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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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Chatron N, Boulven M, Montagut-Romans A, Ponsot F, Jacolot M, Caruel H, Benoît E, Popowycz F, Lattard V. Design of a structure-activity relationship model of vitamin K epoxide reductase (VKORC1) inhibitors combining chemical synthesis of new compounds, enzymatic assays and molecular modelling. Bioorg Med Chem 2023; 94:117453. [PMID: 37741121 DOI: 10.1016/j.bmc.2023.117453] [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: 05/05/2023] [Revised: 08/13/2023] [Accepted: 08/21/2023] [Indexed: 09/25/2023]
Abstract
Vitamin K antagonists (VKAs) anticoagulants have been used since the 1950s as medicines and rodenticides. These molecules are mainly 4-hydroxycoumarin derivatives and act by inhibiting the vitamin K epoxide reductase (VKORC1), an endoplasmic reticulum membrane resident enzyme. However, many VKORC1 mutations have been reported over the last decade, inducing VKAs resistances and thus treatments failures. Although studies have reported experimental and computational investigations of VKAs based on VKORC1 structural homology models, the development of new effective anticoagulants has been quite complex due to the lack of structural data and reliable structure-activity relationships. However, the recent publication of VKORC1 crystal structure provides new information for further studies. Based on these findings, we combined chemical synthesis, enzymatic assays and molecular modelling methods to design a structure-activity relationship (SAR) model. Our results proved that the lipophilicity, the membrane permeability of inhibitors and their affinity towards human VKORC1 enzyme are the main characteristics for potent anticoagulants. Our SAR model managed to rank compounds according to their ability to inhibit the human VKORC1. Such a tool might constitute an alternative to evaluate new molecules potency before their chemical synthesis and biological assessment and might assist the development of new VKAs.
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Affiliation(s)
- Nolan Chatron
- USC 1233 RS2GP, VetAgro Sup, INRAE, University of Lyon, 69280 Marcy L'Etoile, France.
| | - Manon Boulven
- Univ Lyon, INSA Lyon, Université Lyon 1, CNRS, CPE Lyon, UMR 5246, ICBMS, 1 rue Victor Grignard, 69621 Villeurbanne Cedex, France; Liphatech, Bonnel, 47480 Pont-du-Casse, France
| | - Adrien Montagut-Romans
- Univ Lyon, INSA Lyon, Université Lyon 1, CNRS, CPE Lyon, UMR 5246, ICBMS, 1 rue Victor Grignard, 69621 Villeurbanne Cedex, France; Liphatech, Bonnel, 47480 Pont-du-Casse, France
| | - Flavien Ponsot
- Univ Lyon, INSA Lyon, Université Lyon 1, CNRS, CPE Lyon, UMR 5246, ICBMS, 1 rue Victor Grignard, 69621 Villeurbanne Cedex, France
| | - Maïwenn Jacolot
- Univ Lyon, INSA Lyon, Université Lyon 1, CNRS, CPE Lyon, UMR 5246, ICBMS, 1 rue Victor Grignard, 69621 Villeurbanne Cedex, France
| | | | - Etienne Benoît
- USC 1233 RS2GP, VetAgro Sup, INRAE, University of Lyon, 69280 Marcy L'Etoile, France
| | - Florence Popowycz
- Univ Lyon, INSA Lyon, Université Lyon 1, CNRS, CPE Lyon, UMR 5246, ICBMS, 1 rue Victor Grignard, 69621 Villeurbanne Cedex, France
| | - Virginie Lattard
- USC 1233 RS2GP, VetAgro Sup, INRAE, University of Lyon, 69280 Marcy L'Etoile, France
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Zhao Q, Chen Y, Huang W, Zhou H, Zhang W. Drug-microbiota interactions: an emerging priority for precision medicine. Signal Transduct Target Ther 2023; 8:386. [PMID: 37806986 PMCID: PMC10560686 DOI: 10.1038/s41392-023-01619-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 07/20/2023] [Accepted: 08/24/2023] [Indexed: 10/10/2023] Open
Abstract
Individual variability in drug response (IVDR) can be a major cause of adverse drug reactions (ADRs) and prolonged therapy, resulting in a substantial health and economic burden. Despite extensive research in pharmacogenomics regarding the impact of individual genetic background on pharmacokinetics (PK) and pharmacodynamics (PD), genetic diversity explains only a limited proportion of IVDR. The role of gut microbiota, also known as the second genome, and its metabolites in modulating therapeutic outcomes in human diseases have been highlighted by recent studies. Consequently, the burgeoning field of pharmacomicrobiomics aims to explore the correlation between microbiota variation and IVDR or ADRs. This review presents an up-to-date overview of the intricate interactions between gut microbiota and classical therapeutic agents for human systemic diseases, including cancer, cardiovascular diseases (CVDs), endocrine diseases, and others. We summarise how microbiota, directly and indirectly, modify the absorption, distribution, metabolism, and excretion (ADME) of drugs. Conversely, drugs can also modulate the composition and function of gut microbiota, leading to changes in microbial metabolism and immune response. We also discuss the practical challenges, strategies, and opportunities in this field, emphasizing the critical need to develop an innovative approach to multi-omics, integrate various data types, including human and microbiota genomic data, as well as translate lab data into clinical practice. To sum up, pharmacomicrobiomics represents a promising avenue to address IVDR and improve patient outcomes, and further research in this field is imperative to unlock its full potential for precision medicine.
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Affiliation(s)
- Qing Zhao
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, PR China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, 110 Xiangya Road, Changsha, 410078, PR China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, PR China
- National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, PR China
| | - Yao Chen
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, PR China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, 110 Xiangya Road, Changsha, 410078, PR China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, PR China
- National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, PR China
| | - Weihua Huang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, PR China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, 110 Xiangya Road, Changsha, 410078, PR China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, PR China
- National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, PR China
| | - Honghao Zhou
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, PR China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, 110 Xiangya Road, Changsha, 410078, PR China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, PR China
- National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, PR China
| | - Wei Zhang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, PR China.
- The First Affiliated Hospital of Shantou University Medical College, Shantou, 515041, PR China.
- The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, 510080, PR China.
- Central Laboratory of Hunan Cancer Hospital, Central South University, 283 Tongzipo Road, Changsha, 410013, PR China.
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Simic J, Mihajlovic M, Zec N, Kovacevic V, Marinkovic M, Mujovic N, Potpara T. The impact of anticoagulation therapy on kidney function in patients with atrial fibrillation and chronic kidney disease. Expert Rev Cardiovasc Ther 2023; 21:937-945. [PMID: 37842943 DOI: 10.1080/14779072.2023.2270909] [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: 07/27/2023] [Accepted: 10/11/2023] [Indexed: 10/17/2023]
Abstract
INTRODUCTION Atrial fibrillation (AF) and chronic kidney disease (CKD) are closely related. These diseases share common risk factors and are associated with increased risk of thromboembolic events. Choosing the appropriate oral anticoagulant therapy (OAC) in patients with AF and CKD is challenging. Deterioration of renal function is common in patients with AF treated with OACs, although not all OACs affect the kidneys equally. AREAS COVERED In this review, we aim to summarize the current knowledge of the prevention of thromboembolic events in patients with AF and CKD, focusing on the impact of specific OAC agents on renal function. EXPERT OPINION Consideration of OAC use is mandatory in patients with AF and CKD who are at increased risk of stroke or systemic embolism. Available evidence suggests that the use of non-vitamin K antagonist oral anticoagulants (NOACs) is associated with slower deterioration of renal function in comparison to Vitamin K antagonists (VKAs). Hence, a NOAC should be used in preference to VKAs in all NOAC-eligible patients with AF and CKD. Regarding patients with end-stage renal dysfunction and those on dialysis or renal replacement therapy, the use of NOAC should be considered in line with locally relevant formal recommendations.
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Affiliation(s)
- Jelena Simic
- Cardiology Clinic, University Clinical Centre of Serbia, Belgrade, Serbia
| | | | - Nevena Zec
- School of Medicine, University of Belgrade, Belgrade, Serbia
| | - Vladan Kovacevic
- Cardiology Clinic, University Clinical Centre of Serbia, Belgrade, Serbia
| | - Milan Marinkovic
- Cardiology Clinic, University Clinical Centre of Serbia, Belgrade, Serbia
- School of Medicine, University of Belgrade, Belgrade, Serbia
| | - Nebojsa Mujovic
- Cardiology Clinic, University Clinical Centre of Serbia, Belgrade, Serbia
- School of Medicine, University of Belgrade, Belgrade, Serbia
| | - Tatjana Potpara
- Cardiology Clinic, University Clinical Centre of Serbia, Belgrade, Serbia
- School of Medicine, University of Belgrade, Belgrade, Serbia
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Yadav T, Vishwkarma A, Mandal M, Karmakar I, Pathak A, Brahmachari G, Tripathi P, Maddheshiya A, Yadav N, Mahapatra C. Molecular modeling, vibrational dynamics and NBO analysis of a synthetic bio-relevant warfarin analog. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2023.135347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2023]
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Furukawa N, Chen X, Asano S, Matsumoto M, Wu Y, Murata K, Takeuchi A, Tode C, Homma T, Koharazawa R, Usami K, Tie JK, Hirota Y, Suhara Y. Synthesis of new vitamin K derivatives with a ketone group at the C-1′ position of the side chain and their conversion to menaquinone-4. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.134614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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7
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Ahmad I, Pawara R, Patel H. In silico toxicity investigation of Methaqualone’s conjunctival, retinal, and gastrointestinal hemorrhage by molecular modelling approach. MOLECULAR SIMULATION 2022. [DOI: 10.1080/08927022.2022.2113412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Affiliation(s)
- Iqrar Ahmad
- Division of Computer-Aided Drug Design, Dept. of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, India
| | - Rahul Pawara
- Division of Computer-Aided Drug Design, Dept. of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, India
| | - Harun Patel
- Division of Computer-Aided Drug Design, Dept. of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, India
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Chen X, Furukawa N, Jin DY, Liu Y, Stafford DW, Williams CM, Suhara Y, Tie JK. Naturally occurring UBIAD1 mutations differentially affect menaquinone biosynthesis and vitamin K-dependent carboxylation. FEBS J 2021; 289:2613-2627. [PMID: 34813684 PMCID: PMC9064899 DOI: 10.1111/febs.16291] [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: 07/12/2021] [Revised: 10/15/2021] [Accepted: 11/22/2021] [Indexed: 11/30/2022]
Abstract
UbiA prenyltransferase domain-containing protein-1 (UBIAD1) is responsible for the biosynthesis of menaquinone-4 (MK-4), a cofactor for extrahepatic carboxylation of vitamin K-dependent (VKD) proteins. Genetic variations of UBIAD1 are mainly associated with Schnyder corneal dystrophy (SCD), a disease characterized by abnormal accumulation of cholesterol in the cornea. Results from in vitro studies demonstrate that SCD-associated UBIAD1 mutations are defective in MK-4 biosynthesis. However, SCD patients do not exhibit typical phenotypes associated with defects of MK-4 or VKD carboxylation. Here, we coupled UBIAD1's biosynthetic activity of MK-4 with VKD carboxylation in HEK293 cells that stably express a chimeric VKD reporter protein. The endogenous Ubiad1 gene in these cells was knocked out by CRISPR-Cas9-mediated genome editing. The effect of UBIAD1 mutations on MK-4 biosynthesis and VKD carboxylation was evaluated in Ubiad1-deficient reporter cells by determining the production of MK-4 or by measuring the efficiency of reporter-protein carboxylation. Our results show that the hot-spot mutation N102S has a moderate impact on MK-4 biosynthesis (retained ˜ 82% activity) but does not affect VKD carboxylation. However, the G186R mutation significantly affected both MK-4 biosynthesis and VKD carboxylation. Other mutations exhibit varying degrees of effects on MK-4 biosynthesis and VKD carboxylation. These results are consistent with in vivo results obtained from gene knock-in mice and SCD patients. Our findings suggest that UBIAD1's MK-4 biosynthetic activity does not directly correlate with the phenotypes of SCD patients. The established cell-based assays in this study provide a powerful tool for the functional studies of UBIAD1 in a cellular milieu.
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Affiliation(s)
- Xuejie Chen
- Department of Biology, University of North Carolina at Chapel Hill, NC, USA
| | - Natsuko Furukawa
- Department of Bioscience and Engineering, College of Systems Engineering and Science, Shibaura Institute of Technology, Saitama, Japan
| | - Da-Yun Jin
- Department of Biology, University of North Carolina at Chapel Hill, NC, USA
| | - Yizhou Liu
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD, Australia
| | - Darrel W Stafford
- Department of Biology, University of North Carolina at Chapel Hill, NC, USA
| | - Craig M Williams
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD, Australia
| | - Yoshitomo Suhara
- Department of Bioscience and Engineering, College of Systems Engineering and Science, Shibaura Institute of Technology, Saitama, Japan
| | - Jian-Ke Tie
- Department of Biology, University of North Carolina at Chapel Hill, NC, USA
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