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Du X, Yang X, Zhao J, Zhang J, Yu J, Ma L, Zhang W, Cen S, Ren X, He X. Design of novel broad-spectrum antiviral nucleoside analogues using natural bases ring-opening strategy. Drug Dev Res 2024; 85:e22237. [PMID: 39032059 DOI: 10.1002/ddr.22237] [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: 12/18/2023] [Revised: 06/19/2024] [Accepted: 07/07/2024] [Indexed: 07/22/2024]
Abstract
The global prevalence of RNA virus infections has presented significant challenges to public health in recent years, necessitating the expansion of its alternative therapeutic library. Due to its evolutional conservation, RNA-dependent RNA polymerase (RdRp) has emerged as a potential target for broad-spectrum antiviral nucleoside analogues. However, after over half a century of structural modification, exploring unclaimed chemical space using frequently-used structural substitution methods to design new nucleoside analogues is challenging. In this study, we explore the use of the "ring-opening" strategy to design new base mimics, thereby using these base mimics to design new nucleoside analogues with broad-spectrum antiviral activities. A total of 29 compounds were synthesized. Their activity against viral RdRp was initially screened using an influenza A virus RdRp high-throughput screening model. Then, the antiviral activity of 38a was verified against influenza virus strain A/PR/8/34 (H1N1), demonstrating a 50% inhibitory concentration (IC50) value of 9.95 μM, which was superior to that of ribavirin (the positive control, IC50 = 11.43 μM). Moreover, 38a also has inhibitory activity against coronavirus 229E with an IC50 of 30.82 μM. In addition, compounds 42 and 46f exhibit an 82% inhibition rate against vesicular stomatitis virus at a concentration of 20 μM and hardly induce cytotoxicity in host cells. This work demonstrates the feasibility of designing nucleoside analogues with "ring-opening" bases and suggests the "ring-opening" nucleosides may have greater polarity, and designing prodrugs is an important aspect of optimizing their antiviral activity. Future research should focus on enhancing the conformational restriction of open-loop bases to mimic Watson-Crick base pairing better and improve antiviral activity.
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Affiliation(s)
- Xingyi Du
- Key Laboratory of Structure-Based Drug Design and Discovery, Shenyang Pharmaceutical University, Shenyang, China
- Nanhu Laboratory, National Center of Biomedical Analysis, Beijing, China
| | - Xingxing Yang
- Key Laboratory of Structure-Based Drug Design and Discovery, Shenyang Pharmaceutical University, Shenyang, China
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, China
| | - Jianyuan Zhao
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science, Beijing, China
| | - Jinyan Zhang
- Key Laboratory of Structure-Based Drug Design and Discovery, Shenyang Pharmaceutical University, Shenyang, China
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, China
| | - Jiahui Yu
- Key Laboratory of Structure-Based Drug Design and Discovery, Shenyang Pharmaceutical University, Shenyang, China
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, China
| | - Ling Ma
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science, Beijing, China
| | - Weina Zhang
- Nanhu Laboratory, National Center of Biomedical Analysis, Beijing, China
- State Key Laboratory of Proteomics, Institute of Basic Medical Sciences, National Center of Biomedical Analysis, Beijing, China
| | - Shan Cen
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science, Beijing, China
| | - Xuhong Ren
- Key Laboratory of Structure-Based Drug Design and Discovery, Shenyang Pharmaceutical University, Shenyang, China
| | - Xinhua He
- Nanhu Laboratory, National Center of Biomedical Analysis, Beijing, China
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, China
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Ciardullo G, Parise A, Prejanò M, Marino T. Viral RNA Replication Suppression of SARS-CoV-2: Atomistic Insights into Inhibition Mechanisms of RdRp Machinery by ddhCTP. J Chem Inf Model 2024; 64:1593-1604. [PMID: 38412057 DOI: 10.1021/acs.jcim.3c01919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/29/2024]
Abstract
The nonstructural protein 12, known as RNA-dependent RNA polymerase (RdRp), is essential for both replication and repair of the viral genome. The RdRp of SARS-CoV-2 has been used as a promising candidate for drug development since the inception of the COVID-19 spread. In this work, we performed an in silico investigation on the insertion of the naturally modified pyrimidine nucleobase ddhCTP into the SARS-CoV-2 RdRp active site, in a comparative analysis with the natural one (CTP). The modification in ddhCTP involves the removal of the 3'-hydroxyl group that prevents the addition of subsequent nucleotides into the nascent strand, acting as an RNA chain terminator inhibitor. Quantum mechanical investigations helped to shed light on the mechanistic source of RdRp activity on the selected nucleobases, and comprehensive all-atom simulations provided insights about the structural rearrangements occurring in the active-site region when inorganic pyrophosphate (PPi) is formed. Subsequently, the intricate pathways for the release of PPi, the catalytic product of RdRp, were investigated using Umbrella Sampling simulations. The results are in line with the available experimental data and contribute to a more comprehensive point of view on such an important viral enzyme.
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Affiliation(s)
- Giada Ciardullo
- Dipartimento di Chimica E Tecnologie Chimiche, Laboratorio PROMOCS Cubo 14C, Università della Calabria, RENDE (CS) I-87036, Italy
| | - Angela Parise
- Consiglio Nazionale Delle Ricerche (CNR)-IOM C/O International School for Advanced Studies (SISSA/ISAS), Via Bonomea 265, Trieste 34136, Italy
| | - Mario Prejanò
- Dipartimento di Chimica E Tecnologie Chimiche, Laboratorio PROMOCS Cubo 14C, Università della Calabria, RENDE (CS) I-87036, Italy
| | - Tiziana Marino
- Dipartimento di Chimica E Tecnologie Chimiche, Laboratorio PROMOCS Cubo 14C, Università della Calabria, RENDE (CS) I-87036, Italy
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Ma Z, Xu J, Wang C, Liu Z, Zhu G. Molecular dynamics simulation study on the binding mechanism between carbon nanotubes and RNA-dependent RNA polymerase. J Biomol Struct Dyn 2024:1-10. [PMID: 38263694 DOI: 10.1080/07391102.2024.2308781] [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: 08/30/2023] [Accepted: 01/14/2024] [Indexed: 01/25/2024]
Abstract
Carbon nanotubes (CNTs) have potential prospects in disease treatment, so it is of great significance to study CNTs as the possible inhibitors of RNA-dependent RNA polymerase (RdRp). Through the way of using the RdRp of SARS-COV-2 as a model, five armchair single-walled carbon nanotubes (SWCNTs) (namely Dn, which stands for CNTs (n, m = n), n = 3-7) and RdRp have been selected to study the interactions by means of molecular docking and molecular dynamics simulation. After five SWCNT-RdRp complex systems have been subjected to the molecular dynamics simulations of 100 ns, and Molecular Mechanics Poisson - Boltzmann Surface Area (MMPBSA) has been used to calculate the binding free energy, it is found that the binding free energy of the D6 system (-189.541 kJ/mol) is significantly higher than that of the other four systems, and most of the amino acids with strong positive effects on binding are usually basic amino acids. What's more, in the further investigation of the specific interaction mechanism between CNT (6,6) and RdRp, it is revealed that the three amino acid residues LYS545, ARG553 and ARG555 located in the nucleoside triphosphate (NTP) entry channel all have strong effects. In addition, it is also observed that when ARG555 has been inserted into SWCNT, a stable structure will be formed, which will break the original NTP entry channel structure and inhibit virus replication. Therefore, it can be concluded that certain specific types of SWCNT, such as CNT (6,6), could be potential small molecule inhibitors in the treatment of coronavirus.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Zhaopeng Ma
- Anhui Province Key Laboratory of Optoelectronic Materials Science and Technology, School of Physics and Electronic Information, Anhui Normal University, Wuhu, China
| | - Jianqiang Xu
- Anhui Province Key Laboratory of Optoelectronic Materials Science and Technology, School of Physics and Electronic Information, Anhui Normal University, Wuhu, China
| | - Chenchen Wang
- Anhui Province Key Laboratory of Optoelectronic Materials Science and Technology, School of Physics and Electronic Information, Anhui Normal University, Wuhu, China
| | - Zhicong Liu
- Anhui Province Key Laboratory of Optoelectronic Materials Science and Technology, School of Physics and Electronic Information, Anhui Normal University, Wuhu, China
| | - Guanglai Zhu
- Anhui Province Key Laboratory of Optoelectronic Materials Science and Technology, School of Physics and Electronic Information, Anhui Normal University, Wuhu, China
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Matsuzaka Y, Yashiro R. Extracellular Vesicle-Based SARS-CoV-2 Vaccine. Vaccines (Basel) 2023; 11:vaccines11030539. [PMID: 36992123 DOI: 10.3390/vaccines11030539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 02/06/2023] [Accepted: 02/22/2023] [Indexed: 03/02/2023] Open
Abstract
Messenger ribonucleic acid (RNA) vaccines are mainly used as SARS-CoV-2 vaccines. Despite several issues concerning storage, stability, effective period, and side effects, viral vector vaccines are widely used for the prevention and treatment of various diseases. Recently, viral vector-encapsulated extracellular vesicles (EVs) have been suggested as useful tools, owing to their safety and ability to escape from neutral antibodies. Herein, we summarize the possible cellular mechanisms underlying EV-based SARS-CoV-2 vaccines.
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Affiliation(s)
- Yasunari Matsuzaka
- Division of Molecular and Medical Genetics, The Institute of Medical Science, Center for Gene and Cell Therapy, University of Tokyo, Minato-ku, Tokyo 108-8639, Japan
- Administrative Section of Radiation Protection, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Tokyo 187-8551, Japan
| | - Ryu Yashiro
- Administrative Section of Radiation Protection, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Tokyo 187-8551, Japan
- Department of Infectious Diseases, Kyorin University School of Medicine, 6-20-2 Shinkawa, Mitaka-shi, Tokyo 181-8611, Japan
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