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Qin B, Wu C, Zhao B, Li G, Wang B, Ou M, Li Z, Lang X, Li P, Liu J, Cui S, Huang H. Design, Synthesis, and Biological Evaluation of 1,2,4-Oxadiazole Derivatives Containing an Aryl Carboxylic Acid Moiety as Potent Sarbecovirus Papain-like Protease Inhibitors. J Med Chem 2024; 67:10211-10232. [PMID: 38871484 DOI: 10.1021/acs.jmedchem.4c00534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2024]
Abstract
Papain-like protease (PLpro) is a promising therapeutic target for its pivotal role in the life cycle of SARS-CoV-2. A series of 1,2,4-oxadiazole derivatives was designed and synthesized via a ring formation strategy based on SARS-CoV-2 PLpro-GRL0617 complex structure. Systematic structure-activity relationship studies revealed that introducing oxadiazole and aryl carboxylic acid moieties to GRL0617 enhanced the enzymatic inhibition activity, affinity, and deubiquitination capacity toward PLpro. 1,2,4-Oxadiazole compounds 13f and 26r, which had PLpro inhibition activity (IC50 = 1.8 and 1.0 μM) and antiviral activity against SARS-CoV-2 (EC50 = 5.4 and 4.3 μM), exhibited good metabolic stability (t1/2 > 93.2 min) and higher plasma exposure (AUC0-t = 17,380.08 and 24,289.76 ng·h/mL) in mice. Especially, compound 26r with moderate oral bioavailability of 39.1% and potent antiviral activity is worthy of further studies in vivo. Our findings provide a new insight for the discovery of antiviral agents targeting PLpro.
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Affiliation(s)
- Bo Qin
- NHC Key Laboratory of Systems Biology of Pathogens, National Institute of Pathogen Biology, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, P. R. China
| | - Chengwei Wu
- Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100050, P. R. China
| | - Binbin Zhao
- National Center of Technology Innovation for Animal Models, NHC Key Laboratory of Human Disease Comparative Medicine, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College, Beijing 100021, P. R. China
| | - Gang Li
- Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100050, P. R. China
- State Key Laboratory of Respiratory Health and Multimorbidity, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, P. R. China
| | - Baolian Wang
- Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100050, P. R. China
| | - Mengdie Ou
- NHC Key Laboratory of Systems Biology of Pathogens, National Institute of Pathogen Biology, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, P. R. China
| | - Ziheng Li
- NHC Key Laboratory of Systems Biology of Pathogens, National Institute of Pathogen Biology, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, P. R. China
| | - Xuli Lang
- Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100050, P. R. China
| | - Peng Li
- Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100050, P. R. China
| | - Jiangning Liu
- National Center of Technology Innovation for Animal Models, NHC Key Laboratory of Human Disease Comparative Medicine, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College, Beijing 100021, P. R. China
| | - Sheng Cui
- NHC Key Laboratory of Systems Biology of Pathogens, National Institute of Pathogen Biology, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, P. R. China
- State Key Laboratory of Respiratory Health and Multimorbidity, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, P. R. China
| | - Haihong Huang
- Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100050, P. R. China
- State Key Laboratory of Respiratory Health and Multimorbidity, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, P. R. China
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Valdés-Albuernes JL, Díaz-Pico E, Alfaro S, Caballero J. Modeling of noncovalent inhibitors of the papain-like protease (PLpro) from SARS-CoV-2 considering the protein flexibility by using molecular dynamics and cross-docking. Front Mol Biosci 2024; 11:1374364. [PMID: 38601323 PMCID: PMC11004324 DOI: 10.3389/fmolb.2024.1374364] [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: 01/22/2024] [Accepted: 03/11/2024] [Indexed: 04/12/2024] Open
Abstract
The papain-like protease (PLpro) found in coronaviruses that can be transmitted from animals to humans is a critical target in respiratory diseases linked to Severe Acute Respiratory Syndrome (SARS-CoV). Researchers have proposed designing PLpro inhibitors. In this study, a set of 89 compounds, including recently reported 2-phenylthiophenes with nanomolar inhibitory potency, were investigated as PLpro noncovalent inhibitors using advanced molecular modeling techniques. To develop the work with these inhibitors, multiple structures of the SARS-CoV-2 PLpro binding site were generated using a molecular sampling method. These structures were then clustered to select a group that represents the flexibility of the site. Subsequently, models of the protein-ligand complexes were created for the set of inhibitors within the chosen conformations. The quality of the complex models was assessed using LigRMSD software to verify similarities in the orientations of the congeneric series and interaction fingerprints to determine the recurrence of chemical interactions. With the multiple models constructed, a protocol was established to choose one per ligand, optimizing the correlation between the calculated docking energy values and the biological activities while incorporating the effect of the binding site's flexibility. A strong correlation (R2 = 0.922) was found when employing this flexible docking protocol.
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Affiliation(s)
| | | | | | - Julio Caballero
- Centro de Bioinformática, Simulación y Modelado (CBSM), Facultad de Ingeniería, Universidad de Talca, Talca, Chile
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Cockram PE, Walters BT, Lictao A, Shanahan F, Wertz IE, Foster SA, Rudolph J. Allosteric Inhibitors of the SARS-COV-2 Papain-like Protease Domain Induce Proteasomal Degradation of Its Parent Protein NSP3. ACS Chem Biol 2024; 19:22-36. [PMID: 38150587 DOI: 10.1021/acschembio.3c00312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2023]
Abstract
The papain-like protease of SARS-COV-2 is essential for viral replication and pathogenesis. Its location within a much larger multifunctional protein, NSP3, makes it an ideal candidate for a targeted degradation approach capable of eliminating multiple functions with a single-molecule treatment. In this work, we have developed a HiBiT-based cellular model to study NSP3 degradation and used this platform for the discovery of monovalent NSP3 degraders. We present previously unreported degradation activity of published papain-like protease inhibitors. Follow-up exploration of structure-activity relationships and mechanism-of-action studies points to the recruitment of the ubiquitin-proteasome machinery that is solely driven by site occupancy, regardless of molecular features of the ligand. Supported by HDX data, we hypothesize that binding-induced structural changes in NSP3 trigger the recruitment of an E3 ligase and lead to proteasomal degradation.
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Affiliation(s)
- Peter E Cockram
- Discovery Chemistry, Genentech, South San Francisco, California 94080, United States
- Discovery Oncology, Genentech, South San Francisco, California 94080, United States
| | - Benjamin T Walters
- Biochemical and Cellular Pharmacology, Genentech, South San Francisco, California 94080, United States
| | - Aaron Lictao
- Biochemical and Cellular Pharmacology, Genentech, South San Francisco, California 94080, United States
| | - Frances Shanahan
- Discovery Oncology, Genentech, South San Francisco, California 94080, United States
| | - Ingrid E Wertz
- Discovery Oncology, Genentech, South San Francisco, California 94080, United States
| | - Scott A Foster
- Discovery Oncology, Genentech, South San Francisco, California 94080, United States
| | - Joachim Rudolph
- Discovery Chemistry, Genentech, South San Francisco, California 94080, United States
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4
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Li X, Song Y. Targeting SARS-CoV-2 nonstructural protein 3: Function, structure, inhibition, and perspective in drug discovery. Drug Discov Today 2024; 29:103832. [PMID: 37977285 PMCID: PMC10872262 DOI: 10.1016/j.drudis.2023.103832] [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: 09/22/2023] [Revised: 11/06/2023] [Accepted: 11/13/2023] [Indexed: 11/19/2023]
Abstract
As a highly contagious human pathogen, severe acute respiratory syndrome-associated coronavirus-2 (SARS-CoV-2) has infected billions of people worldwide with more than 6 million deaths. With several effective vaccines and antiviral drugs now available, the SARS-CoV-2 pandemic been brought under control. However, a new pathogenic coronavirus could emerge in the future, given the zoonotic nature of this virus. Natural evolution and drug-induced mutations of SARS-CoV-2 also require continued efforts for new anti-coronavirus drugs. Nonstructural protein (nsp) 3 of CoVs is a large, multifunctional protein, containing a papain-like protease (PLpro) and a macrodomain (Mac1), which are essential for viral replication. Here, we provide a comprehensive review of the function, structure, and inhibition of SARS-CoV/-CoV-2 PLpro and Mac1. We also discuss advances in, and challenges to, the discovery of drugs against these targets.
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Affiliation(s)
- Xin Li
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA.
| | - Yongcheng Song
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA.
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5
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Ghosh AK, Shahabi D, Imhoff MEC, Kovela S, Sharma A, Hattori SI, Higashi-Kuwata N, Mitsuya H, Mesecar AD. SARS-CoV-2 papain-like protease (PLpro) inhibitory and antiviral activity of small molecule derivatives for drug leads. Bioorg Med Chem Lett 2023; 96:129489. [PMID: 37770002 PMCID: PMC10842477 DOI: 10.1016/j.bmcl.2023.129489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 09/20/2023] [Accepted: 09/25/2023] [Indexed: 10/03/2023]
Abstract
We report here the synthesis and biological evaluation of a series of small molecule SARS-CoV-2 PLpro inhibitors. We compared the activity of selected compounds in both SARS-CoV-1 and SARS-CoV-2 PLpro inhibitory and antiviral assays. We have synthesized and evaluated several new structural variants of previous leads against SARS-CoV-2 PLpro. The replacement of the carboxamide functionality with sulfonamide derivatives resulted in PLpro inhibitors with potent PLpro inhibitory and antiviral activity in VeroE6 cells similar to GRL0617. To obtain molecular insight, we created an optimized model of a potent sulfonamide derivative in the SARS-CoV-2 PLpro active site.
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Affiliation(s)
- Arun K Ghosh
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907 USA.
| | - Dana Shahabi
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907 USA
| | | | - Satish Kovela
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907 USA
| | - Ashish Sharma
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907 USA
| | - Shin-Ichiro Hattori
- Department of Refractory Viral Diseases, National Center for Global Health and Medicine, Shinjuku, Tokyo 162-8655 Japan
| | - Nobuyo Higashi-Kuwata
- Department of Refractory Viral Diseases, National Center for Global Health and Medicine, Shinjuku, Tokyo 162-8655 Japan
| | - Hiroaki Mitsuya
- Department of Refractory Viral Diseases, National Center for Global Health and Medicine, Shinjuku, Tokyo 162-8655 Japan; Department of Clinical Sciences, Kumamoto University Hospital, Kumamoto 860-8556 Japan; Experimental Retrovirology Section, HIV and AIDS Malignancy Branch National Cancer Institute, Bethesda, MD 20892 USA
| | - Andrew D Mesecar
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907 USA
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6
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Castillo-Campos L, Velázquez-Libera JL, Caballero J. Computational study of the binding orientation and affinity of noncovalent inhibitors of the papain-like protease (PLpro) from SARS-CoV-1 considering the protein flexibility by using molecular dynamics and cross-docking. Front Mol Biosci 2023; 10:1215499. [PMID: 37426421 PMCID: PMC10326900 DOI: 10.3389/fmolb.2023.1215499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 06/12/2023] [Indexed: 07/11/2023] Open
Abstract
The papain-like protease (PLpro) from zoonotic coronaviruses (CoVs) has been identified as a target with an essential role in viral respiratory diseases caused by Severe Acute Respiratory Syndrome-associated coronaviruses (SARS-CoVs). The design of PLpro inhibitors has been proposed as an alternative to developing potential drugs against this disease. In this work, 67 naphthalene-derived compounds as noncovalent PLpro inhibitors were studied using molecular modeling methods. Structural characteristics of the bioactive conformations of these inhibitors and their interactions at the SARS-CoV-1 PLpro binding site were reported here in detail, taking into account the flexibility of the protein residues. Firstly, a molecular docking protocol was used to obtain the orientations of the inhibitors. After this, the orientations were compared, and the recurrent interactions between the PLpro residues and ligand chemical groups were described (with LigRMSD and interaction fingerprints methods). In addition, efforts were made to find correlations between docking energy values and experimentally determined binding affinities. For this, the PLpro was sampled by using Gaussian Accelerated Molecular Dynamics (GaMD), generating multiple conformations of the binding site. Diverse protein conformations were selected and a cross-docking experiment was performed, yielding models of the 67 naphthalene-derived compounds adopting different binding modes. Representative complexes for each ligand were selected to obtain the highest correlation between docking energies and activities. A good correlation (R 2 = 0.948) was found when this flexible docking protocol was performed.
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7
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Identifying Drug Candidates for COVID-19 with Large-Scale Drug Screening. Int J Mol Sci 2023; 24:ijms24054397. [PMID: 36901828 PMCID: PMC10002104 DOI: 10.3390/ijms24054397] [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: 01/03/2023] [Revised: 02/11/2023] [Accepted: 02/16/2023] [Indexed: 02/25/2023] Open
Abstract
Papain-like protease (PLpro) is critical to COVID-19 infection. Therefore, it is a significant target protein for drug development. We virtually screened a 26,193 compound library against the PLpro of SARS-CoV-2 and identified several drug candidates with convincing binding affinities. The three best compounds all had better estimated binding energy than those of the drug candidates proposed in previous studies. By analyzing the docking results for the drug candidates identified in this and previous studies, we demonstrate that the critical interactions between the compounds and PLpro proposed by the computational approaches are consistent with those proposed by the biological experiments. In addition, the predicted binding energies of the compounds in the dataset showed a similar trend as their IC50 values. The predicted ADME and drug-likeness properties also suggested that these identified compounds can be used for COVID-19 treatment.
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8
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Gurjar V, Iqra Kamil S, Chandra A, Qamar I, Singh N. Drugs swapping in coronavirus strains: a structural biology view. J Biomol Struct Dyn 2023; 41:13488-13495. [PMID: 36744537 DOI: 10.1080/07391102.2023.2175037] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 01/26/2023] [Indexed: 02/07/2023]
Abstract
Coronavirus belongs to the coronaviridae family, having a single-stranded RNA as genetic material of 26-42 kb in size. The first coronavirus infection emerged in 2002, caused by SARS-CoV1. Since then, genome sequences and three-dimensional structures of crucial proteins and enzymes of the virus have been studied in detail. The novel coronavirus (nCoV) outbreak has caused the COVID19 pandemic, which is responsible for the deaths of millions of people worldwide. The nCoV was later renamed as SARS-CoV2. The details of most of the COV proteins are available at the atomic and molecular levels. The entire genome is made up of 12 open reading frames that code for 27 different proteins. The spike surface glycoprotein, the envelope protein, the nucleocapsid protein, and the membrane protein are the four structural proteins which are required for virus attachment, entrance, assembly, and pathogenicity. The remaining proteins encoded are called non-structural (NSPs) and support the survival of the virus. Several non-structural proteins are also validated targets for drug development against coronavirus and are being used for drug design purposes. To perform a comparative study, sequences and three-dimensional structures of four crucial viral enzymes, Mpro, PLpro, RdRp, and EndoU from SARS-CoV1 and SARS-CoV2 variants were analyzed. The key structural elements and ligands recognizing amino acid residues were found to be similar in enzymes from both strains. The significant sequences and structural resemblance also suggest that a drug developed either for SARS-CoV1 or SARS-CoV2 using these enzymes may also have the potential to cross-react.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Vaishali Gurjar
- School of Biotechnology, Gautam Buddha University, Gautam Budh Nagar, Uttar Pradesh, India
| | - Saiyada Iqra Kamil
- School of Biotechnology, Gautam Buddha University, Gautam Budh Nagar, Uttar Pradesh, India
| | - Anshuman Chandra
- School of Biotechnology, Gautam Buddha University, Gautam Budh Nagar, Uttar Pradesh, India
| | - Imteyaz Qamar
- School of Biotechnology, Gautam Buddha University, Gautam Budh Nagar, Uttar Pradesh, India
| | - Nagendra Singh
- School of Biotechnology, Gautam Buddha University, Gautam Budh Nagar, Uttar Pradesh, India
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Cho H, Kim YJ, Chae JW, Meyer MR, Kim SK, Ryu CS. In vitro metabolic characterization of the SARS-CoV-2 papain-like protease inhibitors GRL0617 and HY-17542. Front Pharmacol 2023; 14:1067408. [PMID: 36874001 PMCID: PMC9975351 DOI: 10.3389/fphar.2023.1067408] [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: 10/11/2022] [Accepted: 02/03/2023] [Indexed: 02/17/2023] Open
Abstract
The SARS-CoV-2 pandemic requires a new therapeutic target for viral infection, and papain-like protease (Plpro) has been suggested as a druggable target. This in-vitro study was conducted to examine the drug metabolism of the GRL0617 and HY-17542, Plpro inhibitors. Metabolism of these inhibitors was studied to predict the pharmacokinetics in human liver microsomes. The hepatic cytochrome P450 (CYP) isoforms responsible for their metabolism were identified using recombinant enzymes. The drug-drug interaction potential mediated by cytochrome P450 inhibition was estimated. In human liver microsomes, the Plpro inhibitors had phase I and phase I + II metabolism with half-lives of 26.35 and 29.53 min, respectively. Hydroxylation (M1) and desaturation (-H2, M3) of the para-amino toluene side chain were the predominant reactions mediated with CYP3A4 and CYP3A5. CYP2D6 is responsible for the hydroxylation of the naphthalene side ring. GRL0617 inhibits major drug-metabolizing enzymes, including CYP2C9 and CYP3A4. HY-17542 is structural analog of GRL0617 and it is metabolized to GRL0617 through non-cytochrome P450 reactions in human liver microsomes without NADPH. Like GRL0617 and HY-17542 undergoes additional hepatic metabolism. The in-vitro hepatic metabolism of the Plpro inhibitors featured short half-lives; preclinical metabolism studies are needed to determine therapeutic doses for these inhibitors.
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Affiliation(s)
- Hyunki Cho
- Environmental Safety Group, KIST Europe Forschungsgesellschaft mbH, Saarbrücken, Germany.,Department of Pharmacy, Saarland University, Saarbrücken, Germany
| | - Young Jun Kim
- Environmental Safety Group, KIST Europe Forschungsgesellschaft mbH, Saarbrücken, Germany
| | - Jung-Woo Chae
- College of Pharmacy, Chungnam National Univerisity, Daejeon, Republic of Korea
| | - Markus R Meyer
- Department of Experimental and Clinical Toxicology, Center for Molecular Signaling (PZMS), Institute of Experimental and Clinical Pharmacology and Toxicology, Saarland University, Homburg, Germany
| | - Sang Kyum Kim
- College of Pharmacy, Chungnam National Univerisity, Daejeon, Republic of Korea
| | - Chang Seon Ryu
- Environmental Safety Group, KIST Europe Forschungsgesellschaft mbH, Saarbrücken, Germany
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Flavonoids from the roots and rhizomes of Sophoratonkinensis and their in vitro anti-SARS-CoV-2 activity. Chin J Nat Med 2023; 21:65-80. [PMID: 36641234 PMCID: PMC9836829 DOI: 10.1016/s1875-5364(23)60386-3] [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: 07/26/2022] [Indexed: 01/14/2023]
Abstract
Acute respiratory infection caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) had caused a global pandemic since 2019, and posed a serious threat to global health security. Traditional Chinese medicine (TCM) has played an indispensable role in the battle against the epidemic. Many components originated from TCMs were found to inhibit the production of SARS-CoV-2 3C-like protease (3CLpro) and papain-like protease (PLpro), which are two promising therapeutic targets to inhibit SARS-CoV-2. This study describes a systematic investigation of the roots and rhizomes of Sophora tonkinensis, which results in the characterization of 12 new flavonoids, including seven prenylated flavanones (1-7), one prenylated flavonol (8), two prenylated chalcones (9-10), one isoflavanone (11), and one isoflavan dimer (12), together with 43 known compounds (13-55). Their structures including the absolute configurations were elucidated by comprehensive analysis of MS, 1D and 2D NMR data, and time-dependent density functional theory electronic circular dichroism (TDDFT ECD) calculations. Compounds 12 and 51 exhibited inhibitory effects against SARS-CoV-2 3CLpro with IC50 values of 34.89 and 19.88 μmol·L-1, repectively while compounds 9, 43 and 47 exhibited inhibitory effects against PLpro with IC50 values of 32.67, 79.38, and 16.74 μmol·L-1, respectively.
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11
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Hu H, Wang Q, Su H, Shao Q, Zhao W, Chen G, Li M, Xu Y. Identification of Cysteine 270 as a Novel Site for Allosteric Modulators of SARS-CoV-2 Papain-Like Protease. Angew Chem Int Ed Engl 2022; 61:e202212378. [PMID: 36308706 PMCID: PMC9874598 DOI: 10.1002/anie.202212378] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Indexed: 11/06/2022]
Abstract
The coronavirus papain-like protease (PLpro ) plays an important role in the proteolytic processing of viral polyproteins and the dysregulation of the host immune response, providing a promising therapeutic target. However, the development of inhibitors against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) PLpro is challenging owing to the restricted S1/S2 sites in the substrate binding pocket. Here we report the discovery of two activators of SARS-CoV-2 PLpro and the identification of the unique residue, cysteine 270 (C270), as an allosteric and covalent regulatory site for the activators. This site is also specifically modified by glutathione, resulting in protease activation. Furthermore, a compound was found to allosterically inhibit the protease activity by covalent binding to C270. Together, these results elucidate an unrevealed molecular mechanism for allosteric modulation of SARS-CoV-2 PLpro and provid a novel site for allosteric inhibitors design.
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Affiliation(s)
- Hangchen Hu
- School of Pharmaceutical Science and TechnologyHangzhou Institute for Advanced StudyUniversity of Chinese Academy of SciencesHangzhou310024China,CAS Key Laboratory of Receptor Research and State Key Laboratory of Drug ResearchShanghai Institute of Materia MedicaChinese Academy of SciencesShanghai201203China,University of Chinese Academy of SciencesBeijing100049China
| | - Qian Wang
- School of Chinese Materia MedicaNanjing University of Chinese MedicineNanjing210023China
| | - Haixia Su
- CAS Key Laboratory of Receptor Research and State Key Laboratory of Drug ResearchShanghai Institute of Materia MedicaChinese Academy of SciencesShanghai201203China
| | - Qiang Shao
- CAS Key Laboratory of Receptor Research and State Key Laboratory of Drug ResearchShanghai Institute of Materia MedicaChinese Academy of SciencesShanghai201203China
| | - Wenfeng Zhao
- CAS Key Laboratory of Receptor Research and State Key Laboratory of Drug ResearchShanghai Institute of Materia MedicaChinese Academy of SciencesShanghai201203China
| | - Guofeng Chen
- CAS Key Laboratory of Receptor Research and State Key Laboratory of Drug ResearchShanghai Institute of Materia MedicaChinese Academy of SciencesShanghai201203China,University of Chinese Academy of SciencesBeijing100049China
| | - Minjun Li
- Shanghai Synchrotron Radiation FacilityShanghai Advanced Research InstituteChinese Academy of SciencesShanghai201203China
| | - Yechun Xu
- School of Pharmaceutical Science and TechnologyHangzhou Institute for Advanced StudyUniversity of Chinese Academy of SciencesHangzhou310024China,CAS Key Laboratory of Receptor Research and State Key Laboratory of Drug ResearchShanghai Institute of Materia MedicaChinese Academy of SciencesShanghai201203China,University of Chinese Academy of SciencesBeijing100049China,School of Chinese Materia MedicaNanjing University of Chinese MedicineNanjing210023China
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12
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Pathfinder-Driven Chemical Space Exploration and Multiparameter Optimization in Tandem with Glide/IFD and QSAR-Based Active Learning Approach to Prioritize Design Ideas for FEP+ Calculations of SARS-CoV-2 PL pro Inhibitors. Molecules 2022; 27:molecules27238569. [PMID: 36500659 PMCID: PMC9741453 DOI: 10.3390/molecules27238569] [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: 10/29/2022] [Revised: 11/25/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022] Open
Abstract
A global pandemic caused by the SARS-CoV-2 virus that started in 2020 and has wreaked havoc on humanity still ravages up until now. As a result, the negative impact of travel restrictions and lockdowns has underscored the importance of our preparedness for future pandemics. The main thrust of this work was based on addressing this need by traversing chemical space to design inhibitors that target the SARS-CoV-2 papain-like protease (PLpro). Pathfinder-based retrosynthesis analysis was used to generate analogs of GRL-0617 using commercially available building blocks by replacing the naphthalene moiety. A total of 10 models were built using active learning QSAR, which achieved good statistical results such as an R2 > 0.70, Q2 > 0.64, STD Dev < 0.30, and RMSE < 0.31, on average for all models. A total of 35 ideas were further prioritized for FEP+ calculations. The FEP+ results revealed that compound 45 was the most active compound in this series with a ΔG of −7.28 ± 0.96 kcal/mol. Compound 5 exhibited a ΔG of −6.78 ± 1.30 kcal/mol. The inactive compounds in this series were compound 91 and compound 23 with a ΔG of −5.74 ± 1.06 and −3.11 ± 1.45 kcal/mol. The combined strategy employed here is envisaged to be of great utility in multiparameter lead optimization efforts, to traverse chemical space, maintaining and/or improving the potency as well as the property space of synthetically aware design ideas.
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13
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Ghosh AK, Mishevich JL, Mesecar A, Mitsuya H. Recent Drug Development and Medicinal Chemistry Approaches for the Treatment of SARS-CoV-2 Infection and COVID-19. ChemMedChem 2022; 17:e202200440. [PMID: 36165855 PMCID: PMC9538661 DOI: 10.1002/cmdc.202200440] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 09/21/2022] [Indexed: 01/14/2023]
Abstract
COVID-19, caused by SARS-CoV-2 infection, continues to be a major public health crisis around the globe. Development of vaccines and the first cluster of antiviral drugs has brought promise and hope for prevention and treatment of severe coronavirus disease. However, continued development of newer, safer, and more effective antiviral drugs are critically important to combat COVID-19 and counter the looming pathogenic variants. Studies of the coronavirus life cycle revealed several important biochemical targets for drug development. In the present review, we focus on recent drug design and medicinal chemistry efforts in small molecule drug discovery, including the development of nirmatrelvir that targets viral protein synthesis and remdesivir and molnupiravir that target viral RdRp. These are recent FDA approved drugs for the treatment of COVID-19.
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Affiliation(s)
- Arun K Ghosh
- Purdue UniversityDepartments of Chemistry and Medicinal Chemistry560 Oval Drive47907West LafayetteUNITED STATES
| | | | - Andrew Mesecar
- Purdue University College of ScienceBiochemistryUNITED STATES
| | - Hiroaki Mitsuya
- National Cancer InstituteHIV and AIDS Malignancy BranchUNITED STATES
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14
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Speck-Planche A, Kleandrova VV. Multi-Condition QSAR Model for the Virtual Design of Chemicals with Dual Pan-Antiviral and Anti-Cytokine Storm Profiles. ACS OMEGA 2022; 7:32119-32130. [PMID: 36120024 PMCID: PMC9476185 DOI: 10.1021/acsomega.2c03363] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 08/19/2022] [Indexed: 06/15/2023]
Abstract
Respiratory viruses are infectious agents, which can cause pandemics. Although nowadays the danger associated with respiratory viruses continues to be evidenced by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) as the virus responsible for the current COVID-19 pandemic, other viruses such as SARS-CoV-1, the influenza A and B viruses (IAV and IBV, respectively), and the respiratory syncytial virus (RSV) can lead to globally spread viral diseases. Also, from a biological point of view, most of these viruses can cause an organ-damaging hyperinflammatory response known as the cytokine storm (CS). Computational approaches constitute an essential component of modern drug development campaigns, and therefore, they have the potential to accelerate the discovery of chemicals able to simultaneously inhibit multiple molecular and nonmolecular targets. We report here the first multicondition model based on quantitative structure-activity relationships and an artificial neural network (mtc-QSAR-ANN) for the virtual design and prediction of molecules with dual pan-antiviral and anti-CS profiles. Our mtc-QSAR-ANN model exhibited an accuracy higher than 80%. By interpreting the different descriptors present in the mtc-QSAR-ANN model, we could retrieve several molecular fragments whose assembly led to new molecules with drug-like properties and predicted pan-antiviral and anti-CS activities.
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Affiliation(s)
- Alejandro Speck-Planche
- Grupo
de Química Computacional y Teórica (QCT-USFQ), Departamento
de Ingeniería Química, Universidad
San Francisco de Quito, Diego de Robles y vía Interoceánica, Quito 170901, Ecuador
| | - Valeria V. Kleandrova
- Laboratory
of Fundamental and Applied Research of Quality and Technology of Food
Production, Moscow State University of Food
Production, Volokolamskoe
shosse 11, 125080, Moscow, Russian Federation
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15
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Zou Z, Shan H, Sun D, Xia L, Shi Y, Wan J, Zhou A, Wu Y, Xu H, Lei H, Xu Z, Wu Y. Parthenolide reveals an allosteric mode to inhibit the deISGylation activity of SARS-CoV‑2 papain-like protease. Acta Biochim Biophys Sin (Shanghai) 2022; 54:1133-1139. [PMID: 35866602 PMCID: PMC9827819 DOI: 10.3724/abbs.2022092] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The coronavirus papain-like protease (PLpro) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for viral polypeptide cleavage and the deISGylation of interferon-stimulated gene 15 (ISG15), which enable it to participate in virus replication and host innate immune pathways. Therefore, PLpro is considered an attractive antiviral drug target. Here, we show that parthenolide, a germacrane sesquiterpene lactone, has SARS-CoV-2 PLpro inhibitory activity. Parthenolide covalently binds to Cys-191 or Cys-194 of the PLpro protein, but not the Cys-111 at the PLpro catalytic site. Mutation of Cys-191 or Cys-194 reduces the activity of PLpro. Molecular docking studies show that parthenolide may also form hydrogen bonds with Lys-192, Thr-193, and Gln-231. Furthermore, parthenolide inhibits the deISGylation but not the deubiquitinating activity of PLpro in vitro. These results reveal that parthenolide inhibits PLpro activity by allosteric regulation.
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Affiliation(s)
- Zhihui Zou
- Hongqiao International Institute of MedicineShanghai Tongren Hospital / Faculty of Basic MedicineChemical Biology Division of Shanghai Universities E-InstitutesKey Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of EducationChinese Academy of Medical Sciences Research Unit 2019RU043Shanghai Jiao Tong University School of Medicine (SJTU-SM)Shanghai200025China
| | - Huizhuang Shan
- Hongqiao International Institute of MedicineShanghai Tongren Hospital / Faculty of Basic MedicineChemical Biology Division of Shanghai Universities E-InstitutesKey Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of EducationChinese Academy of Medical Sciences Research Unit 2019RU043Shanghai Jiao Tong University School of Medicine (SJTU-SM)Shanghai200025China,Laboratory MedicineGuangdong Provincial People’s HospitalGuangdong Academy of Medical SciencesGuangzhouGuangdong510000China
| | - Demeng Sun
- Tsinghua-Peking Center for Life SciencesKey Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education)Beijing Advanced Innovation Center for Structural BiologyDepartment of ChemistryTsinghua UniversityBeijing100084China
| | - Li Xia
- Hongqiao International Institute of MedicineShanghai Tongren Hospital / Faculty of Basic MedicineChemical Biology Division of Shanghai Universities E-InstitutesKey Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of EducationChinese Academy of Medical Sciences Research Unit 2019RU043Shanghai Jiao Tong University School of Medicine (SJTU-SM)Shanghai200025China
| | - Yulong Shi
- CAS Key Laboratory of Receptor ResearchDrug Discovery and Design CenterShanghai Institute of Materia MedicaChinese Academy of SciencesShanghai201203China
| | - Jiahui Wan
- Hongqiao International Institute of MedicineShanghai Tongren Hospital / Faculty of Basic MedicineChemical Biology Division of Shanghai Universities E-InstitutesKey Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of EducationChinese Academy of Medical Sciences Research Unit 2019RU043Shanghai Jiao Tong University School of Medicine (SJTU-SM)Shanghai200025China
| | - Aiwu Zhou
- Hongqiao International Institute of MedicineShanghai Tongren Hospital / Faculty of Basic MedicineChemical Biology Division of Shanghai Universities E-InstitutesKey Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of EducationChinese Academy of Medical Sciences Research Unit 2019RU043Shanghai Jiao Tong University School of Medicine (SJTU-SM)Shanghai200025China
| | - Yunzhao Wu
- Hongqiao International Institute of MedicineShanghai Tongren Hospital / Faculty of Basic MedicineChemical Biology Division of Shanghai Universities E-InstitutesKey Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of EducationChinese Academy of Medical Sciences Research Unit 2019RU043Shanghai Jiao Tong University School of Medicine (SJTU-SM)Shanghai200025China
| | - Hanzhang Xu
- Hongqiao International Institute of MedicineShanghai Tongren Hospital / Faculty of Basic MedicineChemical Biology Division of Shanghai Universities E-InstitutesKey Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of EducationChinese Academy of Medical Sciences Research Unit 2019RU043Shanghai Jiao Tong University School of Medicine (SJTU-SM)Shanghai200025China
| | - Hu Lei
- Hongqiao International Institute of MedicineShanghai Tongren Hospital / Faculty of Basic MedicineChemical Biology Division of Shanghai Universities E-InstitutesKey Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of EducationChinese Academy of Medical Sciences Research Unit 2019RU043Shanghai Jiao Tong University School of Medicine (SJTU-SM)Shanghai200025China
| | - Zhijian Xu
- CAS Key Laboratory of Receptor ResearchDrug Discovery and Design CenterShanghai Institute of Materia MedicaChinese Academy of SciencesShanghai201203China,Correspondence address. +86-21-63846590-776916; E-mail: (Y.W.) / Tel: +86-21-50806600-1304; E-mail: (Z.X.) @simm.ac.cn
| | - Yingli Wu
- Hongqiao International Institute of MedicineShanghai Tongren Hospital / Faculty of Basic MedicineChemical Biology Division of Shanghai Universities E-InstitutesKey Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of EducationChinese Academy of Medical Sciences Research Unit 2019RU043Shanghai Jiao Tong University School of Medicine (SJTU-SM)Shanghai200025China,Correspondence address. +86-21-63846590-776916; E-mail: (Y.W.) / Tel: +86-21-50806600-1304; E-mail: (Z.X.) @simm.ac.cn
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16
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Chalcone-amide, a privileged backbone for the design and development of selective SARS-CoV/SARS-CoV-2 papain-like protease inhibitors. Eur J Med Chem 2022; 240:114572. [PMID: 35797899 PMCID: PMC9250826 DOI: 10.1016/j.ejmech.2022.114572] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 06/22/2022] [Accepted: 06/23/2022] [Indexed: 11/23/2022]
Abstract
The newly emerged coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that caused the COVID-19 pandemic, is the closest relative of SARS-CoV with high genetic similarity. The papain-like protease (PLpro) is an important SARS-CoV/SARS-CoV-2 nonstructural protein that plays a critical role in some infection processes such as the generation of the functional replication complex, maturation of crude polyproteins, and regulation of the host antiviral immune responses. Therefore, the research to discover SARS-CoV-2 PLpro inhibitors could be a sensible strategy to obtain therapeutic agents for the treatment of COVID-19. Aiming to find SARS-CoV/SARS-CoV-2 PLpro inhibitors, various high throughput screenings (HTS) have been performed over the past two decades. Interestingly, the result of these efforts is the identification of hit/lead compounds whose structures have one important feature in common, namely having a chalcone-amide (N-benzylbenzamide) backbone. Structure-activity relationship (SAR) studies have shown that placing an (R)-configurated methyl group on the middle carbon adjacent to the amide group creates a unique backbone called (R)-methyl chalcone-amide, which dramatically increases PLpro inhibitory potency. Although this scaffold has not yet been introduced by medicinal chemists as a specific skeleton for the design of PLpro inhibitors, structural considerations show that the most reported PLpro inhibitors have this skeleton. This review suggests the (R)-methyl chalcone-amide scaffold as a key backbone for the design and development of selective SARS-CoV-2 PLpro inhibitors. Understanding the SAR and binding mode of these inhibitors in the active site of SARS-CoV-2 PLpro can aid the future development of anti-COVID-19 agents.
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17
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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.
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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
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18
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Antiviral Drug Discovery for the Treatment of COVID-19 Infections. Viruses 2022; 14:v14050961. [PMID: 35632703 PMCID: PMC9143071 DOI: 10.3390/v14050961] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 04/28/2022] [Accepted: 04/29/2022] [Indexed: 02/04/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a recently emerged human coronavirus. COVID-19 vaccines have proven to be successful in protecting the vaccinated from infection, reducing the severity of disease, and deterring the transmission of infection. However, COVID-19 vaccination faces many challenges, such as the decline in vaccine-induced immunity over time, and the decrease in potency against some SARS-CoV-2 variants including the recently emerged Omicron variant, resulting in breakthrough infections. The challenges that COVID-19 vaccination is facing highlight the importance of the discovery of antivirals to serve as another means to tackle the pandemic. To date, neutralizing antibodies that block viral entry by targeting the viral spike protein make up the largest class of antivirals that has received US FDA emergency use authorization (EUA) for COVID-19 treatment. In addition to the spike protein, other key targets for the discovery of direct-acting antivirals include viral enzymes that are essential for SARS-CoV-2 replication, such as RNA-dependent RNA polymerase and proteases, as judged by US FDA approval for remdesivir, and EUA for Paxlovid (nirmatrelvir + ritonavir) for treating COVID-19 infections. This review presents an overview of the current status and future direction of antiviral drug discovery for treating SARS-CoV-2 infections, covering important antiviral targets such as the viral spike protein, non-structural protein (nsp) 3 papain-like protease, nsp5 main protease, and the nsp12/nsp7/nsp8 RNA-dependent RNA polymerase complex.
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19
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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.
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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
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20
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Calleja DJ, Kuchel N, Lu BGC, Birkinshaw RW, Klemm T, Doerflinger M, Cooney JP, Mackiewicz L, Au AE, Yap YQ, Blackmore TR, Katneni K, Crighton E, Newman J, Jarman KE, Call MJ, Lechtenberg BC, Czabotar PE, Pellegrini M, Charman SA, Lowes KN, Mitchell JP, Nachbur U, Lessene G, Komander D. Insights Into Drug Repurposing, as Well as Specificity and Compound Properties of Piperidine-Based SARS-CoV-2 PLpro Inhibitors. Front Chem 2022; 10:861209. [PMID: 35494659 PMCID: PMC9039177 DOI: 10.3389/fchem.2022.861209] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 03/15/2022] [Indexed: 11/25/2022] Open
Abstract
The COVID-19 pandemic continues unabated, emphasizing the need for additional antiviral treatment options to prevent hospitalization and death of patients infected with SARS-CoV-2. The papain-like protease (PLpro) domain is part of the SARS-CoV-2 non-structural protein (nsp)-3, and represents an essential protease and validated drug target for preventing viral replication. PLpro moonlights as a deubiquitinating (DUB) and deISGylating enzyme, enabling adaptation of a DUB high throughput (HTS) screen to identify PLpro inhibitors. Drug repurposing has been a major focus through the COVID-19 pandemic as it may provide a fast and efficient route for identifying clinic-ready, safe-in-human antivirals. We here report our effort to identify PLpro inhibitors by screening the ReFRAME library of 11,804 compounds, showing that none inhibit PLpro with any reasonable activity or specificity to justify further progression towards the clinic. We also report our latest efforts to improve piperidine-scaffold inhibitors, 5c and 3k, originally developed for SARS-CoV PLpro. We report molecular details of binding and selectivity, as well as in vitro absorption, distribution, metabolism and excretion (ADME) studies of this scaffold. A co-crystal structure of SARS-CoV-2 PLpro bound to inhibitor 3k guides medicinal chemistry efforts to improve binding and ADME characteristics. We arrive at compounds with improved and favorable solubility and stability characteristics that are tested for inhibiting viral replication. Whilst still requiring significant improvement, our optimized small molecule inhibitors of PLpro display decent antiviral activity in an in vitro SARS-CoV-2 infection model, justifying further optimization.
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Affiliation(s)
- Dale J. Calleja
- Department of Medical Biology, Walter and Eliza Hall Institute, University of Melbourne, Melbourne, VIC, Australia
| | - Nathan Kuchel
- Department of Medical Biology, Walter and Eliza Hall Institute, University of Melbourne, Melbourne, VIC, Australia
| | - Bernadine G. C. Lu
- Department of Medical Biology, Walter and Eliza Hall Institute, University of Melbourne, Melbourne, VIC, Australia
| | - Richard W. Birkinshaw
- Department of Medical Biology, Walter and Eliza Hall Institute, University of Melbourne, Melbourne, VIC, Australia
| | - Theresa Klemm
- Department of Medical Biology, Walter and Eliza Hall Institute, University of Melbourne, Melbourne, VIC, Australia
| | - Marcel Doerflinger
- Department of Medical Biology, Walter and Eliza Hall Institute, University of Melbourne, Melbourne, VIC, Australia
| | - James P. Cooney
- Department of Medical Biology, Walter and Eliza Hall Institute, University of Melbourne, Melbourne, VIC, Australia
| | - Liana Mackiewicz
- Department of Medical Biology, Walter and Eliza Hall Institute, University of Melbourne, Melbourne, VIC, Australia
| | - Amanda E. Au
- Department of Medical Biology, Walter and Eliza Hall Institute, University of Melbourne, Melbourne, VIC, Australia
| | - Yu Q. Yap
- Department of Medical Biology, Walter and Eliza Hall Institute, University of Melbourne, Melbourne, VIC, Australia
| | - Timothy R Blackmore
- Department of Medical Biology, Walter and Eliza Hall Institute, University of Melbourne, Melbourne, VIC, Australia
| | - Kasiram Katneni
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia
| | - Elly Crighton
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia
| | - Janet Newman
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Biomedical Program, Parkville, VIC, Australia
| | - Kate E. Jarman
- Department of Medical Biology, Walter and Eliza Hall Institute, University of Melbourne, Melbourne, VIC, Australia
| | - Melissa J. Call
- Department of Medical Biology, Walter and Eliza Hall Institute, University of Melbourne, Melbourne, VIC, Australia
| | - Bernhard C. Lechtenberg
- Department of Medical Biology, Walter and Eliza Hall Institute, University of Melbourne, Melbourne, VIC, Australia
| | - Peter E. Czabotar
- Department of Medical Biology, Walter and Eliza Hall Institute, University of Melbourne, Melbourne, VIC, Australia
| | - Marc Pellegrini
- Department of Medical Biology, Walter and Eliza Hall Institute, University of Melbourne, Melbourne, VIC, Australia
| | - Susan A. Charman
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia
| | - Kym N. Lowes
- Department of Medical Biology, Walter and Eliza Hall Institute, University of Melbourne, Melbourne, VIC, Australia
| | - Jeffrey P. Mitchell
- Department of Medical Biology, Walter and Eliza Hall Institute, University of Melbourne, Melbourne, VIC, Australia
| | - Ueli Nachbur
- Department of Medical Biology, Walter and Eliza Hall Institute, University of Melbourne, Melbourne, VIC, Australia
| | - Guillaume Lessene
- Department of Medical Biology, Walter and Eliza Hall Institute, University of Melbourne, Melbourne, VIC, Australia
- Department of Pharmacology and Therapeutics, The University of Melbourne, Melbourne, VIC, Australia
| | - David Komander
- Department of Medical Biology, Walter and Eliza Hall Institute, University of Melbourne, Melbourne, VIC, Australia
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21
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Shen Z, Ratia K, Cooper L, Kong D, Lee H, Kwon Y, Li Y, Alqarni S, Huang F, Dubrovskyi O, Rong L, Thatcher G, Xiong R. Design of SARS-CoV-2 PLpro Inhibitors for COVID-19 Antiviral Therapy Leveraging Binding Cooperativity. J Med Chem 2022; 65:2940-2955. [PMID: 34665619 PMCID: PMC8547495 DOI: 10.1021/acs.jmedchem.1c01307] [Citation(s) in RCA: 91] [Impact Index Per Article: 45.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Indexed: 12/29/2022]
Abstract
Antiviral agents that complement vaccination are urgently needed to end the COVID-19 pandemic. The SARS-CoV-2 papain-like protease (PLpro), one of only two essential cysteine proteases that regulate viral replication, also dysregulates host immune sensing by binding and deubiquitination of host protein substrates. PLpro is a promising therapeutic target, albeit challenging owing to featureless P1 and P2 sites recognizing glycine. To overcome this challenge, we leveraged the cooperativity of multiple shallow binding sites on the PLpro surface, yielding novel 2-phenylthiophenes with nanomolar inhibitory potency. New cocrystal structures confirmed that ligand binding induces new interactions with PLpro: by closing of the BL2 loop of PLpro forming a novel "BL2 groove" and by mimicking the binding interaction of ubiquitin with Glu167 of PLpro. Together, this binding cooperativity translates to the most potent PLpro inhibitors reported to date, with slow off-rates, improved binding affinities, and low micromolar antiviral potency in SARS-CoV-2-infected human cells.
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Affiliation(s)
- Zhengnan Shen
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago (UIC), Chicago, IL, 60612, USA
- UICentre (Drug Discovery @ UIC), University of Illinois at Chicago (UIC), Chicago, IL, 60612, USA
- Department of Pharmacology & Toxicology, College of Pharmacy, University of Arizona, Tucson, AZ, 85721, USA
| | - Kiira Ratia
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago (UIC), Chicago, IL, 60612, USA
- Research Resources Center, University of Illinois at Chicago (UIC), Chicago, IL, 60612, USA
| | - Laura Cooper
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago (UIC), Chicago, IL, 60612, USA
- Department of Microbiology, College of Medicine, University of Illinois at Chicago (UIC), Chicago, IL, 60612, USA
| | - Deyu Kong
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago (UIC), Chicago, IL, 60612, USA
- UICentre (Drug Discovery @ UIC), University of Illinois at Chicago (UIC), Chicago, IL, 60612, USA
| | - Hyun Lee
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago (UIC), Chicago, IL, 60612, USA
- Research Resources Center, University of Illinois at Chicago (UIC), Chicago, IL, 60612, USA
| | - Youngjin Kwon
- Research Resources Center, University of Illinois at Chicago (UIC), Chicago, IL, 60612, USA
| | - Yangfeng Li
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago (UIC), Chicago, IL, 60612, USA
- UICentre (Drug Discovery @ UIC), University of Illinois at Chicago (UIC), Chicago, IL, 60612, USA
| | - Saad Alqarni
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago (UIC), Chicago, IL, 60612, USA
| | - Fei Huang
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago (UIC), Chicago, IL, 60612, USA
- UICentre (Drug Discovery @ UIC), University of Illinois at Chicago (UIC), Chicago, IL, 60612, USA
| | - Oleksii Dubrovskyi
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago (UIC), Chicago, IL, 60612, USA
- UICentre (Drug Discovery @ UIC), University of Illinois at Chicago (UIC), Chicago, IL, 60612, USA
| | - Lijun Rong
- Department of Microbiology, College of Medicine, University of Illinois at Chicago (UIC), Chicago, IL, 60612, USA
| | - Gregory Thatcher
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago (UIC), Chicago, IL, 60612, USA
- Department of Pharmacology & Toxicology, College of Pharmacy, University of Arizona, Tucson, AZ, 85721, USA
| | - Rui Xiong
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago (UIC), Chicago, IL, 60612, USA
- UICentre (Drug Discovery @ UIC), University of Illinois at Chicago (UIC), Chicago, IL, 60612, USA
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22
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Cannalire R, Cerchia C, Beccari AR, Di Leva FS, Summa V. Targeting SARS-CoV-2 Proteases and Polymerase for COVID-19 Treatment: State of the Art and Future Opportunities. J Med Chem 2022; 65:2716-2746. [PMID: 33186044 PMCID: PMC7688049 DOI: 10.1021/acs.jmedchem.0c01140] [Citation(s) in RCA: 124] [Impact Index Per Article: 62.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Indexed: 02/07/2023]
Abstract
The newly emerged coronavirus, called SARS-CoV-2, is the causing pathogen of pandemic COVID-19. The identification of drugs to treat COVID-19 and other coronavirus diseases is an urgent global need, thus different strategies targeting either virus or host cell are still under investigation. Direct-acting agents, targeting protease and polymerase functionalities, represent a milestone in antiviral therapy. The 3C-like (or Main) protease (3CLpro) and the nsp12 RNA-dependent RNA-polymerase (RdRp) are the best characterized SARS-CoV-2 targets and show the highest degree of conservation across coronaviruses fostering the identification of broad-spectrum inhibitors. Coronaviruses also possess a papain-like protease, another essential enzyme, still poorly characterized and not equally conserved, limiting the identification of broad-spectrum agents. Herein, we provide an exhaustive comparative analysis of SARS-CoV-2 proteases and RdRp with respect to other coronavirus homologues. Moreover, we highlight the most promising inhibitors of these proteins reported so far, including the possible strategies for their further development.
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Affiliation(s)
- Rolando Cannalire
- Department
of Pharmacy, University of Naples “Federico
II”, via D. Montesano 49, 80131 Napoli, Italy
| | - Carmen Cerchia
- Department
of Pharmacy, University of Naples “Federico
II”, via D. Montesano 49, 80131 Napoli, Italy
| | | | - Francesco Saverio Di Leva
- Department
of Pharmacy, University of Naples “Federico
II”, via D. Montesano 49, 80131 Napoli, Italy
| | - Vincenzo Summa
- Department
of Pharmacy, University of Naples “Federico
II”, via D. Montesano 49, 80131 Napoli, Italy
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23
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Cannalire R, Cerchia C, Beccari AR, Di Leva FS, Summa V. Targeting SARS-CoV-2 Proteases and Polymerase for COVID-19 Treatment: State of the Art and Future Opportunities. J Med Chem 2022. [PMID: 33186044 DOI: 10.1021/acs.jmedchem.0c01140/suppl_file/jm0c01140_si_001.pdf] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The newly emerged coronavirus, called SARS-CoV-2, is the causing pathogen of pandemic COVID-19. The identification of drugs to treat COVID-19 and other coronavirus diseases is an urgent global need, thus different strategies targeting either virus or host cell are still under investigation. Direct-acting agents, targeting protease and polymerase functionalities, represent a milestone in antiviral therapy. The 3C-like (or Main) protease (3CLpro) and the nsp12 RNA-dependent RNA-polymerase (RdRp) are the best characterized SARS-CoV-2 targets and show the highest degree of conservation across coronaviruses fostering the identification of broad-spectrum inhibitors. Coronaviruses also possess a papain-like protease, another essential enzyme, still poorly characterized and not equally conserved, limiting the identification of broad-spectrum agents. Herein, we provide an exhaustive comparative analysis of SARS-CoV-2 proteases and RdRp with respect to other coronavirus homologues. Moreover, we highlight the most promising inhibitors of these proteins reported so far, including the possible strategies for their further development.
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Affiliation(s)
- Rolando Cannalire
- Department of Pharmacy, University of Naples "Federico II", via D. Montesano 49, 80131 Napoli, Italy
| | - Carmen Cerchia
- Department of Pharmacy, University of Naples "Federico II", via D. Montesano 49, 80131 Napoli, Italy
| | - Andrea R Beccari
- Dompé Farmaceutici SpA, via Campo di Pile, 67100 L'Aquila, Italy
| | - Francesco Saverio Di Leva
- Department of Pharmacy, University of Naples "Federico II", via D. Montesano 49, 80131 Napoli, Italy
| | - Vincenzo Summa
- Department of Pharmacy, University of Naples "Federico II", via D. Montesano 49, 80131 Napoli, Italy
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24
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Lv Z, Cano KE, Jia L, Drag M, Huang TT, Olsen SK. Targeting SARS-CoV-2 Proteases for COVID-19 Antiviral Development. Front Chem 2022; 9:819165. [PMID: 35186898 PMCID: PMC8850931 DOI: 10.3389/fchem.2021.819165] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 12/20/2021] [Indexed: 12/18/2022] Open
Abstract
The emergence of severe acute respiratory syndrome (SARS-CoV-2) in 2019 marked the third occurrence of a highly pathogenic coronavirus in the human population since 2003. As the death toll surpasses 5 million globally and economic losses continue, designing drugs that could curtail infection and disease progression is critical. In the US, three highly effective Food and Drug Administration (FDA)-authorized vaccines are currently available, and Remdesivir is approved for the treatment of hospitalized patients. However, moderate vaccination rates and the sustained evolution of new viral variants necessitate the ongoing search for new antivirals. Several viral proteins have been prioritized as SARS-CoV-2 antiviral drug targets, among them the papain-like protease (PLpro) and the main protease (Mpro). Inhibition of these proteases would target viral replication, viral maturation, and suppression of host innate immune responses. Knowledge of inhibitors and assays for viruses were quickly adopted for SARS-CoV-2 protease research. Potential candidates have been identified to show inhibitory effects against PLpro and Mpro, both in biochemical assays and viral replication in cells. These results encourage further optimizations to improve prophylactic and therapeutic efficacy. In this review, we examine the latest developments of potential small-molecule inhibitors and peptide inhibitors for PLpro and Mpro, and how structural biology greatly facilitates this process.
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Affiliation(s)
- Zongyang Lv
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Kristin E. Cano
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Lijia Jia
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Marcin Drag
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, Wroclaw, Poland
| | - Tony T. Huang
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, United States
| | - Shaun K. Olsen
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
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25
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Inhibition of XPO-1 Mediated Nuclear Export through the Michael-Acceptor Character of Chalcones. Pharmaceuticals (Basel) 2021; 14:ph14111131. [PMID: 34832913 PMCID: PMC8621101 DOI: 10.3390/ph14111131] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 11/02/2021] [Accepted: 11/04/2021] [Indexed: 01/10/2023] Open
Abstract
The nuclear export receptor exportin-1 (XPO1, CRM1) mediates the nuclear export of proteins that contain a leucine-rich nuclear export signal (NES) towards the cytoplasm. XPO1 is considered a relevant target in different human diseases, particularly in hematological malignancies, tumor resistance, inflammation, neurodegeneration and viral infections. Thus, its pharmacological inhibition is of significant therapeutic interest. The best inhibitors described so far (leptomycin B and SINE compounds) interact with XPO1 through a covalent interaction with Cys528 located in the NES-binding cleft of XPO1. Based on the well-established feature of chalcone derivatives to react with thiol groups via hetero-Michael addition reactions, we have synthesized two series of chalcones. Their capacity to react with thiol groups was tested by incubation with GSH to afford the hetero-Michael adducts that evolved backwards to the initial chalcone through a retro-Michael reaction, supporting that the covalent interaction with thiols could be reversible. The chalcone derivatives were evaluated in antiproliferative assays against a panel of cancer cell lines and as XPO1 inhibitors, and a good correlation was observed with the results obtained in both assays. Moreover, no inhibition of the cargo export was observed when the two prototype chalcones 9 and 10 were tested against a XPO1-mutated Jurkat cell line (XPO1C528S), highlighting the importance of the Cys at the NES-binding cleft for inhibition. Finally, their interaction at the molecular level at the NES-binding cleft was studied by applying the computational tool CovDock.
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26
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Tomazou M, Bourdakou MM, Minadakis G, Zachariou M, Oulas A, Karatzas E, Loizidou EM, Kakouri AC, Christodoulou CC, Savva K, Zanti M, Onisiforou A, Afxenti S, Richter J, Christodoulou CG, Kyprianou T, Kolios G, Dietis N, Spyrou GM. Multi-omics data integration and network-based analysis drives a multiplex drug repurposing approach to a shortlist of candidate drugs against COVID-19. Brief Bioinform 2021; 22:bbab114. [PMID: 34009288 PMCID: PMC8135326 DOI: 10.1093/bib/bbab114] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 02/01/2021] [Accepted: 03/13/2021] [Indexed: 02/06/2023] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic is undeniably the most severe global health emergency since the 1918 Influenza outbreak. Depending on its evolutionary trajectory, the virus is expected to establish itself as an endemic infectious respiratory disease exhibiting seasonal flare-ups. Therefore, despite the unprecedented rally to reach a vaccine that can offer widespread immunization, it is equally important to reach effective prevention and treatment regimens for coronavirus disease 2019 (COVID-19). Contributing to this effort, we have curated and analyzed multi-source and multi-omics publicly available data from patients, cell lines and databases in order to fuel a multiplex computational drug repurposing approach. We devised a network-based integration of multi-omic data to prioritize the most important genes related to COVID-19 and subsequently re-rank the identified candidate drugs. Our approach resulted in a highly informed integrated drug shortlist by combining structural diversity filtering along with experts' curation and drug-target mapping on the depicted molecular pathways. In addition to the recently proposed drugs that are already generating promising results such as dexamethasone and remdesivir, our list includes inhibitors of Src tyrosine kinase (bosutinib, dasatinib, cytarabine and saracatinib), which appear to be involved in multiple COVID-19 pathophysiological mechanisms. In addition, we highlight specific immunomodulators and anti-inflammatory drugs like dactolisib and methotrexate and inhibitors of histone deacetylase like hydroquinone and vorinostat with potential beneficial effects in their mechanisms of action. Overall, this multiplex drug repurposing approach, developed and utilized herein specifically for SARS-CoV-2, can offer a rapid mapping and drug prioritization against any pathogen-related disease.
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Affiliation(s)
- Marios Tomazou
- Bioinformatics Department, The Cyprus Institute of Neurology and Genetics, Cyprus
- The Cyprus School of Molecular Medicine, Cyprus
- Neurogenetics Department, The Cyprus Institute of Neurology and Genetics, Cyprus
| | - Marilena M Bourdakou
- Bioinformatics Department, The Cyprus Institute of Neurology and Genetics, Cyprus
- Laboratory of Pharmacology, Faculty of Medicine, Democritus University of Thrace, Greece
| | - George Minadakis
- Bioinformatics Department, The Cyprus Institute of Neurology and Genetics, Cyprus
- The Cyprus School of Molecular Medicine, Cyprus
| | - Margarita Zachariou
- Bioinformatics Department, The Cyprus Institute of Neurology and Genetics, Cyprus
- The Cyprus School of Molecular Medicine, Cyprus
| | - Anastasis Oulas
- Bioinformatics Department, The Cyprus Institute of Neurology and Genetics, Cyprus
- The Cyprus School of Molecular Medicine, Cyprus
| | - Evangelos Karatzas
- Bioinformatics Department, The Cyprus Institute of Neurology and Genetics, Cyprus
- Institute for Fundamental Biomedical Research, BSRC “Alexander Fleming”, Vari, Greece
| | - Eleni M Loizidou
- Bioinformatics Department, The Cyprus Institute of Neurology and Genetics, Cyprus
- Institute for Fundamental Biomedical Research, BSRC “Alexander Fleming”, Vari, Greece
| | - Andrea C Kakouri
- Bioinformatics Department, The Cyprus Institute of Neurology and Genetics, Cyprus
- The Cyprus School of Molecular Medicine, Cyprus
- Neurogenetics Department, The Cyprus Institute of Neurology and Genetics, Cyprus
| | - Christiana C Christodoulou
- Bioinformatics Department, The Cyprus Institute of Neurology and Genetics, Cyprus
- The Cyprus School of Molecular Medicine, Cyprus
- Neuroepidemiology Department, The Cyprus Institute of Neurology and Genetics, Cyprus
| | - Kyriaki Savva
- Bioinformatics Department, The Cyprus Institute of Neurology and Genetics, Cyprus
- The Cyprus School of Molecular Medicine, Cyprus
| | - Maria Zanti
- Bioinformatics Department, The Cyprus Institute of Neurology and Genetics, Cyprus
- The Cyprus School of Molecular Medicine, Cyprus
- Cancer Genetics, Therapeutics … Ultrastructural Pathology, The Cyprus Institute of Neurology and Genetics, Cyprus
| | - Anna Onisiforou
- Bioinformatics Department, The Cyprus Institute of Neurology and Genetics, Cyprus
- The Cyprus School of Molecular Medicine, Cyprus
| | - Sotiroula Afxenti
- Bioinformatics Department, The Cyprus Institute of Neurology and Genetics, Cyprus
- The Cyprus School of Molecular Medicine, Cyprus
- Neuroimmunology Department, The Cyprus Institute of Neurology and Genetics, Cyprus
| | - Jan Richter
- Department of Molecular Virology, The Cyprus Institute of Neurology and Genetics, Cyprus
- The Cyprus School of Molecular Medicine, Cyprus
| | - Christina G Christodoulou
- Department of Molecular Virology, The Cyprus Institute of Neurology and Genetics, Cyprus
- The Cyprus School of Molecular Medicine, Cyprus
| | - Theodoros Kyprianou
- Medical School, University of Nicosia, Cyprus
- University Hospitals Bristol and Weston NHS Foundation Trust, United Kingdom
| | - George Kolios
- Laboratory of Pharmacology, Faculty of Medicine, Democritus University of Thrace, Greece
| | - Nikolas Dietis
- Experimental Pharmacology Laboratory, Medical School, University of Cyprus, Cyprus
| | - George M Spyrou
- Bioinformatics Department, The Cyprus Institute of Neurology and Genetics, Cyprus
- The Cyprus School of Molecular Medicine, Cyprus
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27
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Gunaratna MJ, Hao B, Zhang M, Nakagomi M, Ito A, Iwamoto T, Hua DH. SYNTHESIS OF PROBE MOLECULES, 6-(DIMETHYLAMINO)-2-PHENYLISOINDOLIN-1-ONES, FOR MECHANISTIC STUDIES OF FIREFLY LUCIFERASE INHIBITION. HETEROCYCLES 2021; 103:231-248. [PMID: 34566248 DOI: 10.3987/com-20-s(k)1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Firefly luciferase is used in high-throughput screening based on the detection of chemiluminescence. It catalyzes an esterification reaction of luciferin with adenosine 5'-triphosphate (ATP) followed by decarbonylation with oxygen and concomitance of light. Previously, we reported that firefly luciferase also possesses acyl-CoA synthetase activity and catalyzes an aromatic carboxylic acid group of F-53, using ATP, Mg2+ and coenzyme A (CoA), to produce F-53 covalently attached to active-site lysine-529 residue of firefly luciferase through the formation of an amide group. The amidation of lysine-529 resulted in a deactivation of luciferase. In order to probe firefly luciferase inhibition's mechanism, we synthesized two probe molecules 1 and 2, mimicking F-53. Molecule 1 contains an azido-appended side chain in the aromatic ring of F-53, while 2 possesses an azido and a carboxylic acid group appended side chains. Both synthetic schemes are readily amenable to large-scale syntheses. Molecule 1 was made from 2-allylaniline, which was derived from a thermal-induced aromatic-Claisen rearrangement of N-allylaniline. The azido-appended side chain of 2 was installed from a Horner-Wadsworth-Emmons reaction and the carboxylic acid side chain from a Sonogashira reaction.
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Affiliation(s)
- Medha J Gunaratna
- Department of Chemistry, 1212 Mid Campus Drive N., Kansas State University, Manhattan, KS 66506, U.S.A
| | - Bo Hao
- Department of Chemistry, 1212 Mid Campus Drive N., Kansas State University, Manhattan, KS 66506, U.S.A
| | - Man Zhang
- Department of Chemistry, 1212 Mid Campus Drive N., Kansas State University, Manhattan, KS 66506, U.S.A
| | - Madoka Nakagomi
- Research Foundation ITSUU Laboratory, C1232 Kanagawa Science Park R&D Building, 3-2-1 Sakado, Takatsu-ku, Kawasaki, Kanagawa, 213-0012, Japan
| | - Ai Ito
- Showa Pharmaceutical University, 3-3165 Higashi-Tamagawagakuen, Machida, Tokyo, 194-8543, Japan
| | - Takeo Iwamoto
- Core Research Facilities, The Jikei University School of Medicine, Tokyo, 105-8461, Japan
| | - Duy H Hua
- Department of Chemistry, 1212 Mid Campus Drive N., Kansas State University, Manhattan, KS 66506, U.S.A
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28
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Ghosh K, Amin SA, Gayen S, Jha T. Unmasking of crucial structural fragments for coronavirus protease inhibitors and its implications in COVID-19 drug discovery. J Mol Struct 2021; 1237:130366. [PMID: 33814612 PMCID: PMC7997030 DOI: 10.1016/j.molstruc.2021.130366] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 03/19/2021] [Accepted: 03/20/2021] [Indexed: 12/19/2022]
Abstract
Fragment based drug discovery (FBDD) by the aid of different modelling techniques have been emerged as a key drug discovery tool in the area of pharmaceutical science and technology. The merits of employing these methods, in place of other conventional molecular modelling techniques, endorsed clear detection of the possible structural fragments present in diverse set of investigated compounds and can create alternate possibilities of lead optimization in drug discovery. In this work, two fragment identification tools namely SARpy and Laplacian-corrected Bayesian analysis were used for previous SARS-CoV PLpro and 3CLpro inhibitors. A robust and predictive SARpy based fragments identification was performed which have been validated further by Laplacian-corrected Bayesian model. These comprehensive approaches have advantages since fragments are straight forward to interpret. Moreover, distinguishing the key molecular features (with respect to ECFP_6 fingerprint) revealed good or bad influences for the SARS-CoV protease inhibitory activities. Furthermore, the identified fragments could be implemented in the medicinal chemistry endeavors of COVID-19 drug discovery.
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Affiliation(s)
- Kalyan Ghosh
- Laboratory of Drug Design and Discovery, Department of Pharmaceutical Sciences, Dr. Harisingh Gour University, Sagar, MP, India
| | - Sk Abdul Amin
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - Shovanlal Gayen
- Laboratory of Drug Design and Discovery, Department of Pharmaceutical Sciences, Dr. Harisingh Gour University, Sagar, MP, India
| | - Tarun Jha
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
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29
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High-Throughput Fluorescent Assay for Inhibitor Screening of Proteases from RNA Viruses. Molecules 2021; 26:molecules26133792. [PMID: 34206406 PMCID: PMC8270262 DOI: 10.3390/molecules26133792] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 06/11/2021] [Accepted: 06/14/2021] [Indexed: 01/07/2023] Open
Abstract
Spanish flu, polio epidemics, and the ongoing COVID-19 pandemic are the most profound examples of severe widespread diseases caused by RNA viruses. The coronavirus pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) demands affordable and reliable assays for testing antivirals. To test inhibitors of viral proteases, we have developed an inexpensive high-throughput assay based on fluorescent energy transfer (FRET). We assayed an array of inhibitors for papain-like protease from SARS-CoV-2 and validated it on protease from the tick-borne encephalitis virus to emphasize its versatility. The reaction progress is monitored as loss of FRET signal of the substrate. This robust and reproducible assay can be used for testing the inhibitors in 96- or 384-well plates.
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30
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Small molecules as tools for functional assessment of deubiquitinating enzyme function. Cell Chem Biol 2021; 28:1090-1100. [PMID: 34089649 DOI: 10.1016/j.chembiol.2021.04.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 04/05/2021] [Accepted: 04/23/2021] [Indexed: 12/11/2022]
Abstract
Deubiquitinating enzymes (DUBs) are a largely understudied and untapped resource in the toolkit of protein degradation functionalities. They comprise a large repertoire of enzymes that remove ubiquitin from substrates in a variety of cellular and pathophysiological contexts, and have enormous potential for research and clinical use. It is only within the last 5 years that potent, selective, and well-characterized small-molecule inhibitors of DUBs have been described. These compounds are now being used to study the biological roles of DUBs. Here, we describe downstream applications of small-molecule inhibitors for studying DUBs and provide a framework for future studies. We highlight recent examples of using these inhibitors to confirm and explore the role of these enzymes in both normal and pathological contexts. These studies represent the first steps in the burgeoning field of pharmacological and chemoproteomic studies of DUBs, which will be critical for the continued advancement of DUB field.
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31
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Advancements in macromolecular crystallography: from past to present. Emerg Top Life Sci 2021; 5:127-149. [PMID: 33969867 DOI: 10.1042/etls20200316] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 04/09/2021] [Accepted: 04/15/2021] [Indexed: 11/17/2022]
Abstract
Protein Crystallography or Macromolecular Crystallography (MX) started as a new discipline of science with the pioneering work on the determination of the protein crystal structures by John Kendrew in 1958 and Max Perutz in 1960. The incredible achievements in MX are attributed to the development of advanced tools, methodologies, and automation in every aspect of the structure determination process, which have reduced the time required for solving protein structures from years to a few days, as evident from the tens of thousands of crystal structures of macromolecules available in PDB. The advent of brilliant synchrotron sources, fast detectors, and novel sample delivery methods has shifted the paradigm from static structures to understanding the dynamic picture of macromolecules; further propelled by X-ray Free Electron Lasers (XFELs) that explore the femtosecond regime. The revival of the Laue diffraction has also enabled the understanding of macromolecules through time-resolved crystallography. In this review, we present some of the astonishing method-related and technological advancements that have contributed to the progress of MX. Even with the rapid evolution of several methods for structure determination, the developments in MX will keep this technique relevant and it will continue to play a pivotal role in gaining unprecedented atomic-level details as well as revealing the dynamics of biological macromolecules. With many exciting developments awaiting in the upcoming years, MX has the potential to contribute significantly to the growth of modern biology by unraveling the mechanisms of complex biological processes as well as impacting the area of drug designing.
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32
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Shiryaev VA, Klimochkin YN. Main Chemotypes of SARS-CoV-2 Reproduction Inhibitors. RUSSIAN JOURNAL OF ORGANIC CHEMISTRY 2021. [PMCID: PMC8188765 DOI: 10.1134/s107042802105002x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The COVID-19 pandemic has forced scientists all over the world to focus their effort on searching for targeted drugs for coronavirus chemotherapy. The present review is an attempt to systematize low-molecular-weight compounds, including well-known pharmaceuticals and natural substances that have exhibited high anti-coronavirus activity, not in terms of action on their targets, but in terms of their structural type.
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Affiliation(s)
- V. A. Shiryaev
- Samara State Technical University, 443100 Samara, Russia
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33
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Wang R, Stephen P, Tao Y, Zhang W, Lin SX. Human endeavor for anti-SARS-CoV-2 pharmacotherapy: A major strategy to fight the pandemic. Biomed Pharmacother 2021; 137:111232. [PMID: 33486202 PMCID: PMC7834004 DOI: 10.1016/j.biopha.2021.111232] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 12/25/2020] [Accepted: 12/31/2020] [Indexed: 12/22/2022] Open
Abstract
The global spread of COVID-19 constitutes the most dangerous pandemic to emerge during the last one hundred years. About seventy-nine million infections and more than 1.7 million death have been reported to date, along with destruction of the global economy. With the uncertainty evolved by alarming level of genome mutations, coupled with likelihood of generating only a short lived immune response by the vaccine injections, the identification of antiviral drugs for direct therapy is the need of the hour. Strategies to inhibit virus infection and replication focus on targets such as the spike protein and non-structural proteins including the highly conserved RNA-dependent-RNA-polymerase, nucleotidyl-transferases, main protease and papain-like proteases. There is also an indirect option to target the host cell recognition systems such as angiotensin-converting enzyme 2 (ACE2), transmembrane protease, serine 2, host cell expressed CD147, and the host furin. A drug search strategy consensus in tandem with analysis of currently available information is extremely important for the rapid identification of anti-viral. An unprecedented display of cooperation among the scientific community regarding SARS-CoV-2 research has resulted in the accumulation of an enormous amount of literature that requires curation. Drug repurposing and drug combinations have drawn tremendous attention for rapid therapeutic application, while high throughput screening and virtual searches support de novo drug identification. Here, we examine how certain approved drugs targeting different viruses can play a role in combating this new virus and analyze how they demonstrate efficacy under clinical assessment. Suggestions on repurposing and de novo strategies are proposed to facilitate the fight against the COVID-19 pandemic.
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Affiliation(s)
- Ruixuan Wang
- Axe Molecular Endocrinology and Nephrology, CHU Research Center and Laval University, Quebec City, Quebec, G1V 4G2, Canada
| | - Preyesh Stephen
- Axe Molecular Endocrinology and Nephrology, CHU Research Center and Laval University, Quebec City, Quebec, G1V 4G2, Canada
| | - Yi Tao
- Axe Molecular Endocrinology and Nephrology, CHU Research Center and Laval University, Quebec City, Quebec, G1V 4G2, Canada
| | - Wenfa Zhang
- Axe Molecular Endocrinology and Nephrology, CHU Research Center and Laval University, Quebec City, Quebec, G1V 4G2, Canada
| | - Sheng-Xiang Lin
- Axe Molecular Endocrinology and Nephrology, CHU Research Center and Laval University, Quebec City, Quebec, G1V 4G2, Canada.
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34
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Amin SA, Banerjee S, Gayen S, Jha T. Protease targeted COVID-19 drug discovery: What we have learned from the past SARS-CoV inhibitors? Eur J Med Chem 2021; 215:113294. [PMID: 33618158 PMCID: PMC7880840 DOI: 10.1016/j.ejmech.2021.113294] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 02/06/2021] [Accepted: 02/08/2021] [Indexed: 12/25/2022]
Abstract
The fascinating similarity between the SARS-CoV and SARS-CoV-2, inspires scientific community to investigate deeper into the SARS-CoV proteases such as main protease (Mpro) and papain-like protease (PLpro) and their inhibitors for the discovery of SARS-CoV-2 protease inhibitors. Because of the similarity in the proteases of these two corona viruses, there is a greater chance for the previous SARS-CoV Mpro and PLpro inhibitors to provide effective results against SARS-CoV-2. In this context, the molecular fragments from the SARS-CoV protease inhibitors through the fragment-based drug design and discovery technique can be useful guidance for COVID-19 drug discovery. Here, we have focused on the structure-activity relationship studies of previous SARS-CoV protease inhibitors and discussed about crucial fragments generated from previous SARS-CoV protease inhibitors important for the lead optimization of SARS-CoV-2 protease inhibitors. This study surely offers different strategic options of lead optimization to the medicinal chemists to discover effective anti-viral agent against the devastating disease, COVID-19.
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Affiliation(s)
- Sk Abdul Amin
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, P. O. Box 17020, Jadavpur University, Kolkata, 700032, India
| | - Suvankar Banerjee
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, P. O. Box 17020, Jadavpur University, Kolkata, 700032, India
| | - Shovanlal Gayen
- Laboratory of Drug Design and Discovery, Department of Pharmaceutical Sciences, Dr. Harisingh Gour University, Sagar, MP, India.
| | - Tarun Jha
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, P. O. Box 17020, Jadavpur University, Kolkata, 700032, India.
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Waidha K, Saxena A, Kumar P, Sharma S, Ray D, Saha B. Design and identification of novel annomontine analogues against SARS-CoV-2: An in-silico approach. Heliyon 2021; 7:e06657. [PMID: 33824915 PMCID: PMC8017494 DOI: 10.1016/j.heliyon.2021.e06657] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 08/20/2020] [Accepted: 03/29/2021] [Indexed: 12/27/2022] Open
Abstract
AIMS COVID-19 has currently emerged as the major global pandemic affecting the lives of people across the globe. It broke out from Wuhan Province of China, first reported to WHO on 31st December 2019 as "Pneumonia of unknown cause". Over time more people were infected with this virus, and the only tactic to ensure safety was to take precautionary measures due to the lack of any effective treatment or vaccines. As a result of unavailability of desired efficacy for previously repurposed drugs, exploring novel scaffolds against the virus has become the need of the hour. MAIN METHODS In the present study, 23 new annomontine analogues were designed representing β-Carboline based scaffolds. A hypothesis on its role as an effective ligand was laid for target-specific binding in SARS-CoV-2. These molecules were used for molecular docking analysis against the multiple possible drug targets using the Maestro Interface. To ensure the drug safety of these molecules ADME/Tox analysis was also performed. KEY FINDINGS The molecular docking analysis of the 23 novel molecules indicated the efficiency of these derivates against COVID-19. The efficiency of molecules was computed by the summation of the docking score against each target defined as LigE Score and compared against Hydroxycholoquine as a standard. Based on the docking score, the majority of the annomontine derivatives were found to have increased binding affinity with targets as compared to hydroxycholoquine. SIGNIFICANCE Due to the lack of efficiency, effectiveness, and failure of already repurposed drugs against the COVID-19, the exploration of the novel scaffold that can act as effective treatment is much needed. The current study hence emphasizes the potential of Annomontine based - β- Carboline derivatives as a potential drug candidate against COVID-19.
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Affiliation(s)
- Kamran Waidha
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, 125, 201301, India
| | - Anjali Saxena
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, 125, 201301, India
| | - Prashant Kumar
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, 125, 201301, India
| | - Sunil Sharma
- Chemical Engineering Department, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Devalina Ray
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, 125, 201301, India
| | - Biswajit Saha
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, 125, 201301, India
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Kinetic Characterization and Inhibitor Screening for the Proteases Leading to Identification of Drugs against SARS-CoV-2. Antimicrob Agents Chemother 2021; 65:AAC.02577-20. [PMID: 33526482 PMCID: PMC8097444 DOI: 10.1128/aac.02577-20] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 01/13/2021] [Indexed: 12/13/2022] Open
Abstract
Coronavirus (CoV) disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has claimed many lives worldwide and is still spreading since December 2019. The 3C-like protease (3CLpro) and papain-like protease (PLpro) are essential for maturation of viral polyproteins in SARS-CoV-2 life cycle and thus regarded as key drug targets for the disease. Coronavirus (CoV) disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has claimed many lives worldwide and is still spreading since December 2019. The 3C-like protease (3CLpro) and papain-like protease (PLpro) are essential for maturation of viral polyproteins in SARS-CoV-2 life cycle and thus regarded as key drug targets for the disease. In this study, 3CLpro and PLpro assay platforms were established, and their substrate specificities were characterized. The assays were used to screen collections of 1,068 and 2,701 FDA-approved drugs. After excluding the externally used drugs which are too toxic, we totally identified 12 drugs as 3CLpro inhibitors and 36 drugs as PLpro inhibitors active at 10 μM. Among these inhibitors, six drugs were found to suppress SARS-CoV-2 with the half-maximal effective concentration (EC50) below or close to 10 μM. This study enhances our understanding on the proteases and provides FDA-approved drugs for prevention and/or treatment of COVID-19.
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Chukwudozie OS, Duru VC, Ndiribe CC, Aborode AT, Oyebanji VO, Emikpe BO. The Relevance of Bioinformatics Applications in the Discovery of Vaccine Candidates and Potential Drugs for COVID-19 Treatment. Bioinform Biol Insights 2021; 15:11779322211002168. [PMID: 33795932 PMCID: PMC7968009 DOI: 10.1177/11779322211002168] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Accepted: 02/14/2021] [Indexed: 12/16/2022] Open
Abstract
The application of bioinformatics to vaccine research and drug discovery has never been so essential in the fight against infectious diseases. The greatest combat of the 21st century against a debilitating disease agent SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) virus discovered in Wuhan, China, December 2019, has piqued an unprecedented usage of bioinformatics tools in deciphering the molecular characterizations of infectious pathogens. With the viral genome data of SARS-COV-2 been made available barely weeks after the reported outbreak, bioinformatics platforms have become an all-time critical tool to gain time in the fight against the disease pandemic. Before the outbreak, different platforms have been developed to explore antigenic epitopes, predict peptide-protein docking and antibody structures, and simulate antigen-antibody reactions and lots more. However, the advent of the pandemic witnessed an upsurge in the application of these pipelines with the development of newer ones such as the Coronavirus Explorer in the development of efficacious vaccines, drug repurposing, and/or discovery. In this review, we have explored the various pipelines available for use, their relevance, and limitations in the timely development of useful therapeutic candidates from genomic data knowledge to clinical therapy.
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Affiliation(s)
| | - Vincent C Duru
- Molecular Genetics Unit, Institute of Child Health, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Charlotte C Ndiribe
- Department of Cell Biology and Genetics, University of Lagos, Lagos, Nigeria
| | | | - Victor O Oyebanji
- Department of Veterinary Pathology, University of Ibadan, Ibadan, Nigeria
| | - Benjamin O Emikpe
- Department of Veterinary Pathology, University of Ibadan, Ibadan, Nigeria
- School of Veterinary Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
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38
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Exploring naphthyl derivatives as SARS-CoV papain-like protease (PLpro) inhibitors and its implications in COVID-19 drug discovery. Mol Divers 2021; 26:215-228. [PMID: 33675510 PMCID: PMC7936608 DOI: 10.1007/s11030-021-10198-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 02/05/2021] [Indexed: 11/23/2022]
Abstract
Abstract Novel coronavirus disease 2019 (COVID-19) emerges as a serious threat to public health globally. The rapid spreading of COVID-19, caused by severe acute respiratory syndrome (SARS) coronavirus 2 (SARS-CoV-2), proclaimed the multitude of applied research needed not only to save the human health but also for the environmental safety. As per the recent World Health Organization reports, the novel corona virus may never be wiped out completely from the world. In this connection, the inhibitors already designed against different targets of previous human coronavirus (HCoV) infections will be a great starting point for further optimization. Pinpointing biochemical events censorious to the HCoV lifecycle has provided two proteases: a papain-like protease (PLpro) and a 3C-like protease (3CLpro) enzyme essential for viral replication. In this study, naphthyl derivatives inhibiting PLpro enzyme were subjected to robust molecular modelling approaches to understand different structural fingerprints important for the inhibition. Here, we cover two main aspects such as (a) exploration of naphthyl derivatives by classification QSAR analyses to find important fingerprints that module the SARS-CoV PLpro inhibition and (b) implications of naphthyl derivatives against SARS-CoV-2 PLpro enzyme through detailed ligand–receptor interaction analysis. The modelling insights will help in the speedy design of potent broad spectrum PLpro inhibitors against infectious SARS-CoV and SARS-CoV-2 in the future. Graphical Abstract ![]()
Supplementary Information The online version contains supplementary material available at(10.1007/s11030-021-10198-3) .
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Shen Z, Ratia K, Cooper L, Kong D, Lee H, Kwon Y, Li Y, Alqarni S, Huang F, Dubrovskyi O, Rong L, Thatcher GR, Xiong R. Potent, Novel SARS-CoV-2 PLpro Inhibitors Block Viral Replication in Monkey and Human Cell Cultures. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021. [PMID: 33594371 DOI: 10.1101/2021.02.13.431008] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Antiviral agents blocking SARS-CoV-2 viral replication are desperately needed to complement vaccination to end the COVID-19 pandemic. Viral replication and assembly are entirely dependent on two viral cysteine proteases: 3C-like protease (3CLpro) and the papain-like protease (PLpro). PLpro also has deubiquitinase (DUB) activity, removing ubiquitin (Ub) and Ub-like modifications from host proteins, disrupting the host immune response. 3CLpro is inhibited by many known cysteine protease inhibitors, whereas PLpro is a relatively unusual cysteine protease, being resistant to blockade by such inhibitors. A high-throughput screen of biased and unbiased libraries gave a low hit rate, identifying only CPI-169 and the positive control, GRL0617, as inhibitors with good potency (IC50 < 10 lower case Greek μM). Analogues of both inhibitors were designed to develop structure-activity relationships; however, without a co-crystal structure of the CPI-169 series, we focused on GRL0617 as a starting point for structure-based drug design, obtaining several co-crystal structures to guide optimization. A series of novel 2-phenylthiophene-based non-covalent SARS-CoV-2 PLpro inhibitors were obtained, culminating in low nanomolar potency. The high potency and slow inhibitor off-rate were rationalized by newly identified ligand interactions with a 'BL2 groove' that is distal from the active site cysteine. Trapping of the conformationally flexible BL2 loop by these inhibitors blocks binding of viral and host protein substrates; however, until now it has not been demonstrated that this mechanism can induce potent and efficacious antiviral activity. In this study, we report that novel PLpro inhibitors have excellent antiviral efficacy and potency against infectious SARS-CoV-2 replication in cell cultures. Together, our data provide structural insights into the design of potent PLpro inhibitors and the first validation that non-covalent inhibitors of SARS-CoV-2 PLpro can block infection of human cells with low micromolar potency.
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40
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Anirudhan V, Lee H, Cheng H, Cooper L, Rong L. Targeting SARS-CoV-2 viral proteases as a therapeutic strategy to treat COVID-19. J Med Virol 2021; 93:2722-2734. [PMID: 33475167 PMCID: PMC8014870 DOI: 10.1002/jmv.26814] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 01/15/2021] [Accepted: 01/18/2021] [Indexed: 12/14/2022]
Abstract
The 21st century has witnessed three outbreaks of coronavirus (CoVs) infections caused by severe acute respiratory syndrome (SARS)‐CoV, Middle East respiratory syndrome (MERS)‐CoV, and SARS‐CoV‐2. Coronavirus disease 2019 (COVID‐19), caused by SARS‐CoV‐2, spreads rapidly and since the discovery of the first COVID‐19 infection in December 2019, has caused 1.2 million deaths worldwide and 226,777 deaths in the United States alone. The high amino acid similarity between SARS‐CoV and SARS‐CoV‐2 viral proteins supports testing therapeutic molecules that were designed to treat SARS infections during the 2003 epidemic. In this review, we provide information on possible COVID‐19 treatment strategies that act via inhibition of the two essential proteins of the virus, 3C‐like protease (3CLpro) or papain‐like protease (PLpro). This highlights the importance of 3CLpro and PLpro as theraputic targets for drug design and development of SARS‐CoV‐2 inhibitors to prevent COVID‐19.
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Affiliation(s)
- Varada Anirudhan
- Department of Microbiology and Immunology, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Hyun Lee
- Department of Pharmaceutical Sciences, Center for Biomolecular Sciences, College of Pharmacy, Biophysics Core at Research Resources Center, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Han Cheng
- Department of Microbiology and Immunology, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Laura Cooper
- Department of Microbiology and Immunology, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Lijun Rong
- Department of Microbiology and Immunology, University of Illinois at Chicago, Chicago, Illinois, USA
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41
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Cockram PE, Kist M, Prakash S, Chen SH, Wertz IE, Vucic D. Ubiquitination in the regulation of inflammatory cell death and cancer. Cell Death Differ 2021; 28:591-605. [PMID: 33432113 PMCID: PMC7798376 DOI: 10.1038/s41418-020-00708-5] [Citation(s) in RCA: 163] [Impact Index Per Article: 54.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 12/03/2020] [Accepted: 12/04/2020] [Indexed: 12/12/2022] Open
Abstract
The ubiquitin system is complex, multifaceted, and is crucial for the modulation of a vast number of cellular processes. Ubiquitination is tightly regulated at different levels by a range of enzymes including E1s, E2s, and E3s, and an array of DUBs. The UPS directs protein degradation through the proteasome, and regulates a wide array of cellular processes including transcription and epigenetic factors as well as key oncoproteins. Ubiquitination is key to the dynamic regulation of programmed cell death. Notably, the TNF signaling pathway is controlled by competing ubiquitin conjugation and deubiquitination, which governs both proteasomal degradation and signaling complex formation. In the inflammatory response, ubiquitination is capable of both activating and dampening inflammasome activation through the control of either protein stability, complex formation, or, in some cases, directly affecting receptor activity. In this review, we discuss the enzymes and targets in the ubiquitin system that regulate fundamental cellular processes regulating cell death, and inflammation, as well as disease consequences resulting from their dysregulation. Finally, we highlight several pre-clinical and clinical compounds that regulate ubiquitin system enzymes, with the aim of restoring homeostasis and ameliorating diseases.
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Affiliation(s)
- Peter E Cockram
- Departments of Discovery Oncology, Genentech, 1 DNA Way, South San Francisco, CA, 94080, USA.,Departments of Discovery Chemistry, Genentech, 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Matthias Kist
- Departments of Early Discovery Biochemistry, Genentech, 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Sumit Prakash
- Departments of Discovery Oncology, Genentech, 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Si-Han Chen
- Departments of Discovery Oncology, Genentech, 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Ingrid E Wertz
- Departments of Discovery Oncology, Genentech, 1 DNA Way, South San Francisco, CA, 94080, USA. .,Departments of Early Discovery Biochemistry, Genentech, 1 DNA Way, South San Francisco, CA, 94080, USA.
| | - Domagoj Vucic
- Departments of Early Discovery Biochemistry, Genentech, 1 DNA Way, South San Francisco, CA, 94080, USA.
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42
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Zong Z, Zhang Z, Wu L, Zhang L, Zhou F. The Functional Deubiquitinating Enzymes in Control of Innate Antiviral Immunity. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:2002484. [PMID: 33511009 PMCID: PMC7816709 DOI: 10.1002/advs.202002484] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 09/09/2020] [Indexed: 05/11/2023]
Abstract
Innate antiviral immunity is the first line of host defense against invading viral pathogens. Immunity activation primarily relies on the recognition of pathogen-associated molecular patterns (PAMPs) by pattern recognition receptors (PRRs). Viral proteins or nucleic acids mainly engage three classes of PRRs: Toll-like receptors (TLRs), retinoic acid-inducible gene I (RIG-I)-like receptors (RLRs), and DNA sensor cyclic GMP-AMP (cGAMP) synthase (cGAS). These receptors initiate a series of signaling cascades that lead to the production of proinflammatory cytokines and type I interferon (IFN-I) in response to viral infection. This system requires precise regulation to avoid aberrant activation. Emerging evidence has unveiled the crucial roles that the ubiquitin system, especially deubiquitinating enzymes (DUBs), play in controlling immune responses. In this review, an overview of the most current findings on the function of DUBs in the innate antiviral immune pathways is provided. Insights into the role of viral DUBs in counteracting host immune responses are also provided. Furthermore, the prospects and challenges of utilizing DUBs as therapeutic targets for infectious diseases are discussed.
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Affiliation(s)
- Zhi Zong
- Department of Hepatobiliary and Pancreatic SurgeryThe First Affiliated HospitalZhejiang University School of MedicineHangzhou310003P. R. China
- MOE Key Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling NetworkLife Sciences InstituteZhejiang UniversityHangzhou310058P. R. China
| | - Zhengkui Zhang
- Institute of Biology and Medical ScienceSoochow UniversitySuzhou215123P. R. China
| | - Liming Wu
- Department of Hepatobiliary and Pancreatic SurgeryThe First Affiliated HospitalZhejiang University School of MedicineHangzhou310003P. R. China
| | - Long Zhang
- Department of Hepatobiliary and Pancreatic SurgeryThe First Affiliated HospitalZhejiang University School of MedicineHangzhou310003P. R. China
- MOE Key Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling NetworkLife Sciences InstituteZhejiang UniversityHangzhou310058P. R. China
| | - Fangfang Zhou
- Institute of Biology and Medical ScienceSoochow UniversitySuzhou215123P. R. China
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43
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Xu C, Ke Z, Liu C, Wang Z, Liu D, Zhang L, Wang J, He W, Xu Z, Li Y, Yang Y, Huang Z, Lv P, Wang X, Han D, Li Y, Qiao N, Liu B. Systemic In Silico Screening in Drug Discovery for Coronavirus Disease (COVID-19) with an Online Interactive Web Server. J Chem Inf Model 2020; 60:5735-5745. [PMID: 32786695 PMCID: PMC7460831 DOI: 10.1021/acs.jcim.0c00821] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Indexed: 01/18/2023]
Abstract
The emergence of the new coronavirus (nCoV-19) has impacted human health on a global scale, while the interaction between the virus and the host is the foundation of the disease. The viral genome codes a cluster of proteins, each with a unique function in the event of host invasion or viral development. Under the current adverse situation, we employ virtual screening tools in searching for drugs and natural products which have been already deposited in DrugBank in an attempt to accelerate the drug discovery process. This study provides an initial evaluation of current drug candidates from various reports using our systemic in silico drug screening based on structures of viral proteins and human ACE2 receptor. Additionally, we have built an interactive online platform (https://shennongproject.ai/) for browsing these results with the visual display of a small molecule docked on its potential target protein, without installing any specialized structural software. With continuous maintenance and incorporation of data from laboratory work, it may serve not only as the assessment tool for the new drug discovery but also an educational web site for the public.
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Affiliation(s)
- Chi Xu
- Laboratory of Health Intelligence,
Huawei Technologies Co., Ltd,
Shenzhen 518100, China
| | - Zunhui Ke
- Wuhan Children’s Hospital,
Tongji Medical College, Huazhong University of Science
& Technology, Wuhan 430000,
China
| | - Chuandong Liu
- Key Laboratory of Genomic and Precision
Medicine, Beijing Institute of Genomics, Chinese Academy
of Sciences, Beijing 100101,
China
- College of Future Technology,
Sino-Danish College, University of Chinese Academy of
Sciences, Beijing, 100049
China
| | - Zhihao Wang
- BioBank, The First
Affiliated Hospital of Xi’an Jiaotong
University, Shaanxi 710061,
China
- MRC Centre for Molecular Bacteriology and
Infection, Imperial College London, London
SW7 2AZ, U.K.
| | - Denghui Liu
- Laboratory of Health Intelligence,
Huawei Technologies Co., Ltd,
Shenzhen 518100, China
| | - Lei Zhang
- Laboratory of Health Intelligence,
Huawei Technologies Co., Ltd,
Shenzhen 518100, China
| | - Jingning Wang
- Department of Pathogen Biology, School
of Basic Medicine, Tongji Medical College, Huazhong
University of Science and Technology, Wuhan
430030, China
| | - Wenjun He
- Laboratory of Health Intelligence,
Huawei Technologies Co., Ltd,
Shenzhen 518100, China
| | - Zhimeng Xu
- Laboratory of Health Intelligence,
Huawei Technologies Co., Ltd,
Shenzhen 518100, China
| | - Yanqing Li
- BioBank, The First
Affiliated Hospital of Xi’an Jiaotong
University, Shaanxi 710061,
China
| | - Yanan Yang
- BioBank, The First
Affiliated Hospital of Xi’an Jiaotong
University, Shaanxi 710061,
China
| | - Zhaowei Huang
- Laboratory of Health Intelligence,
Huawei Technologies Co., Ltd,
Shenzhen 518100, China
| | - Panjing Lv
- Department of Pathogen Biology, School
of Basic Medicine, Tongji Medical College, Huazhong
University of Science and Technology, Wuhan
430030, China
| | - Xin Wang
- BioBank, The First
Affiliated Hospital of Xi’an Jiaotong
University, Shaanxi 710061,
China
| | - Dali Han
- Key Laboratory of Genomic and Precision
Medicine, Beijing Institute of Genomics, Chinese Academy
of Sciences, Beijing 100101,
China
- College of Future Technology,
Sino-Danish College, University of Chinese Academy of
Sciences, Beijing, 100049
China
- Institute for
Stem Cell and Regeneration, Chinese Academy of
Sciences, Beijing 100101,
China
- China National Center for
Bioinformation, Beijing 100101,
China
| | - Yan Li
- Department of Pathogen Biology, School
of Basic Medicine, Tongji Medical College, Huazhong
University of Science and Technology, Wuhan
430030, China
- Department of Pediatrics, Tongji
Hospital, Tongji Medical College, Huazhong University of
Science and Technology, Wuhan 430030,
China
| | - Nan Qiao
- Laboratory of Health Intelligence,
Huawei Technologies Co., Ltd,
Shenzhen 518100, China
| | - Bing Liu
- BioBank, The First
Affiliated Hospital of Xi’an Jiaotong
University, Shaanxi 710061,
China
- MRC Centre for Molecular Bacteriology and
Infection, Imperial College London, London
SW7 2AZ, U.K.
- Instrument Analysis
Centre, of Xi’an Jiaotong University,
Shaanxi 710049, China
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Gil‐Moles M, Basu U, Büssing R, Hoffmeister H, Türck S, Varchmin A, Ott I. Gold Metallodrugs to Target Coronavirus Proteins: Inhibitory Effects on the Spike-ACE2 Interaction and on PLpro Protease Activity by Auranofin and Gold Organometallics*. Chemistry 2020; 26:15140-15144. [PMID: 32915473 PMCID: PMC7756435 DOI: 10.1002/chem.202004112] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Indexed: 02/06/2023]
Abstract
Gold complexes have a long tradition in medicine and for many examples antirheumatic, anticancer or anti-infective effects have been confirmed. Herein, we evaluated the lead compound Auranofin and five selected gold organometallics as inhibitors of two relevant drug targets of severe acute respiratory syndrome coronaviruses (SARS-CoV). The gold metallodrugs were effective inhibitors of the interaction of the SARS-CoV-2 spike protein with the angiotensin converting enzyme 2 (ACE2) host receptor and might thus interfere with the viral entry process. The gold metallodrugs were also efficient inhibitors of the papain-like protease (PLpro) of SARS-CoV-1 and SARS-CoV-2, which is a key enzyme in the viral replication. Regarding PLpro from SARS-CoV-2, the here reported inhibitors are among the very first experimentally confirmed examples with activity against this target enzyme. Importantly, the activity of the complexes against both PLpro enzymes correlated with the ability of the inhibitors to remove zinc ions from the labile zinc center of the enzyme. Taken together, the results of this pilot study suggest further evaluation of gold complexes as SARS-CoV antiviral drugs.
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Affiliation(s)
- Maria Gil‐Moles
- Institute of Medicinal and Pharmaceutical ChemistryTechnische Universität BraunschweigBeethovenstrasse 5538106BraunschweigGermany
| | - Uttara Basu
- Institute of Medicinal and Pharmaceutical ChemistryTechnische Universität BraunschweigBeethovenstrasse 5538106BraunschweigGermany
| | - Rolf Büssing
- Institute of Medicinal and Pharmaceutical ChemistryTechnische Universität BraunschweigBeethovenstrasse 5538106BraunschweigGermany
| | - Henrik Hoffmeister
- Institute of Medicinal and Pharmaceutical ChemistryTechnische Universität BraunschweigBeethovenstrasse 5538106BraunschweigGermany
| | - Sebastian Türck
- Institute of Medicinal and Pharmaceutical ChemistryTechnische Universität BraunschweigBeethovenstrasse 5538106BraunschweigGermany
| | - Agnieszka Varchmin
- Institute of Medicinal and Pharmaceutical ChemistryTechnische Universität BraunschweigBeethovenstrasse 5538106BraunschweigGermany
| | - Ingo Ott
- Institute of Medicinal and Pharmaceutical ChemistryTechnische Universität BraunschweigBeethovenstrasse 5538106BraunschweigGermany
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45
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Wade AD, Huggins DJ. Identification of Optimal Ligand Growth Vectors Using an Alchemical Free-Energy Method. J Chem Inf Model 2020; 60:5580-5594. [PMID: 32810401 DOI: 10.1021/acs.jcim.0c00610] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this work, a novel method to rationally design inhibitors with improved steric contacts and enhanced binding free energies is presented. This new method uses alchemical single step perturbation calculations to rapidly optimize the van der Waals interactions of a small molecule in a protein-ligand complex in order to maximize its binding affinity. The results of the optimizer are used to predict beneficial growth vectors on the ligand, and good agreement is found between the predictions from the optimizer and a more rigorous free energy calculation, with a Spearman's rank order correlation of 0.59. The advantage of the method presented here is the significant speed up of over 10-fold compared to traditional free energy calculations and sublinear scaling with the number of growth vectors assessed. Where experimental data were available, mutations from hydrogen to a methyl group at sites highlighted by the optimizer were calculated with MBAR, and the mean unsigned error between experimental and calculated values of the binding free energy was 0.83 kcal/mol.
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Affiliation(s)
- Alexander D Wade
- TCM Group, Cavendish Laboratory, University of Cambridge, 19 J J Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - David J Huggins
- Tri-Institutional Therapeutics Discovery Institute, Belfer Research Building, 413 East 69th Street, 16th Floor, Box 300, New York, United States.,Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, New York 10065, United States
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46
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Liu XH, Zhang X, Lu ZH, Zhu YS, Wang T. Potential molecular targets of nonstructural proteins for the development of antiviral drugs against SARS-CoV-2 infection. Biomed Pharmacother 2020; 133:111035. [PMID: 33254013 PMCID: PMC7671653 DOI: 10.1016/j.biopha.2020.111035] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 11/10/2020] [Accepted: 11/15/2020] [Indexed: 02/08/2023] Open
Abstract
The pandemic of SARS-CoV-2 has posed significant threats to public health worldwide. Target-based drug development is a promising approach against SARS-CoV-2 infection. Nonstructural proteins may play critical roles from drug design perspectives. Insights into NSPs of different viruses could streamline novel drug development.
Outbreaks of severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome coronavirus (MERS-CoV), and SARS-CoV-2 have produced high pathogenicity and mortality rates in human populations. However, to meet the increasing demand for treatment of these pathogenic coronaviruses, accelerating novel antiviral drug development as much as possible has become a public concern. Target-based drug development may be a promising approach to achieve this goal. In this review, the relevant features of potential molecular targets in human coronaviruses (HCoVs) are highlighted, including the viral protease, RNA-dependent RNA polymerase, and methyltransferases. Additionally, recent advances in the development of antivirals based on these targets are summarized. This review is expected to provide new insights and potential strategies for the development of novel antiviral drugs to treat SARS-CoV-2 infection.
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Affiliation(s)
- Xiao-Huan Liu
- School of Biological Science, Jining Medical University, Jining, China
| | - Xiao Zhang
- School of Biological Science, Jining Medical University, Jining, China
| | - Zhen-Hua Lu
- College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - You-Shuang Zhu
- School of Biological Science, Jining Medical University, Jining, China
| | - Tao Wang
- School of Biological Science, Jining Medical University, Jining, China.
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Patel D, Athar M, Jha PC. Computational investigation of binding of chloroquinone and hydroxychloroquinone against PLPro of SARS-CoV-2. J Biomol Struct Dyn 2020; 40:3071-3081. [PMID: 33200683 PMCID: PMC7682385 DOI: 10.1080/07391102.2020.1844804] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Novel coronavirus SARS-CoV-2 has infected 18 million people with 700,000+ mortalities worldwide and this deadly numeric figure is rapidly rising. With very few success stories, the therapeutic targeting of this epidemic has been mainly attributed to main protease (Mpro), whilst Papain-like proteases (PLpro) also plays a vital role in the processing of replicase polyprotein. Multifunctional roles of PLpro such as viral polypeptide cleavage, de-ISGlyation and immune suppression have made it a promising drug target for therapeutic interventions. Whilst there have been a number of studies and others are on-going on repurposing and new-small molecule screening, albeit previously FDA approved drugs viz. Chloroquine (CQ) and Hydroxychloroquine (HCQ) have only been found effective against this pandemic. Inspired by this fact, we have carried out molecular docking and dynamics simulation studies of FDA approved CQ and HCQ against SARS-CoV-2 PLpro. The end aim is to characterise the binding mode of CQ and HCQ and identify the key amino acid residues involved in the mechanism of action. Further, molecular dynamics simulations (MDS) were carried out with the docked complex to search for the conformational space and for understanding the integrity of binding mode. We showed that the CQ and HCQ can bind with better binding affinity with PLpro as compared to reference known PLpro inhibitor. Based on the presented findings, it can be anticipated that the SARS-CoV-2 PLpro may act as molecular target of CQ and HCQ, and can be projected for further exploration to design potent inhibitors of SARS-CoV-2 PLpro in the near future.
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Affiliation(s)
- Dhaval Patel
- Department of Biological Sciences and Biotechnology, Indian Institute of Advanced Research, Gandhinagar, India
| | - Mohd Athar
- Center for Chemical Biology and Therapeutics, InStem, Bangalore, India
| | - P C Jha
- School of Applied Material Sciences, Central University of Gujarat, Gandhinagar, India
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Silva LR, da Silva Santos-Júnior PF, de Andrade Brandão J, Anderson L, Bassi ÊJ, Xavier de Araújo-Júnior J, Cardoso SH, da Silva-Júnior EF. Druggable targets from coronaviruses for designing new antiviral drugs. Bioorg Med Chem 2020; 28:115745. [PMID: 33007557 PMCID: PMC7836322 DOI: 10.1016/j.bmc.2020.115745] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 08/26/2020] [Accepted: 08/29/2020] [Indexed: 01/18/2023]
Abstract
Severe respiratory infections were highlighted in the SARS-CoV outbreak in 2002, as well as MERS-CoV, in 2012. Recently, the novel CoV (COVID-19) has led to severe respiratory damage to humans and deaths in Asia, Europe, and Americas, which allowed the WHO to declare the pandemic state. Notwithstanding all impacts caused by Coronaviruses, it is evident that the development of new antiviral agents is an unmet need. In this review, we provide a complete compilation of all potential antiviral agents targeting macromolecular structures from these Coronaviruses (Coronaviridae), providing a medicinal chemistry viewpoint that could be useful for designing new therapeutic agents.
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Affiliation(s)
- Leandro Rocha Silva
- Chemistry and Biotechnology Institute, Federal University of Alagoas, Campus A.C. Simões, Lourival Melo Mota Avenue, Maceió 57072-970, Brazil; Laboratory of Organic and Medicinal Synthesis, Federal University of Alagoas, Campus Arapiraca, Manoel Severino Barbosa Avenue, Arapiraca 57309-005, Brazil
| | | | - Júlia de Andrade Brandão
- IMUNOREG - Immunoregulation Research Group, Laboratory of Research in Virology and Immunology, Institute of Biological Sciences and Health, Federal University of Alagoas, Campus AC. Simões, Lourival Melo Mota Avenue, Maceió 57072-970, Brazil
| | - Letícia Anderson
- IMUNOREG - Immunoregulation Research Group, Laboratory of Research in Virology and Immunology, Institute of Biological Sciences and Health, Federal University of Alagoas, Campus AC. Simões, Lourival Melo Mota Avenue, Maceió 57072-970, Brazil; CESMAC University Center, Cônego Machado Street, Maceió 57051-160, Brazil
| | - Ênio José Bassi
- IMUNOREG - Immunoregulation Research Group, Laboratory of Research in Virology and Immunology, Institute of Biological Sciences and Health, Federal University of Alagoas, Campus AC. Simões, Lourival Melo Mota Avenue, Maceió 57072-970, Brazil
| | - João Xavier de Araújo-Júnior
- Chemistry and Biotechnology Institute, Federal University of Alagoas, Campus A.C. Simões, Lourival Melo Mota Avenue, Maceió 57072-970, Brazil; Laboratory of Medicinal Chemistry, Pharmaceutical Sciences Institute, Federal University of Alagoas, Campus A.C. Simões, Lourival Melo Mota Avenue, Maceió 57072-970, Brazil
| | - Sílvia Helena Cardoso
- Laboratory of Organic and Medicinal Synthesis, Federal University of Alagoas, Campus Arapiraca, Manoel Severino Barbosa Avenue, Arapiraca 57309-005, Brazil
| | - Edeildo Ferreira da Silva-Júnior
- Chemistry and Biotechnology Institute, Federal University of Alagoas, Campus A.C. Simões, Lourival Melo Mota Avenue, Maceió 57072-970, Brazil; Laboratory of Medicinal Chemistry, Pharmaceutical Sciences Institute, Federal University of Alagoas, Campus A.C. Simões, Lourival Melo Mota Avenue, Maceió 57072-970, Brazil.
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49
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Ibrahim TM, Ismail MI, Bauer MR, Bekhit AA, Boeckler FM. Supporting SARS-CoV-2 Papain-Like Protease Drug Discovery: In silico Methods and Benchmarking. Front Chem 2020; 8:592289. [PMID: 33251185 PMCID: PMC7674952 DOI: 10.3389/fchem.2020.592289] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 09/29/2020] [Indexed: 12/17/2022] Open
Abstract
The coronavirus disease 19 (COVID-19) is a rapidly growing pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Its papain-like protease (SARS-CoV-2 PLpro) is a crucial target to halt virus replication. SARS-CoV PLpro and SARS-CoV-2 PLpro share an 82.9% sequence identity and a 100% sequence identity for the binding site reported to accommodate small molecules in SARS-CoV. The flexible key binding site residues Tyr269 and Gln270 for small-molecule recognition in SARS-CoV PLpro exist also in SARS-CoV-2 PLpro. This inspired us to use the reported small-molecule binders to SARS-CoV PLpro to generate a high-quality DEKOIS 2.0 benchmark set. Accordingly, we used them in a cross-benchmarking study against SARS-CoV-2 PLpro. As there is no SARS-CoV-2 PLpro structure complexed with a small-molecule ligand publicly available at the time of manuscript submission, we built a homology model based on the ligand-bound SARS-CoV structure for benchmarking and docking purposes. Three publicly available docking tools FRED, AutoDock Vina, and PLANTS were benchmarked. All showed better-than-random performances, with FRED performing best against the built model. Detailed performance analysis via pROC-Chemotype plots showed a strong enrichment of the most potent bioactives in the early docking ranks. Cross-benchmarking against the X-ray structure complexed with a peptide-like inhibitor confirmed that FRED is the best-performing tool. Furthermore, we performed cross-benchmarking against the newly introduced X-ray structure complexed with a small-molecule ligand. Interestingly, its benchmarking profile and chemotype enrichment were comparable to the built model. Accordingly, we used FRED in a prospective virtual screen of the DrugBank database. In conclusion, this study provides an example of how to harness a custom-made DEKOIS 2.0 benchmark set as an approach to enhance the virtual screening success rate against a vital target of the rapidly emerging pandemic.
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Affiliation(s)
- Tamer M. Ibrahim
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh, Egypt
| | - Muhammad I. Ismail
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, The British University in Egypt, Cairo, Egypt
| | - Matthias R. Bauer
- Structure, Biophysics and Fragment-Based Lead Generation, Discovery Sciences, R&D, AstraZeneca, Cambridge, United Kingdom
- Department of Pharmacy, Eberhard-Karls University, Tuebingen, Germany
| | - Adnan A. Bekhit
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Alexandria University, Alexandria, Egypt
- Pharmacy Program, Allied Health Department, College of Health and Sport Sciences, University of Bahrain, Zallaq, Bahrain
| | - Frank M. Boeckler
- Department of Pharmacy, Eberhard-Karls University, Tuebingen, Germany
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Cuesta-Galisteo S, Schörgenhumer J, Wei X, Merino E, Nevado C. Nickel-Catalyzed Asymmetric Synthesis of α-Arylbenzamides. Angew Chem Int Ed Engl 2020; 60:1605-1609. [PMID: 33015909 DOI: 10.1002/anie.202011342] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Indexed: 12/16/2022]
Abstract
A nickel-catalyzed asymmetric reductive hydroarylation of vinyl amides to produce enantioenriched α-arylbenzamides is reported. The use of a chiral bisimidazoline (BIm) ligand, in combination with diethoxymethylsilane and aryl halides, enables the regioselective introduction of aryl groups to the internal position of the olefin, forging a new stereogenic center α to the N atom. The use of neutral reagents and mild reaction conditions provides simple access to pharmacologically relevant motifs present in anticancer, SARS-CoV PLpro inhibitors, and KCNQ channel openers.
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Affiliation(s)
- Sergio Cuesta-Galisteo
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH 8057, Zurich, Switzerland
| | - Johannes Schörgenhumer
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH 8057, Zurich, Switzerland
| | - Xiaofeng Wei
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH 8057, Zurich, Switzerland
| | - Estíbaliz Merino
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH 8057, Zurich, Switzerland.,Current address: Department of Organic and Inorganic Chemistry, University of Alcalá, 28805-Alcalá de Henares, Madrid, Spain
| | - Cristina Nevado
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH 8057, Zurich, Switzerland
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