1
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Wu J, Shi Y, Zhou M, Chen M, Ji S, Liu X, Zhou M, Xia R, Zheng X, Wang W. Nutrient vitamins enabled metabolic regulation of ferroptosis via reactive oxygen species biology. Front Pharmacol 2024; 15:1434088. [PMID: 39092216 PMCID: PMC11291210 DOI: 10.3389/fphar.2024.1434088] [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: 05/17/2024] [Accepted: 07/01/2024] [Indexed: 08/04/2024] Open
Abstract
Vitamins are dietary components necessary for cellular metabolic balance, especially redox homeostasis; deficient or excessive supply may give rise to symptoms of psychiatric disorders. Exploring the nutritional and metabolic pathways of vitamins could contribute to uncovering the underlying pathogenesis of ferroptosis-associated diseases. This mini-review aims to provide insights into vitamins closely linked to the regulation of ferroptosis from the perspective of cellular reactive oxygen species biology. The mainstream reprogramming mechanisms of ferroptosis are overviewed, focusing on unique biological processes of iron metabolism, lipid metabolism, and amino acid metabolism. Moreover, recent breakthroughs in therapeutic interventions targeting ferroptosis via fully utilizing vitamin-based pharmacological tools were overviewed, covering vitamins (B, C, E, and K). Finally, mechanism insight related to vitamin-associated nutrient signaling was provided, highlighting the pharmacological benefits of metabolically reprogramming ferroptosis-associated diseases.
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Affiliation(s)
- Junjie Wu
- School of Pharmacy, Nantong University, Nantong, Jiangsu, China
| | - Yanting Shi
- School of Pharmacy, Nantong University, Nantong, Jiangsu, China
| | - Man Zhou
- School of Pharmacy, Nantong University, Nantong, Jiangsu, China
| | - Min Chen
- School of Pharmacy, Nantong University, Nantong, Jiangsu, China
| | - Shuying Ji
- School of Pharmacy, Nantong University, Nantong, Jiangsu, China
| | - Xingxing Liu
- School of Pharmacy, Nantong University, Nantong, Jiangsu, China
| | - Mengjiao Zhou
- School of Pharmacy, Nantong University, Nantong, Jiangsu, China
| | - Rui Xia
- School of Public Health, Nantong University, Nantong, Jiangsu, China
| | - Xiaohua Zheng
- School of Pharmacy, Nantong University, Nantong, Jiangsu, China
| | - Weiqi Wang
- School of Pharmacy, Nantong University, Nantong, Jiangsu, China
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2
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Xiao YQ, Long J, Zhang SS, Zhu YY, Gu SX. Non-peptidic inhibitors targeting SARS-CoV-2 main protease: A review. Bioorg Chem 2024; 147:107380. [PMID: 38636432 DOI: 10.1016/j.bioorg.2024.107380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 04/11/2024] [Accepted: 04/14/2024] [Indexed: 04/20/2024]
Abstract
The COVID-19 pandemic continues to pose a threat to global health, and sounds the alarm for research & development of effective anti-coronavirus drugs, which are crucial for the patients and urgently needed for the current epidemic and future crisis. The main protease (Mpro) stands as an essential enzyme in the maturation process of SARS-CoV-2, playing an irreplaceable role in regulating viral RNA replication and transcription. It has emerged as an ideal target for developing antiviral agents against SARS-CoV-2 due to its high conservation and the absence of homologous proteases in the human body. Among the SARS-CoV-2 Mpro inhibitors, non-peptidic compounds hold promising prospects owing to their excellent antiviral activity and improved metabolic stability. In this review, we offer an overview of research progress concerning non-peptidic SARS-CoV-2 Mpro inhibitors since 2020. The efforts delved into molecular structures, structure-activity relationships (SARs), biological activity, and binding modes of these inhibitors with Mpro. This review aims to provide valuable clues and insights for the development of anti-SARS-CoV-2 agents as well as broad-spectrum coronavirus Mpro inhibitors.
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Affiliation(s)
- Ya-Qi Xiao
- School of Chemical Engineering and Pharmacy, Pharmaceutical Research Institute, Wuhan Institute of Technology, Wuhan 430205, China
| | - Jiao Long
- School of Chemical Engineering and Pharmacy, Pharmaceutical Research Institute, Wuhan Institute of Technology, Wuhan 430205, China
| | - Shuang-Shuang Zhang
- School of Chemical Engineering and Pharmacy, Pharmaceutical Research Institute, Wuhan Institute of Technology, Wuhan 430205, China.
| | - Yuan-Yuan Zhu
- School of Chemistry and Environmental Engineering, Wuhan Institute of Technology, Wuhan 430205, China.
| | - Shuang-Xi Gu
- School of Chemical Engineering and Pharmacy, Pharmaceutical Research Institute, Wuhan Institute of Technology, Wuhan 430205, China.
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3
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Li H, Sun M, Lei F, Liu J, Chen X, Li Y, Wang Y, Lu J, Yu D, Gao Y, Xu J, Chen H, Li M, Yi Z, He X, Chen L. Methyl rosmarinate is an allosteric inhibitor of SARS-CoV-2 3 CL protease as a potential candidate against SARS-cov-2 infection. Antiviral Res 2024; 224:105841. [PMID: 38408645 DOI: 10.1016/j.antiviral.2024.105841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 02/09/2024] [Accepted: 02/24/2024] [Indexed: 02/28/2024]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been ongoing for more than three years and urgently needs to be addressed. Traditional Chinese medicine (TCM) prescriptions have played an important role in the clinical treatment of patients with COVID-19 in China. However, it is difficult to uncover the potential molecular mechanisms of the active ingredients in these TCM prescriptions. In this paper, we developed a new approach by integrating the experimental assay, virtual screening, and the experimental verification, exploring the rapid discovery of active ingredients from TCM prescriptions. To achieve this goal, 4 TCM prescriptions in clinical use for different indications were selected to find the antiviral active ingredients in TCMs. The 3-chymotrypsin-like protease (3CLpro), an important target for fighting COVID-19, was utilized to determine the inhibitory activity of the TCM prescriptions and single herb. It was found that 10 single herbs had better inhibitory activity than other herbs by using a fluorescence resonance energy transfer (FRET) - based enzymatic assay of SARS-CoV-2 3CLpro. The ingredients contained in 10 herbs were thus virtually screened and the predicted active ingredients were experimentally validated. Thus, such a research strategy firstly removed many single herbs with no inhibitory activity against SARS-CoV-2 3CLpro at the very beginning by FRET-based assay, making our subsequent virtual screening more effective. Finally, 4 active components were found to have stronger inhibitory effects on SARS-CoV-2 3CLpro, and their inhibitory mechanism was subsequently investigated. Among of them, methyl rosmarinate as an allosteric inhibitor of SARS-CoV-2 3CLpro was confirmed and its ability to inhibit viral replication was demonstrated by the SARS-CoV-2 replicon system. To validate the binding mode via docking, the mutation experiment, circular dichroism (CD), enzymatic inhibition and surface plasmon resonance (SPR) assay were performed, demonstrating that methyl rosmarinate bound to the allosteric site of SARS-CoV-2 3CLpro. In conclusion, this paper provides the new ideas for the rapid discovery of active ingredients in TCM prescriptions based on a specific target, and methyl rosmarinate has the potential to be developed as an antiviral therapeutic candidate against SARS-CoV-2 infection.
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Affiliation(s)
- Hongtao Li
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Meng Sun
- Department of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Fuzhi Lei
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, and Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
| | - Jinfeng Liu
- Department of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 210009, China; Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062, China
| | - Xixiang Chen
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Yaqi Li
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha 410081, China; Institute of Interdisciplinary Studies, Hunan Normal University, Changsha 410081, China; Peptide and small Molecule Drug R&D Plateform, Furong Laboratory, Hunan Normal University, Changsha 410081, Hunan, China; DP Technology, Beijing, China
| | - Ying Wang
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha 410081, China; Institute of Interdisciplinary Studies, Hunan Normal University, Changsha 410081, China; Peptide and small Molecule Drug R&D Plateform, Furong Laboratory, Hunan Normal University, Changsha 410081, Hunan, China
| | - Jiani Lu
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Danmei Yu
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Yueqiu Gao
- Department of Hepatopathy, Shuguang Hospital, Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China; Laboratory of Cellular Immunity, Shuguang Hospital, Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China; Institute of Infectious Diseases of Integrated Traditional Chinese and Western Medicine, China
| | - Jianrong Xu
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Hongzhuan Chen
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Man Li
- Laboratory of Cellular Immunity, Shuguang Hospital, Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China.
| | - Zhigang Yi
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, and Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China; Shanghai Public Health Clinical Center, Fudan University, Shanghai, China.
| | - Xiao He
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062, China; New York University-East China Normal University Center for Computational Chemistry, New York University Shanghai, Shanghai, 200062, China.
| | - Lili Chen
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China; Longhua Hospital Shanghai University of Traditional Chinese Medicine, 725 South Wanping Road, Shanghai, 200032, China.
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4
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Koharazawa R, Hayakawa M, Takeda K, Miyazaki K, Tode C, Hirota Y, Suhara Y. Exploring 2-methyl-substituted vitamin K 3 derivatives with potent inhibitory activity against the 3CL protease of SARS-CoV-2. Bioorg Med Chem Lett 2024; 100:129642. [PMID: 38310976 DOI: 10.1016/j.bmcl.2024.129642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 01/19/2024] [Accepted: 01/30/2024] [Indexed: 02/06/2024]
Abstract
Since the outbreak of the pandemic, various anti-SARS-CoV-2 drugs have been developed. In particular, 3CL protease (3C-like protease, 3CLpro) is an attractive drug target because it is an essential enzyme for viral multiplication and is present only in viruses, not in humans. To date, 3CLpro inhibitors against SARS-CoV-2 such as nirmatrelvir and ensitrelvir have been launched as oral drugs in Japan, but there is still no potent drug against SARS-CoV-2, due to issues of in vivo absorption and stability. Recently, vitamin K3 was reported to show inhibitory activity against 3CLpro of SARS-CoV-2, and the mechanism of action was predicted to be the formation of a covalent bond between the thiol group of cysteine 145, the active center of 3CLpro, and the C-3 position of vitamin K3. Therefore, we synthesized derivatives in which the 2-methyl group of the vitamin K3 was systematically converted to other substituents and examined their inhibitory activity against 3CLpro of SARS-CoV-2. The results showed that the compounds with the sulfide structure showed an approximately 4-fold increase in activity over vitamin K3. These results indicated the possibility of creating new inhibitors based on vitamin K3 and its derivatives.
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Affiliation(s)
- Ryohto Koharazawa
- Laboratory of Organic Synthesis and Medicinal Chemistry, Department of Bioscience and Engineering, College of Systems Engineering and Science, Shibaura Institute of Technology, 307 Fukasaku, Minuma-ku, Saitama 337-8570, Japan
| | - Mayu Hayakawa
- Laboratory of Biochemistry, Department of Bioscience and Engineering, College of Systems Engineering and Science, Shibaura Institute of Technology, 307 Fukasaku, Minuma-ku, Saitama 337-8570, Japan
| | - Kazuki Takeda
- Laboratory of Toxicology, School of Veterinary Medicine, Kitasato University, E23-35-1, Towada, Aomori 034-0021, Japan; Department of Computer Science, Tokyo Institute of Technology, 4259-J3-1818, Nagatsuta-cho, Midori-ku, Yokohama-shi, Kanagawa 226-0026, Japan
| | - Kotone Miyazaki
- Laboratory of Organic Synthesis and Medicinal Chemistry, Department of Bioscience and Engineering, College of Systems Engineering and Science, Shibaura Institute of Technology, 307 Fukasaku, Minuma-ku, Saitama 337-8570, Japan
| | - Chisato Tode
- Instrumental Analysis Center, Kobe Pharmaceutical University, 4-19-1 Motoyamakita-machi, Higashinada-ku, Kobe 658-8558, Japan
| | - Yoshihisa Hirota
- Laboratory of Biochemistry, Department of Bioscience and Engineering, College of Systems Engineering and Science, Shibaura Institute of Technology, 307 Fukasaku, Minuma-ku, Saitama 337-8570, Japan
| | - Yoshitomo Suhara
- Laboratory of Organic Synthesis and Medicinal Chemistry, Department of Bioscience and Engineering, College of Systems Engineering and Science, Shibaura Institute of Technology, 307 Fukasaku, Minuma-ku, Saitama 337-8570, Japan.
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5
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Wang R, Chen X, Li H, Chen X, Sun D, Yu D, Lu J, Xie Y, Zhang Q, Xu J, Zhang W, Chen H, Liu S, Chen L. Danshensu inhibits SARS-CoV-2 by targeting its main protease as a specific covalent inhibitor and discovery of bifunctional compounds eliciting antiviral and anti-inflammatory activity. Int J Biol Macromol 2024; 257:128623. [PMID: 38070810 DOI: 10.1016/j.ijbiomac.2023.128623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 11/30/2023] [Accepted: 12/02/2023] [Indexed: 12/17/2023]
Abstract
The coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has posed a serious threat to human. Since there are still no effective treatment options against the new emerging variants of SARS-CoV-2, it is necessary to devote a continuous endeavor for more targeted drugs and the preparation for the next pandemic. Salvia miltiorrhiza and its active ingredients possess wide antiviral activities, including against SARS-CoV-2. Danshensu, as one of the most important active ingredients in Salvia miltiorrhiza, has been reported to inhibit the entry of SARS-CoV-2 into ACE2 (angiotensin-converting enzyme 2)-overexpressed HEK-293T cells and Vero-E6 cells. However, there is a paucity of information regarding its detailed target and mechanism against SARS-CoV-2. Here, we present Danshensu as a covalent inhibitor of 3-chymotrypsin-like protease (3CLpro) against SARS-CoV-2 by the time-dependent inhibition assay (TDI) and mass spectrometry analysis. Further molecular docking, site-directed mutagenesis, circular dichroism (CD) and fluorescence spectra revealed that Danshensu covalently binds to C145 of SARS-CoV-2 3CLpro, meanwhile forming the hydrogen bonds with S144, H163 and E166 in the S1 site. Structure-based optimization of Danshensu led to the discovery of the promising compounds with good inhibitory activity and microsomal stability in vitro. Due to Danshensu inhibiting lung inflammation in the mouse model, we found that Danshensu derivatives also showed better anti-inflammatory activity than Danshensu in lipopolysaccharide (LPS)-stimulated RAW264.7 macrophage cells. Thus, our study provides not only the clue of the efficacy of Salvia miltiorrhiza against SARS-CoV-2, but also a detailed mechanistic insight into the covalent mode of action of Danshensu for design of covalent inhibitors against SARS-CoV-2 3CLpro, highlighting its potential as a bifunctional molecule with antivirus and anti-inflammation.
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Affiliation(s)
- Ruyu Wang
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Xuwen Chen
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Hongtao Li
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Xixiang Chen
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Donghui Sun
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Danmei Yu
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Jiani Lu
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Yuanyuan Xie
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China; Academy of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai 201203, China
| | - Qian Zhang
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Jianrong Xu
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China; Academy of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai 201203, China
| | - Weidong Zhang
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China; Shanghai Institute of Infectious Diseases and Biosafety, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Hongzhuan Chen
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Shunying Liu
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China.
| | - Lili Chen
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China.
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6
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Li X, Song Y. Structure and function of SARS-CoV and SARS-CoV-2 main proteases and their inhibition: A comprehensive review. Eur J Med Chem 2023; 260:115772. [PMID: 37659195 PMCID: PMC10529944 DOI: 10.1016/j.ejmech.2023.115772] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/24/2023] [Accepted: 08/26/2023] [Indexed: 09/04/2023]
Abstract
Severe acute respiratory syndrome-associated coronavirus (SARS-CoV) identified in 2003 infected ∼8000 people in 26 countries with 800 deaths, which was soon contained and eradicated by syndromic surveillance and enhanced quarantine. A closely related coronavirus SARS-CoV-2, the causative agent of COVID-19 identified in 2019, has been dramatically more contagious and catastrophic. It has infected and caused various flu-like symptoms of billions of people in >200 countries, including >6 million people died of or with the virus. Despite the availability of several vaccines and antiviral drugs against SARS-CoV-2, finding new therapeutics is needed because of viral evolution and a possible emerging coronavirus in the future. The main protease (Mpro) of these coronaviruses plays important roles in their life cycle and is essential for the viral replication. This article represents a comprehensive review of the function, structure and inhibition of SARS-CoV and -CoV-2 Mpro, including structure-activity relationships, protein-inhibitor interactions and clinical trial status.
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Affiliation(s)
- Xin Li
- Department of Pharmacology and Chemical Biology, 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
- Department of Pharmacology and Chemical Biology, 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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7
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Homma T, Okamoto M, Koharazawa R, Hayakawa M, Fushimi T, Tode C, Hirota Y, Osakabe N, Baba M, Suhara Y. Exploring Novel Vitamin K Derivatives with Anti-SARS-CoV-2 Activity. ACS OMEGA 2023; 8:42248-42263. [PMID: 38024673 PMCID: PMC10652723 DOI: 10.1021/acsomega.3c04175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 10/07/2023] [Accepted: 10/13/2023] [Indexed: 12/01/2023]
Abstract
From our compound library of vitamin K derivatives, we found that some compounds exhibited anti-SARS-CoV-2 activity in VeroE6/TMPRSS2 cells. The common structure of these compounds was menaquinone-2 (MK-2) with either the m-methylphenyl or the 1-naphthyl group introduced at the end of the side chain. Therefore, new vitamin K derivatives having more potent anti-SARS-CoV-2 activity were explored by introducing various functional groups at the ω-position of the side chain. MK-2 derivatives with a purine moiety showed the most potent antiviral activity among the derivatives. We also found that their mechanism of action was the inhibition of RNA-dependent RNA polymerase (RdRp) of SARS-CoV-2. The chemical structures of our compounds were completely different from those of nucleic acid derivatives such as remdesivir and molnupiravir, clinically approved RdRp inhibitors for COVID-19 treatment, suggesting that our compounds may be effective against viruses resistant to these nucleic acid derivatives.
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Affiliation(s)
- Taiki Homma
- Department
of Bioscience and Engineering, College of Systems Engineering and
Science, Shibaura Institute of Technology, 307 Fukasaku, Minuma-ku, Saitama 337-8570, Japan
| | - Mika Okamoto
- Division
of Infection Control Research, Center for Advanced Science Research
and Promotion, Kagoshima University, Kagoshima 890-8580, Japan
| | - Ryohto Koharazawa
- Department
of Bioscience and Engineering, College of Systems Engineering and
Science, Shibaura Institute of Technology, 307 Fukasaku, Minuma-ku, Saitama 337-8570, Japan
| | - Mayu Hayakawa
- Department
of Bioscience and Engineering, College of Systems Engineering and
Science, Shibaura Institute of Technology, 307 Fukasaku, Minuma-ku, Saitama 337-8570, Japan
| | - Taiki Fushimi
- Functional
Control Systems, Graduate School of Engineering and Science, Shibaura Institute of Technology, 307 Fukasaku, Minuma-ku, Saitama 337-8570, Japan
| | - Chisato Tode
- Instrumental
Analysis Center, Kobe Pharmaceutical University, 4-19-1 Motoyamakita-machi, Higashinada-ku, Kobe 658-8558, Japan
| | - Yoshihisa Hirota
- Department
of Bioscience and Engineering, College of Systems Engineering and
Science, Shibaura Institute of Technology, 307 Fukasaku, Minuma-ku, Saitama 337-8570, Japan
- Functional
Control Systems, Graduate School of Engineering and Science, Shibaura Institute of Technology, 307 Fukasaku, Minuma-ku, Saitama 337-8570, Japan
| | - Naomi Osakabe
- Department
of Bioscience and Engineering, College of Systems Engineering and
Science, Shibaura Institute of Technology, 307 Fukasaku, Minuma-ku, Saitama 337-8570, Japan
- Functional
Control Systems, Graduate School of Engineering and Science, Shibaura Institute of Technology, 307 Fukasaku, Minuma-ku, Saitama 337-8570, Japan
| | - Masanori Baba
- Division
of Infection Control Research, Center for Advanced Science Research
and Promotion, Kagoshima University, Kagoshima 890-8580, Japan
| | - Yoshitomo Suhara
- Department
of Bioscience and Engineering, College of Systems Engineering and
Science, Shibaura Institute of Technology, 307 Fukasaku, Minuma-ku, Saitama 337-8570, Japan
- Functional
Control Systems, Graduate School of Engineering and Science, Shibaura Institute of Technology, 307 Fukasaku, Minuma-ku, Saitama 337-8570, Japan
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8
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Kato Y, Sakanishi A, Matsuda K, Hattori M, Kaneko I, Nishikawa M, Ikushiro S. Covalent adduction of serotonin-derived quinones to the SARS-CoV-2 main protease expressed in a cultured cell. Free Radic Biol Med 2023; 206:74-82. [PMID: 37391098 PMCID: PMC10300202 DOI: 10.1016/j.freeradbiomed.2023.06.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 06/18/2023] [Accepted: 06/20/2023] [Indexed: 07/02/2023]
Abstract
The SARS-CoV-2 main protease is an essential molecule for viral replication and is often targeted by medications to treat the infection. In this study, we investigated the possible inhibitory action of endogenous quinones on the enzyme. Recombinant SARS-CoV-2 main protease was exposed to tryptamine-4,5-dione (TD) or quinone from 5-hydroxyindoleacetic acid (Q5HIAA). As a result, the protease activity was considerably decreased in a dose-dependent manner. The IC50 values of the quinones toward the enzyme were approximately 0.28 μM (TD) and 0.49 μM (Q5HIAA). Blot analyses using specific antibodies to quinone-modified proteins revealed that quinones were adducted to the enzyme at concentrations as low as 0.12 μM. Intact mass analyses showed that one or two quinone molecules were covalently adducted onto the main protease. Chymotrypsin-digested main protease analyses revealed that the quinones bind to thiol residues at the enzyme's active site. When TD or Q5HIAA were exposed to cultured cells expressing the viral enzyme, quinone-modified enzyme was identified in the cell lysate, suggesting that even extracellularly generated quinones could react with the viral enzyme expressed in an infected cell. Thus, these endogenous quinones could act as inhibitors of the viral enzyme.
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Affiliation(s)
- Yoji Kato
- School of Human Science and Environment, University of Hyogo, Himeji, Hyogo, 670-0092, Japan; Research Institute for Food and Nutritional Sciences, University of Hyogo, Himeji, Hyogo, 670-0092, Japan.
| | - Asahi Sakanishi
- School of Human Science and Environment, University of Hyogo, Himeji, Hyogo, 670-0092, Japan
| | - Kaoru Matsuda
- School of Human Science and Environment, University of Hyogo, Himeji, Hyogo, 670-0092, Japan
| | - Mai Hattori
- School of Human Science and Environment, University of Hyogo, Himeji, Hyogo, 670-0092, Japan
| | - Ichiro Kaneko
- School of Human Science and Environment, University of Hyogo, Himeji, Hyogo, 670-0092, Japan; Research Institute for Food and Nutritional Sciences, University of Hyogo, Himeji, Hyogo, 670-0092, Japan
| | - Miyu Nishikawa
- Department of Biotechnology, Faculty of Engineering, Toyama Prefectural University, Imizu, Toyama, 939-0398, Japan
| | - Shinichi Ikushiro
- Department of Biotechnology, Faculty of Engineering, Toyama Prefectural University, Imizu, Toyama, 939-0398, Japan
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9
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Zhan Y, Zha D, Lin H, Mao X, Yang L, Huang H, He Z, Zhou S, Xu F, Qian Y, Liu Y. Protective Role of Vitamin K3 on SARS-CoV-2 Structural Protein-Induced Inflammation and Cell Death. Pharmaceuticals (Basel) 2023; 16:1101. [PMID: 37631016 PMCID: PMC10457795 DOI: 10.3390/ph16081101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 07/28/2023] [Accepted: 07/28/2023] [Indexed: 08/27/2023] Open
Abstract
The structure proteins of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), such as nucleocapsid protein (N protein) and envelop protein (E protein), are considered to be the critical pro-inflammatory factors in coronavirus disease 2019 (COVID-19). Vitamin K3 has been reported to exert an anti-inflammatory effect. In this study, we investigated the protective effects of vitamin K3 on SARS-CoV-2 N protein induced-endothelial activation and SARS-CoV-2 E protein induced-cell death in THP-1 cells. The results showed that vitamin K3 reduced N protein-induced monocyte adhesion, suppressed the expression of adhesion molecules, and decreased the mRNA levels of pro-inflammatory cytokines in HLMECs. We confirmed that the effects of vitamin K3 on endothelial activation may be related to the inhibition of the NF-κB signal pathway. In addition, vitamin K3 reversed E protein-induced pyroptosis, inhibited NLRP3/GSDMD signal pathway and reduced the mRNA expression of pro-inflammatory cytokines in THP-1 cells. Our results also showed the protective effects of vitamin K3 on the SARS-CoV-2 structural protein-induced THP-1 cells pyroptosis and endothelial activation via NF-κB signaling pathway. These findings suggested that vitamin K3 potently suppressed the inflammatory response to prevent endothelial activation and monocyte pyroptosis induced by SARS-CoV-2 proteins. This may provide a new strategy for the treatment of COVID-19.
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Affiliation(s)
- Yixiong Zhan
- Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Nanchang University, Nanchang 330006, China; (Y.Z.); (F.X.)
- The National Engineering Research Center for Bioengineering Drugs and the Technologies, Institute of Translational Medicine, Nanchang University, Nanchang 330031, China; (D.Z.); (H.L.); (X.M.); (L.Y.); (H.H.); (S.Z.)
- Chongqing Research Institute, Nanchang University, Chongqing 402660, China
| | - Duoduo Zha
- The National Engineering Research Center for Bioengineering Drugs and the Technologies, Institute of Translational Medicine, Nanchang University, Nanchang 330031, China; (D.Z.); (H.L.); (X.M.); (L.Y.); (H.H.); (S.Z.)
| | - Hongru Lin
- The National Engineering Research Center for Bioengineering Drugs and the Technologies, Institute of Translational Medicine, Nanchang University, Nanchang 330031, China; (D.Z.); (H.L.); (X.M.); (L.Y.); (H.H.); (S.Z.)
| | - Xianxian Mao
- The National Engineering Research Center for Bioengineering Drugs and the Technologies, Institute of Translational Medicine, Nanchang University, Nanchang 330031, China; (D.Z.); (H.L.); (X.M.); (L.Y.); (H.H.); (S.Z.)
| | - Lingyi Yang
- The National Engineering Research Center for Bioengineering Drugs and the Technologies, Institute of Translational Medicine, Nanchang University, Nanchang 330031, China; (D.Z.); (H.L.); (X.M.); (L.Y.); (H.H.); (S.Z.)
| | - Houda Huang
- The National Engineering Research Center for Bioengineering Drugs and the Technologies, Institute of Translational Medicine, Nanchang University, Nanchang 330031, China; (D.Z.); (H.L.); (X.M.); (L.Y.); (H.H.); (S.Z.)
| | - Zongnan He
- Department of Pediatrics, Pingxiang Maternity and Child Care Hospital, Pingxiang 337055, China;
| | - Sheng Zhou
- The National Engineering Research Center for Bioengineering Drugs and the Technologies, Institute of Translational Medicine, Nanchang University, Nanchang 330031, China; (D.Z.); (H.L.); (X.M.); (L.Y.); (H.H.); (S.Z.)
| | - Fei Xu
- Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Nanchang University, Nanchang 330006, China; (Y.Z.); (F.X.)
| | - Yisong Qian
- The National Engineering Research Center for Bioengineering Drugs and the Technologies, Institute of Translational Medicine, Nanchang University, Nanchang 330031, China; (D.Z.); (H.L.); (X.M.); (L.Y.); (H.H.); (S.Z.)
- Chongqing Research Institute, Nanchang University, Chongqing 402660, China
| | - Yu Liu
- Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Nanchang University, Nanchang 330006, China; (Y.Z.); (F.X.)
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10
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Zhang YN, Zhu GH, Liu W, Xiong Y, Hu Q, Zhuang XY, Jia GH, Zhang WD, Ge GB. Discovery and characterization of the covalent SARS-CoV-2 3CL pro inhibitors from Ginkgo biloba extract via integrating chemoproteomic and biochemical approaches. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2023; 114:154796. [PMID: 37037086 PMCID: PMC10052880 DOI: 10.1016/j.phymed.2023.154796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 03/07/2023] [Accepted: 03/29/2023] [Indexed: 06/19/2023]
Abstract
BACKGROUND The 3C-like proteases (3CLpros) are cysteine-rich homodimeric proteins and can be covalently modified by numerous natural and synthetic compounds, which in turn, block the proteolytic activity or the formation of enzymatically active dimeric forms. Although herbal medicines have been widely used to treat COVID-19, identification of the key herbal constituents that can covalently modify the 3CLpros in β-coronaviruses (CoVs) remains a big challenge. AIMS To construct a comprehensive approach for efficient discovering the covalent SARS-CoV-2 3CLpro inhibitors from herbal medicines. To decipher the key anti-SARS-CoV-2 3CLpro constituents in Ginkgo biloba extract 50 (GBE50) and to study their anti-SARS-CoV-2 3CLpro mechanisms. METHODS SARS-CoV-2 3CLpro inhibition assay including time-dependent inhibition assays and inactivation kinetic analyses were conducted using a fluorescence-based biochemical assay. The constituents in GBE50 were analyzed by UHPLC-Q-Exactive Orbitrap HRMS. The peptides modified by herbal constituents were characterized by using nanoLC-MS/MS. RESULTS Following testing the anti-SARS-CoV-2 3CLpro effects of 104 herbal medicines, it was found that Ginkgo biloba extract 50 (GBE50) potently inhibited SARS-CoV-2 3CLpro in dose- and time-dependent manners. A total of 38 constituents were identified from GBE50 by UHPLC-Q-Exactive Orbitrap HRMS, while 26 peptides modified by 18 constituents were identified by chemoproteomic profiling. The anti-SARS-CoV-2 3CLpro effects of 18 identified covalent inhibitors were then validated by performing time-dependent inhibition assays. The results clearly demonstrated that most tested constituents showed time-dependent inhibition on SARS-CoV-2 3CLpro, while gallocatechin and sciadopitysin displayed the most potent anti-SARS-CoV-2 3CLpro effects. CONCLUSION Collectively, GBE50 and some constituents in this herbal product could strongly inhibit SARS-CoV-2 3CLpro in dose- and time-dependent manner. Gallocatechin and sciadopitysin were identified as potent SARS-CoV-2 3CLpro inhibitors, which offers promising lead compounds for the development of novel anti-SARS-CoV-2 drugs.
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Affiliation(s)
- Ya-Ni Zhang
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Guang-Hao Zhu
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Wei Liu
- Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yuan Xiong
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Qing Hu
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China; Clinical Pharmacy Center, Cancer Center, Department of Pharmacy, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang 310014, China
| | - Xiao-Yu Zhuang
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Gui-Hua Jia
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Wei-Dong Zhang
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Guang-Bo Ge
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China.
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11
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Wang Y, Gao Q, Yao P, Yao Q, Zhang J. Multidimensional virtual screening approaches combined with drug repurposing to identify potential covalent inhibitors of SARS-CoV-2 3CL protease. J Biomol Struct Dyn 2023; 41:15262-15285. [PMID: 36961210 DOI: 10.1080/07391102.2023.2193994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Accepted: 02/26/2023] [Indexed: 03/25/2023]
Abstract
The outbreak of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has caused an unprecedented global pandemic, and new cases are still on the rise due to the absence of effective medicines. However, developing new drugs within a short time is extremely difficult. Repurposing the existing drugs provides a fast and effective strategy to identify promising inhibitors. Here we focus on the screening of drugs database for discovering potential covalent inhibitors that target 3-chymotrypsin-like protease (3CLpro), an essential enzyme mediating viral replication and transcription. Firstly, we constructed a receptor-ligand pharmacophore model and verified it through decoy set. The importance of pharmacophore features was evaluated by combining molecular dynamics simulation with interaction analyses. Then, covalent docking was used to perform further screening. According to docking score and Prime/Molecular Mechanics Generalized Born Surface Area (MM-GBSA) score, total ten compounds obtained good scores and successfully established covalent bonds with the catalytic Cys145 residue. They also formed favorable interactions with key residues in active sites and closely integrated with 3CLpro with binding modes similar to known 3CLpro inhibitor. Finally, the top four hits DB08732, DB04653, DB01871 and DB07299 were further subjected to 100 ns molecular dynamics (MD) simulation and MM-GBSA binding free energy calculations. The results suggest that the four candidates show good binding affinities for 3CLpro, which warrants further evaluation for their in-vitro/in-vivo activities. Overall, our research methods provide a valuable reference for discovering promising inhibitors against SARS-CoV-2 and help to fight against the epidemic.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ying Wang
- Department of Physical Chemistry, China Pharmaceutical University, Nanjing, People's Republic of China
| | - Qiushuang Gao
- Department of Physical Chemistry, China Pharmaceutical University, Nanjing, People's Republic of China
| | - Peng Yao
- Department of Physical Chemistry, China Pharmaceutical University, Nanjing, People's Republic of China
| | - Qizheng Yao
- School of Pharmacy, China Pharmaceutical University, Nanjing, People's Republic of China
| | - Ji Zhang
- Department of Physical Chemistry, China Pharmaceutical University, Nanjing, People's Republic of China
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, People's Republic of China
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12
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Liang J, Zheng M, Xu W, Chen Y, Tang P, Wu G, Zou P, Li H, Chen L. Acriflavine and proflavine hemisulfate as potential antivirals by targeting M pro. Bioorg Chem 2022; 129:106185. [PMID: 36240541 PMCID: PMC9540699 DOI: 10.1016/j.bioorg.2022.106185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 09/18/2022] [Accepted: 09/26/2022] [Indexed: 11/02/2022]
Abstract
The evolving SARS-CoV-2 epidemic buffets the world, and the concerted efforts are needed to explore effective drugs. Mpro is an intriguing antiviral target for interfering with viral RNA replication and transcription. In order to get potential anti-SARS-CoV-2 agents, we established an enzymatic assay using a fluorogenic substrate to screen the inhibitors of Mpro. Fortunately, Acriflavine (ACF) and Proflavine Hemisulfate (PRF) with the same acridine scaffold were picked out for their good inhibitory activity against Mpro with IC50 of 5.60 ± 0.29 μM and 2.07 ± 0.01 μM, respectively. Further evaluation of MST assay and enzymatic kinetics experiment in vitro showed that they had a certain affinity to SARS-CoV-2 Mpro and were both non-competitive inhibitors. In addition, they inhibited about 90 % HCoV-OC43 replication in BHK-21 cells at 1 μM. Both compounds showed nano-molar activities against SARS-CoV-2 virus, which were superior to GC376 for anti-HCoV-43, and equivalent to the standard molecule remdesivir. Our study demonstrated that ACF and PRF were inhibitors of Mpro, and ACF has been previously reported as a PLpro inhibitor. Taken together, ACF and PRF might be dual-targeted inhibitors to provide protection against infections of coronaviruses.
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Affiliation(s)
- Jing Liang
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Mengzhu Zheng
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Wei Xu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai 200032, China
| | - Yongkang Chen
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai 200032, China
| | - Piyu Tang
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Guoyi Wu
- Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China,Corresponding authors at: Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China (H. Li and L. Chen)
| | - Peng Zou
- Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China,Corresponding authors at: Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China (H. Li and L. Chen)
| | - Hua Li
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China,Institute of Structural Pharmacology & TCM Chemical Biology, College of Pharmacy, Fujian University of Traditional Chinese Medicine, Fuzhou 350122, China,School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China,Corresponding authors at: Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China (H. Li and L. Chen)
| | - Lixia Chen
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China,Corresponding authors at: Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China (H. Li and L. Chen)
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13
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Discovery and mechanism of action of Thonzonium bromide from an FDA-approved drug library with potent and broad-spectrum inhibitory activity against main proteases of human coronaviruses. Bioorg Chem 2022; 130:106264. [PMCID: PMC9643332 DOI: 10.1016/j.bioorg.2022.106264] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Revised: 10/28/2022] [Accepted: 11/04/2022] [Indexed: 11/10/2022]
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14
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La Monica G, Bono A, Lauria A, Martorana A. Targeting SARS-CoV-2 Main Protease for Treatment of COVID-19: Covalent Inhibitors Structure-Activity Relationship Insights and Evolution Perspectives. J Med Chem 2022; 65:12500-12534. [PMID: 36169610 PMCID: PMC9528073 DOI: 10.1021/acs.jmedchem.2c01005] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Indexed: 02/07/2023]
Abstract
The viral main protease is one of the most attractive targets among all key enzymes involved in the SARS-CoV-2 life cycle. Covalent inhibition of the cysteine145 of SARS-CoV-2 MPRO with selective antiviral drugs will arrest the replication process of the virus without affecting human catalytic pathways. In this Perspective, we analyzed the in silico, in vitro, and in vivo data of the most representative examples of covalent SARS-CoV-2 MPRO inhibitors reported in the literature to date. In particular, the studied molecules were classified into eight different categories according to their reactive electrophilic warheads, highlighting the differences between their reversible/irreversible mechanism of inhibition. Furthermore, the analyses of the most recurrent pharmacophoric moieties and stereochemistry of chiral carbons were reported. The analyses of noncovalent and covalent in silico protocols, provided in this Perspective, would be useful for the scientific community to discover new and more efficient covalent SARS-CoV-2 MPRO inhibitors.
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Affiliation(s)
| | | | - Antonino Lauria
- Dipartimento di Scienze e
Tecnologie Biologiche Chimiche e Farmaceutiche, University of Palermo, Viale delle Scienze, Ed. 17, I-90128 Palermo, Italy
| | - Annamaria Martorana
- Dipartimento di Scienze e
Tecnologie Biologiche Chimiche e Farmaceutiche, University of Palermo, Viale delle Scienze, Ed. 17, I-90128 Palermo, Italy
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15
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The inhibitory activity of methoxyl flavonoids derived from Inula britannica flowers on SARS-CoV-2 3CLpro. Int J Biol Macromol 2022; 222:2098-2104. [PMID: 36208809 PMCID: PMC9534544 DOI: 10.1016/j.ijbiomac.2022.10.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 09/26/2022] [Accepted: 10/02/2022] [Indexed: 11/21/2022]
Abstract
In our ongoing efforts to identify effective natural antiviral agents, four methoxy flavonoids (1-4) were isolated from the Inula britannica flower extract. Their structures were elucidated using nuclear magnetic resonance. Flavonoids 1-4 exhibited inhibitory activity against SARS- CoV-2 3CLpro with IC50 values of 41.6 ± 2.5, 35.9 ± 0.9, 32.8 ± 1.2, and 96.6 ± 3.4 μM, respectively. Flavonoids 1-3 inhibited 3CLpro in a competitive manner. Based on molecular simulations, key amino acids that form hydrogen bond with inhibitor 3 were identified. Finally, we found that inhibitors (1-3) suppressed HCoV-OC43 coronavirus proliferation at micromole concentrations.
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16
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Hu Q, Xiong Y, Zhu GH, Zhang YN, Zhang YW, Huang P, Ge GB. The SARS-CoV-2 main protease (M pro): Structure, function, and emerging therapies for COVID-19. MedComm (Beijing) 2022; 3:e151. [PMID: 35845352 PMCID: PMC9283855 DOI: 10.1002/mco2.151] [Citation(s) in RCA: 61] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 06/06/2022] [Accepted: 06/06/2022] [Indexed: 12/21/2022] Open
Abstract
The main proteases (Mpro), also termed 3‐chymotrypsin‐like proteases (3CLpro), are a class of highly conserved cysteine hydrolases in β‐coronaviruses. Increasing evidence has demonstrated that 3CLpros play an indispensable role in viral replication and have been recognized as key targets for preventing and treating coronavirus‐caused infectious diseases, including COVID‐19. This review is focused on the structural features and biological function of the severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) main protease Mpro (also known as 3CLpro), as well as recent advances in discovering and developing SARS‐CoV‐2 3CLpro inhibitors. To better understand the characteristics of SARS‐CoV‐2 3CLpro inhibitors, the inhibition activities, inhibitory mechanisms, and key structural features of various 3CLpro inhibitors (including marketed drugs, peptidomimetic, and non‐peptidomimetic synthetic compounds, as well as natural compounds and their derivatives) are summarized comprehensively. Meanwhile, the challenges in this field are highlighted, while future directions for designing and developing efficacious 3CLpro inhibitors as novel anti‐coronavirus therapies are also proposed. Collectively, all information and knowledge presented here are very helpful for understanding the structural features and inhibitory mechanisms of SARS‐CoV‐2 3CLpro inhibitors, which offers new insights or inspiration to medicinal chemists for designing and developing more efficacious 3CLpro inhibitors as novel anti‐coronavirus agents.
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Affiliation(s)
- Qing Hu
- Shanghai Frontiers Science Center of TCM Chemical Biology Institute of Interdisciplinary Integrative Medicine Research Shanghai University of Traditional Chinese Medicine Shanghai China.,Clinical Pharmacy Center Cancer Center Department of Pharmacy Zhejiang Provincial People's Hospital Affiliated People's Hospital Hangzhou Medical College, Hangzhou Zhejiang China
| | - Yuan Xiong
- Shanghai Frontiers Science Center of TCM Chemical Biology Institute of Interdisciplinary Integrative Medicine Research Shanghai University of Traditional Chinese Medicine Shanghai China
| | - Guang-Hao Zhu
- Shanghai Frontiers Science Center of TCM Chemical Biology Institute of Interdisciplinary Integrative Medicine Research Shanghai University of Traditional Chinese Medicine Shanghai China
| | - Ya-Ni Zhang
- Shanghai Frontiers Science Center of TCM Chemical Biology Institute of Interdisciplinary Integrative Medicine Research Shanghai University of Traditional Chinese Medicine Shanghai China
| | - Yi-Wen Zhang
- Clinical Pharmacy Center Cancer Center Department of Pharmacy Zhejiang Provincial People's Hospital Affiliated People's Hospital Hangzhou Medical College, Hangzhou Zhejiang China
| | - Ping Huang
- Clinical Pharmacy Center Cancer Center Department of Pharmacy Zhejiang Provincial People's Hospital Affiliated People's Hospital Hangzhou Medical College, Hangzhou Zhejiang China
| | - Guang-Bo Ge
- Shanghai Frontiers Science Center of TCM Chemical Biology Institute of Interdisciplinary Integrative Medicine Research Shanghai University of Traditional Chinese Medicine Shanghai China
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17
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Sun H, Xi M, Jin Q, Zhu Z, Zhang Y, Jia G, Zhu G, Sun M, Zhang H, Ren X, Zhang Y, Xu Z, Huang H, Shen J, Li B, Ge G, Chen K, Zhu W. Chemo- and Site-Selective Lysine Modification of Peptides and Proteins under Native Conditions Using the Water-Soluble Zolinium. J Med Chem 2022; 65:11840-11853. [DOI: 10.1021/acs.jmedchem.2c00937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Haiguo Sun
- CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Mengyu Xi
- CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Qiang Jin
- Shanghai Frontiers Science Center of TCM Chemical Biology; Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai 201203, China
| | - Zhengdan Zhu
- CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Yani Zhang
- Shanghai Frontiers Science Center of TCM Chemical Biology; Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai 201203, China
| | - Guihua Jia
- Shanghai Frontiers Science Center of TCM Chemical Biology; Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai 201203, China
| | - Guanghao Zhu
- Shanghai Frontiers Science Center of TCM Chemical Biology; Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai 201203, China
| | - Mengru Sun
- Shanghai Frontiers Science Center of TCM Chemical Biology; Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai 201203, China
| | - Hongwei Zhang
- Shanghai Frontiers Science Center of TCM Chemical Biology; Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai 201203, China
| | - Xuelian Ren
- CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Yong Zhang
- CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Zhijian Xu
- CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - He Huang
- CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Jingshan Shen
- CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Bo Li
- CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, No. 38 Xue Yuan Road, Haidian District, Beijing 100191, China
| | - Guangbo Ge
- Shanghai Frontiers Science Center of TCM Chemical Biology; Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai 201203, China
| | - Kaixian Chen
- CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- Shanghai Frontiers Science Center of TCM Chemical Biology; Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Weiliang Zhu
- CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- Shanghai Frontiers Science Center of TCM Chemical Biology; Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
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18
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Kandhasamy S, Zeng Y. Fabrication of vitamin K3-carnosine peptide-loaded spun silk fibroin fibers/collagen bi-layered architecture for bronchopleural fistula tissue repair and regeneration applications. BIOMATERIALS ADVANCES 2022; 137:212817. [PMID: 35929255 DOI: 10.1016/j.bioadv.2022.212817] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 04/15/2022] [Accepted: 04/18/2022] [Indexed: 06/15/2023]
Abstract
Bronchial and pleural injuries with persistent air leak pose a threat in the repair and regeneration of pulmonary diseases. The need to arrive at a highly efficient therapy for closure of bronchopleural fistula (BPF) so as to effectively suppress inflammation, infection and repair the damaged pleural space caused by cancer as well as contractile restoration of bronchopleural scars remain a significant clinical challenge. Herein, we have designed and developed potent bioactive vitamin K3 carnosine peptide (VKC)-loaded spun SF fibroin fibers/collagen bi-layered 3D scaffold for bronchopleural fistula tissue engineering applications. The VKC drug showed excellent cell viability in human bronchial epithelial cells (HBECs), in addition to its pronounced higher cytotoxicity against the A549 lung cancer cell line with an IC50 of 5 μg/mL. Furthermore, VKC displayed a strong affinity with the catalytic site of EGFR (PDB ID: 1M17) and VEGFR2 (PDB ID: 4AGD, 4ASD) receptors in molecular docking studies. Following which the spun SF-VKC (primary layer) and collagen film (top layer) constructed bi-layered CSVKC were structurally elucidated and its morphological, physicochemical and biological characterizations were well examined. The bi-layered scaffold showed superior biocompatibility and cell migration ability in HBECs than other scaffolds. Interestingly, the CSVKC revealed rapid HBECs motility towards scratched regions for fast healing in vitro bronchial tissue engineering. In vivo biocompatibility and angiogenesis studies of the prepared scaffolds were evaluated and the results obtained demonstrated excellent new tissue formation and neovascularization in the bi-layered architecture rather than others. Therefore, our results suggest that the potent antibacterial and anticancer therapeutic agent (VKC)-impregnated silk fibroin fibers/collagen bi-layered 3D biomaterial could be useful in treating cancerous BPF and pulmonary diseases in future.
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Affiliation(s)
- Subramani Kandhasamy
- Department of Respiratory Diseases, Clinical Center for Molecular Diagnosis and Therapy, The Second Affiliated Hospital of Fujian Medical University, Quanzhou 362000, China
| | - Yiming Zeng
- Department of Respiratory Diseases, Clinical Center for Molecular Diagnosis and Therapy, The Second Affiliated Hospital of Fujian Medical University, Quanzhou 362000, China.
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Shimizu N, Shigemitsu H, Kida T, Bach T, Mori T. Visible Light-Induced Regio- and Enantiodifferentiating [2 + 2] Photocycloaddition of 1,4-Naphthoquinones Mediated by Oppositely Coordinating 1,3,2-Oxazaborolidine Chiral Lewis Acid. J Org Chem 2022; 87:8071-8083. [PMID: 35652135 DOI: 10.1021/acs.joc.2c00730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A range of asymmetric photochemical transformations using visible light have recently become considerably attractive. Among the various approaches, chiral Lewis acid association to enones for [2 + 2] and ortho photocycloadditions and oxadi-π-methane rearrangements have shown to be very promising. Naturally, chiral Lewis acid coordination protects one of the prochiral faces of the C═C double bond, which enables an effective enantiodifferentiation in the following bond-forming process(es). Here, we studied regio- and enantiodifferentiating [2 + 2] photocycloaddition reactions of naphthoquinone derivatives mediated by chiral oxazaborolidines. A stereochemical control was quite challenging for the 2-ene-1,4-dione substrate, as a double coordination of Lewis acid essentially cancels out the face selectivity, and a mono-coordination to each carbonyl group leads to an opposite stereochemical outcome. Furthermore, a stepwise coordination in the ground state of Lewis acid in a 1:1 fashion was practically inaccessible. We found that the excited-state decomplexation is a key to accomplish high regio- and enantioselectivities in the photocycloaddition of an ene-dione.
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Affiliation(s)
- Nao Shimizu
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Hajime Shigemitsu
- Integrated Frontier Research for Medical Science Division Institute for OTRI, Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Toshiyuki Kida
- Integrated Frontier Research for Medical Science Division Institute for OTRI, Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Thorsten Bach
- Department Chemie and Catalysis Research Center (CRC), Technische Universität München, Lichtenbergstrasse 4, Garching 85747, Germany
| | - Tadashi Mori
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita, Osaka 565-0871, Japan
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Sreelatha S, Devang N, Marathe A. Vitamin K: A Simple and Efficient Add-on to the Current Treatment Regime of COVID-19. CURRENT NUTRITION & FOOD SCIENCE 2022. [DOI: 10.2174/1573401318666220405134759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
: Intravascular thrombosis and pulmonary fibrosis in COVID-19 patients with pneumonia is significantly associated with the severity of disease. Vitamin K is known to balance the coagulation mechanisms and also prevents calcification and fibrosis of the extrahepatic soft tissues. This narrative review focuses on the role of Vitamin K as a linking factor for thrombotic as well as pulmonary complications of COVID-19.
Methods and Results:
Article search was performed in databases of WHO, PubMed, Scopus and Clinical Trial Registry using appropriate key words. Original articles included very few observational studies which showed a reduced level of Vitamin K as well as activated extrahepatic Vitamin K Dependent Proteins (VKDP) in COVID-19 patients when compared to healthy controls. Chronic treatment with Vitamin K Antagonists did not reduce the risk of in-hospital death. Docking study was performed using Swiss dock and it gave a significant interaction between menaquinone and SARS-CoV-2 main Protease (SARS-CoV-2 Mpro).
Discussion:
Deficiency of Vitamin K in COVID-19 can be due to excess use of antagonists or defective ingestion or absorption. This triggers an imbalance in the normal coagulation-anticoagulation mechanism by channelling the available Vitamin K to the liver and thereby causing a deficiency of the same in extrahepatic tissues and finally leading to thrombosis. This also prevents carboxylation and activation of extrahepatic VKDP required to prevent the calcification of soft tissues and thus leading to lung fibrosis.
Conclutions:
Supplementation of Vitamin K should be considered as a potentially modifiable risk factor in severe COVID-19. Randomized control trials are highly recommended to give clearer evidence on the same.
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Affiliation(s)
- Souparnika Sreelatha
- Department of Biochemistry, Assistant Professor, K S Hegde Medical Academy, NITTE University, Deralakkatte, Mangalore, Karnataka, India
| | - Nayana Devang
- Department of Biochemistry, Assistant Professor, Kanachur Institute of Medical Sciences, Natekal, University Road, Mangalore, Karnataka, India
| | - Aradhana Marathe
- Department of Biochemistry, Tutor, Kasturba Medical College, Mangalore, Manipal Academy of Higher Education, Manipal, Karnataka, India
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