1
|
Nazir F, John Kombe Kombe A, Khalid Z, Bibi S, Zhang H, Wu S, Jin T. SARS-CoV-2 replication and drug discovery. Mol Cell Probes 2024; 77:101973. [PMID: 39025272 DOI: 10.1016/j.mcp.2024.101973] [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: 01/11/2024] [Revised: 07/14/2024] [Accepted: 07/15/2024] [Indexed: 07/20/2024]
Abstract
The coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has killed millions of people and continues to wreak havoc across the globe. This sudden and deadly pandemic emphasizes the necessity for anti-viral drug development that can be rapidly administered to reduce morbidity, mortality, and virus propagation. Thus, lacking efficient anti-COVID-19 treatment, and especially given the lengthy drug development process as well as the critical death tool that has been associated with SARS-CoV-2 since its outbreak, drug repurposing (or repositioning) constitutes so far, the ideal and ready-to-go best approach in mitigating viral spread, containing the infection, and reducing the COVID-19-associated death rate. Indeed, based on the molecular similarity approach of SARS-CoV-2 with previous coronaviruses (CoVs), repurposed drugs have been reported to hamper SARS-CoV-2 replication. Therefore, understanding the inhibition mechanisms of viral replication by repurposed anti-viral drugs and chemicals known to block CoV and SARS-CoV-2 multiplication is crucial, and it opens the way for particular treatment options and COVID-19 therapeutics. In this review, we highlighted molecular basics underlying drug-repurposing strategies against SARS-CoV-2. Notably, we discussed inhibition mechanisms of viral replication, involving and including inhibition of SARS-CoV-2 proteases (3C-like protease, 3CLpro or Papain-like protease, PLpro) by protease inhibitors such as Carmofur, Ebselen, and GRL017, polymerases (RNA-dependent RNA-polymerase, RdRp) by drugs like Suramin, Remdesivir, or Favipiravir, and proteins/peptides inhibiting virus-cell fusion and host cell replication pathways, such as Disulfiram, GC376, and Molnupiravir. When applicable, comparisons with SARS-CoV inhibitors approved for clinical use were made to provide further insights to understand molecular basics in inhibiting SARS-CoV-2 replication and draw conclusions for future drug discovery research.
Collapse
Affiliation(s)
- Farah Nazir
- Center of Disease Immunity and Investigation, College of Medicine, Lishui University, Lishui, 323000, China
| | - Arnaud John Kombe Kombe
- Laboratory of Structural Immunology, Key Laboratory of Immune Response and Immunotherapy, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Zunera Khalid
- Laboratory of Structural Immunology, Key Laboratory of Immune Response and Immunotherapy, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Shaheen Bibi
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, University of Science and Technology of China, Anhui, China
| | - Hongliang Zhang
- Center of Disease Immunity and Investigation, College of Medicine, Lishui University, Lishui, 323000, China
| | - Songquan Wu
- Center of Disease Immunity and Investigation, College of Medicine, Lishui University, Lishui, 323000, China.
| | - Tengchuan Jin
- Center of Disease Immunity and Investigation, College of Medicine, Lishui University, Lishui, 323000, China; Laboratory of Structural Immunology, Key Laboratory of Immune Response and Immunotherapy, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China; Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, University of Science and Technology of China, Anhui, China; Institute of Health and Medicine, Hefei Comprehensive National Science Center, Hefei, Anhui, China; Biomedical Sciences and Health Laboratory of Anhui Province, University of Science & Technology of China, Hefei, 230027, China; Clinical Research Hospital of Chinese Academy of Sciences (Hefei), University of Science and Technology of China, Hefei, 230001, China.
| |
Collapse
|
2
|
Zhang Z, Sun Z, Liu JL. Developing Device of Death Operation (DODO) to Detect Apoptosis in 2D and 3D Cultures. Cells 2024; 13:1224. [PMID: 39056805 PMCID: PMC11274962 DOI: 10.3390/cells13141224] [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: 05/11/2024] [Revised: 07/05/2024] [Accepted: 07/18/2024] [Indexed: 07/28/2024] Open
Abstract
The real-time detection of intracellular biological processes by encoded sensors has broad application prospects. Here, we developed a degron-based modular reporting system, the Device of Death Operation (DODO), that can monitor various biological processes. The DODO system consists of a "reporter", an "inductor", and a "degron". After zymogen activation and cleavage, the degron will be released from the "reporter", which eventually leads to the stabilization of the "reporter", and can be detected. By replacing different "inductors" and "reporters", a series of biological processes can be reported through various signals. The system can effectively report the existence of TEV protease. To prove this concept, we successfully applied the DODO system to report apoptosis in 2D and 3D cultures. In addition, the reporter based on degron will help to design protease reporters other than caspase.
Collapse
Affiliation(s)
- Ziheng Zhang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Zhe Sun
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Ji-Long Liu
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3PT, UK
| |
Collapse
|
3
|
Sokolinskaya EL, Ivanova ON, Fedyakina IT, Ivanov AV, Lukyanov KA. Natural-Target-Mimicking Translocation-Based Fluorescent Sensor for Detection of SARS-CoV-2 PLpro Protease Activity and Virus Infection in Living Cells. Int J Mol Sci 2024; 25:6635. [PMID: 38928340 PMCID: PMC11203561 DOI: 10.3390/ijms25126635] [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: 05/11/2024] [Revised: 06/13/2024] [Accepted: 06/15/2024] [Indexed: 06/28/2024] Open
Abstract
Papain-like protease PLpro, a domain within a large polyfunctional protein, nsp3, plays key roles in the life cycle of SARS-CoV-2, being responsible for the first events of cleavage of a polyprotein into individual proteins (nsp1-4) as well as for the suppression of cellular immunity. Here, we developed a new genetically encoded fluorescent sensor, named PLpro-ERNuc, for detection of PLpro activity in living cells using a translocation-based readout. The sensor was designed as follows. A fragment of nsp3 protein was used to direct the sensor on the cytoplasmic surface of the endoplasmic reticulum (ER) membrane, thus closely mimicking the natural target of PLpro. The fluorescent part included two bright fluorescent proteins-red mScarlet I and green mNeonGreen-separated by a linker with the PLpro cleavage site. A nuclear localization signal (NLS) was attached to ensure accumulation of mNeonGreen into the nucleus upon cleavage. We tested PLpro-ERNuc in a model of recombinant PLpro expressed in HeLa cells. The sensor demonstrated the expected cytoplasmic reticular network in the red and green channels in the absence of protease, and efficient translocation of the green signal into nuclei in the PLpro-expressing cells (14-fold increase in the nucleus/cytoplasm ratio). Then, we used PLpro-ERNuc in a model of Huh7.5 cells infected with the SARS-CoV-2 virus, where it showed robust ER-to-nucleus translocation of the green signal in the infected cells 24 h post infection. We believe that PLpro-ERNuc represents a useful tool for screening PLpro inhibitors as well as for monitoring virus spread in a culture.
Collapse
Affiliation(s)
- Elena L. Sokolinskaya
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia;
| | - Olga N. Ivanova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (O.N.I.); (A.V.I.)
| | - Irina T. Fedyakina
- Gamaleya National Research Centre for Epidemiology and Microbiology of the Ministry of Russia, 132098 Moscow, Russia;
| | - Alexander V. Ivanov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (O.N.I.); (A.V.I.)
| | - Konstantin A. Lukyanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia;
| |
Collapse
|
4
|
Li C, Schneider JM, Schneider EM. Disulfiram Inhibits Opsonin-Independent Phagocytosis and Migration of Human Long-Lived In Vitro Cultured Phagocytes from Multiple Inflammatory Diseases. Cells 2024; 13:535. [PMID: 38534379 DOI: 10.3390/cells13060535] [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: 01/22/2024] [Revised: 03/07/2024] [Accepted: 03/11/2024] [Indexed: 03/28/2024] Open
Abstract
Disulfiram (DSF), an anti-alcoholism medicine, exerts treatment effects in patients suffering from persistent Borreliosis and also exhibits anti-cancer effects through its copper chelating derivatives and induction of oxidative stress in mitochondria. Since chronic/persistent borreliosis is characterized by increased amounts of pro-inflammatory macrophages, this study investigated opsonin-independent phagocytosis, migration, and surface marker expression of in vivo activated and in vitro cultured human monocyte-derived phagocytes (macrophages and dendritic cells) with and without DSF treatment. Phagocytosis of non-opsonized Dynabeads® M-450 and migration of macrophages and dendritic cells were monitored using live cell analyzer Juli™ Br for 24 h, imaging every 3.5 min. To simultaneously monitor phagocyte function, results were analyzed by a newly developed software based on the differential phase contrast images of cells before and after ingestion of Dynabeads. DSF decreased the phagocytic capacities exhibited by in vitro enriched and long-lived phagocytes. Although no chemotactic gradient was applied to the test system, vigorous spontaneous migration was observed. We therefore set up an algorithm to monitor and quantify both phagocytosis and migration simultaneously. DSF not only reduced phagocytosis in a majority of these long-lived phagocytes but also impaired their migration. Despite these selective effects by DSF, we found that DSF reduced the expression densities of surface antigens CD45 and CD14 in all of our long-lived phagocytes. In cells with a high metabolic activity and high mitochondrial contents, DSF led to cell death corresponding to mitochondrial oxidative stress, whereas metabolically inactive phagocytes survived our DSF treatment protocol. In conclusion, DSF affects the viability of metabolically active phagocytes by inducing mitochondrial stress and secondly attenuates phagocytosis and migration in some long-lived phagocytes.
Collapse
Affiliation(s)
- Chen Li
- Clinic for Anaesthesiology and Intensive Care Medicine, Ulm University Hospital, Albert-Einstein-Allee 23, 89081 Ulm, Germany
| | - Julian M Schneider
- Clinic for Anaesthesiology and Intensive Care Medicine, Ulm University Hospital, Albert-Einstein-Allee 23, 89081 Ulm, Germany
| | - E Marion Schneider
- Clinic for Anaesthesiology and Intensive Care Medicine, Ulm University Hospital, Albert-Einstein-Allee 23, 89081 Ulm, Germany
| |
Collapse
|
5
|
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.
Collapse
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
| |
Collapse
|
6
|
Bischof E. Mitigating COVID-19 Mortality and Morbidity in China's Aging Population: A Focus on Available Medications and Future Developments. Aging Dis 2023; 14:1967-1976. [PMID: 37199593 PMCID: PMC10676792 DOI: 10.14336/ad.2023.0318] [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: 02/15/2023] [Accepted: 03/18/2023] [Indexed: 05/19/2023] Open
Abstract
The COVID-19 pandemic, often referred to as the geropandemic, has put immense pressure on global healthcare systems worldwide, leading to a rush in the development and approval of medications for the treatment of the viral infection. Clinical trials on efficacy and safety had a limited spectrum on inclusion and endpoints because of the urgent need for fast results. The chronologically and biologically aged population is especially at risk for severe or lethal disease, as well as treatment-associated toxicity. In China, the growing elderly population segment has been a focus in public health measurements of COVID-19, guiding towards herd immunity with a mild variant, thus minimizing overall deaths and morbidity. While the COVID-19 pandemic has now been reclassified and the virus weakened, there is a clear need for novel therapies to protect the elderly. This paper reviews the current safety and efficacy of available COVID-19 medications in China, with a specific focus on 3CL protease inhibitors and the aging population. The current COVID wave in China has demonstrated a significant impact on the elderly and the need for new drugs that are effective at low doses and can be used alone, without harmful side effects, generation of viral resistance, and drug-drug interactions. The rush to develop and approve COVID-19 medications has brought up important questions about the balance between speed and caution, resulting in a pipeline of novel therapies now moving through clinical trials, including third-generation 3CL protease inhibitors. A majority of those therapeutics are being developed in China.
Collapse
Affiliation(s)
- Evelyne Bischof
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Department of Oncology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
- Department of Advanced Biomedical Sciences, Federico II University of Naples, Naples, Italy.
- Shanghai University of Medicine and Health Sciences, Shanghai, China.
| |
Collapse
|
7
|
Pérez-Vargas J, Worrall LJ, Olmstead AD, Ton AT, Lee J, Villanueva I, Thompson CAH, Dudek S, Ennis S, Smith JR, Shapira T, De Guzman J, Gang S, Ban F, Vuckovic M, Bielecki M, Kovacic S, Kenward C, Hong CY, Gordon DG, Levett PN, Krajden M, Leduc R, Boudreault PL, Niikura M, Paetzel M, Young RN, Cherkasov A, Strynadka NCJ, Jean F. A novel class of broad-spectrum active-site-directed 3C-like protease inhibitors with nanomolar antiviral activity against highly immune-evasive SARS-CoV-2 Omicron subvariants. Emerg Microbes Infect 2023; 12:2246594. [PMID: 37555275 PMCID: PMC10453993 DOI: 10.1080/22221751.2023.2246594] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 07/31/2023] [Accepted: 08/06/2023] [Indexed: 08/10/2023]
Abstract
Antivirals with broad coronavirus activity are important for treating high-risk individuals exposed to the constantly evolving SARS-CoV-2 variants of concern (VOCs) as well as emerging drug-resistant variants. We developed and characterized a novel class of active-site-directed 3-chymotrypsin-like protease (3CLpro) inhibitors (C2-C5a). Our lead direct-acting antiviral (DAA), C5a, is a non-covalent, non-peptide with a dissociation constant of 170 nM against recombinant SARS-CoV-2 3CLpro. The compounds C2-C5a exhibit broad-spectrum activity against Omicron subvariants (BA.5, BQ.1.1, and XBB.1.5) and seasonal human coronavirus-229E infection in human cells. Notably, C5a has median effective concentrations of 30-50 nM against BQ.1.1 and XBB.1.5 in two different human cell lines. X-ray crystallography has confirmed the unique binding modes of C2-C5a to the 3CLpro, which can limit virus cross-resistance to emerging Paxlovid-resistant variants. We tested the effect of C5a with two of our newly discovered host-directed antivirals (HDAs): N-0385, a TMPRSS2 inhibitor, and bafilomycin D (BafD), a human vacuolar H+-ATPase [V-ATPase] inhibitor. We demonstrated a synergistic action of C5a in combination with N-0385 and BafD against Omicron BA.5 infection in human Calu-3 lung cells. Our findings underscore that a SARS-CoV-2 multi-targeted treatment for circulating Omicron subvariants based on DAAs (C5a) and HDAs (N-0385 or BafD) can lead to therapeutic benefits by enhancing treatment efficacy. Furthermore, the high-resolution structures of SARS-CoV-2 3CLpro in complex with C2-C5a will facilitate future rational optimization of our novel broad-spectrum active-site-directed 3C-like protease inhibitors.
Collapse
Affiliation(s)
- Jimena Pérez-Vargas
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Liam J. Worrall
- Department of Biochemistry and Molecular Biology and Centre for Blood Research, University of British Columbia, Vancouver, Canada
| | - Andrea D. Olmstead
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Anh-Tien Ton
- Vancouver Prostate Centre, University of British Columbia, Vancouver, Canada
| | - Jaeyong Lee
- Department of Biochemistry and Molecular Biology and Centre for Blood Research, University of British Columbia, Vancouver, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada
| | - Ivan Villanueva
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Connor A. H. Thompson
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Svenja Dudek
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Siobhan Ennis
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Jason R. Smith
- Vancouver Prostate Centre, University of British Columbia, Vancouver, Canada
- Department of Chemistry, Simon Fraser University, Burnaby, Canada
| | - Tirosh Shapira
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Joshua De Guzman
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Shutong Gang
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Fuqiang Ban
- Vancouver Prostate Centre, University of British Columbia, Vancouver, Canada
| | - Marija Vuckovic
- Department of Biochemistry and Molecular Biology and Centre for Blood Research, University of British Columbia, Vancouver, Canada
| | - Michael Bielecki
- Department of Chemistry, Simon Fraser University, Burnaby, Canada
| | - Suzana Kovacic
- Department of Chemistry, Simon Fraser University, Burnaby, Canada
| | - Calem Kenward
- Department of Biochemistry and Molecular Biology and Centre for Blood Research, University of British Columbia, Vancouver, Canada
| | - Christopher Yee Hong
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Danielle G. Gordon
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Paul N. Levett
- British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Mel Krajden
- British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Richard Leduc
- Department of Pharmacology-Physiology, Faculty of Medicine and Health Sciences, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, Sherbrooke, Canada
| | - Pierre-Luc Boudreault
- Department of Pharmacology-Physiology, Faculty of Medicine and Health Sciences, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, Sherbrooke, Canada
| | - Masahiro Niikura
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Mark Paetzel
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada
| | - Robert N. Young
- Department of Chemistry, Simon Fraser University, Burnaby, Canada
| | - Artem Cherkasov
- Vancouver Prostate Centre, University of British Columbia, Vancouver, Canada
| | - Natalie C. J. Strynadka
- Department of Biochemistry and Molecular Biology and Centre for Blood Research, University of British Columbia, Vancouver, Canada
| | - François Jean
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| |
Collapse
|
8
|
To TL, Li X, Shu X. Spying on SARS-CoV-2 with Fluorescent Tags and Protease Reporters. Viruses 2023; 15:2005. [PMID: 37896782 PMCID: PMC10612051 DOI: 10.3390/v15102005] [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: 09/06/2023] [Revised: 09/23/2023] [Accepted: 09/26/2023] [Indexed: 10/29/2023] Open
Abstract
The SARS-CoV-2 coronavirus has caused worldwide disruption through the COVID-19 pandemic, providing a sobering reminder of the profound impact viruses can have on human well-being. Understanding virus life cycles and interactions with host cells lays the groundwork for exploring therapeutic strategies against virus-related diseases. Fluorescence microscopy plays a vital role in virus imaging, offering high spatiotemporal resolution, sensitivity, and spectroscopic versatility. In this opinion piece, we first highlight two recent techniques, SunTag and StayGold, for the in situ imaging of viral RNA translation and viral assembly. Next, we discuss a new class of genetically encoded fluorogenic protease reporters, such as FlipGFP, which can be customized to monitor SARS-CoV-2's main (Mpro) or papain-like (PLpro) protease activity. These assays have proven effective in identifying potential antivirals through high-throughput screening, making fluorogenic viral protease reporters a promising platform for viral disease diagnostics and therapeutics.
Collapse
Affiliation(s)
| | - Xiaoquan Li
- Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, UC San Francisco, San Francisco, CA 94158, USA
| | - Xiaokun Shu
- Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, UC San Francisco, San Francisco, CA 94158, USA
| |
Collapse
|
9
|
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.
Collapse
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
| |
Collapse
|
10
|
Beia ZC, Yu H, Wang H, Li Q, Wang B, Zhang D, Xu L, Zhao L, Dong S, Song Y. Orthogonal dual reporter-based gain-of-signal assay for probing SARS-CoV-2 3CL protease activity in living cells: inhibitor identification and mutation investigation. Emerg Microbes Infect 2023; 12:2211688. [PMID: 37144395 DOI: 10.1080/22221751.2023.2211688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The main protease (3-chymotrypsin-like protease, 3CLpro) of SARS-CoV-2 has become a focus of anti-coronavirus research. Despite efforts, drug development targeting 3CLpro has been hampered by limitations in the currently available activity assays. Additionally, the emergence of 3CLpro mutations in circulating SARS-CoV-2 variants has raised concerns about potential resistance. Both emphasize the need for a more reliable, sensitive, and facile 3CLpro assay. Here, we report an orthogonal dual reporter-based gain-of-signal assay for measuring 3CLpro activity in living cells. It builds on the finding that 3CLpro induces cytotoxicity and reporter expression suppression, which can be rescued by its inhibitor or mutation. This assay circumvents most limitations in previously reported assays, especially false positives caused by nonspecific compounds and signal interference from test compounds. It is also convenient and robust for high throughput screening of compounds and comparing the drug susceptibilities of mutants. Using this assay, we screened 1789 compounds, including natural products and protease inhibitors, with 45 compounds that have been reported to inhibit SARS-CoV-2 3CLpro among them. Except for the approved drug PF-07321332, only five of these inhibit 3CLpro in our assays: GC376; PF-00835231; S-217622; Boceprevir; and Z-FA-FMK. The susceptibilities of seven 3CLpro mutants prevalent in circulating variants to PF-07321332, S-217622, and GC376 were also assessed. Three mutants were identified as being less susceptible to PF-07321322 (P132H) and S-217622 (G15S, T21I). This assay should greatly facilitate the development of novel 3CLpro-targeted drugs and the monitoring of the susceptibility of emerging SARS-CoV-2 variants to 3CLpro inhibitors.
Collapse
Affiliation(s)
- Zhu-Chun Beia
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Huanhuan Yu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
- The Affiliated AnNing First Hospital, Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China
| | - Hong Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Qingyun Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
- Clinical laboratory, No.985 hospital, Joint Support Unit, Chinese People's Liberation Army, Taiyuan, 030001, China
| | - Baogang Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Dongna Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Likun Xu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Liangliang Zhao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Shuwei Dong
- The Affiliated AnNing First Hospital, Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China
| | - Yabin Song
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| |
Collapse
|
11
|
Tan H, Hu Y, Wang J. FlipGFP protease assay for evaluating in vitro inhibitory activity against SARS-CoV-2 M pro and PL pro. STAR Protoc 2023; 4:102323. [PMID: 37329507 PMCID: PMC10156985 DOI: 10.1016/j.xpro.2023.102323] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 03/22/2023] [Accepted: 04/28/2023] [Indexed: 06/19/2023] Open
Abstract
FlipGFP assay characterizes the intracellular drug target engagement to Mpro and PLpro and can be performed in the biosafety level 1/2 settings. Here, we provide the detailed protocol for the cell-based FlipGFP assay to identify and characterize SARS-CoV-2 Mpro and PLpro inhibitors. We describe steps for cell passage and seeding, transfection, addition of compounds, and their incubation and timing. We then detail the quantification of the fluorescence signal of the assay For complete details on the use and execution of this protocol, please refer to Ma et al.1.
Collapse
Affiliation(s)
- Haozhou Tan
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
| | - Yanmei Hu
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
| | - Jun Wang
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA.
| |
Collapse
|
12
|
Hassan H, Chiavaralli J, Hassan A, Bedda L, Krischuns T, Chen KY, Li ASM, Delpal A, Decroly E, Vedadi M, Naffakh N, Agou F, Mallart S, Arafa RK, Arimondo PB. Design and synthesis of naturally-inspired SARS-CoV-2 inhibitors. RSC Med Chem 2023; 14:507-519. [PMID: 36970153 PMCID: PMC10034039 DOI: 10.1039/d2md00149g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 01/13/2023] [Indexed: 01/26/2023] Open
Abstract
A naturally inspired chemical library of 25 molecules was synthesised guided by 3-D dimensionality and natural product likeness factors to explore a new chemical space. The synthesised chemical library, consisting of fused-bridged dodecahydro-2a,6-epoxyazepino[3,4,5-c,d]indole skeletons, followed lead likeness factors in terms of molecular weight, C-sp3 fraction and Clog P. Screening of the 25 compounds against lung cells infected with SARS-CoV-2 led to the identification of 2 hits. Although the chemical library showed cytotoxicity, the two hits (3b, 9e) showed the highest antiviral activity (EC50 values of 3.7 and 1.4 μM, respectively) with an acceptable cytotoxicity difference. Computational analysis based on docking and molecular dynamics simulations against main protein targets in SARS-CoV-2 (main protease Mpro, nucleocapsid phosphoprotein, non-structural protein nsp10-nsp16 complex and RBD/ACE2 complex) were performed. The computational analysis proposed the possible binding targets to be either Mpro or the nsp10-nsp16 complex. Biological assays were performed to confirm this proposition. A cell-based assay for Mpro protease activity using a reverse-nanoluciferase (Rev-Nluc) reporter confirmed that 3b targets Mpro. These results open the way towards further hit-to-lead optimisations.
Collapse
Affiliation(s)
- Haitham Hassan
- Institut Pasteur, Department of Structural Biology and Chemistry, CNRS UMR no 3523 Chem4Life, Epigenetic Chemical Biology, Université Paris Cité F-75015 Paris France
| | - Jeanne Chiavaralli
- Institut Pasteur, Center for Technological Resources and Research (C2RT), CNRS UMR no 3523 Chem4Life, Chemogenomic and Biological Screening platform, Université Paris Cité F-75015 Paris France
| | - Afnan Hassan
- Drug Design and Discovery Lab, Zewail City of Science and Technology 12578 Cairo Egypt
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology 12578 Cairo Egypt
| | - Loay Bedda
- Drug Design and Discovery Lab, Zewail City of Science and Technology 12578 Cairo Egypt
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology 12578 Cairo Egypt
| | - Tim Krischuns
- Institut Pasteur, Unité Biologie des ARN et Virus Influenza, CNRS UMR3569, Université Paris Cité F-75015 Paris France
| | - Kuang-Yu Chen
- Institut Pasteur, Unité Biologie des ARN et Virus Influenza, CNRS UMR3569, Université Paris Cité F-75015 Paris France
| | - Alice Shi Ming Li
- Department of Pharmacology and Toxicology, University of Toronto Canada
| | - Adrien Delpal
- CNRS - UMR7257 - AFMB - Aix-Marseille Université Marseille France
| | - Etienne Decroly
- CNRS - UMR7257 - AFMB - Aix-Marseille Université Marseille France
| | - Masoud Vedadi
- Department of Pharmacology and Toxicology, University of Toronto Canada
- QBI COVID-19 Research Group (QCRG) San Francisco CA USA
| | - Nadia Naffakh
- Institut Pasteur, Unité Biologie des ARN et Virus Influenza, CNRS UMR3569, Université Paris Cité F-75015 Paris France
| | - Fabrice Agou
- Institut Pasteur, Center for Technological Resources and Research (C2RT), CNRS UMR no 3523 Chem4Life, Chemogenomic and Biological Screening platform, Université Paris Cité F-75015 Paris France
| | - Sergio Mallart
- Institut Pasteur, Department of Structural Biology and Chemistry, CNRS UMR no 3523 Chem4Life, Epigenetic Chemical Biology, Université Paris Cité F-75015 Paris France
| | - Reem K Arafa
- Drug Design and Discovery Lab, Zewail City of Science and Technology 12578 Cairo Egypt
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology 12578 Cairo Egypt
| | - Paola B Arimondo
- Institut Pasteur, Department of Structural Biology and Chemistry, CNRS UMR no 3523 Chem4Life, Epigenetic Chemical Biology, Université Paris Cité F-75015 Paris France
| |
Collapse
|
13
|
Arakawa M, Yoshida A, Okamura S, Ebina H, Morita E. A highly sensitive NanoLuc-based protease biosensor for detecting apoptosis and SARS-CoV-2 infection. Sci Rep 2023; 13:1753. [PMID: 36720982 PMCID: PMC9887574 DOI: 10.1038/s41598-023-28984-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 01/27/2023] [Indexed: 02/02/2023] Open
Abstract
Proteases play critical roles in various biological processes, including apoptosis and viral infection. Several protease biosensors have been developed; however, obtaining a reliable signal from a very low level of endogenous protease activity remains a challenge. In this study, we developed a highly sensitive protease biosensor, named FlipNanoLuc, based on the Oplophorus gracilirostris NanoLuc luciferase. The flipped β-strand was restored by protease activation and cleavage, resulting in the reconstitution of luciferase and enzymatic activity. By making several modifications, such as introducing NanoBiT technology and CL1-PEST1 degradation tag, the FlipNanoLuc-based protease biosensor system achieved more than 500-fold luminescence increase in the corresponding protease-overexpressing cells. We demonstrated that the FlipNanoLuc-based caspase sensor can be utilized for the detection of staurosporine-induced apoptosis with sixfold increase in luminescence. Furthermore, we also demonstrated that the FlipNanoLuc-based coronavirus 3CL-protease sensor can be used to detect human coronavirus OC43 with tenfold increase in luminescence and severe acute respiratory syndrome-coronavirus-2 infections with 20-fold increase in luminescence by introducing the stem-loop 1 sequence to prevent the virus inducing global translational shutdown.
Collapse
Affiliation(s)
- Masashi Arakawa
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo-Cho, Hirosaki-Shi, Aomori, 036-8561, Japan.,Division of Biomolecular Function, Bioresources Science, United Graduate School of Agricultural Sciences, Iwate University, Morioka, 020-0066, Japan
| | - Akiho Yoshida
- Virus Vaccine Group, BIKEN Innovative Vaccine Research Alliance Laboratories, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Osaka, Japan.,The Research Foundation for Microbial Diseases of Osaka University, Suita, Osaka, Japan
| | - Shinya Okamura
- Virus Vaccine Group, BIKEN Innovative Vaccine Research Alliance Laboratories, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Osaka, Japan.,The Research Foundation for Microbial Diseases of Osaka University, Suita, Osaka, Japan
| | - Hirotaka Ebina
- Virus Vaccine Group, BIKEN Innovative Vaccine Research Alliance Laboratories, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Osaka, Japan.,Virus Vaccine Group, BIKEN Innovative Vaccine Research Alliance Laboratories, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan.,The Research Foundation for Microbial Diseases of Osaka University, Suita, Osaka, Japan
| | - Eiji Morita
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo-Cho, Hirosaki-Shi, Aomori, 036-8561, Japan. .,Division of Biomolecular Function, Bioresources Science, United Graduate School of Agricultural Sciences, Iwate University, Morioka, 020-0066, Japan.
| |
Collapse
|
14
|
Yang Z, Cai X, Ye Q, Zhao Y, Li X, Zhang S, Zhang L. High-Throughput Screening for the Potential Inhibitors of SARS-CoV-2 with Essential Dynamic Behavior. Curr Drug Targets 2023; 24:532-545. [PMID: 36876836 DOI: 10.2174/1389450124666230306141725] [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: 06/18/2022] [Revised: 11/09/2022] [Accepted: 01/11/2023] [Indexed: 03/07/2023]
Abstract
Global health security has been challenged by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) pandemic. Due to the lengthy process of generating vaccinations, it is vital to reposition currently available drugs in order to relieve anti-epidemic tensions and accelerate the development of therapies for Coronavirus Disease 2019 (COVID-19), the public threat caused by SARS-CoV-2. High throughput screening techniques have established their roles in the evaluation of already available medications and the search for novel potential agents with desirable chemical space and more cost-effectiveness. Here, we present the architectural aspects of highthroughput screening for SARS-CoV-2 inhibitors, especially three generations of virtual screening methodologies with structural dynamics: ligand-based screening, receptor-based screening, and machine learning (ML)-based scoring functions (SFs). By outlining the benefits and drawbacks, we hope that researchers will be motivated to adopt these methods in the development of novel anti- SARS-CoV-2 agents.
Collapse
Affiliation(s)
- Zhiwei Yang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an710049, China
| | - Xinhui Cai
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an710049, China
| | - Qiushi Ye
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an710049, China
| | - Yizhen Zhao
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an710049, China
| | - Xuhua Li
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an710049, China
| | - Shengli Zhang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an710049, China
| | - Lei Zhang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an710049, China
| |
Collapse
|
15
|
Bram Y, Duan X, Nilsson-Payant BE, Chandar V, Wu H, Shore D, Fajardo A, Sinha S, Hassan N, Weinstein H, TenOever BR, Chen S, Schwartz RE. Dual-Reporter System for Real-Time Monitoring of SARS-CoV-2 Main Protease Activity in Live Cells Enables Identification of an Allosteric Inhibition Path. ACS BIO & MED CHEM AU 2022; 2:627-641. [PMID: 36570071 PMCID: PMC9603010 DOI: 10.1021/acsbiomedchemau.2c00034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 09/21/2022] [Accepted: 09/21/2022] [Indexed: 11/17/2022]
Abstract
The SARS-CoV-2 pandemic is an ongoing threat to global health, and the continuing emergence of contagious variants highlights the urgent need for additional antiviral therapy to attenuate COVID-19 disease. The SARS-CoV-2 main protease (3CLpro) presents an attractive target for such therapy due to its high sequence conservation and key role in the viral life cycle. In this study, we designed a fluorescent-luminescent cell-based reporter for the detection and quantification of 3CLpro intracellular activity. Employing this platform, we examined the efficiency of known protease inhibitors against 3CLpro and further identified potent inhibitors through high-throughput chemical screening. Computational analysis confirmed a direct interaction of the lead compounds with the protease catalytic site and identified a prototype for efficient allosteric inhibition. These developments address a pressing need for a convenient sensor and specific targets for both virus detection and rapid discovery of potential inhibitors.
Collapse
Affiliation(s)
- Yaron Bram
- Division
of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, New York 10065, United States
| | - Xiaohua Duan
- Department
of Surgery, Weill Cornell Medicine, 1300 York Avenue, New York, New York 10065, United States
| | - Benjamin E. Nilsson-Payant
- Department
of Microbiology, Icahn School of Medicine
at Mount Sinai, One Gustav L Levy Place, New York, New York 10029, United
States
| | - Vasuretha Chandar
- Division
of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, New York 10065, United States
| | - Hao Wu
- Department
of Physiology, Biophysics, Weill Cornell
Medicine, 1300 York Avenue, New York, New York 10065, United States
| | - Derek Shore
- Department
of Physiology, Biophysics, Weill Cornell
Medicine, 1300 York Avenue, New York, New York 10065, United States
| | - Alvaro Fajardo
- Division
of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, New York 10065, United States
| | - Saloni Sinha
- Division
of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, New York 10065, United States
| | - Nora Hassan
- Division
of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, New York 10065, United States
| | - Harel Weinstein
- Department
of Physiology, Biophysics, Weill Cornell
Medicine, 1300 York Avenue, New York, New York 10065, United States,
| | - Benjamin R. TenOever
- Department
of Microbiology, Icahn School of Medicine
at Mount Sinai, One Gustav L Levy Place, New York, New York 10029, United
States,
| | - Shuibing Chen
- Department
of Surgery, Weill Cornell Medicine, 1300 York Avenue, New York, New York 10065, United States,
| | - Robert E. Schwartz
- Division
of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, New York 10065, United States,Department
of Physiology, Biophysics, Weill Cornell
Medicine, 1300 York Avenue, New York, New York 10065, United States,
| |
Collapse
|
16
|
de Souza AS, de Souza RF, Guzzo CR. Quantitative structure-activity relationships, molecular docking and molecular dynamics simulations reveal drug repurposing candidates as potent SARS-CoV-2 main protease inhibitors. J Biomol Struct Dyn 2022; 40:11339-11356. [PMID: 34370631 DOI: 10.1080/07391102.2021.1958700] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The current outbreak of COVID-19 is leading an unprecedented scientific effort focusing on targeting SARS-CoV-2 proteins critical for its viral replication. Herein, we performed high-throughput virtual screening of more than eleven thousand FDA-approved drugs using backpropagation-based artificial neural networks (q2LOO = 0.60, r2 = 0.80 and r2pred = 0.91), partial-least-square (PLS) regression (q2LOO = 0.83, r2 = 0.62 and r2pred = 0.70) and sequential minimal optimization (SMO) regression (q2LOO = 0.70, r2 = 0.80 and r2pred = 0.89). We simulated the stability of Acarbose-derived hexasaccharide, Naratriptan, Peramivir, Dihydrostreptomycin, Enviomycin, Rolitetracycline, Viomycin, Angiotensin II, Angiotensin 1-7, Angiotensinamide, Fenoterol, Zanamivir, Laninamivir and Laninamivir octanoate with 3CLpro by 100 ns and calculated binding free energy using molecular mechanics combined with Poisson-Boltzmann surface area (MM-PBSA). Our QSAR models and molecular dynamics data suggest that seven repurposed-drug candidates such as Acarbose-derived Hexasaccharide, Angiotensinamide, Dihydrostreptomycin, Enviomycin, Fenoterol, Naratriptan and Viomycin are potential SARS-CoV-2 main protease inhibitors. In addition, our QSAR models and molecular dynamics simulations revealed that His41, Asn142, Cys145, Glu166 and Gln189 are potential pharmacophoric centers for 3CLpro inhibitors. Glu166 is a potential pharmacophore for drug design and inhibitors that interact with this residue may be critical to avoid dimerization of 3CLpro. Our results will contribute to future investigations of novel chemical scaffolds and the discovery of novel hits in high-throughput screening as potential anti-SARS-CoV-2 properties.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Anacleto Silva de Souza
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Robson Francisco de Souza
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Cristiane Rodrigues Guzzo
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| |
Collapse
|
17
|
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.
Collapse
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
| |
Collapse
|
18
|
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.
Collapse
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
| |
Collapse
|
19
|
Xu M, Zhou J, Cheng Y, Jin Z, Clark AE, He T, Yim W, Li Y, Chang YC, Wu Z, Fajtová P, O’Donoghue AJ, Carlin AF, Todd MD, Jokerst JV. A Self-Immolative Fluorescent Probe for Selective Detection of SARS-CoV-2 Main Protease. Anal Chem 2022; 94:11728-11733. [PMID: 35973073 PMCID: PMC9396966 DOI: 10.1021/acs.analchem.2c02381] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 08/10/2022] [Indexed: 02/06/2023]
Abstract
Existing tools to detect and visualize severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) suffer from low selectivity, poor cell permeability, and high cytotoxicity. Here we report a novel self-immolative fluorescent probe (MP590) for the highly selective and sensitive detection of the SARS-CoV-2 main protease (Mpro). This fluorescent probe was prepared by connecting a Mpro-cleavable peptide (N-acetyl-Abu-Tle-Leu-Gln) with a fluorophore (i.e., resorufin) via a self-immolative aromatic linker. Fluorescent titration results show that MP590 can detect Mpro with a limit of detection (LoD) of 35 nM and is selective over interferents such as hemoglobin, bovine serum albumin (BSA), thrombin, amylase, SARS-CoV-2 papain-like protease (PLpro), and trypsin. The cell imaging data indicate that this probe can report Mpro in HEK 293T cells transfected with a Mpro expression plasmid as well as in TMPRSS2-VeroE6 cells infected with SARS-CoV-2. Our results suggest that MP590 can both measure and monitor Mpro activity and quantitatively evaluate Mpro inhibition in infected cells, making it an important tool for diagnostic and therapeutic research on SARS-CoV-2.
Collapse
Affiliation(s)
- Ming Xu
- Department of NanoEngineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Jiajing Zhou
- Department of NanoEngineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Yong Cheng
- Department of NanoEngineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Zhicheng Jin
- Department of NanoEngineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Alex E. Clark
- Department of Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Tengyu He
- Materials Science and Engineering Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Wonjun Yim
- Materials Science and Engineering Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Yi Li
- Department of NanoEngineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Yu-Ci Chang
- Materials Science and Engineering Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Zhuohong Wu
- Department of NanoEngineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Pavla Fajtová
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Anthony J. O’Donoghue
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Aaron F. Carlin
- Department of Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Michael D. Todd
- Department of Structural Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Jesse V. Jokerst
- Department of NanoEngineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
- Materials Science and Engineering Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
- Department of Radiology, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| |
Collapse
|
20
|
Cheng Y, Clark AE, Zhou J, He T, Li Y, Borum RM, Creyer MN, Xu M, Jin Z, Zhou J, Yim W, Wu Z, Fajtová P, O’Donoghue AJ, Carlin AF, Jokerst JV. Protease-Responsive Peptide-Conjugated Mitochondrial-Targeting AIEgens for Selective Imaging and Inhibition of SARS-CoV-2-Infected Cells. ACS NANO 2022; 16:12305-12317. [PMID: 35878004 PMCID: PMC9344892 DOI: 10.1021/acsnano.2c03219] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 07/11/2022] [Indexed: 05/06/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a serious threat to human health and lacks an effective treatment. There is an urgent need for both real-time tracking and precise treatment of the SARS-CoV-2-infected cells to mitigate and ultimately prevent viral transmission. However, selective triggering and tracking of the therapeutic process in the infected cells remains challenging. Here, we report a main protease (Mpro)-responsive, mitochondrial-targeting, and modular-peptide-conjugated probe (PSGMR) for selective imaging and inhibition of SARS-CoV-2-infected cells via enzyme-instructed self-assembly and aggregation-induced emission (AIE) effect. The amphiphilic PSGMR was constructed with tunable structure and responsive efficiency and validated with recombinant proteins, cells transfected with Mpro plasmid or infected by SARS-CoV-2, and a Mpro inhibitor. By rational construction of AIE luminogen (AIEgen) with modular peptides and Mpro, we verified that the cleavage of PSGMR yielded gradual aggregation with bright fluorescence and enhanced cytotoxicity to induce mitochondrial interference of the infected cells. This strategy may have value for selective detection and treatment of SARS-CoV-2-infected cells.
Collapse
Affiliation(s)
- Yong Cheng
- Department of NanoEngineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Alex E. Clark
- Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Jiajing Zhou
- Department of NanoEngineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Tengyu He
- Materials Science and Engineering Program, University of California, San Diego, La Jolla, CA 92093, USA
| | - Yi Li
- Department of NanoEngineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Raina M. Borum
- Department of NanoEngineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Matthew N. Creyer
- Department of NanoEngineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Ming Xu
- Department of NanoEngineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Zhicheng Jin
- Department of NanoEngineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jingcheng Zhou
- Department of NanoEngineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Wonjun Yim
- Materials Science and Engineering Program, University of California, San Diego, La Jolla, CA 92093, USA
| | - Zhuohong Wu
- Department of NanoEngineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Pavla Fajtová
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Anthony J. O’Donoghue
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Aaron F. Carlin
- Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Jesse V. Jokerst
- Department of NanoEngineering, University of California, San Diego, La Jolla, CA 92093, USA
- Materials Science and Engineering Program, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Radiology, University of California, San Diego, La Jolla, CA 92093, USA
| |
Collapse
|
21
|
The Main Protease of SARS-CoV-2 as a Target for Phytochemicals against Coronavirus. PLANTS 2022; 11:plants11141862. [PMID: 35890496 PMCID: PMC9319234 DOI: 10.3390/plants11141862] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 07/12/2022] [Accepted: 07/15/2022] [Indexed: 11/23/2022]
Abstract
In late December 2019, the first cases of COVID-19 emerged as an outbreak in Wuhan, China that later spread vastly around the world, evolving into a pandemic and one of the worst global health crises in modern history. The causative agent was identified as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Although several vaccines were authorized for emergency use, constantly emerging new viral mutants and limited treatment options for COVID-19 drastically highlighted the need for developing an efficient treatment for this disease. One of the most important viral components to target for this purpose is the main protease of the coronavirus (Mpro). This enzyme is an excellent target for a potential drug, as it is essential for viral replication and has no closely related homologues in humans, making its inhibitors unlikely to be toxic. Our review describes a variety of approaches that could be applied in search of potential inhibitors among plant-derived compounds, including virtual in silico screening (a data-driven approach), which could be structure-based or fragment-guided, the classical approach of high-throughput screening, and antiviral activity cell-based assays. We will focus on several classes of compounds reported to be potential inhibitors of Mpro, including phenols and polyphenols, alkaloids, and terpenoids.
Collapse
|
22
|
Sokolinskaya EL, Putlyaeva LV, Polinovskaya VS, Lukyanov KA. Genetically Encoded Fluorescent Sensors for SARS-CoV-2 Papain-like Protease PLpro. Int J Mol Sci 2022; 23:ijms23147826. [PMID: 35887174 PMCID: PMC9318946 DOI: 10.3390/ijms23147826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 07/07/2022] [Accepted: 07/14/2022] [Indexed: 02/04/2023] Open
Abstract
In the SARS-CoV-2 lifecycle, papain-like protease PLpro cuts off the non-structural proteins nsp1, nsp2, and nsp3 from a large polyprotein. This is the earliest viral enzymatic activity, which is crucial for all downstream steps. Here, we designed two genetically encoded fluorescent sensors for the real-time detection of PLpro activity in live cells. The first sensor was based on the Förster resonance energy transfer (FRET) between the red fluorescent protein mScarlet as a donor and the biliverdin-binding near-infrared fluorescent protein miRFP670 as an acceptor. A linker with the PLpro recognition site LKGG in between made this FRET pair sensitive to PLpro cleavage. Upon the co-expression of mScarlet-LKGG-miRFP670 and PLpro in HeLa cells, we observed a gradual increase in the donor fluorescence intensity of about 1.5-fold. In the second sensor, both PLpro and its target—green mNeonGreen and red mScarletI fluorescent proteins separated by an LKGG-containing linker—were attached to the endoplasmic reticulum (ER) membrane. Upon cleavage by PLpro, mScarletI diffused from the ER throughout the cell. About a two-fold increase in the nucleus/cytoplasm ratio was observed as a result of the PLpro action. We believe that the new PLpro sensors can potentially be used to detect the earliest stages of SARS-CoV-2 propagation in live cells as well as for the screening of PLpro inhibitors.
Collapse
|
23
|
Abstract
The main protease, Mpro, of SARS-CoV-2 is required to cleave the viral polyprotein into precise functional units for virus replication and pathogenesis. Here, we report quantitative reporters for Mpro function in living cells in which protease inhibition by genetic or chemical methods results in robust signal readouts by fluorescence (enhanced green fluorescent protein [eGFP]) or bioluminescence (firefly luciferase). These gain-of-signal systems are scalable to high-throughput platforms for quantitative discrimination between Mpro mutants and/or inhibitor potencies as evidenced by validation of several reported inhibitors. Additional utility is shown by single Mpro amino acid variants and structural information combining to demonstrate that both inhibitor conformational dynamics and amino acid differences are able to influence inhibitor potency. We further show that a recent variant of concern (Omicron) has an unchanged response to a clinically approved drug, nirmatrelvir, whereas proteases from divergent coronavirus species show differential susceptibility. Together, we demonstrate that these gain-of-signal systems serve as robust, facile, and scalable assays for live cell quantification of Mpro inhibition, which will help expedite the development of next-generation antivirals and enable the rapid testing of emerging variants. IMPORTANCE The main protease, Mpro, of SARS-CoV-2 is an essential viral protein required for the earliest steps of infection. It is therefore an attractive target for antiviral drug development. Here, we report the development and implementation of two complementary cell-based systems for quantification of Mpro inhibition by genetic or chemical approaches. The first is fluorescence based (eGFP), and the second is luminescence based (firefly luciferase). Importantly, both systems rely upon gain-of-signal readouts such that stronger inhibitors yield higher fluorescent or luminescent signal. The high versatility and utility of these systems are demonstrated by characterizing Mpro mutants and natural variants, including Omicron, as well as a panel of existing inhibitors. These systems rapidly, safely, and sensitively identify Mpro variants with altered susceptibilities to inhibition, triage-nonspecific, or off-target molecules and validate bona fide inhibitors, with the most potent thus far being the first-in-class drug nirmatrelvir.
Collapse
|
24
|
Production of a functionally active recombinant SARS-CoV-2 (COVID-19) 3C-Like protease and a soluble inactive 3C-like protease-RBD chimeric in a prokaryotic expression system. Epidemiol Infect 2022; 150:e128. [PMID: 35723031 PMCID: PMC9300977 DOI: 10.1017/s0950268822001078] [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] [Indexed: 11/10/2022] Open
Abstract
During the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) intracellular life-cycle, two large polyproteins, pp1a and pp1ab, are produced. Processing of these by viral cysteine proteases, the papain-like protease (PLpro) and the chymotrypsin-like 3C-like protease (3CL-pro) release non-structural proteins necessary for the establishment of the viral replication and transcription complex (RTC), crucial for viral replication. Hence, these proteases are considered prime targets against which anti-coronavirus disease 2019 (COVID-19) drugs could be developed. Here, we describe the expression of a highly soluble and functionally active recombinant 3CL-pro using Escherichia coli BL21 cells. We show that the enzyme functions in a dimeric form and exhibits an unexpected inhibitory profile because its activity is potently blocked by serine rather than cysteine protease inhibitors. In addition, we assessed the ability of our 3CL-pro to function as a carrier for the receptor binding domain (RBD) of the Spike protein. The co-expressed chimeric protein, 3CLpro-RBD, did not exhibit 3CL-pro activity, but its enhanced solubility made purification easier and improved RBD antigenicity when tested against serum from vaccinated individuals in ELISAs. Chimeric proteins containing the 3CL-pro could represent an innovative approach to developing new COVID-19 vaccines.
Collapse
|
25
|
Tan H, Hu Y, Jadhav P, Tan B, Wang J. Progress and Challenges in Targeting the SARS-CoV-2 Papain-like Protease. J Med Chem 2022; 65:7561-7580. [PMID: 35620927 PMCID: PMC9159073 DOI: 10.1021/acs.jmedchem.2c00303] [Citation(s) in RCA: 59] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Indexed: 01/18/2023]
Abstract
SARS-CoV-2 is the causative agent of the COVID-19 pandemic. The approval of vaccines and small-molecule antivirals is vital in combating the pandemic. The viral polymerase inhibitors remdesivir and molnupiravir and the viral main protease inhibitor nirmatrelvir/ritonavir have been approved by the U.S. FDA. However, the emergence of variants of concern/interest calls for additional antivirals with novel mechanisms of action. The SARS-CoV-2 papain-like protease (PLpro) mediates the cleavage of viral polyprotein and modulates the host's innate immune response upon viral infection, rendering it a promising antiviral drug target. This Perspective highlights major achievements in structure-based design and high-throughput screening of SARS-CoV-2 PLpro inhibitors since the beginning of the pandemic. Encouraging progress includes the design of non-covalent PLpro inhibitors with favorable pharmacokinetic properties and the first-in-class covalent PLpro inhibitors. In addition, we offer our opinion on the knowledge gaps that need to be filled to advance PLpro inhibitors to the clinic.
Collapse
Affiliation(s)
- Haozhou Tan
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Yanmei Hu
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Prakash Jadhav
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Bin Tan
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Jun Wang
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, New Jersey 08854, United States
| |
Collapse
|
26
|
Hognon C, Marazzi M, García-Iriepa C. Atomistic-Level Description of the Covalent Inhibition of SARS-CoV-2 Papain-like Protease. Int J Mol Sci 2022; 23:5855. [PMID: 35628665 PMCID: PMC9143025 DOI: 10.3390/ijms23105855] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 05/13/2022] [Accepted: 05/21/2022] [Indexed: 12/25/2022] Open
Abstract
Inhibition of the papain-like protease (PLpro) of SARS-CoV-2 has been demonstrated to be a successful target to prevent the spreading of the coronavirus in the infected body. In this regard, covalent inhibitors, such as the recently proposed VIR251 ligand, can irreversibly inactivate PLpro by forming a covalent bond with a specific residue of the catalytic site (Cys111), through a Michael addition reaction. An inhibition mechanism can therefore be proposed, including four steps: (i) ligand entry into the protease pocket; (ii) Cys111 deprotonation of the thiol group by a Brønsted-Lowry base; (iii) Cys111-S- addition to the ligand; and (iv) proton transfer from the protonated base to the covalently bound ligand. Evaluating the energetics and PLpro conformational changes at each of these steps could aid the design of more efficient and selective covalent inhibitors. For this aim, we have studied by means of MD simulations and QM/MM calculations the whole mechanism. Regarding the first step, we show that the inhibitor entry in the PLpro pocket is thermodynamically favorable only when considering the neutral Cys111, that is, prior to the Cys111 deprotonation. For the second step, MD simulations revealed that His272 would deprotonate Cys111 after overcoming an energy barrier of ca. 32 kcal/mol (at the QM/MM level), but implying a decrease of the inhibitor stability inside the protease pocket. This information points to a reversible Cys111 deprotonation, whose equilibrium is largely shifted toward the neutral Cys111 form. Although thermodynamically disfavored, if Cys111 is deprotonated in close proximity to the vinylic carbon of the ligand, then covalent binding takes place in an irreversible way (third step) to form the enolate intermediate. Finally, due to Cys111-S- negative charge redistribution over the bound ligand, proton transfer from the initially protonated His272 is favored, finally leading to an irreversibly modified Cys111 and a restored His272. These results elucidate the selectivity of Cys111 to enable formation of a covalent bond, even if a weak proton acceptor is available, as His272.
Collapse
Affiliation(s)
- Cécilia Hognon
- Grupo de Reactividad y Estructura Molecular (RESMOL), Departamento de Química Analítica, Química Física e Ingeniería Química, Universidad de Alcalá, Alcalá de Henares, 28801 Madrid, Spain;
| | - Marco Marazzi
- Grupo de Reactividad y Estructura Molecular (RESMOL), Departamento de Química Analítica, Química Física e Ingeniería Química, Universidad de Alcalá, Alcalá de Henares, 28801 Madrid, Spain;
- Instituto de Investigación Química “Andrés M. del Río” (IQAR), Universidad de Alcalá, Alcalá de Henares, 28801 Madrid, Spain
| | - Cristina García-Iriepa
- Grupo de Reactividad y Estructura Molecular (RESMOL), Departamento de Química Analítica, Química Física e Ingeniería Química, Universidad de Alcalá, Alcalá de Henares, 28801 Madrid, Spain;
- Instituto de Investigación Química “Andrés M. del Río” (IQAR), Universidad de Alcalá, Alcalá de Henares, 28801 Madrid, Spain
| |
Collapse
|
27
|
Ma C, Hu Y, Wang Y, Choza J, Wang J. Drug-Repurposing Screening Identified Tropifexor as a SARS-CoV-2 Papain-like Protease Inhibitor. ACS Infect Dis 2022; 8:1022-1030. [PMID: 35404564 PMCID: PMC9017246 DOI: 10.1021/acsinfecdis.1c00629] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Indexed: 12/24/2022]
Abstract
The global COVID-19 pandemic underscores the dire need for effective antivirals. Encouraging progress has been made in developing small-molecule inhibitors targeting the SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) and main protease (Mpro). However, the development of papain-like protease (PLpro) inhibitors faces several obstacles. Nevertheless, PLpro represents a high-profile drug target given its multifaceted roles in viral replication. PLpro is involved in not only the cleavage of viral polyprotein but also the modulation of host immune response. In this study, we conducted a drug-repurposing screening of PLpro against the MedChemExpress bioactive compound library and identified three hits, EACC, KY-226, and tropifexor, as potent PLpro inhibitors with IC50 values ranging from 3.39 to 8.28 μM. The three hits showed dose-dependent binding to PLpro in the thermal shift assay. In addition, tropifexor inhibited the cellular PLpro activity in the FlipGFP assay with an IC50 of 10.6 μM. Gratifyingly, tropifexor showed antiviral activity against SARS-CoV-2 in Calu-3 cells at noncytotoxic concentrations. Overall, tropifexor represents a novel PLpro inhibitor that can be further developed as SARS-CoV-2 antivirals.
Collapse
Affiliation(s)
- Chunlong Ma
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, Arizona 85721, United States
| | - Yanmei Hu
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, Arizona 85721, United States
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Yuyin Wang
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, Arizona 85721, United States
| | - Juliana Choza
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, Arizona 85721, United States
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Jun Wang
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, Arizona 85721, United States
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, New Jersey 08854, United States
| |
Collapse
|
28
|
Tan H, Ma C, Wang J. Invalidation of dieckol and 1,2,3,4,6-pentagalloylglucose (PGG) as SARS-CoV-2 main protease inhibitors and the discovery of PGG as a papain-like protease inhibitor. Med Chem Res 2022; 31:1147-1153. [PMID: 35578732 PMCID: PMC9095416 DOI: 10.1007/s00044-022-02903-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 05/02/2022] [Indexed: 11/24/2022]
Abstract
The COVID-19 pandemic spurred a broad interest in antiviral drug discovery. The SARS-CoV-2 main protease (Mpro) and papain-like protease (PLpro) are attractive antiviral drug targets given their vital roles in viral replication and modulation of host immune response. Structurally disparate compounds were reported as Mpro and PLpro inhibitors from either drug repurposing or rational design. Two polyphenols dieckol and 1,2,3,4,6-pentagalloylglucose (PGG) were recently reported as SARS-CoV-2 Mpro inhibitors. With our continuous interest in studying the mechanism of inhibition and resistance of Mpro inhibitors, we report herein our independent validation/invalidation of these two natural products. Our FRET-based enzymatic assay showed that neither dieckol nor PGG inhibited SARS-CoV-2 Mpro (IC50 > 20 µM), which is in contrary to previous reports. Serendipitously, PGG was found to inhibit the SARS-CoV-2 PLpro with an IC50 of 3.90 µM. The binding of PGG to PLpro was further confirmed in the thermal shift assay. However, PGG was cytotoxic in 293T-ACE2 cells (CC50 = 7.7 µM), so its intracellular PLpro inhibitory activity could not be quantified by the cell-based Flip-GFP PLpro assay. In addition, we also invalidated ebselen, disulfiram, carmofur, PX12, and tideglusib as SARS-CoV-2 PLpro inhibitors using the Flip-GFP assay. Overall, our results call for stringent hit validation, and the serendipitous discovery of PGG as a putative PLpro inhibitor might worth further pursuing. Graphical abstract ![]()
Collapse
|
29
|
Zhang Y, Li C, Ke X, Luo D, Liu Y, Chen Q, Wang H, Song X, Zheng Z. Development of a biosensor assessing SARS-CoV-2 main protease proteolytic activity in living cells for antiviral drugs screening. Virol Sin 2022; 37:459-461. [PMID: 35513272 PMCID: PMC9060717 DOI: 10.1016/j.virs.2022.04.002] [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: 07/23/2021] [Accepted: 04/01/2022] [Indexed: 11/25/2022] Open
Abstract
The biosensor reported in our study can monitor SARS-CoV-2 Mpro activity in living cells instead of in vitro solutions. The biosensor reported in our study is sensitive and easy to operate. It is suitable for high-throughput screening. It has the potential to be used in small animal models.
Collapse
Affiliation(s)
- Yuan Zhang
- Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Chunjie Li
- Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Xianliang Ke
- Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Dan Luo
- Department of Gastroenterology, Wuhan Children's Hospital, Tongji Medical College, Huazhong University of Science & Technology, Wuhan 430015, China
| | - Yan Liu
- Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Quanjiao Chen
- Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Hanzhong Wang
- Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Xiaohui Song
- Department of Obstetrics, Wuhan Children's Hospital, Wuhan Maternal and Child Healthcare Hospital, Tongji Medical College, Huazhong University of Science & Technology, Wuhan 430015, China.
| | - Zhenhua Zheng
- Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China.
| |
Collapse
|
30
|
A VSV-based assay quantifies coronavirus Mpro/3CLpro/Nsp5 main protease activity and chemical inhibition. Commun Biol 2022; 5:391. [PMID: 35478219 PMCID: PMC9046202 DOI: 10.1038/s42003-022-03277-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 03/15/2022] [Indexed: 11/08/2022] Open
Abstract
Protease inhibitors are among the most powerful antiviral drugs. However, for SARS-CoV-2 only a small number of protease inhibitors have been identified thus far and there is still a great need for assays that efficiently report protease activity and inhibition in living cells. Here, we engineer a safe VSV-based system to report both gain- and loss-of-function of coronavirus main protease (Mpro/3CLpro/Nsp5) activity in living cells. We use SARS-CoV-2 3CLpro in this system to confirm susceptibility to known inhibitors (boceprevir, GC376, PF-00835231, and PF-07321332/nirmatrelvir) and reevaluate other reported inhibitors (baicalein, ebselen, carmofur, ethacridine, ivermectin, masitinib, darunavir, and atazanavir). Moreover, we show that the system can be adapted to report both the function and the chemical inhibition of proteases from different coronavirus species as well as from distantly related viruses. Together with the fact that live cell assays also reflect compound permeability and toxicity, we anticipate that this system will be useful for both identification and optimization of additional coronavirus protease inhibitors.
Collapse
|
31
|
Calleja DJ, Lessene G, Komander D. Inhibitors of SARS-CoV-2 PLpro. Front Chem 2022; 10:876212. [PMID: 35559224 PMCID: PMC9086436 DOI: 10.3389/fchem.2022.876212] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 03/28/2022] [Indexed: 12/12/2022] Open
Abstract
The emergence of SARS-CoV-2 causing the COVID-19 pandemic, has highlighted how a combination of urgency, collaboration and building on existing research can enable rapid vaccine development to fight disease outbreaks. However, even countries with high vaccination rates still see surges in case numbers and high numbers of hospitalized patients. The development of antiviral treatments hence remains a top priority in preventing hospitalization and death of COVID-19 patients, and eventually bringing an end to the SARS-CoV-2 pandemic. The SARS-CoV-2 proteome contains several essential enzymatic activities embedded within its non-structural proteins (nsps). We here focus on nsp3, that harbours an essential papain-like protease (PLpro) domain responsible for cleaving the viral polyprotein as part of viral processing. Moreover, nsp3/PLpro also cleaves ubiquitin and ISG15 modifications within the host cell, derailing innate immune responses. Small molecule inhibition of the PLpro protease domain significantly reduces viral loads in SARS-CoV-2 infection models, suggesting that PLpro is an excellent drug target for next generation antivirals. In this review we discuss the conserved structure and function of PLpro and the ongoing efforts to design small molecule PLpro inhibitors that exploit this knowledge. We first discuss the many drug repurposing attempts, concluding that it is unlikely that PLpro-targeting drugs already exist. We next discuss the wealth of structural information on SARS-CoV-2 PLpro inhibition, for which there are now ∼30 distinct crystal structures with small molecule inhibitors bound in a surprising number of distinct crystallographic settings. We focus on optimisation of an existing compound class, based on SARS-CoV PLpro inhibitor GRL-0617, and recapitulate how new GRL-0617 derivatives exploit different features of PLpro, to overcome some compound liabilities.
Collapse
Affiliation(s)
- Dale J. Calleja
- Walter and Eliza Hall Institute, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Guillaume Lessene
- Walter and Eliza Hall Institute, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
- Department of Pharmacology and Therapeutics, The University of Melbourne, Melbourne, VIC, Australia
| | - David Komander
- Walter and Eliza Hall Institute, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| |
Collapse
|
32
|
Ma C, Tan H, Choza J, Wang Y, Wang J. Validation and invalidation of SARS-CoV-2 main protease inhibitors using the Flip-GFP and Protease-Glo luciferase assays. Acta Pharm Sin B 2022; 12:1636-1651. [PMID: 34745850 PMCID: PMC8558150 DOI: 10.1016/j.apsb.2021.10.026] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 09/24/2021] [Accepted: 10/14/2021] [Indexed: 12/14/2022] Open
Abstract
SARS-CoV-2 main protease (Mpro) is one of the most extensively exploited drug targets for COVID-19. Structurally disparate compounds have been reported as Mpro inhibitors, raising the question of their target specificity. To elucidate the target specificity and the cellular target engagement of the claimed Mpro inhibitors, we systematically characterize their mechanism of action using the cell-free FRET assay, the thermal shift-binding assay, the cell lysate Protease-Glo luciferase assay, and the cell-based FlipGFP assay. Collectively, our results have shown that majority of the Mpro inhibitors identified from drug repurposing including ebselen, carmofur, disulfiram, and shikonin are promiscuous cysteine inhibitors that are not specific to Mpro, while chloroquine, oxytetracycline, montelukast, candesartan, and dipyridamole do not inhibit Mpro in any of the assays tested. Overall, our study highlights the need of stringent hit validation at the early stage of drug discovery.
Collapse
|
33
|
Tan H, Ma C, Wang J. Invalidation of dieckol and 1,2,3,4,6-pentagalloylglucose (PGG) as SARS-CoV-2 main protease inhibitors and the discovery of PGG as a papain-like protease inhibitor. RESEARCH SQUARE 2022:rs.3.rs-1490282. [PMID: 35378761 PMCID: PMC8978949 DOI: 10.21203/rs.3.rs-1490282/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The COVID-19 pandemic spurred a broad interest in antiviral drug discovery. The SARS-CoV-2 main protease (M pro ) and papain-like protease (PL pro ) are attractive antiviral drug targets given their vital roles in viral replication and modulation of host immune response. Structurally disparate compounds were reported as M pro and PL pro inhibitors from either drug repurposing or rational design. Two polyphenols dieckol and 1,2,3,4,6-pentagalloylglucose (PGG) were recently reported as SARS-CoV-2 main protease (M pro ) inhibitors. With our continuous interest in studying the mechanism of inhibition and resistance of M pro inhibitors, we report herein our independent validation/invalidation of these two natural products. Our FRET-based enzymatic assay showed that neither dieckol nor PGG inhibited SARS-CoV-2 M pro (IC 50 > 20 µM), which is in contrary to previous reports. Serendipitously, PGG was found to inhibit the SARS-CoV-2 papain-like protease (PL pro ) with an IC 50 of 3.90 µM. The binding of PGG to PL pro was further confirmed in the thermal shift assay. However, PGG was cytotoxic in 293T-ACE2 cells (CC 50 = 7.7 µM), so its intracellular PL pro inhibitory activity could not be quantified by the cell-based Flip-GFP PL pro assay. In addition, we also invalidated ebselen, disulfiram, carmofur, PX12, and tideglusib as SARS-CoV-2 PL pro inhibitors using the Flip-GFP assay. Overall, our results call for stringent hit validation, and the serendipitous discovery of PGG as a putative PL pro inhibitor might worth further pursuing.
Collapse
Affiliation(s)
| | - Chunlong Ma
- University of Arizona College of Pharmacy: The University of Arizona College of Medicine Phoenix
| | - Jun Wang
- Rutgers The State University of New Jersey
| |
Collapse
|
34
|
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.
Collapse
|
35
|
Joshi N, Shukla S, Narayan RJ. Novel photonic methods for diagnosis of SARS-CoV-2 infection. TRANSLATIONAL BIOPHOTONICS 2022; 4:e202200001. [PMID: 35602265 PMCID: PMC9111306 DOI: 10.1002/tbio.202200001] [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: 01/24/2022] [Revised: 02/27/2022] [Accepted: 03/02/2022] [Indexed: 11/08/2022] Open
Abstract
The COVID-19 pandemic that began in March 2020 continues in many countries. The ongoing pandemic makes early diagnosis a crucial part of efforts to prevent the spread of SARS-CoV-2 infections. As such, the development of a rapid, reliable, and low-cost technique with increased sensitivity for detection of SARS-CoV-2 is an important priority of the scientific community. At present, nucleic acid-based techniques are primarily used as the reference approach for the detection of SARS-CoV-2 infection. However, in several cases, false positive results have been observed with these techniques. Due to the drawbacks associated with existing techniques, the development of new techniques for the diagnosis of COVID-19 is an important research activity. We provide an overview of novel diagnostic methods for SARS-CoV-2 diagnosis that integrate photonic technology with artificial intelligence. Recent developments in emerging diagnostic techniques based on the principles of advanced molecular spectroscopy and microscopy are considered.
Collapse
Affiliation(s)
- Naveen Joshi
- Department of Materials Science and EngineeringNorth Carolina State UniversityRaleighNorth CarolinaUSA
| | - Shubhangi Shukla
- Joint Department of Biomedical EngineeringNorth Carolina State UniversityRaleighNorth CarolinaUSA
| | - Roger J. Narayan
- Joint Department of Biomedical EngineeringNorth Carolina State UniversityRaleighNorth CarolinaUSA
| |
Collapse
|
36
|
Cheng Y, Borum RM, Clark AE, Jin Z, Moore C, Fajtová P, O'Donoghue AJ, Carlin AF, Jokerst JV. A Dual-Color Fluorescent Probe Allows Simultaneous Imaging of Main and Papain-like Proteases of SARS-CoV-2-Infected Cells for Accurate Detection and Rapid Inhibitor Screening. Angew Chem Int Ed Engl 2022; 61:e202113617. [PMID: 34889013 PMCID: PMC8854376 DOI: 10.1002/anie.202113617] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Indexed: 11/15/2022]
Abstract
The main protease (Mpro ) and papain-like protease (PLpro ) play critical roles in SARS-CoV-2 replication and are promising targets for antiviral inhibitors. The simultaneous visualization of Mpro and PLpro is extremely valuable for SARS-CoV-2 detection and rapid inhibitor screening. However, such a crucial investigation has remained challenging because of the lack of suitable probes. We have now developed a dual-color probe (3MBP5) for the simultaneous detection of Mpro and PLpro by fluorescence (or Förster) resonance energy transfer (FRET). This probe produces fluorescence from both the Cy3 and Cy5 fluorophores that are cleaved by Mpro and PLpro . 3MBP5-activatable specificity was demonstrated with recombinant proteins, inhibitors, plasmid-transfected HEK 293T cells, and SARS-CoV-2-infected TMPRSS2-Vero cells. Results from the dual-color probe first verified the simultaneous detection and intracellular distribution of SARS-CoV-2 Mpro and PLpro . This is a powerful tool for the simultaneous detection of different proteases with value for the rapid screening of inhibitors.
Collapse
Affiliation(s)
- Yong Cheng
- Department of NanoEngineeringUniversity of California, San DiegoLa JollaCA 92093USA
| | - Raina M. Borum
- Department of NanoEngineeringUniversity of California, San DiegoLa JollaCA 92093USA
| | - Alex E. Clark
- Department of MedicineUniversity of California, San DiegoLa JollaCA 92093USA
| | - Zhicheng Jin
- Department of NanoEngineeringUniversity of California, San DiegoLa JollaCA 92093USA
| | - Colman Moore
- Department of NanoEngineeringUniversity of California, San DiegoLa JollaCA 92093USA
| | - Pavla Fajtová
- Skaggs School of Pharmacy and Pharmaceutical SciencesUniversity of California, San DiegoLa JollaCA 92093USA
| | - Anthony J. O'Donoghue
- Skaggs School of Pharmacy and Pharmaceutical SciencesUniversity of California, San DiegoLa JollaCA 92093USA
| | - Aaron F. Carlin
- Department of MedicineUniversity of California, San DiegoLa JollaCA 92093USA
| | - Jesse V. Jokerst
- Department of NanoEngineeringUniversity of California, San DiegoLa JollaCA 92093USA
- Materials Science and Engineering ProgramUniversity of California, San DiegoLa JollaCA 92093USA
- Department of RadiologyUniversity of California, San DiegoLa JollaCA 92093USA
| |
Collapse
|
37
|
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.
Collapse
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
| |
Collapse
|
38
|
Cheng Y, Borum RM, Clark AE, Jin Z, Moore C, Fajtová P, O'Donoghue AJ, Carlin AF, Jokerst JV. A Dual‐Color Fluorescent Probe Allows Simultaneous Imaging of Main and Papain‐like Proteases of SARS‐CoV‐2‐Infected Cells for Accurate Detection and Rapid Inhibitor Screening. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202113617] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Yong Cheng
- Department of NanoEngineering University of California, San Diego La Jolla CA 92093 USA
| | - Raina M. Borum
- Department of NanoEngineering University of California, San Diego La Jolla CA 92093 USA
| | - Alex E. Clark
- Department of Medicine University of California, San Diego La Jolla CA 92093 USA
| | - Zhicheng Jin
- Department of NanoEngineering University of California, San Diego La Jolla CA 92093 USA
| | - Colman Moore
- Department of NanoEngineering University of California, San Diego La Jolla CA 92093 USA
| | - Pavla Fajtová
- Skaggs School of Pharmacy and Pharmaceutical Sciences University of California, San Diego La Jolla CA 92093 USA
| | - Anthony J. O'Donoghue
- Skaggs School of Pharmacy and Pharmaceutical Sciences University of California, San Diego La Jolla CA 92093 USA
| | - Aaron F. Carlin
- Department of Medicine University of California, San Diego La Jolla CA 92093 USA
| | - Jesse V. Jokerst
- Department of NanoEngineering University of California, San Diego La Jolla CA 92093 USA
- Materials Science and Engineering Program University of California, San Diego La Jolla CA 92093 USA
- Department of Radiology University of California, San Diego La Jolla CA 92093 USA
| |
Collapse
|
39
|
Structure-based inhibitor design and repurposing clinical drugs to target SARS-CoV-2 proteases. Biochem Soc Trans 2022; 50:151-165. [PMID: 35015073 DOI: 10.1042/bst20211180] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 12/15/2021] [Accepted: 12/16/2021] [Indexed: 01/01/2023]
Abstract
SARS-CoV-2, the coronavirus responsible for the current COVID-19 pandemic, encodes two proteases, 3CLpro and PLpro, two of the main antiviral research targets. Here we provide an overview of the structures and functions of 3CLpro and PLpro and examine strategies of structure-based drug designing and drug repurposing against these proteases. Rational structure-based drug design enables the generation of potent and target-specific antivirals. Drug repurposing offers an attractive prospect with an accelerated turnaround. Thus far, several protease inhibitors have been identified, and some candidates are undergoing trials that may well prove to be effective antivirals against SARS-CoV-2.
Collapse
|
40
|
Proteases of SARS Coronaviruses. REFERENCE MODULE IN LIFE SCIENCES 2022. [PMCID: PMC9308495 DOI: 10.1016/b978-0-12-821618-7.00111-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Coronaviruses such as SARS and SARS-CoV-2 have established themselves as a global health concern after causing an epidemic and a pandemic in the last twenty years. Understanding the life cycle of such viruses is critical to reveal their pathogenic potential. As one of the essential viral enzymes, SARS proteases are indispensable for the processing of viral polypeptides and for the replication of the virus. SARS-CoV and SARS-CoV-2 encode for 2 viral proteases: the main protease (3CLpro) and the papain-like protease (PLPro), which are conserved among different coronaviruses and are absent in humans. This review summarizes the existing literature on the structure and function of these proteases; highlighting the similarity and differences between the enzymes of SARS and SARS-CoV-2. It also discusses the development of inhibitors to target viral proteases.
Collapse
|
41
|
Morales Vasquez D, Chiem K, Ye C, Martinez-Sobrido L. Bioluminescent and Fluorescent Reporter-Expressing Recombinant SARS-CoV-2. Methods Mol Biol 2022; 2524:235-248. [PMID: 35821476 DOI: 10.1007/978-1-0716-2453-1_18] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Reporter-expressing recombinant severe acute respiratory syndrome coronavirus 2 (rSARS-CoV-2) represents an excellent tool to understand the biology of and ease studying viral infections in vitro and in vivo. The broad range of applications of reporter-expressing recombinant viruses is due to the facilitated expression of fluorescence or bioluminescence readouts. In this chapter, we describe a detailed protocol on the generation of rSARS-CoV-2 expressing Venus, mCherry, and NLuc that represents a valid surrogate to track viral infections.
Collapse
Affiliation(s)
| | - Kevin Chiem
- Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Chengjin Ye
- Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Luis Martinez-Sobrido
- Texas Biomedical Research Institute, San Antonio, TX, USA.
- Department of Disease Prevention and Intervention, Texas Biomedical Research Institute, San Antonio, TX, USA.
| |
Collapse
|
42
|
Chen J, Zhang Y, Zeng D, Zhang B, Ye X, Zeng Z, Zhang XK, Wang Z, Zhou H. Merbromin is a mixed-type inhibitor of 3-chyomotrypsin like protease of SARS-CoV-2. Biochem Biophys Res Commun 2021; 591:118-123. [PMID: 35007835 PMCID: PMC8716398 DOI: 10.1016/j.bbrc.2021.12.108] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 12/27/2021] [Indexed: 12/23/2022]
Abstract
3-chyomotrypsin like protease (3CLpro) has been considered as a promising target for developing anti-SARS-CoV-2 drugs. Herein, about 6000 compounds were analyzed by high-throughput screening using enzyme activity model, and Merbromin, an antibacterial agent, was identified as a potent inhibitor of 3CLpro. Merbromin strongly inhibited the proteolytic activity of 3CLpro but not the other three proteases Proteinase K, Trypsin and Papain. Michaelis-Menten kinetic analysis showed that Merbromin was a mixed-type inhibitor of 3CLpro, due to its ability of increasing the KM and decreasing the Kcat of 3CLpro. The binding assays and molecular docking suggested that 3CLpro possessed two binding sites for Merbromin. Consistently, Merbromin showed a weak binding to the other three proteases. Together, these findings demonstrated that Merbromin is a selective inhibitor of 3CLpro and provided a scaffold to design effective inhibitors of SARS-CoV-2.
Collapse
Affiliation(s)
- Junjie Chen
- School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, China; High Throughput Drug Screening Platform of Xiamen University, China
| | - Yaya Zhang
- Department of Neurosurgery, Xiamen Key Laboratory of Brain Center, The First Affiliated Hospital of Xiamen University, China
| | - Dequan Zeng
- School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, China; High Throughput Drug Screening Platform of Xiamen University, China
| | - Bingchang Zhang
- Department of Neurosurgery, Xiamen Key Laboratory of Brain Center, The First Affiliated Hospital of Xiamen University, China
| | - Xiaohong Ye
- School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, China; High Throughput Drug Screening Platform of Xiamen University, China
| | - Zhiping Zeng
- School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, China; High Throughput Drug Screening Platform of Xiamen University, China
| | - Xiao-Kun Zhang
- School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, China; High Throughput Drug Screening Platform of Xiamen University, China
| | - Zhanxiang Wang
- Department of Neurosurgery, Xiamen Key Laboratory of Brain Center, The First Affiliated Hospital of Xiamen University, China; School of Medicine, Xiamen University, Xiamen, Fujian, 361102, China.
| | - Hu Zhou
- School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, China; High Throughput Drug Screening Platform of Xiamen University, China.
| |
Collapse
|
43
|
Macip G, Garcia-Segura P, Mestres-Truyol J, Saldivar-Espinoza B, Pujadas G, Garcia-Vallvé S. A Review of the Current Landscape of SARS-CoV-2 Main Protease Inhibitors: Have We Hit the Bullseye Yet? Int J Mol Sci 2021; 23:259. [PMID: 35008685 PMCID: PMC8745775 DOI: 10.3390/ijms23010259] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 12/24/2021] [Accepted: 12/25/2021] [Indexed: 01/01/2023] Open
Abstract
In this review, we collected 1765 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) M-pro inhibitors from the bibliography and other sources, such as the COVID Moonshot project and the ChEMBL database. This set of inhibitors includes only those compounds whose inhibitory capacity, mainly expressed as the half-maximal inhibitory concentration (IC50) value, against M-pro from SARS-CoV-2 has been determined. Several covalent warheads are used to treat covalent and non-covalent inhibitors separately. Chemical space, the variation of the IC50 inhibitory activity when measured by different methods or laboratories, and the influence of 1,4-dithiothreitol (DTT) are discussed. When available, we have collected the values of inhibition of viral replication measured with a cellular antiviral assay and expressed as half maximal effective concentration (EC50) values, and their possible relationship to inhibitory potency against M-pro is analyzed. Finally, the most potent covalent and non-covalent inhibitors that simultaneously inhibit the SARS-CoV-2 M-pro and the virus replication in vitro are discussed.
Collapse
Affiliation(s)
| | | | | | | | - Gerard Pujadas
- Research Group in Cheminformatics & Nutrition, Departament de Bioquímica i Biotecnologia, Campus Sescelades, Universitat Rovira i Virgili, 43007 Tarragona, Catalonia, Spain; (G.M.); (P.G.-S.); (J.M.-T.); (B.S.-E.)
| | - Santiago Garcia-Vallvé
- Research Group in Cheminformatics & Nutrition, Departament de Bioquímica i Biotecnologia, Campus Sescelades, Universitat Rovira i Virgili, 43007 Tarragona, Catalonia, Spain; (G.M.); (P.G.-S.); (J.M.-T.); (B.S.-E.)
| |
Collapse
|
44
|
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.
Collapse
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
| |
Collapse
|
45
|
Yan G, Li D, Lin Y, Fu Z, Qi H, Liu X, Zhang J, Si S, Chen Y. Development of a simple and miniaturized sandwich-like fluorescence polarization assay for rapid screening of SARS-CoV-2 main protease inhibitors. Cell Biosci 2021; 11:199. [PMID: 34865653 PMCID: PMC8645223 DOI: 10.1186/s13578-021-00720-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 11/19/2021] [Indexed: 12/14/2022] Open
Abstract
Background Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is highly transmissible and has caused a pandemic named coronavirus disease 2019 (COVID-19), which has quickly spread worldwide. Although several therapeutic agents have been evaluated or approved for the treatment of COVID-19 patients, efficacious antiviral agents are still lacking. An attractive therapeutic target for SARS-CoV-2 is the main protease (Mpro), as this highly conserved enzyme plays a key role in viral polyprotein processing and genomic RNA replication. Therefore, the identification of efficacious antiviral agents against SARS-CoV-2 Mpro using a rapid, miniaturized and economical high-throughput screening (HTS) assay is of the highest importance at the present. Results In this study, we first combined the fluorescence polarization (FP) technique with biotin-avidin system (BAS) to develop a novel and step-by-step sandwich-like FP screening assay to quickly identify SARS-CoV-2 Mpro inhibitors from a natural product library. Using this screening assay, dieckol, a natural phlorotannin component extracted from a Chinese traditional medicine Ecklonia cava, was identified as a novel competitive inhibitor against SARS-CoV-2 Mpro in vitro with an IC50 value of 4.5 ± 0.4 µM. Additionally, dieckol exhibited a high affinity with SARS-CoV-2 Mpro using surface plasmon resonance (SPR) analysis and could bind to the catalytic sites of Mpro through hydrogen-bond interactions in the predicted docking model. Conclusions This innovative sandwich-like FP screening assay enables the rapid discovery of antiviral agents targeting viral proteases, and dieckol will be an excellent lead compound for generating more potent and selective antiviral agents targeting SARS-CoV-2 Mpro.
Collapse
Affiliation(s)
- Gangan Yan
- Institute for Drug Screening and Evaluation, Wannan Medical College, 241002, Wuhu, China
| | - Dongsheng Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100050, Beijing, China
| | - Yuan Lin
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, 100050, Beijing, China
| | - Zhenghao Fu
- Institute for Drug Screening and Evaluation, Wannan Medical College, 241002, Wuhu, China
| | - Haiyan Qi
- Institute for Drug Screening and Evaluation, Wannan Medical College, 241002, Wuhu, China
| | - Xiaoping Liu
- Institute for Drug Screening and Evaluation, Wannan Medical College, 241002, Wuhu, China
| | - Jing Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100050, Beijing, China.
| | - Shuyi Si
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100050, Beijing, China.
| | - Yunyu Chen
- Institute for Drug Screening and Evaluation, Wannan Medical College, 241002, Wuhu, China. .,Anhui Provincial Engineering Laboratory for Screening and Reevaluation of Bioactive Compounds of Herbal Medicines in Southern Anhui, Wannan Medical College, 241002, Wuhu, China.
| |
Collapse
|
46
|
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.
Collapse
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.
| |
Collapse
|
47
|
A fluorescence-based, gain-of-signal, live cell system to evaluate SARS-CoV-2 main protease inhibition. Antiviral Res 2021; 195:105183. [PMID: 34626674 PMCID: PMC8495046 DOI: 10.1016/j.antiviral.2021.105183] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 09/17/2021] [Accepted: 09/25/2021] [Indexed: 02/03/2023]
Abstract
The likelihood of continued circulation of COVID-19 and its variants, and novel coronaviruses due to future zoonotic transmissions, combined with the current paucity of coronavirus antivirals, emphasize the need for improved screening in developing effective antivirals for the treatment of infection by SARS-CoV-2 (CoV2) and other coronaviruses. Here we report the development of a live-cell based assay for evaluating the intracellular function of the critical, highly-conserved CoV2 target, the Main 3C-like protease (Mpro). This assay is based on expression of native wild-type mature CoV2 Mpro, the function of which is quantitatively evaluated in living cells through cleavage of a biosensor leading to loss of fluorescence. Evaluation does not require cell harvesting, allowing for multiple measurements from the same cells facilitating quantification of Mpro inhibition, as well as recovery of function upon removal of inhibitory drugs. The pan-coronavirus Mpro inhibitor, GC376, was utilized in this assay and effective inhibition of intracellular CoV2 Mpro was found to be consistent with levels required to inhibit CoV2 infection of human lung cells. We demonstrate that GC376 is an effective inhibitor of intracellular CoV2 Mpro at low micromolar levels, while other predicted Mpro inhibitors, bepridil and alverine, are not. Results indicate this system can provide a highly effective high-throughput coronavirus Mpro screening system.
Collapse
|
48
|
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.
Collapse
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.)
| |
Collapse
|
49
|
Duarte RRR, Copertino DC, Iñiguez LP, Marston JL, Bram Y, Han Y, Schwartz RE, Chen S, Nixon DF, Powell TR. Identifying FDA-approved drugs with multimodal properties against COVID-19 using a data-driven approach and a lung organoid model of SARS-CoV-2 entry. Mol Med 2021; 27:105. [PMID: 34503440 PMCID: PMC8426591 DOI: 10.1186/s10020-021-00356-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 08/16/2021] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Vaccination programs have been launched worldwide to halt the spread of COVID-19. However, the identification of existing, safe compounds with combined treatment and prophylactic properties would be beneficial to individuals who are waiting to be vaccinated, particularly in less economically developed countries, where vaccine availability may be initially limited. METHODS We used a data-driven approach, combining results from the screening of a large transcriptomic database (L1000) and molecular docking analyses, with in vitro tests using a lung organoid model of SARS-CoV-2 entry, to identify drugs with putative multimodal properties against COVID-19. RESULTS Out of thousands of FDA-approved drugs considered, we observed that atorvastatin was the most promising candidate, as its effects negatively correlated with the transcriptional changes associated with infection. Atorvastatin was further predicted to bind to SARS-CoV-2's main protease and RNA-dependent RNA polymerase, and was shown to inhibit viral entry in our lung organoid model. CONCLUSIONS Small clinical studies reported that general statin use, and specifically, atorvastatin use, are associated with protective effects against COVID-19. Our study corroborrates these findings and supports the investigation of atorvastatin in larger clinical studies. Ultimately, our framework demonstrates one promising way to fast-track the identification of compounds for COVID-19, which could similarly be applied when tackling future pandemics.
Collapse
Affiliation(s)
- Rodrigo R R Duarte
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, Cornell University, Belfer Research Building, 5th floor, 413 E. 69th St., New York, NY, 10021, USA.
- Social, Genetic & Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK.
| | - Dennis C Copertino
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, Cornell University, Belfer Research Building, 5th floor, 413 E. 69th St., New York, NY, 10021, USA
| | - Luis P Iñiguez
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, Cornell University, Belfer Research Building, 5th floor, 413 E. 69th St., New York, NY, 10021, USA
| | - Jez L Marston
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, Cornell University, Belfer Research Building, 5th floor, 413 E. 69th St., New York, NY, 10021, USA
| | - Yaron Bram
- Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Yuling Han
- Department of Surgery, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Robert E Schwartz
- Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Shuibing Chen
- Department of Surgery, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Douglas F Nixon
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, Cornell University, Belfer Research Building, 5th floor, 413 E. 69th St., New York, NY, 10021, USA
| | - Timothy R Powell
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, Cornell University, Belfer Research Building, 5th floor, 413 E. 69th St., New York, NY, 10021, USA
- Social, Genetic & Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| |
Collapse
|
50
|
Tarannum H, Rashmi Km, Nandi S. Exploring the SARS-CoV-2 main protease (Mpro) and RdRp targets by updating current structure-based drug design utilizing co-crystals to combat COVID-19. Curr Drug Targets 2021; 23:802-817. [PMID: 34488580 DOI: 10.2174/1389450122666210906154849] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 07/03/2021] [Accepted: 07/31/2021] [Indexed: 01/18/2023]
Abstract
The unprecedented pandemic of COVID-19 caused by the novel strain of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) engulfs millions of death worldwide. It has directly hit the socio-economic status of the affected countries. There are more than 219 countries badly affected by the COVID-19. There are no particular small molecule inhibitors to combat the dreadful virus. Many antivirals, antimalarials, antiparasitic, antibacterials, immunosuppressive anti-inflammatory, and immune stimulatory agents have been repurposed for the treatment of COVID19. But the exact mechanism of action of these drugs towards COVID-19 targets has not been experimented with yet. Under the effect of chemotherapeutics, the virus may change its genetic material and produces various strains, which are the main reasons behind the dreadful attack of COVID-19. The nuclear genetic components are composed of main protease and RNA-dependent RNA polymerase (RdRp) which are responsible for producing nascent virion and viral replication in the host cells. To explore the biochemical mechanisms of various small molecule inhibitors, structure-based drug design can be attempted utilizing NMR crystallography. The process identifies and validates the target protein involved in the disease pathogenesis by the binding of a chemical ligand at a well-defined pocket on the protein surface. In this way, the mode of binding of the ligands inside the target cavity can be predicted for the design of potent SARS-CoV-2 inhibitors.
Collapse
Affiliation(s)
- Heena Tarannum
- Six Sigma Institute of Technology and Science, Dineshpur, Rudrapur-263153. India
| | - Rashmi Km
- Global Institute of Pharmaceutical Education and Research, Kashipur-244713. India
| | - Sisir Nandi
- Global Institute of Pharmaceutical Education and Research, Kashipur-244713. India
| |
Collapse
|