republic of China
| | - Hessamaddin Sohrabi
- Department of Analytical Chemistry, Faculty of Chemistry, University of Tabriz, Tabriz, 51666-16471 Iran
| | - Nima Hemmat
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Fatemeh Oroojalian
- Department of Advanced Sciences and Technologies in Medicine, School of Medicine, North Khorasan University of Medical Sciences, Bojnurd, Iran
| | - Behzad Baradaran
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ahad Mokhtarzadeh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohamad Mohaghegh
- Department of Nanobiotechnology, School of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Hassan Karimi-Maleh
- Department of Chemical Engineering, Laboratory of Nanotechnology, Quchan University of Technology, Quchan, Islamic Republic of Iran
- School of Resources and Environment, University of Electronic Science and Technology of China, Xiyuan Ave, Chengdu, 611731 People’s Republic of China
- Department of Chemical Sciences, University of Johannesburg, Doornfontein Campus, PO Box 17011, Johannesburg, 2028 South Africa
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Development of a Fluorescence-Based, High-Throughput SARS-CoV-2 3CL pro Reporter Assay. J Virol 2020; 94:JVI.01265-20. [PMID: 32843534 PMCID: PMC7592234 DOI: 10.1128/jvi.01265-20] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 08/20/2020] [Indexed: 12/27/2022] Open
Abstract
The COVID-19 pandemic has already led to more than 700,000 deaths and innumerable changes to daily life worldwide. Along with development of a vaccine, identification of effective antivirals to treat infected patients is of the highest importance. However, rapid drug discovery requires efficient methods to identify novel compounds that can inhibit the virus. In this work, we present a method for identifying inhibitors of the SARS-CoV-2 main protease, 3CLpro. This reporter-based assay allows for antiviral drug screening in human cell culture at biosafety level 2 (BSL2) with high-throughput compatible sample processing and analysis. This assay may help identify novel antivirals to control the COVID-19 pandemic. In late 2019, a human coronavirus, now known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), emerged, likely from a zoonotic reservoir. This virus causes COVID-19, has infected millions of people, and has led to hundreds of thousands of deaths across the globe. While the best interventions to control and ultimately stop the pandemic are prophylactic vaccines, antiviral therapeutics are important to limit morbidity and mortality in those already infected. At this time, only one FDA-approved anti-SARS-CoV-2 antiviral drug, remdesivir, is available, and unfortunately, its efficacy appears to be limited. Thus, the identification of new and efficacious antivirals is of the highest importance. In order to facilitate rapid drug discovery, flexible, sensitive, and high-throughput screening methods are required. With respect to drug targets, most attention is focused on either the viral RNA-dependent RNA polymerase or the main viral protease, 3CLpro. 3CLpro is an attractive target for antiviral therapeutics, as it is essential for processing newly translated viral proteins and the viral life cycle cannot be completed without protease activity. In this work, we report a new assay to identify inhibitors of 3CLpro. Our reporter is based on a green fluorescent protein (GFP)-derived protein that fluoresces only after cleavage by 3CLpro. This experimentally optimized reporter assay allows for antiviral drug screening in human cell culture at biosafety level 2 (BSL2) with high-throughput compatible protocols. Using this screening approach in combination with existing drug libraries may lead to the rapid identification of novel antivirals to suppress SARS-CoV-2 replication and spread. IMPORTANCE The COVID-19 pandemic has already led to more than 700,000 deaths and innumerable changes to daily life worldwide. Along with development of a vaccine, identification of effective antivirals to treat infected patients is of the highest importance. However, rapid drug discovery requires efficient methods to identify novel compounds that can inhibit the virus. In this work, we present a method for identifying inhibitors of the SARS-CoV-2 main protease, 3CLpro. This reporter-based assay allows for antiviral drug screening in human cell culture at biosafety level 2 (BSL2) with high-throughput compatible sample processing and analysis. This assay may help identify novel antivirals to control the COVID-19 pandemic.
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Brown AS, Ackerley DF, Calcott MJ. High-Throughput Screening for Inhibitors of the SARS-CoV-2 Protease Using a FRET-Biosensor. Molecules 2020; 25:molecules25204666. [PMID: 33066278 PMCID: PMC7587356 DOI: 10.3390/molecules25204666] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 10/09/2020] [Accepted: 10/12/2020] [Indexed: 11/18/2022] Open
Abstract
The global SARS-CoV-2 pandemic started late 2019 and currently continues unabated. The lag-time for developing vaccines means it is of paramount importance to be able to quickly develop and repurpose therapeutic drugs. Protein-based biosensors allow screening to be performed using routine molecular laboratory equipment without a need for expensive chemical reagents. Here we present a biosensor for the 3-chymotrypsin-like cysteine protease from SARS-CoV-2, comprising a FRET-capable pair of fluorescent proteins held in proximity by a protease cleavable linker. We demonstrate the utility of this biosensor for inhibitor discovery by screening 1280 compounds from the Library of Pharmaceutically Active Compounds collection. The screening identified 65 inhibitors, with the 20 most active exhibiting sub-micromolar inhibition of 3CLpro in follow-up EC50 assays. The top hits included several compounds not previously identified as 3CLpro inhibitors, in particular five members of a family of aporphine alkaloids that offer promise as new antiviral drug leads.
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Drayman N, Jones KA, Azizi SA, Froggatt HM, Tan K, Maltseva NI, Chen S, Nicolaescu V, Dvorkin S, Furlong K, Kathayat RS, Firpo MR, Mastrodomenico V, Bruce EA, Schmidt MM, Jedrzejczak R, Muñoz-Alía MÁ, Schuster B, Nair V, Botten JW, Brooke CB, Baker SC, Mounce BC, Heaton NS, Dickinson BC, Jaochimiak A, Randall G, Tay S. Drug repurposing screen identifies masitinib as a 3CLpro inhibitor that blocks replication of SARS-CoV-2 in vitro. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020. [PMID: 32908976 DOI: 10.1101/2020.08.31.274639] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
There is an urgent need for anti-viral agents that treat SARS-CoV-2 infection. The shortest path to clinical use is repurposing of drugs that have an established safety profile in humans. Here, we first screened a library of 1,900 clinically safe drugs for inhibiting replication of OC43, a human beta-coronavirus that causes the common-cold and is a relative of SARS-CoV-2, and identified 108 effective drugs. We further evaluated the top 26 hits and determined their ability to inhibit SARS-CoV-2, as well as other pathogenic RNA viruses. 20 of the 26 drugs significantly inhibited SARS-CoV-2 replication in human lung cells (A549 epithelial cell line), with EC50 values ranging from 0.1 to 8 micromolar. We investigated the mechanism of action for these and found that masitinib, a drug originally developed as a tyrosine-kinase inhibitor for cancer treatment, strongly inhibited the activity of the SARS-CoV-2 main protease 3CLpro. X-ray crystallography revealed that masitinib directly binds to the active site of 3CLpro, thereby blocking its enzymatic activity. Mastinib also inhibited the related viral protease of picornaviruses and blocked picornaviruses replication. Thus, our results show that masitinib has broad anti-viral activity against two distinct beta-coronaviruses and multiple picornaviruses that cause human disease and is a strong candidate for clinical trials to treat SARS-CoV-2 infection.
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Akaji K, Konno H. Design and Evaluation of Anti-SARS-Coronavirus Agents Based on Molecular Interactions with the Viral Protease. Molecules 2020; 25:molecules25173920. [PMID: 32867349 PMCID: PMC7504761 DOI: 10.3390/molecules25173920] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 08/14/2020] [Accepted: 08/21/2020] [Indexed: 11/16/2022] Open
Abstract
Three types of new coronaviruses (CoVs) have been identified recently as the causative viruses for the severe pneumonia-like respiratory illnesses, severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS), and corona-virus disease 2019 (COVID-19). Neither therapeutic agents nor vaccines have been developed to date, which is a major drawback in controlling the present global pandemic of COVID-19 caused by SARS coronavirus 2 (SARS-CoV-2) and has resulted in more than 20,439,814 cases and 744,385 deaths. Each of the 3C-like (3CL) proteases of the three CoVs is essential for the proliferation of the CoVs, and an inhibitor of the 3CL protease (3CLpro) is thought to be an ideal therapeutic agent against SARS, MERS, or COVID-19. Among these, SARS-CoV is the first corona-virus isolated and has been studied in detail since the first pandemic in 2003. This article briefly reviews a series of studies on SARS-CoV, focusing on the development of inhibitors for the SARS-CoV 3CLpro based on molecular interactions with the 3CL protease. Our recent approach, based on the structure-based rational design of a novel scaffold for SARS-CoV 3CLpro inhibitor, is also included. The achievements summarized in this short review would be useful for the design of a variety of novel inhibitors for corona-viruses, including SARS-CoV-2.
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Affiliation(s)
- Kenichi Akaji
- Department of Medicinal Chemistry, Kyoto Pharmaceutical University, Yamashina, Kyoto 607-8414, Japan
- Hamari Chemicals, Ltd., Suminoe-ku, Osaka 559-0034, Japan
- Correspondence:
| | - Hiroyuki Konno
- Chemical Engineering and Biochemical Engineering, Yamagata University, Yonezawa, Yamagata 992-8510, Japan;
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