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Kurosawa M, Kato F, Hishiki T, Ito S, Fujisawa H, Yamaguchi T, Moriguchi M, Hosokawa K, Watanabe T, Saito-Tarashima N, Minakawa N, Fujimuro M. Sofosbuvir Suppresses the Genome Replication of DENV1 in Human Hepatic Huh7 Cells. Int J Mol Sci 2024; 25:2022. [PMID: 38396699 PMCID: PMC10889370 DOI: 10.3390/ijms25042022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 02/02/2024] [Accepted: 02/04/2024] [Indexed: 02/25/2024] Open
Abstract
Dengue virus (DENV) causes dengue fever and dengue hemorrhagic fever, and DENV infection kills 20,000 people annually worldwide. Therefore, the development of anti-DENV drugs is urgently needed. Sofosbuvir (SOF) is an effective drug for HCV-related diseases, and its triphosphorylated metabolite inhibits viral RNA synthesis by the RNA-dependent RNA polymerase (RdRp) of HCV. (2'R)-2'-Deoxy-2'-fluoro-2'-methyluridine (FMeU) is the dephosphorylated metabolite produced from SOF. The effects of SOF and FMeU on DENV1 replication were analyzed using two DENV1 replicon-based methods that we previously established. First, a replicon-harboring cell assay showed that DENV1 replicon replication in human hepatic Huh7 cells was decreased by SOF but not by FMeU. Second, a transient replicon assay showed that DENV1 replicon replication in Huh7 cells was decreased by SOF; however, in hamster kidney BHK-21 cells, it was not suppressed by SOF. Additionally, the replicon replication in Huh7 and BHK-21 cells was not affected by FMeU. Moreover, we assessed the effects of SOF on infectious DENV1 production. SOF suppressed infectious DENV1 production in Huh7 cells but not in monkey kidney Vero cells. To examine the substrate recognition of the HCV and DENV1 RdRps, the complex conformation of SOF-containing DENV1 RdRp or HCV RdRp was predicted using AlphaFold 2. These results indicate that SOF may be used as a treatment for DENV1 infection.
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Affiliation(s)
- Madoka Kurosawa
- Department of Cell Biology, Kyoto Pharmaceutical University, Kyoto 607-8412, Japan; (M.K.); (S.I.); (H.F.); (T.Y.); (M.M.); (K.H.)
| | - Fumihiro Kato
- Department of Virology III, National Institute of Infectious Diseases, Tokyo 208-0011, Japan;
| | - Takayuki Hishiki
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo 162-8640, Japan;
| | - Saori Ito
- Department of Cell Biology, Kyoto Pharmaceutical University, Kyoto 607-8412, Japan; (M.K.); (S.I.); (H.F.); (T.Y.); (M.M.); (K.H.)
| | - Hiroki Fujisawa
- Department of Cell Biology, Kyoto Pharmaceutical University, Kyoto 607-8412, Japan; (M.K.); (S.I.); (H.F.); (T.Y.); (M.M.); (K.H.)
| | - Tatsuo Yamaguchi
- Department of Cell Biology, Kyoto Pharmaceutical University, Kyoto 607-8412, Japan; (M.K.); (S.I.); (H.F.); (T.Y.); (M.M.); (K.H.)
| | - Misato Moriguchi
- Department of Cell Biology, Kyoto Pharmaceutical University, Kyoto 607-8412, Japan; (M.K.); (S.I.); (H.F.); (T.Y.); (M.M.); (K.H.)
| | - Kohei Hosokawa
- Department of Cell Biology, Kyoto Pharmaceutical University, Kyoto 607-8412, Japan; (M.K.); (S.I.); (H.F.); (T.Y.); (M.M.); (K.H.)
| | - Tadashi Watanabe
- Department of Virology, Graduate School of Medicine, University of the Ryukyus, Okinawa 903-0215, Japan;
| | - Noriko Saito-Tarashima
- Graduate School of Pharmaceutical Science, Tokushima University, Tokushima 770-8505, Japan; (N.S.-T.); (N.M.)
| | - Noriaki Minakawa
- Graduate School of Pharmaceutical Science, Tokushima University, Tokushima 770-8505, Japan; (N.S.-T.); (N.M.)
| | - Masahiro Fujimuro
- Department of Cell Biology, Kyoto Pharmaceutical University, Kyoto 607-8412, Japan; (M.K.); (S.I.); (H.F.); (T.Y.); (M.M.); (K.H.)
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2
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Shehzadi K, Saba A, Yu M, Liang J. Structure-Based Drug Design of RdRp Inhibitors against SARS-CoV-2. Top Curr Chem (Cham) 2023; 381:22. [PMID: 37318607 DOI: 10.1007/s41061-023-00432-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 05/15/2023] [Indexed: 06/16/2023]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a worldwide pandemic since 2019, spreading rapidly and posing a significant threat to human health and life. With over 6 billion confirmed cases of the virus, the need for effective therapeutic drugs has become more urgent than ever before. RNA-dependent RNA polymerase (RdRp) is crucial in viral replication and transcription, catalysing viral RNA synthesis and serving as a promising therapeutic target for developing antiviral drugs. In this article, we explore the inhibition of RdRp as a potential treatment for viral diseases, analysing the structural information of RdRp in virus proliferation and summarizing the reported inhibitors' pharmacophore features and structure-activity relationship profiles. We hope that the information provided by this review will aid in structure-based drug design and aid in the global fight against SARS-CoV-2 infection.
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Affiliation(s)
- Kiran Shehzadi
- Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 10081, China
| | - Afsheen Saba
- Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 10081, China
| | - Mingjia Yu
- Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 10081, China.
| | - Jianhua Liang
- Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 10081, China.
- Yangtze Delta Region Academy of Beijing Institute of Technology, Jiaxing, 314019, China.
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3
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Zhou GF, Qian W, Li F, Yang RH, Wang N, Zheng CB, Li CY, Gu XR, Yang LM, Liu J, Xiong SD, Zhou GC, Zheng YT. Discovery of ZFD-10 of a pyridazino[4,5-b]indol-4(5H)-one derivative as an anti-ZIKV agent and a ZIKV NS5 RdRp inhibitor. Antiviral Res 2023; 214:105607. [PMID: 37088168 DOI: 10.1016/j.antiviral.2023.105607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 04/17/2023] [Accepted: 04/18/2023] [Indexed: 04/25/2023]
Abstract
Zika virus (ZIKV) infection is associated with the birth defect microcephaly and Guillain-Barré syndrome in adults. There is no approved vaccine or specific antiviral agent against ZIKV. ZFD-10, a novel structural skeleton of 1H-pyridazino[4,5-b]indol-4(5H)-one, was firstly synthesized and discovered to be a potent anti-ZIKV inhibitor with very low cytotoxicity. ZFD-10's anti-ZIKV potency is independent of cell lines and ZFD-10 mainly targets the post-entry stages of ZIKV life cycle. Time-of-addition and time-of-withdrawal assays showed that 10 μM ZFD-10 displayed the ability to decrease mainly at the RNA level and weakly the viral progeny particle load. Furthermore, ZFD-10 could protect ZIKV NS5 from thermal unfolding and aggregation and increase the Tagg value of ZIKV NS5 protein from 44.6 to 49.3 °C, while ZFD-10 dose-dependently inhibits ZIKV NS5 RdRp activity using in vitro RNA polymerase assays. Molecular docking study suggests that ZFD-10 affects RdRp enzymatic function through interfering with the fingers and thumb subdomains. These results supported that ZFD-10's cell-based anti-ZIKV activity is related to its anti-RdRp activity of ZIKV NS5. The in vivo anti-ZIKV study shows that the middle-dose (4.77 mg/kg/d) of ZFD-10 protected mice from ZIKV infection and the viral loads of the blood, liver, kidney and brain in the middle-dose and high-dose (9.54 mg/kg/d) were significantly reduced compared to those of the ZIKV control. These results confirm that ZFD-10 has a certain antiviral effect against ZIKV infection in vivo.
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Affiliation(s)
- Guang-Feng Zhou
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, Key Laboratory of Bioactive Peptides of Yunnan Province, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China; College of Pharmacy, Soochow University, Suzhou, 215021, China
| | - Weiyi Qian
- School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing, 211816, Jiangsu, China
| | - Feng Li
- School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing, 211816, Jiangsu, China
| | - Ren-Hua Yang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, Key Laboratory of Bioactive Peptides of Yunnan Province, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China; School of Pharmaceutical Science & Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, Kunming, 650500, China
| | - Na Wang
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Chang-Bo Zheng
- School of Pharmaceutical Science & Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, Kunming, 650500, China
| | - Chun-Yan Li
- College of Pharmacy, Dali University, Dali, 671000, Yunnan, China
| | - Xue-Rong Gu
- School of Pharmaceutical Science & Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, Kunming, 650500, China
| | - Liu-Meng Yang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, Key Laboratory of Bioactive Peptides of Yunnan Province, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
| | - Jinsong Liu
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Si-Dong Xiong
- College of Pharmacy, Soochow University, Suzhou, 215021, China.
| | - Guo-Chun Zhou
- School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing, 211816, Jiangsu, China.
| | - Yong-Tang Zheng
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, Key Laboratory of Bioactive Peptides of Yunnan Province, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China.
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4
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Zhou GF, Li F, Xue JX, Qian W, Gu XR, Zheng CB, Li C, Yang LM, Xiong SD, Zhou GC, Zheng YT. Antiviral effects of the fused tricyclic derivatives of indoline and imidazolidinone on ZIKV infection and RdRp activities of ZIKV and DENV. Virus Res 2023; 326:199062. [PMID: 36746341 DOI: 10.1016/j.virusres.2023.199062] [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: 07/25/2022] [Revised: 01/10/2023] [Accepted: 02/01/2023] [Indexed: 02/08/2023]
Abstract
The prevalence and ravages of Zika virus (ZIKV) seriously endanger human health, especially causing significant neurological defects in both neonates as pediatric microcephaly and adults as Guillain-Barré syndrome. In this work, we studied anti-ZIKV effects of the fused tricyclic derivatives of indoline and imidazolidinone and discovered that some of them are valuable leads for drug discovery of anti-ZIKV agents. The current results show that certain compounds are broad-spectrum inhibitors of ZIKV- and dengue virus (DENV)-infection while distinctive compounds are selective ZIKV inhibitors or selective DENV inhibitors. Compounds of 12, 17 and 28 are more active against Asian ZIKV SZ-VIV01 strain than African ZIKV MR766 strain. It is valued that silylation makes six TBS compounds of 4-nitrophenyl hydrazine series and phenyl hydrazine series more active against ZIKV infection than their phenols. Time-of-addition and withdrawal studies indicate that compound 12 majorly acts on post-infection of RNA synthesis stage of ZIKV life cycle. Moreover, compounds of 12, 17 and 18 are anti-ZIKV agents with the inhibitory activities to ZIKV NS5 RdRp while 12 doesn't inhibit DENV infection even though it is a DENV RdRp inhibitor, 17 is an active agent against DENV infection but is only a weak DENV NS5 RdRp inhibitor, and 28 is inactive against DENV infection and not a DENV NS5 RdRp inhibitor. As a result, a compound's antiviral difference between ZIKV and DENV is not always related to anti-RdRp difference between ZIKV RdRp and DENV RdRp, and structural features of a compound play important roles in executing antiviral and anti-RdRp functions. Further discovery of highly potent broad-spectrum or selective agents against infection by ZIKV and DENV will be facilitated.
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Affiliation(s)
- Guang-Feng Zhou
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; College of Pharmacy, Soochow University, Suzhou 215021, China
| | - Feng Li
- School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing, Jiangsu 211816, China
| | - Jian-Xia Xue
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; Medical College, Kunming University of Science and Technology, Kunming, Yunnan 650223, China
| | - Weiyi Qian
- School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing, Jiangsu 211816, China
| | - Xue-Rong Gu
- School of Pharmaceutical Science and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, Kunming, China
| | - Chang-Bo Zheng
- School of Pharmaceutical Science and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, Kunming, China
| | - Chunyan Li
- College of Pharmacy, Dali University, Dali, Yunnan 671000, China
| | - Liu-Meng Yang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Si-Dong Xiong
- College of Pharmacy, Soochow University, Suzhou 215021, China.
| | - Guo-Chun Zhou
- School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing, Jiangsu 211816, China.
| | - Yong-Tang Zheng
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.
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5
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Genome Editing to Abrogate Muscle Atrophy. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1396:157-176. [DOI: 10.1007/978-981-19-5642-3_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
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6
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Discovery of dehydroandrographolide derivatives with C19 hindered ether as potent anti-ZIKV agents with inhibitory activities to MTase of ZIKV NS5. Eur J Med Chem 2022; 243:114710. [DOI: 10.1016/j.ejmech.2022.114710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 08/20/2022] [Accepted: 08/21/2022] [Indexed: 11/22/2022]
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7
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Grosse S, Tahri A, Raboisson P, Houpis Y, Stoops B, Jacoby E, Neefs JM, Van Loock M, Goethals O, Geluykens P, Bonfanti JF, Jonckers THM. From Oxetane to Thietane: Extending the Antiviral Spectrum of 2′-Spirocyclic Uridines by Substituting Oxygen with Sulfur. ACS Med Chem Lett 2022; 13:1879-1884. [DOI: 10.1021/acsmedchemlett.2c00372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 11/21/2022] [Indexed: 11/30/2022] Open
Affiliation(s)
- Sandrine Grosse
- Janssen Research and Development, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Abdellah Tahri
- Janssen Research and Development, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Pierre Raboisson
- Janssen Research and Development, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Yannis Houpis
- Janssen Research and Development, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Bart Stoops
- Janssen Research and Development, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Edgar Jacoby
- Janssen Research and Development, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Jean-Marc Neefs
- Janssen Research and Development, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Marnix Van Loock
- Janssen Global Public Health, R&D, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Olivia Goethals
- Janssen Global Public Health, R&D, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Peggy Geluykens
- Charles River, Discovery, Turnhoutseweg 30, 2340 Beerse, Belgium
| | | | - Tim H. M. Jonckers
- Janssen Research and Development, Turnhoutseweg 30, 2340 Beerse, Belgium
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8
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Jung E, Soto-Acosta R, Geraghty RJ, Chen L. Zika Virus Inhibitors Based on a 1,3-Disubstituted 1 H-Pyrazolo[3,4- d]pyrimidine-amine Scaffold. Molecules 2022; 27:molecules27186109. [PMID: 36144841 PMCID: PMC9502836 DOI: 10.3390/molecules27186109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 09/13/2022] [Accepted: 09/15/2022] [Indexed: 11/22/2022] Open
Abstract
To search for Zika virus (ZIKV) antivirals, we have further explored previously reported 7H-pyrrolo[2,3-d]pyrimidines by examining an alternative substitution pattern of their central scaffold, leading to compound 5 with low micromolar antiviral activity. To circumvent the synthetic difficulties associated with compound 5, we have exploited a 1H-pyrazolo[3,4-d]pyrimidine scaffold and performed structure-activity relationship studies on its peripheral rings A and B. While ring B is less sensitive to structural modifications, an electron-withdrawing group at the para position of ring A is preferred for enhanced antiviral activity. Overall, we have not only discovered an alternative substitution pattern centered on a 1H-pyrazolo[3,4-d]pyrimidine scaffold but also generated anti-ZIKV compounds including 6 and 13, which possess low micromolar antiviral activity and relatively low cytotoxicity. These compounds represent new chemotypes that will be further optimized in our continued efforts to discover anti-ZIKV agents.
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9
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Synthesis and antiviral properties of biomimetic iminosugar-based nucleosides. Eur J Med Chem 2022; 241:114618. [DOI: 10.1016/j.ejmech.2022.114618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 07/13/2022] [Accepted: 07/14/2022] [Indexed: 11/22/2022]
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10
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Schmitz KS, Lange MV, Gommers L, Handrejk K, Porter DP, Alabi CA, Moscona A, Porotto M, de Vries RD, de Swart RL. Repurposing an In Vitro Measles Virus Dissemination Assay for Screening of Antiviral Compounds. Viruses 2022; 14:v14061186. [PMID: 35746658 PMCID: PMC9230603 DOI: 10.3390/v14061186] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 05/25/2022] [Accepted: 05/25/2022] [Indexed: 02/04/2023] Open
Abstract
Measles virus (MV) is a highly contagious respiratory virus responsible for outbreaks associated with significant morbidity and mortality among children and young adults. Although safe and effective measles vaccines are available, the COVID-19 pandemic has resulted in vaccination coverage gaps that may lead to the resurgence of measles when restrictions are lifted. This puts individuals who cannot be vaccinated, such as young infants and immunocompromised individuals, at risk. Therapeutic interventions are complicated by the long incubation time of measles, resulting in a narrow treatment window. At present, the only available WHO-advised option is treatment with intravenous immunoglobulins, although this is not approved as standard of care. Antivirals against measles may contribute to intervention strategies to limit the impact of future outbreaks. Here, we review previously described antivirals and antiviral assays, evaluate the antiviral efficacy of a number of compounds to inhibit MV dissemination in vitro, and discuss potential application in specific target populations. We conclude that broadly reactive antivirals could strengthen existing intervention strategies to limit the impact of measles outbreaks.
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Affiliation(s)
- Katharina S. Schmitz
- Department of Viroscience, Erasmus MC, 3015 GD Rotterdam, The Netherlands; (K.S.S.); (M.V.L.); (L.G.); (K.H.); (R.D.d.V.)
| | - Mona V. Lange
- Department of Viroscience, Erasmus MC, 3015 GD Rotterdam, The Netherlands; (K.S.S.); (M.V.L.); (L.G.); (K.H.); (R.D.d.V.)
| | - Lennert Gommers
- Department of Viroscience, Erasmus MC, 3015 GD Rotterdam, The Netherlands; (K.S.S.); (M.V.L.); (L.G.); (K.H.); (R.D.d.V.)
| | - Kim Handrejk
- Department of Viroscience, Erasmus MC, 3015 GD Rotterdam, The Netherlands; (K.S.S.); (M.V.L.); (L.G.); (K.H.); (R.D.d.V.)
| | | | - Christopher A. Alabi
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14850, USA;
| | - Anne Moscona
- Department of Pediatrics, Columbia University Medical Center, New York, NY 10032, USA; (A.M.); (M.P.)
- Center for Host–Pathogen Interaction, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Matteo Porotto
- Department of Pediatrics, Columbia University Medical Center, New York, NY 10032, USA; (A.M.); (M.P.)
- Center for Host–Pathogen Interaction, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Experimental Medicine, University of Campania “Luigi Vanvitelli”, 81100 Caserta, Italy
| | - Rory D. de Vries
- Department of Viroscience, Erasmus MC, 3015 GD Rotterdam, The Netherlands; (K.S.S.); (M.V.L.); (L.G.); (K.H.); (R.D.d.V.)
| | - Rik L. de Swart
- Department of Viroscience, Erasmus MC, 3015 GD Rotterdam, The Netherlands; (K.S.S.); (M.V.L.); (L.G.); (K.H.); (R.D.d.V.)
- Correspondence:
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11
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Murali M, Gowtham HG, Ansari MA, Alomary MN, Alghamdi S, Almehmadi M, Singh SB, Shilpa N, Aiyaz M, Kalegowda N, Ledesma AE, Amruthesh KN. Repositioning therapeutics for SARS-CoV-2: Virtual screening of plant-based Anti-HIV compounds as possible inhibitors against COVID-19 viral RdRp. Curr Pharm Des 2022; 28:969-980. [DOI: 10.2174/1381612828666220428120939] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 03/11/2022] [Indexed: 11/22/2022]
Abstract
Background:
Coronavirus disease 2019 (COVID-19) has caused a global pandemic with a high mortality rate and infecting people worldwide. The COVID-19 vaccines that are currently in development or already approved are expected to provide at least some protection against the emerging variants of the virus but the mutations may reduce the efficacy of the existing vaccines. Purified phytochemicals from medicinal plants provide a helpful framework for discovering new therapeutic leads as they have long been employed in traditional medicine to treat many disorders.
Objective:
The objectives of the study are to exploit the anti-HIV bioactive compounds against SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) through molecular docking studies and perform the Absorption, Distribution, Metabolism, Excretion and Toxicity (ADMET) properties of potential compounds.
Methods:
Molecular docking was performed to study the interaction of ligands with the target sites of RdRp protein (PDB: 6M71) using AutoDock Vina. The ADMET properties of potential compounds were predicted using the pkCSM platform.
Results:
A total of 151 phytochemicals derived from the medicinal plants with recognized antiviral activity and 18 anti-HIV drugs were virtually screened against COVID-19 viral RdRp to identify putative inhibitors that facilitate the development of potential anti-COVID-19 drug candidates. The computational studies identified 34 compounds and three drugs inhibiting viral RdRp with binding energies ranging from -10.2 to -8.5 kcal/ mol. Among these, five compounds, namely Michellamine B, Quercetin 3-O-(2'',6''-digalloyl)-beta-D-galactopyranoside, Corilagin, Hypericin, and 1,2,3,4,6-Penta-O-galloyl-beta-D-glucose residues bound efficiently with the binding site of RdRp. Besides, Lopinavir, Maraviroc, and Remdesivir drugs also inhibited SARS-CoV-2 polymerase. In addition, the ADMET properties of top potential compounds were also predicted in comparison to the drugs.
Conclusion:
The present study suggested that these potential drug candidates can be further subjected to in vitro and in vivo studies that may help develop effective anti-COVID-19 drugs.
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Affiliation(s)
- Mahadevamurthy Murali
- Applied Plant Pathology Laboratory, Department of Studies in Botany, University of Mysore, Manasagangotri, Mysuru 570 006, Karnataka, India
| | | | - Mohammad Azam Ansari
- Department of Epidemic Disease Research, Institutes for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, 31441, Dammam, Saudi Arabia
| | - Mohammad N. Alomary
- National Centre for Biotechnology, King Abdulaziz City for Science and Technology (KACST), P.O. Box 6086, Riyadh 11442, Saudi Arabia
| | - Saad Alghamdi
- Laboratory Medicine Department, Faculty of Applied Medical Sciences, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Mazen Almehmadi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif 21944, Saudi Arabia
| | - Sudarshana Brijesh Singh
- Department of Studies in Biotechnology, University of Mysore, Manasagangotri, Mysuru 570 006, Karnataka, India
| | - Natarajamurthy Shilpa
- Department of Studies in Microbiology, University of Mysore, Manasagangotri, Mysuru 570 006, Karnataka, India
| | - Mohammed Aiyaz
- Department of Studies in Biotechnology, University of Mysore, Manasagangotri, Mysuru 570 006, Karnataka, India
| | - Nataraj Kalegowda
- Applied Plant Pathology Laboratory, Department of Studies in Botany, University of Mysore, Manasagangotri, Mysuru 570 006, Karnataka, India
| | - Ana E. Ledesma
- Centro De Investigaciónen Biofísica Aplicada y Alimentos, Universidad Nacional de Santiago del Estero (CIBAAL-UNSE-CONICET), FCEyT, RN 9, km 1125, CP 4206 Santiago del Estero, Argentina
| | - Kestur Nagaraj Amruthesh
- Applied Plant Pathology Laboratory, Department of Studies in Botany, University of Mysore, Manasagangotri, Mysuru 570 006, Karnataka, India
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12
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Abstract
The first appearance of SARS-CoV-2 is dated back to 2019. This new member of the coronavirus family has caused more than 5 million deaths worldwide up until the end of January 2022. At the moment, and after intensive vaccination programmes throughout the world, the pandemic is still active, whilst new mutations constantly appear. Researchers are working intensively to discover antiviral drugs to combat the severe cases in intensive care units, giving the overloaded hospital units a breather. Alongside various research projects focusing on developing small pharmaceutical molecules, a significant proportion of the research community has shifted towards paying attention to metal drugs. In this small review, we make brief reference to the use of metal drugs in therapeutics and provide some examples of metal drugs that are of extreme interest in the current pandemic. At the same time, we will also examine some of their promising mechanisms of action and possible effectiveness against COVID-19.
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13
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Pathania S, Rawal RK, Singh PK. RdRp (RNA-dependent RNA polymerase): A key target providing anti-virals for the management of various viral diseases. J Mol Struct 2022; 1250:131756. [PMID: 34690363 PMCID: PMC8520695 DOI: 10.1016/j.molstruc.2021.131756] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 10/13/2021] [Accepted: 10/15/2021] [Indexed: 01/04/2023]
Abstract
With the arrival of the Covid-19 pandemic, anti-viral agents have regained center stage in the arena of medicine. Out of the various drug targets involved in managing RNA-viral infections, the one that dominates almost all RNA viruses is RdRp (RNA-dependent RNA polymerase). RdRp are proteins that are involved in the replication of RNA-based viruses. Inhibition of RdRps has been an integral approach for managing various viral infections such as dengue, influenza, HCV (Hepatitis), BVDV, etc. Inhibition of the coronavirus RdRp is currently rigorously explored for the treatment of Covid-19 related complications. So, keeping in view the importance and current relevance of this drug target, we have discussed the importance of RdRp in developing anti-viral agents against various viral diseases. Different reported inhibitors have also been discussed, and emphasis has been laid on highlighting the inhibitor's pharmacophoric features and SAR profile.
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Affiliation(s)
- Shelly Pathania
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, Moga-142001, Punjab, India
| | - Ravindra K. Rawal
- Department of Chemistry, Maharishi Markandeshwar (Deemed to be University), Mullana-133207, Haryana, India,CSIR-North East Institute of Science and Technology, Jorhat-785006, Assam, India,Corresponding authors
| | - Pankaj Kumar Singh
- Faculty of Medicine, Integrative Physiology and Pharmacology, Institute of Biomedicine, University of Turku, Turku, FI-20014, Finland,Corresponding authors
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14
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Zhang W, Yang Z, Zhou F, Wei Y, Ma X. Network Pharmacology and Bioinformatics Analysis Identifies Potential Therapeutic Targets of Paxlovid Against LUAD/COVID-19. Front Endocrinol (Lausanne) 2022; 13:935906. [PMID: 36157452 PMCID: PMC9493477 DOI: 10.3389/fendo.2022.935906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 08/09/2022] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has caused a pandemic in many countries around the world. The virus is highly contagious and has a high fatality rate. Lung adenocarcinoma (LUAD) patients may have higher susceptibility and mortality to COVID-19. While Paxlovid is the first oral drug approved by the U.S. Food and Drug Administration (FDA) for COVID-19, its specific drug mechanism for lung cancer patients infected with COVID-19 remains to be further studied. METHODS COVID-19 related genes were obtained from NCBI, GeneCards, and KEGG, and then the transcriptome data for LUAD was downloaded from TCGA. The drug targets of Paxlovid were revealed through BATMAN-TCM, DrugBank, SwissTargetPrediction, and TargetNet. The genes related to susceptibility to COVID-19 in LUAD patients were obtained through differential analysis. The interaction of LUAD/COVID-19 related genes was evaluated and displayed by STRING, and a COX risk regression model was established to screen and evaluate the correlation between genes and clinical characteristics. The Venn diagram was drawn to select the candidate targets of Paxlovid against LUAD/COVID-19, and the functional analysis of the target genes was performed using KEGG and GO enrichment analysis. Finally, Cytoscape was used to screen and visualize the Hub Gene, and Autodock was used for molecular docking between the drug and the target. RESULT Bioinformatics analysis was performed by combining COVID-19-related genes with the gene expression and clinical data of LUAD, including analysis of prognosis-related genes, survival rate, and hub genes screened out by the prognosis model. The key targets of Paxlovid against LUAD/COVID-19 were obtained through network pharmacology, the most important targets include IL6, IL12B, LBP. Furthermore, pathway analysis showed that Paxlovid modulates the IL-17 signaling pathway, the cytokine-cytokine receptor interaction, during LUAD/COVID-19 treatment. CONCLUSIONS Based on bioinformatics and network pharmacology, the prognostic signature of LUAD/COVID-19 patients was screened. And identified the potential therapeutic targets and molecular pathways of Paxlovid Paxlovid in the treatment of LUAD/COVID. As promising features, prognostic signatures and therapeutic targets shed light on improving the personalized management of patients with LUAD.
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Affiliation(s)
- Wentao Zhang
- Tumor Research and Therapy Center, Shandong Provincial Hospital Affiliated to Shandong First Medical Unversity, Jinan, China
- Shandong First Medical Unversity, Jinan, China
| | - Zhe Yang
- Tumor Research and Therapy Center, Shandong Provincial Hospital Affiliated to Shandong First Medical Unversity, Jinan, China
- *Correspondence: Zhe Yang,
| | - Fengge Zhou
- Tumor Research and Therapy Center, Shandong Provincial Hospital Affiliated to Shandong First Medical Unversity, Jinan, China
| | - Yanjun Wei
- Tumor Research and Therapy Center, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Xiaoqing Ma
- Shandong First Medical Unversity, Jinan, China
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15
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Yan L, Cao R, Zhang H, Li Y, Li W, Li X, Fan S, Li S, Zhong W. Design, synthesis and evaluation of 2'-acetylene-7-deaza-adenosine phosphoamidate derivatives as anti-EV71 and anti-EV-D68 agents. Eur J Med Chem 2021; 226:113852. [PMID: 34560428 DOI: 10.1016/j.ejmech.2021.113852] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 09/10/2021] [Accepted: 09/11/2021] [Indexed: 11/29/2022]
Abstract
A series of phosphoamidate derivatives of nucleoside 2'-acetylene-7-deaza-adenosine (NITD008) were synthesized and evaluated for their in vitro antiviral activities against the enteroviruses EV71 and EV-D68. The phosphoamidate (15f) containing a hexyl ester of l-alanine exhibited the most promising activity against EV71 (IC50 = 0.13 ± 0.08 μM) and was 4-times more potent than NITD008. Meanwhile, the derivative containing a cyclohexyl ester of l-alanine (15l) exhibited the most potent activity with high selectivity index against both EV71 (IC50 = 0.19 ± 0.27 μM, SI = 117.00) and EV-D68 (IC50 = 0.17 ± 0.16 μM, SI = 130.76), which were both higher than that of NITD008. The results indicated that the phosphoamidate 15l was the most promising candidate for further development as antiviral agents for the treatment of both EV71 and EV-D68 infection.
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Affiliation(s)
- Linjie Yan
- National Engineering Research Center for the Emergency Drug, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, PR China
| | - Ruiyuan Cao
- National Engineering Research Center for the Emergency Drug, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, PR China
| | - Hongjie Zhang
- National Engineering Research Center for the Emergency Drug, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, PR China
| | - Yuexiang Li
- National Engineering Research Center for the Emergency Drug, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, PR China
| | - Wei Li
- National Engineering Research Center for the Emergency Drug, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, PR China
| | - Xiaoyuan Li
- National Engineering Research Center for the Emergency Drug, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, PR China
| | - Shiyong Fan
- National Engineering Research Center for the Emergency Drug, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, PR China
| | - Song Li
- National Engineering Research Center for the Emergency Drug, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, PR China.
| | - Wu Zhong
- National Engineering Research Center for the Emergency Drug, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, PR China.
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16
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Insights on Dengue and Zika NS5 RNA-dependent RNA polymerase (RdRp) inhibitors. Eur J Med Chem 2021; 224:113698. [PMID: 34274831 DOI: 10.1016/j.ejmech.2021.113698] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 07/09/2021] [Accepted: 07/10/2021] [Indexed: 11/20/2022]
Abstract
Over recent years, many outbreaks caused by (re)emerging RNA viruses have been reported worldwide, including life-threatening Flaviviruses, such as Dengue (DENV) and Zika (ZIKV). Currently, there is only one licensed vaccine against Dengue, Dengvaxia®. However, its administration is not recommended for children under nine years. Still, there are no specific inhibitors available to treat these infectious diseases. Among the flaviviral proteins, NS5 RNA-dependent RNA polymerase (RdRp) is a metalloenzyme essential for viral replication, suggesting that it is a promising macromolecular target since it has no human homolog. Nowadays, several NS5 RdRp inhibitors have been reported, while none inhibitors are currently in clinical development. In this context, this review constitutes a comprehensive work focused on RdRp inhibitors from natural, synthetic, and even repurposing sources. Furthermore, their main aspects associated with the structure-activity relationship (SAR), proposed mechanisms of action, computational studies, and other topics will be discussed in detail.
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17
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Discovery and optimization of 2-((1H-indol-3-yl)thio)-N-benzyl-acetamides as novel SARS-CoV-2 RdRp inhibitors. Eur J Med Chem 2021; 223:113622. [PMID: 34147744 PMCID: PMC8191315 DOI: 10.1016/j.ejmech.2021.113622] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 05/20/2021] [Accepted: 06/04/2021] [Indexed: 12/22/2022]
Abstract
The emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the global pandemic coronavirus disease (COVID-19), but no specific antiviral drug has been proven effective for controlling this pandemic to date. In this study, several 2-((indol-3-yl)thio)-N-benzyl-acetamides were identified as SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) inhibitors. After a two-round optimization, a new series of 2-((indol-3-yl)thio)-N-benzyl-acetamides was designed, synthesized, and evaluated for SARS-CoV-2 RdRp inhibitory effect. Compounds 6b2, 6b5, 6c9, 6d2, and 6d5 were identified as potent inhibitors with IC50 values of 3.35 ± 0.21 μM, 4.55 ± 0.2 μM, 1.65 ± 0.05 μM, 3.76 ± 0.79 μM, and 1.11 ± 0.05 μM, respectively; the IC50 of remdesivir (control) was measured as 1.19 ± 0.36 μM. All of the compounds inhibited RNA synthesis by SARS-CoV-2 RdRp. The most potent compound 6d5, which showed a stronger inhibitory activity against the human coronavirus HCoV-OC43 than remdesivir, is a promising candidate for further investigation.
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