1
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Romero ME, McElhenney SJ, Yu J. Trapping a non-cognate nucleotide upon initial binding for replication fidelity control in SARS-CoV-2 RNA dependent RNA polymerase. Phys Chem Chem Phys 2024; 26:1792-1808. [PMID: 38168789 DOI: 10.1039/d3cp04410f] [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: 01/05/2024]
Abstract
The RNA dependent RNA polymerase (RdRp) in SARS-CoV-2 is a highly conserved enzyme responsible for viral genome replication/transcription. To understand how the viral RdRp achieves fidelity control during such processes, here we computationally investigate the natural non-cognate vs. cognate nucleotide addition and selectivity during viral RdRp elongation. We focus on the nucleotide substrate initial binding (RdRp active site open) to the prechemical insertion (active site closed) of the RdRp. The current studies were first carried out using microsecond ensemble equilibrium all-atom molecular dynamics (MD) simulations. Due to the slow conformational changes (from open to closed) during nucleotide insertion and selection, enhanced or umbrella sampling methods have been further employed to calculate the free energy profiles of the nucleotide insertion. Our studies find notable stability of noncognate dATP and GTP upon initial binding in the active-site open state. The results indicate that while natural cognate ATP and Remdesivir drug analogue (RDV-TP) are biased toward stabilization in the closed state to facilitate insertion, the natural non-cognate dATP and GTP can be well trapped in off-path initial binding configurations and prevented from insertion so that to be further rejected. The current work thus presents the intrinsic nucleotide selectivity of SARS-CoV-2 RdRp for natural substrate fidelity control, which should be considered in antiviral drug design.
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Affiliation(s)
- Moises E Romero
- Department of Chemistry, University of California, Irvine, CA 92697, USA
| | | | - Jin Yu
- Department of Physics and Astronomy, Department of Chemistry, NSF-Simmons Center for Multi-scale Cell Fate Research, University of California, Irvine, CA 92697, USA.
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2
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Lewis J, Gallichotte EN, Randall J, Glass A, Foy BD, Ebel GD, Kading RC. Intrinsic factors driving mosquito vector competence and viral evolution: a review. Front Cell Infect Microbiol 2023; 13:1330600. [PMID: 38188633 PMCID: PMC10771300 DOI: 10.3389/fcimb.2023.1330600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 12/08/2023] [Indexed: 01/09/2024] Open
Abstract
Mosquitoes are responsible for the transmission of numerous viruses of global health significance. The term "vector competence" describes the intrinsic ability of an arthropod vector to transmit an infectious agent. Prior to transmission, the mosquito itself presents a complex and hostile environment through which a virus must transit to ensure propagation and transmission to the next host. Viruses imbibed in an infectious blood meal must pass in and out of the mosquito midgut, traffic through the body cavity or hemocoel, invade the salivary glands, and be expelled with the saliva when the vector takes a subsequent blood meal. Viruses encounter physical, cellular, microbial, and immunological barriers, which are influenced by the genetic background of the mosquito vector as well as environmental conditions. Collectively, these factors place significant selective pressure on the virus that impact its evolution and transmission. Here, we provide an overview of the current state of the field in understanding the mosquito-specific factors that underpin vector competence and how each of these mechanisms may influence virus evolution.
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Affiliation(s)
- Juliette Lewis
- Center for Vector-borne Infectious Diseases, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, United States
| | - Emily N. Gallichotte
- Center for Vector-borne Infectious Diseases, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, United States
| | - Jenna Randall
- Center for Vector-borne Infectious Diseases, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, United States
| | - Arielle Glass
- Department of Cellular and Molecular Biology, Colorado State University, Fort Collins, CO, United States
| | - Brian D. Foy
- Center for Vector-borne Infectious Diseases, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, United States
| | - Gregory D. Ebel
- Center for Vector-borne Infectious Diseases, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, United States
| | - Rebekah C. Kading
- Center for Vector-borne Infectious Diseases, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, United States
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3
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Nicoletto G, Richter SN, Frasson I. Presence, Location and Conservation of Putative G-Quadruplex Forming Sequences in Arboviruses Infecting Humans. Int J Mol Sci 2023; 24:ijms24119523. [PMID: 37298474 DOI: 10.3390/ijms24119523] [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: 03/21/2023] [Revised: 05/12/2023] [Accepted: 05/12/2023] [Indexed: 06/12/2023] Open
Abstract
Guanine quadruplexes (G4s) are non-canonical nucleic acid structures formed by guanine (G)-rich tracts that assemble into a core of stacked planar tetrads. G4s are found in the human genome and in the genomes of human pathogens, where they are involved in the regulation of gene expression and genome replication. G4s have been proposed as novel pharmacological targets in humans and their exploitation for antiviral therapy is an emerging research topic. Here, we report on the presence, conservation and localization of putative G4-forming sequences (PQSs) in human arboviruses. The prediction of PQSs was performed on more than twelve thousand viral genomes, belonging to forty different arboviruses that infect humans, and revealed that the abundance of PQSs in arboviruses is not related to the genomic GC content, but depends on the type of nucleic acid that constitutes the viral genome. Positive-strand ssRNA arboviruses, especially Flaviviruses, are significantly enriched in highly conserved PQSs, located in coding sequences (CDSs) or untranslated regions (UTRs). In contrast, negative-strand ssRNA and dsRNA arboviruses contain few conserved PQSs. Our analyses also revealed the presence of bulged PQSs, accounting for 17-26% of the total predicted PQSs. The data presented highlight the presence of highly conserved PQS in human arboviruses and present non-canonical nucleic acid-structures as promising therapeutic targets in arbovirus infections.
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Affiliation(s)
- Giulia Nicoletto
- Department of Molecular Medicine, University of Padua, Via A. Gabelli 63, 35121 Padua, Italy
| | - Sara N Richter
- Department of Molecular Medicine, University of Padua, Via A. Gabelli 63, 35121 Padua, Italy
| | - Ilaria Frasson
- Department of Molecular Medicine, University of Padua, Via A. Gabelli 63, 35121 Padua, Italy
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4
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Leiva S, Bugnon Valdano M, Gardiol D. Unravelling the epidemiological diversity of Zika virus by analyzing key protein variations. Arch Virol 2023; 168:115. [PMID: 36943525 DOI: 10.1007/s00705-023-05726-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 01/19/2023] [Indexed: 03/23/2023]
Abstract
The consequences of Zika virus (ZIKV) infections were limited to sporadic mild diseases until almost a decade ago, when epidemic outbreaks took place, with quick spread into the Americas. Simultaneously, novel severe neurological manifestations of ZIKV infections were identified, including congenital microcephaly. However, why the epidemic strains behave differently is not yet completely understood, and many questions remain about the actual significance of genetic variations in the epidemiology and biology of ZIKV. In this study, we analysed a large number of viral sequences to identify genes with different levels of variability and patterns of genomic variations that could be associated with ZIKV diversity. We compared numerous epidemic strains with pre-epidemic strains, using the BWA-mem algorithm, and we also examined specific variations among the epidemic ZIKV strains derived from microcephaly cases. We identified several viral genes with dissimilar mutation rates among the ZIKV strain groups and novel protein variation profiles that might be associated with epidemiological particularities. Finally, we assessed the impact of the detected changes on the structure and stability of the NS1, NS5, and E proteins using the I-TASSER, trRosetta, and RaptorX modelling algorithms, and we found some interesting variations that might help to explain the heterogeneous features of the diverse ZIKA strains. This work contributes to the identification of genetic differences in the ZIKV genome that might have a phenotypic impact, providing a basis for future experimental analysis to elucidate the genetic causes of the recent ZIKV emergency.
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Affiliation(s)
- Santiago Leiva
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Instituto de Biología Molecular y Celular de Rosario-CONICET, Universidad Nacional de Rosario, Suipacha 531, 2000, Rosario, Argentina
| | - Marina Bugnon Valdano
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Instituto de Biología Molecular y Celular de Rosario-CONICET, Universidad Nacional de Rosario, Suipacha 531, 2000, Rosario, Argentina.
| | - Daniela Gardiol
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Instituto de Biología Molecular y Celular de Rosario-CONICET, Universidad Nacional de Rosario, Suipacha 531, 2000, Rosario, Argentina.
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5
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Shannon A, Canard B. Kill or corrupt: Mechanisms of action and drug-resistance of nucleotide analogues against SARS-CoV-2. Antiviral Res 2023; 210:105501. [PMID: 36567022 PMCID: PMC9773703 DOI: 10.1016/j.antiviral.2022.105501] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 12/14/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022]
Abstract
Nucleoside/tide analogues (NAs) have long been used in the fight against viral diseases, and now present a promising option for the treatment of COVID-19. Once activated to the 5'-triphosphate state, NAs act by targeting the viral RNA-dependent RNA-polymerase for incorporation into the viral RNA genome. Incorporated analogues can either 'kill' (terminate) synthesis, or 'corrupt' (genetically or chemically) the RNA. Against coronaviruses, the use of NAs has been further complicated by the presence of a virally encoded exonuclease domain (nsp14) with proofreading and repair capacities. Here, we describe the mechanism of action of four promising anti-COVID-19 NAs; remdesivir, molnupiravir, favipiravir and bemnifosbuvir. Their distinct mechanisms of action best exemplify the concept of 'killers' and 'corruptors'. We review available data regarding their ability to be incorporated and excised, and discuss the specific structural features that dictate their overall potency, toxicity, and mutagenic potential. This should guide the synthesis of novel analogues, lend insight into the potential for resistance mutations, and provide a rational basis for upcoming combinations therapies.
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Affiliation(s)
- Ashleigh Shannon
- AFMB, CNRS, Aix-Marseille University, UMR 7257, Case 925, 163 Avenue de Luminy, 13288, Marseille, Cedex 09, France
| | - Bruno Canard
- AFMB, CNRS, Aix-Marseille University, UMR 7257, Case 925, 163 Avenue de Luminy, 13288, Marseille, Cedex 09, France.
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6
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Naidu SAG, Mustafa G, Clemens RA, Naidu AS. Plant-Derived Natural Non-Nucleoside Analog Inhibitors (NNAIs) against RNA-Dependent RNA Polymerase Complex (nsp7/nsp8/nsp12) of SARS-CoV-2. J Diet Suppl 2023; 20:254-283. [PMID: 34850656 DOI: 10.1080/19390211.2021.2006387] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The emergence of fast-spreading SARS-CoV-2 mutants has sparked a new phase of COVID-19 pandemic. There is a dire necessity for antivirals targeting highly conserved genomic domains on SARS-CoV-2 that are less prone to mutation. The nsp12, also known as the RNA-dependent RNA-polymerase (RdRp), the core component of 'SARS-CoV-2 replication-transcription complex', is a potential well-conserved druggable antiviral target. Several FDA-approved RdRp 'nucleotide analog inhibitors (NAIs)' such as remdesivir, have been repurposed to treat COVID-19 infections. The NAIs target RdRp protein translation and competitively block the nucleotide insertion into the RNA chain, resulting in the inhibition of viral replication. However, the replication proofreading function of nsp14-ExoN could provide resistance to SARS-CoV-2 against many NAIs. Conversely, the 'non-nucleoside analog inhibitors (NNAIs)' bind to allosteric sites on viral polymerase surface, change the redox state; thereby, exert antiviral activity by altering interactions between the enzyme substrate and active core catalytic site of the RdRp. NNAIs neither require metabolic activation (unlike NAIs) nor compete with intracellular pool of nucleotide triphosphates (NTPs) for anti-RdRp activity. The NNAIs from phytonutrient origin are potential antiviral candidates compared to their synthetic counterparts. Several in-silico studies reported the antiviral spectrum of natural phytonutrient-NNAIs such as Suramin, Silibinin (flavonolignan), Theaflavin (tea polyphenol), Baicalein (5,6,7-trihydroxyflavone), Corilagin (gallotannin), Hesperidin (citrus bioflavonoid), Lycorine (pyrrolidine alkaloid), with superior redox characteristics (free binding energy, hydrogen-bonds, etc.) than antiviral drugs (i.e. remdesivir, favipiravir). These phytonutrient-NNAIs also exert anti-inflammatory, antioxidant, immunomodulatory and cardioprotective functions, with multifunctional therapeutic benefits in the clinical management of COVID-19.
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Affiliation(s)
| | - Ghulam Mustafa
- Department of Biochemistry, Government College University, Faisalabad, Pakistan
| | - Roger A Clemens
- Department of International Regulatory Science, University of Southern California School of Pharmacy, Los Angeles, CA, USA
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7
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Dey SK, Saini M, Dhembla C, Bhatt S, Rajesh AS, Anand V, Das HK, Kundu S. Suramin, penciclovir, and anidulafungin exhibit potential in the treatment of COVID-19 via binding to nsp12 of SARS-CoV-2. J Biomol Struct Dyn 2022; 40:14067-14083. [PMID: 34784490 DOI: 10.1080/07391102.2021.2000498] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
COVID-19, for which no confirmed therapeutic agents are available, has claimed over 48,14,000 lives globally. A feasible and quicker method to resolve this problem may be 'drug repositioning'. We investigated selected FDA and WHO-EML approved drugs based on their previously promising potential as antivirals, antibacterials or antifungals. These drugs were docked onto the nsp12 protein, which reigns the RNA-dependent RNA polymerase activity of SARS-CoV-2, a key therapeutic target for coronaviruses. Docked complexes were reevaluated using MM-GBSA analysis and the top three inhibitor-protein complexes were subjected to 100 ns long molecular dynamics simulation followed by another round of MM-GBSA analysis. The RMSF plots, binding energies and the mode of physicochemical interaction of the active site of the protein with the drugs were evaluated. Suramin, Penciclovir, and Anidulafungin were found to bind to nsp12 with similar binding energies as that of Remdesivir, which has been used as a therapy for COVID-19. In addition, recent experimental evidences indicate that these drugs exhibit antiviral efficacy against SARS-CoV-2. Such evidence, along with the significant and varied physical interactions of these drugs with the key viral enzyme outlined in this investigation, indicates that they might have a prospective therapeutic potential in the treatment of COVID-19 as monotherapy or combination therapy with Remdesivir.
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Affiliation(s)
- Sanjay Kumar Dey
- Center for Advanced Biotechnology and Medicine, Rutgers University, New Brunswick, New Jersey, USA.,Department of Biochemistry, University of Delhi South Campus, New Delhi, India.,Dr. B.R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi, India
| | - Manisha Saini
- Department of Biochemistry, University of Delhi South Campus, New Delhi, India
| | - Chetna Dhembla
- Department of Biochemistry, University of Delhi South Campus, New Delhi, India
| | - Shruti Bhatt
- Department of Biochemistry, University of Delhi South Campus, New Delhi, India
| | - A Sai Rajesh
- Department of Biosciences and Biotechnology, Fakir Mohan University, Odisha, India
| | - Varnita Anand
- Department of Biochemistry, University of Delhi South Campus, New Delhi, India
| | | | - Suman Kundu
- Department of Biochemistry, University of Delhi South Campus, New Delhi, India
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8
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Qian X, Wu B, Tang H, Luo Z, Xu Z, Ouyang S, Li X, Xie J, Yi Z, Leng Q, Liu Y, Qi Z, Zhao P. Rifapentine is an entry and replication inhibitor against yellow fever virus both in vitro and in vivo. Emerg Microbes Infect 2022; 11:873-884. [PMID: 35249454 PMCID: PMC8942558 DOI: 10.1080/22221751.2022.2049983] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Yellow fever virus (YFV) infection is a major public concern that threatens a large population in South America and Africa. No specific anti-YFV drugs are available till now. Here, we report that rifapentine is a potent YFV inhibitor in various cell lines by high-throughput drugs screening, acting at both cell entry and replication steps. Kinetic test and binding assay suggest that rifapentine interferes the viral attachment to the target cells. The application of YFV replicon and surface plasmon resonance assay indicates that rifapentine suppresses viral replication by binding to the RNA-dependent RNA polymerase (RdRp) domain of viral nonstructural protein NS5. Further molecular docking suggests that it might interact with the active centre of RdRp. Rifapentine significantly improves the survival rate, alleviates clinical signs, and reduces virus load and injury in targeted organs both in YFV-infected type I interferon receptor knockout A129−/− and wild-type C57 mice. The antiviral effect in vivo is robust during both prophylactic intervention and therapeutic treatment, and the activity is superior to sofosbuvir, a previously reported YFV inhibitor in mice. Our data show that rifapentine may serve as an effective anti-YFV agent, providing promising prospects in the development of YFV pharmacotherapy.
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Affiliation(s)
- Xijing Qian
- Department of Microbiology, Faculty of Naval Medicine, Naval Medical University, Shanghai, People's Republic of China
| | - Bingan Wu
- Department of Microbiology, Faculty of Naval Medicine, Naval Medical University, Shanghai, People's Republic of China
| | - Hailin Tang
- Department of Microbiology, Faculty of Naval Medicine, Naval Medical University, Shanghai, People's Republic of China
| | - Zhenghan Luo
- Department of Microbiology, Faculty of Naval Medicine, Naval Medical University, Shanghai, People's Republic of China
| | - Zhenghao Xu
- Department of Microbiology, Faculty of Naval Medicine, Naval Medical University, Shanghai, People's Republic of China
| | - Songying Ouyang
- Key Laboratory of Innate Immune Biology of Fujian Province, College of Life Sciences, Fujian Normal University, Fujian, People's Republic of China
| | - Xiangliang Li
- Key Laboratory of Innate Immune Biology of Fujian Province, College of Life Sciences, Fujian Normal University, Fujian, People's Republic of China
| | - Jianfeng Xie
- Fujian Provincial Center for Disease Control and Prevention, Fujian, People's Republic of China
| | - Zhigang Yi
- Key Laboratory of Medical Molecular Virology and Department of Medical Microbiology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
| | - Qibin Leng
- State Key Laboratory of Respiratory Diseases, Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Yan Liu
- Department of Microbiology, Faculty of Naval Medicine, Naval Medical University, Shanghai, People's Republic of China
| | - Zhongtian Qi
- Department of Microbiology, Faculty of Naval Medicine, Naval Medical University, Shanghai, People's Republic of China
| | - Ping Zhao
- Department of Microbiology, Faculty of Naval Medicine, Naval Medical University, Shanghai, People's Republic of China
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9
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Abstract
The virus-encoded RNA-dependent RNA polymerase (RdRp) is responsible for viral replication, and its fidelity is closely related to viral diversity, pathogenesis, virulence, and fitness. Hepatitis C virus (HCV) and the second human pegivirus (HPgV-2) belong to the family Flaviviridae and share some features, including similar viral genome structure. Unlike HCV, HPgV-2 preserves a highly conserved genome sequence and low intrahost variation. However, the underlying mechanism remains to be elucidated. In this study, we evaluated the fidelity of HPgV-2 and HCV RdRp in an in vitro RNA polymerase reaction system. The results showed higher fidelity of HPgV-2 RdRp than HCV NS5B with respect to the misincorporation rate due to their difference in recognizing nucleoside triphosphate (NTP) substrates. Furthermore, HPgV-2 RdRp showed lower sensitivity than HCV to sofosbuvir, a nucleotide inhibitor against HCV RdRp, which explained the insusceptibility of HPgV-2 to direct-acting antiviral (DAA) therapy against HCV infection. Our results indicate that HPgV-2 could be an excellent model for studying the mechanisms involved in viral polymerase fidelity as well as RNA virus diversity and evolution. IMPORTANCE RNA viruses represent the most important pathogens for humans and animals and exhibit rapid evolution and high adaptive capacity, which is due to the high mutation rates for using the error-prone RNA-dependent RNA polymerase (RdRp) during replication. The fidelity of RdRp is closely associated with viral diversity, fitness, and pathogenesis. Previous studies have shown that the second human pegivirus (HPgV-2) exhibits a highly conserved genome sequence and low intrahost variation, which might be due to the fidelity of HPgV-2 RdRp. In this work, we used a series of in vitro RNA polymerase assays to evaluate the in vitro fidelity of HPgV-2 RdRp and compared it with that of HCV RdRp. The results indicated that HPgV-2 RdRp preserves significantly higher fidelity than HCV RdRp, which might contribute to the conservation of the HPgV-2 genome. The unique feature of HPgV-2 RdRp fidelity provides a new model for investigation of viral RdRp fidelity.
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10
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Inhibition of Viral RNA-Dependent RNA Polymerases by Nucleoside Inhibitors: An Illustration of the Unity and Diversity of Mechanisms. Int J Mol Sci 2022; 23:ijms232012649. [PMID: 36293509 PMCID: PMC9604226 DOI: 10.3390/ijms232012649] [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: 09/25/2022] [Revised: 10/17/2022] [Accepted: 10/19/2022] [Indexed: 11/06/2022] Open
Abstract
RNA-dependent RNA polymerase (RdRP) is essential for the replication and expression of RNA viral genomes. This class of viruses comprise a large number of highly pathogenic agents that infect essentially all species of plants and animals including humans. Infections often lead to epidemics and pandemics that have remained largely out of control due to the lack of specific and reliable preventive and therapeutic regimens. This unmet medical need has led to the exploration of new antiviral targets, of which RdRP is a major one, due to the fact of its obligatory need in virus growth. Recent studies have demonstrated the ability of several synthetic nucleoside analogs to serve as mimics of the corresponding natural nucleosides. These mimics cause stalling/termination of RdRP, or misincorporation, preventing virus replication or promoting large-scale lethal mutations. Several such analogs have received clinical approval and are being routinely used in therapy. In parallel, the molecular structural basis of their inhibitory interactions with RdRP is being elucidated, revealing both traditional and novel mechanisms including a delayed chain termination effect. This review offers a molecular commentary on these mechanisms along with their clinical implications based on analyses of recent results, which should facilitate the rational design of structure-based antiviral drugs.
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11
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Berkhout B, van Hemert FJ. Silent codon positions in the A-rich HIV RNA genome that do not easily become A: Restrictions imposed by the RNA sequence and structure. Virus Evol 2022; 8:veac072. [PMID: 36533144 PMCID: PMC9752802 DOI: 10.1093/ve/veac072] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 07/13/2022] [Accepted: 08/04/2022] [Indexed: 07/30/2023] Open
Abstract
There is a strong evolutionary tendency of the human immunodeficiency virus (HIV) to accumulate A nucleotides in its RNA genome, resulting in a mere 40 per cent A count. This A bias is especially dominant for the so-called silent codon positions where any nucleotide can be present without changing the encoded protein. However, particular silent codon positions in HIV RNA refrain from becoming A, which became apparent upon genome analysis of many virus isolates. We analyzed these 'noA' genome positions to reveal the underlying reason for their inability to facilitate the A nucleotide. We propose that local RNA structure requirements can explain the absence of A at these sites. Thus, noA sites may be prominently involved in the correct folding of the viral RNA. Turning things around, the presence of multiple clustered noA sites may reveal the presence of important sequence and/or structural elements in the HIV RNA genome.
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Affiliation(s)
| | - Formijn J van Hemert
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam University Medical Centers, University of Amsterdam, Meibergdreef 15, 1105AZ Amsterdam, The Netherlands
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12
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Caldwell HS, Pata JD, Ciota AT. The Role of the Flavivirus Replicase in Viral Diversity and Adaptation. Viruses 2022; 14:1076. [PMID: 35632818 PMCID: PMC9143365 DOI: 10.3390/v14051076] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 05/03/2022] [Accepted: 05/06/2022] [Indexed: 02/04/2023] Open
Abstract
Flaviviruses include several emerging and re-emerging arboviruses which cause millions of infections each year. Although relatively well-studied, much remains unknown regarding the mechanisms and means by which these viruses readily alternate and adapt to different hosts and environments. Here, we review a subset of the different aspects of flaviviral biology which impact host switching and viral fitness. These include the mechanism of replication and structural biology of the NS3 and NS5 proteins, which reproduce the viral genome; rates of mutation resulting from this replication and the role of mutational frequency in viral fitness; and the theory of quasispecies evolution and how it contributes to our understanding of genetic and phenotypic plasticity.
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Affiliation(s)
- Haley S. Caldwell
- The Arbovirus Laboratory, Wadsworth Center, New York State Department of Health, Slingerlands, NY 12159, USA;
- Department of Biomedical Sciences, State University of New York at Albany, School of Public Health, Rensselaer, NY 12144, USA;
| | - Janice D. Pata
- Department of Biomedical Sciences, State University of New York at Albany, School of Public Health, Rensselaer, NY 12144, USA;
- Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA
| | - Alexander T. Ciota
- The Arbovirus Laboratory, Wadsworth Center, New York State Department of Health, Slingerlands, NY 12159, USA;
- Department of Biomedical Sciences, State University of New York at Albany, School of Public Health, Rensselaer, NY 12144, USA;
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13
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Li Y, Zhang D, Gao X, Wang X, Zhang L. 2'- and 3'-Ribose Modifications of Nucleotide Analogues Establish the Structural Basis to Inhibit the Viral Replication of SARS-CoV-2. J Phys Chem Lett 2022; 13:4111-4118. [PMID: 35503748 PMCID: PMC9088111 DOI: 10.1021/acs.jpclett.2c00087] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 04/27/2022] [Indexed: 05/12/2023]
Abstract
Inhibition of RNA-dependent RNA polymerase (RdRp) by nucleotide analogues with ribose modification provides a promising antiviral strategy for the treatment of SARS-CoV-2. Previous works have shown that remdesivir carrying 1'-substitution can act as a "delayed chain terminator", while nucleotide analogues with 2'-methyl group substitution could immediately terminate the chain extension. However, how the inhibition can be established by the 3'-ribose modification as well as other 2'-ribose modifications is not fully understood. Herein, we have evaluated the potential of several adenosine analogues with 2'- and/or 3'-modifications as obligate chain terminators by comprehensive structural analysis based on extensive molecular dynamics simulations. Our results suggest that 2'-modification couples with the protein environment to affect the structural stability, while 3'-hydrogen substitution inherently exerts "immediate termination" without compromising the structural stability in the active site. Our study provides an alternative promising modification scheme to orientate the further optimization of obligate terminators for SARS-CoV-2 RdRp.
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Affiliation(s)
- Yongfang Li
- State
Key Laboratory of Structural Chemistry, Fujian Institute of Research
on the Structure of Matter, Chinese Academy
of Sciences, 350002, Fuzhou, Fujian, China
- University
of Chinese Academy of Sciences, 100864, Beijing, China
| | - Dong Zhang
- State
Key Laboratory of Structural Chemistry, Fujian Institute of Research
on the Structure of Matter, Chinese Academy
of Sciences, 350002, Fuzhou, Fujian, China
- University
of Chinese Academy of Sciences, 100864, Beijing, China
| | - Xin Gao
- Computational
Bioscience Research Center (CBRC), Computer, Electrical and Mathematical
Sciences and Engineering Division, King
Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Xiaowei Wang
- Department
of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Kowloon 999077, Hong Kong
| | - Lu Zhang
- State
Key Laboratory of Structural Chemistry, Fujian Institute of Research
on the Structure of Matter, Chinese Academy
of Sciences, 350002, Fuzhou, Fujian, China
- University
of Chinese Academy of Sciences, 100864, Beijing, China
- Fujian
Provincial Key Laboratory of Theoretical and Computational Chemistry, 361005, Xiamen, Fujian, China
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14
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Furtado ND, Raphael LDM, Ribeiro IP, de Mello IS, Fernandes DR, Gómez MM, dos Santos AAC, Nogueira MDS, de Castro MG, de Abreu FVS, Martins LC, Vasconcelos PFDC, Lourenço-de-Oliveira R, Bonaldo MC. Biological Characterization of Yellow Fever Viruses Isolated From Non-human Primates in Brazil With Distinct Genomic Landscapes. Front Microbiol 2022; 13:757084. [PMID: 35237244 PMCID: PMC8882863 DOI: 10.3389/fmicb.2022.757084] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 01/06/2022] [Indexed: 11/13/2022] Open
Abstract
Since the beginning of the XXI Century, the yellow fever virus (YFV) has been cyclically spreading from the Amazon basin to Brazil’s South and Southeast regions, culminating in an unprecedented outbreak that started in 2016. In this work, we studied four YFV isolated from non-human primates obtained during outbreaks in the states of Rio Grande do Sul in 2008 (PR4408), Goiás (GO05), and Espírito Santo (ES-504) in 2017, and Rio de Janeiro (RJ 155) in 2019. These isolates have genomic differences mainly distributed in non-structural proteins. We compared the isolates’ rates of infection in mammal and mosquito cells and neurovirulence in adult mice. RJ 155 and PR4408 YFV isolates exhibited higher infectivity in mammalian cells and neurovirulence in mice. In mosquito Aag2 cells, GO05 and PR4408 displayed the lowest proliferation rates. These results suggest that RJ 155 and PR4408 YFV isolates carry some genomic markers that increase infectivity in mammal hosts. From this characterization, it is possible to contribute to discovering new molecular markers for the virulence of YFV.
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Affiliation(s)
- Nathália Dias Furtado
- Laboratório de Biologia Molecular de Flavivírus, Instituto Oswaldo Cruz/Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, Brazil
| | - Lidiane de Menezes Raphael
- Laboratório de Biologia Molecular de Flavivírus, Instituto Oswaldo Cruz/Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, Brazil
| | - Ieda Pereira Ribeiro
- Laboratório de Biologia Molecular de Flavivírus, Instituto Oswaldo Cruz/Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, Brazil
| | - Iasmim Silva de Mello
- Laboratório de Biologia Molecular de Flavivírus, Instituto Oswaldo Cruz/Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, Brazil
| | - Déberli Ruiz Fernandes
- Laboratório de Biologia Molecular de Flavivírus, Instituto Oswaldo Cruz/Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, Brazil
| | | | | | - Mônica da Silva Nogueira
- Centro de Experimentação Animal, Instituto Oswaldo Cruz/Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, Brazil
| | - Márcia Gonçalves de Castro
- Laboratório de Mosquitos Transmissores de Hematozoários, Instituto Oswaldo Cruz/Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, Brazil
| | - Filipe Vieira Santos de Abreu
- Laboratório de Mosquitos Transmissores de Hematozoários, Instituto Oswaldo Cruz/Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, Brazil
| | - Lívia Carício Martins
- Seção de Arbovirologia e Febres Hemorrágicas, Instituto Evandro Chagas/Fundação Oswaldo Cruz (FIOCRUZ), Pará, Brazil
| | | | - Ricardo Lourenço-de-Oliveira
- Laboratório de Mosquitos Transmissores de Hematozoários, Instituto Oswaldo Cruz/Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, Brazil
| | - Myrna Cristina Bonaldo
- Laboratório de Biologia Molecular de Flavivírus, Instituto Oswaldo Cruz/Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, Brazil
- *Correspondence: Myrna Cristina Bonaldo,
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15
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Xu X, Zhang L, Chu JTS, Wang Y, Chin AWH, Chong TH, Dai Z, Poon LLM, Cheung PPH, Huang X. A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. Nucleic Acids Res 2021; 49:8796-8810. [PMID: 34379778 PMCID: PMC8421151 DOI: 10.1093/nar/gkab660] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/13/2021] [Accepted: 07/26/2021] [Indexed: 11/13/2022] Open
Abstract
During RNA elongation, the influenza A viral (IAV) RNA-dependent RNA polymerase (RdRp) residues in the active site interact with the triphosphate moiety of nucleoside triphosphate (NTP) for catalysis. The molecular mechanisms by which they control the rate and fidelity of NTP incorporation remain elusive. Here, we demonstrated through enzymology, virology and computational approaches that the R239 and K235 in the PB1 subunit of RdRp are critical to controlling the activity and fidelity of transcription. Contrary to common beliefs that high-fidelity RdRp variants exert a slower incorporation rate, we discovered a first-of-its-kind, single lysine-to-arginine mutation on K235 exhibited enhanced fidelity and activity compared with wild-type. In particular, we employed a single-turnover NTP incorporation assay for the first time on IAV RdRp to show that K235R mutant RdRp possessed a 1.9-fold increase in the transcription activity of the cognate NTP and a 4.6-fold increase in fidelity compared to wild-type. Our all-atom molecular dynamics simulations further elucidated that the higher activity is attributed to the shorter distance between K235R and the triphosphate moiety of NTP compared with wild-type. These results provide novel insights into NTP incorporation and fidelity control mechanisms, which lay the foundation for the rational design of IAV vaccine and antiviral targets.
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Affiliation(s)
- Xinzhou Xu
- The Hong Kong University of Science and Technology-Shenzhen Research Institute, Hi-Tech Park, Nanshan, Shenzhen 518057, China.,Bioengineering Graduate Program, Department of Biological and Chemical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Lu Zhang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Julie Tung Sem Chu
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Yuqing Wang
- The Hong Kong University of Science and Technology-Shenzhen Research Institute, Hi-Tech Park, Nanshan, Shenzhen 518057, China.,Bioengineering Graduate Program, Department of Biological and Chemical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Alex Wing Hong Chin
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China.,Centre for Immunity and Infection, Hong Kong Science Park, Hong Kong, China
| | - Tin Hang Chong
- The Hong Kong University of Science and Technology-Shenzhen Research Institute, Hi-Tech Park, Nanshan, Shenzhen 518057, China.,Department of Chemistry, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Kowloon, Hong Kong, China
| | - Zixi Dai
- Department of Chemistry, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Kowloon, Hong Kong, China
| | - Leo Lit Man Poon
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China.,HKU-Pasteur Research Pole, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China.,Centre for Immunity and Infection, Hong Kong Science Park, Hong Kong, China
| | - Peter Pak-Hang Cheung
- The Hong Kong University of Science and Technology-Shenzhen Research Institute, Hi-Tech Park, Nanshan, Shenzhen 518057, China.,Department of Chemistry, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Kowloon, Hong Kong, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong, China.,Li Ka Shing Institute of Health Sciences, Li Ka Shing Medical Sciences Building, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Xuhui Huang
- The Hong Kong University of Science and Technology-Shenzhen Research Institute, Hi-Tech Park, Nanshan, Shenzhen 518057, China.,Department of Chemistry, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Kowloon, Hong Kong, China
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16
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Winston DS, Boehr DD. Allosteric and dynamic control of RNA-dependent RNA polymerase function and fidelity. Enzymes 2021; 49:149-193. [PMID: 34696831 DOI: 10.1016/bs.enz.2021.06.001] [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] [Indexed: 06/13/2023]
Abstract
All RNA viruses encode an RNA-dependent RNA polymerase (RdRp) responsible for genome replication. It is now recognized that enzymes in general, and RdRps specifically, are dynamic macromolecular machines such that their moving parts, including active site loops, play direct functional roles. While X-ray crystallography has provided deep insight into structural elements important for RdRp function, this methodology generally provides only static snapshots, and so is limited in its ability to report on dynamic fluctuations away from the lowest energy conformation. Nuclear magnetic resonance (NMR), molecular dynamics (MD) simulations and other biophysical techniques have brought new insight into RdRp function by their ability to characterize the trajectories, kinetics and thermodynamics of conformational motions. In particular, these methodologies have identified coordinated motions among conserved structural motifs necessary for nucleotide selection and incorporation. Disruption of these motions through amino acid substitutions or inhibitor binding impairs RdRp function. Understanding and re-engineering these motions thus provides exciting new avenues for anti-viral strategies. This chapter outlines the basics of these methodologies, summarizes the dynamic motions observed in different RdRps important for nucleotide selection and incorporation, and illustrates how this information can be leveraged towards rational vaccine strain development and anti-viral drug design.
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Affiliation(s)
- Dennis S Winston
- Department of Chemistry, The Pennsylvania State University, University Park, PA, United States
| | - David D Boehr
- Department of Chemistry, The Pennsylvania State University, University Park, PA, United States.
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17
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Ferrero DS, Falqui M, Verdaguer N. Snapshots of a Non-Canonical RdRP in Action. Viruses 2021; 13:v13071260. [PMID: 34203380 PMCID: PMC8310298 DOI: 10.3390/v13071260] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 06/24/2021] [Accepted: 06/25/2021] [Indexed: 11/17/2022] Open
Abstract
RNA viruses typically encode their own RNA-dependent RNA polymerase (RdRP) to ensure genome replication and transcription. The closed “right hand” architecture of RdRPs encircles seven conserved structural motifs (A to G) that regulate the polymerization activity. The four palm motifs, arranged in the sequential order A to D, are common to all known template dependent polynucleotide polymerases, with motifs A and C containing the catalytic aspartic acid residues. Exceptions to this design have been reported in members of the Permutotetraviridae and Birnaviridae families of positive single stranded (+ss) and double-stranded (ds) RNA viruses, respectively. In these enzymes, motif C is located upstream of motif A, displaying a permuted C–A–B–D connectivity. Here we study the details of the replication elongation process in the non-canonical RdRP of the Thosea asigna virus (TaV), an insect virus from the Permutatetraviridae family. We report the X-ray structures of three replicative complexes of the TaV polymerase obtained with an RNA template-primer in the absence and in the presence of incoming rNTPs. The structures captured different replication events and allowed to define the critical interactions involved in: (i) the positioning of the acceptor base of the template strand, (ii) the positioning of the 3’-OH group of the primer nucleotide during RNA replication and (iii) the recognition and positioning of the incoming nucleotide. Structural comparisons unveiled a closure of the active site on the RNA template-primer binding, before rNTP entry. This conformational rearrangement that also includes the repositioning of the motif A aspartate for the catalytic reaction to take place is maintained on rNTP and metal ion binding and after nucleotide incorporation, before translocation.
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18
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Ferron F, Sama B, Decroly E, Canard B. The enzymes for genome size increase and maintenance of large (+)RNA viruses. Trends Biochem Sci 2021; 46:866-877. [PMID: 34172362 DOI: 10.1016/j.tibs.2021.05.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 05/05/2021] [Accepted: 05/18/2021] [Indexed: 02/08/2023]
Abstract
With sizes <50 kb, viral RNA genomes are at the crossroads of genetic, biophysical, and biochemical stability in their host cell. Here, we analyze the enzymatic assets accompanying large RNA genome viruses, mostly based on recent scientific advances in Coronaviridae. We argue that, in addition to the presence of an RNA exonuclease (ExoN), two markers for the large size of viral RNA genomes are (i) the presence of one or more RNA methyltransferases (MTases) and (ii) a specific architecture of the RNA-dependent RNA polymerase active site. We propose that RNA genome expansion and maintenance are driven by an evolutionary ménage-à-trois made of fast and processive RNA polymerases, RNA repair ExoNs, and RNA MTases that relates to the transition between RNA- to DNA-based life.
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Affiliation(s)
- François Ferron
- Centre National de la Recherche Scientifique, Aix-Marseille Université, CNRS UMR 7257, AFMB, Case 925, 163, Avenue de Luminy, 13009 Marseille, France; European Virus Bioinformatics Center, Leutragraben 1, 07743 Jena, Germany
| | - Bhawna Sama
- Centre National de la Recherche Scientifique, Aix-Marseille Université, CNRS UMR 7257, AFMB, Case 925, 163, Avenue de Luminy, 13009 Marseille, France
| | - Etienne Decroly
- Centre National de la Recherche Scientifique, Aix-Marseille Université, CNRS UMR 7257, AFMB, Case 925, 163, Avenue de Luminy, 13009 Marseille, France
| | - Bruno Canard
- Centre National de la Recherche Scientifique, Aix-Marseille Université, CNRS UMR 7257, AFMB, Case 925, 163, Avenue de Luminy, 13009 Marseille, France; European Virus Bioinformatics Center, Leutragraben 1, 07743 Jena, Germany.
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19
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Long C, Romero ME, La Rocco D, Yu J. Dissecting nucleotide selectivity in viral RNA polymerases. Comput Struct Biotechnol J 2021; 19:3339-3348. [PMID: 34104356 PMCID: PMC8175102 DOI: 10.1016/j.csbj.2021.06.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 05/28/2021] [Accepted: 06/02/2021] [Indexed: 01/18/2023] Open
Abstract
Designing antiviral therapeutics is of great concern per current pandemics caused by novel coronavirus or SARS-CoV-2. The core polymerase enzyme in the viral replication/transcription machinery is generally conserved and serves well for drug target. In this work we briefly review structural biology and computational clues on representative single-subunit viral polymerases that are more or less connected with SARS-CoV-2 RNA dependent RNA polymerase (RdRp), in particular, to elucidate how nucleotide substrates and potential drug analogs are selected in the viral genome synthesis. To do that, we first survey two well studied RdRps from Polio virus and hepatitis C virus in regard to structural motifs and key residues that have been identified for the nucleotide selectivity. Then we focus on related structural and biochemical characteristics discovered for the SARS-CoV-2 RdRp. To further compare, we summarize what we have learned computationally from phage T7 RNA polymerase (RNAP) on its stepwise nucleotide selectivity, and extend discussion to a structurally similar human mitochondria RNAP, which deserves special attention as it cannot be adversely affected by antiviral treatments. We also include viral phi29 DNA polymerase for comparison, which has both helicase and proofreading activities on top of nucleotide selectivity for replication fidelity control. The helicase and proofreading functions are achieved by protein components in addition to RdRp in the coronavirus replication-transcription machine, with the proofreading strategy important for the fidelity control in synthesizing a comparatively large viral genome.
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Affiliation(s)
- Chunhong Long
- School of Science, Chongqing University of Posts and Telecommunications, Chongqing 400065, China
| | | | - Daniel La Rocco
- Department of Physics, University of California, Berkeley, CA 94720, USA
| | - Jin Yu
- Department of Physics and Astronomy, Department of Chemistry, NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, CA 92697, USA
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20
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Global Genomic Analysis of SARS-CoV-2 RNA Dependent RNA Polymerase Evolution and Antiviral Drug Resistance. Microorganisms 2021; 9:microorganisms9051094. [PMID: 34069681 PMCID: PMC8160703 DOI: 10.3390/microorganisms9051094] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 05/09/2021] [Accepted: 05/15/2021] [Indexed: 01/18/2023] Open
Abstract
A variety of antiviral treatments for COVID-19 have been investigated, involving many repurposed drugs. Currently, the SARS-CoV-2 RNA-dependent RNA polymerase (RdRp, encoded by nsp12-nsp7-nsp8) has been targeted by numerous inhibitors, e.g., remdesivir, the only provisionally approved treatment to-date, although the clinical impact of these interventions remains inconclusive. However, the potential emergence of antiviral resistance poses a threat to the efficacy of any successful therapies on a wide scale. Here, we propose a framework to monitor the emergence of antiviral resistance, and as a proof of concept, we address the interaction between RdRp and remdesivir. We show that SARS-CoV-2 RdRp is under purifying selection, that potential escape mutations are rare in circulating lineages, and that those mutations, where present, do not destabilise RdRp. In more than 56,000 viral genomes from 105 countries from the first pandemic wave, we found negative selective pressure affecting nsp12 (Tajima’s D = −2.62), with potential antiviral escape mutations in only 0.3% of sequenced genomes. Potential escape mutations included known key residues, such as Nsp12:Val473 and Nsp12:Arg555. Of the potential escape mutations involved globally, in silico structural models found that they were unlikely to be associated with loss of stability in RdRp. No potential escape mutation was found in a local cohort of remdesivir treated patients. Collectively, these findings indicate that RdRp is a suitable drug target, and that remdesivir does not seem to exert high selective pressure. We anticipate our framework to be the starting point of a larger effort for a global monitoring of drug resistance throughout the COVID-19 pandemic.
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21
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Khani E, Khiali S, Entezari‐Maleki T. Potential COVID-19 Therapeutic Agents and Vaccines: An Evidence-Based Review. J Clin Pharmacol 2021; 61:429-460. [PMID: 33511638 PMCID: PMC8014753 DOI: 10.1002/jcph.1822] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 01/26/2021] [Indexed: 02/06/2023]
Abstract
Since the early days of 2020, the severe acute respiratory syndrome coronavirus 2 pandemic has become a global health concern. Currently, some therapies and vaccines have received US Food and Drug Administration approval or emergency use authorization for the management of coronavirus disease 2019. According to the pathophysiology of the disease, several medications have been evaluated in different clinical conditions of the disease. Evidence-based reviewing and categorizing these medications can guide the clinicians to select the proper medications according to each patient's condition. Therefore, we performed this review to categorize the coronavirus disease 2019 potential therapeutics and vaccines.
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Affiliation(s)
- Elnaz Khani
- Department of Clinical PharmacyFaculty of PharmacyTabriz University of Medical SciencesTabrizIran
| | - Sajad Khiali
- Department of Clinical PharmacyFaculty of PharmacyTabriz University of Medical SciencesTabrizIran
| | - Taher Entezari‐Maleki
- Department of Clinical PharmacyFaculty of PharmacyTabriz University of Medical SciencesTabrizIran
- Cardiovascular Research CenterTabriz University of Medical SciencesTabrizIran
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22
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Harima H, Orba Y, Torii S, Qiu Y, Kajihara M, Eto Y, Matsuta N, Hang'ombe BM, Eshita Y, Uemura K, Matsuno K, Sasaki M, Yoshii K, Nakao R, Hall WW, Takada A, Abe T, Wolfinger MT, Simuunza M, Sawa H. An African tick flavivirus forming an independent clade exhibits unique exoribonuclease-resistant RNA structures in the genomic 3'-untranslated region. Sci Rep 2021; 11:4883. [PMID: 33649491 PMCID: PMC7921595 DOI: 10.1038/s41598-021-84365-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 02/15/2021] [Indexed: 12/16/2022] Open
Abstract
Tick-borne flaviviruses (TBFVs) infect mammalian hosts through tick bites and can cause various serious illnesses, such as encephalitis and hemorrhagic fevers, both in humans and animals. Despite their importance to public health, there is limited epidemiological information on TBFV infection in Africa. Herein, we report that a novel flavivirus, Mpulungu flavivirus (MPFV), was discovered in a Rhipicephalus muhsamae tick in Zambia. MPFV was found to be genetically related to Ngoye virus detected in ticks in Senegal, and these viruses formed a unique lineage in the genus Flavivirus. Analyses of dinucleotide contents of flaviviruses indicated that MPFV was similar to those of other TBFVs with a typical vertebrate genome signature, suggesting that MPFV may infect vertebrate hosts. Bioinformatic analyses of the secondary structures in the 3′-untranslated regions (UTRs) revealed that MPFV exhibited unique exoribonuclease-resistant RNA (xrRNA) structures. Utilizing biochemical approaches, we clarified that two xrRNA structures of MPFV in the 3′-UTR could prevent exoribonuclease activity. In summary, our findings provide new information regarding the geographical distribution of TBFV and xrRNA structures in the 3′-UTR of flaviviruses.
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Affiliation(s)
- Hayato Harima
- Hokudai Center for Zoonosis Control in Zambia, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Yasuko Orba
- Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan.,International Collaboration Unit, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Shiho Torii
- Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Yongjin Qiu
- Hokudai Center for Zoonosis Control in Zambia, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Masahiro Kajihara
- Division of Global Epidemiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Yoshiki Eto
- Division of Global Epidemiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Naoya Matsuta
- Department of Electrical and Information Engineering, Graduate School of Science and Technology, Niigata University, Niigata, Japan
| | - Bernard M Hang'ombe
- Department of Para-Clinical Studies, School of Veterinary Medicine, The University of Zambia, Lusaka, Zambia.,Africa Center of Excellence for Infectious Diseases of Humans and Animals, The University of Zambia, Lusaka, Zambia
| | - Yuki Eshita
- Hokudai Center for Zoonosis Control in Zambia, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Kentaro Uemura
- Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan.,Drug Discovery and Disease Research Laboratory, Shionogi & Co., Ltd., Osaka, Japan
| | - Keita Matsuno
- International Collaboration Unit, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan.,Unit of Risk Analysis and Management, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Michihito Sasaki
- Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Kentaro Yoshii
- Laboratory of Public Health, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan.,National Research Center for the Control and Prevention of Infectious Diseases (CCPID), Nagasaki University, Nagasaki, Japan
| | - Ryo Nakao
- Laboratory of Parasitology, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan
| | - William W Hall
- International Collaboration Unit, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan.,National Virus Reference Laboratory, School of Medicine, University College Dublin, Dublin, Ireland.,Centre for Research in Infectious Diseases, School of Medicine, University College Dublin, Dublin, Ireland.,Global Virus Network, Baltimore, MD, USA
| | - Ayato Takada
- International Collaboration Unit, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan.,Division of Global Epidemiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan.,Africa Center of Excellence for Infectious Diseases of Humans and Animals, The University of Zambia, Lusaka, Zambia.,Department of Disease Control, School of Veterinary Medicine, The University of Zambia, Lusaka, Zambia
| | - Takashi Abe
- Department of Electrical and Information Engineering, Graduate School of Science and Technology, Niigata University, Niigata, Japan
| | - Michael T Wolfinger
- Department of Theoretical Chemistry, University of Vienna, Vienna, Austria.,Research Group Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Vienna, Austria
| | - Martin Simuunza
- Africa Center of Excellence for Infectious Diseases of Humans and Animals, The University of Zambia, Lusaka, Zambia.,Department of Disease Control, School of Veterinary Medicine, The University of Zambia, Lusaka, Zambia
| | - Hirofumi Sawa
- Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan. .,International Collaboration Unit, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan. .,Africa Center of Excellence for Infectious Diseases of Humans and Animals, The University of Zambia, Lusaka, Zambia. .,Global Virus Network, Baltimore, MD, USA. .,Department of Disease Control, School of Veterinary Medicine, The University of Zambia, Lusaka, Zambia.
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23
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Bamford CG, McLauchlan J. An interferon lambda 4-associated variant in the hepatitis C virus RNA polymerase affects viral replication in infected cells. J Gen Virol 2021; 102:001495. [PMID: 32897180 PMCID: PMC8116938 DOI: 10.1099/jgv.0.001495] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 08/18/2020] [Indexed: 01/25/2023] Open
Abstract
Host IFNL4 haplotype status contributes to the development of chronic hepatitis C virus (HCV) infection in individuals who are acutely infected with the virus. In silico studies revealed that specific amino acid variants at multiple sites on the HCV polyprotein correlate with functional single-nucleotide polymorphisms (SNPs) in the IFNL4 locus. Thus, SNPs at the IFNL4 locus may select variants that influence virus replication and thereby the outcome of infection. Here, we examine the most significantly IFNL4-associated amino acid variants that lie in the 'lambda (L) 2 loop' of the HCV NS5B RNA polymerase. L2 loop variants were introduced into both sub-genomic replicon and full-length infectious clones of HCV and viral replication was examined in the presence and absence of exogenous IFNλ4. Our data demonstrate that while mutation of the NS5B L2 loop affects replication, individual IFNL4-associated variants have modest but consistent effects on replication in both the presence and absence of IFNλ4. Given the strong genetic association between these variants and IFNL4, these data suggest a nuanced effect of each individual position on viral replication, the combined effect of which might mediate resistance to the effects of IFNλ4.
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Affiliation(s)
- Connor G.G. Bamford
- MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Rd, Glasgow, G61 1QH, Scotland, UK
- Wellcome-Wolfson Institute for Experimental Medicine, Queen’s University of Belfast, 97 Lisburn Rd, Belfast, BT97BL, Northern Ireland, UK
| | - John McLauchlan
- MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Rd, Glasgow, G61 1QH, Scotland, UK
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24
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Ju J, Li X, Kumar S, Jockusch S, Chien M, Tao C, Morozova I, Kalachikov S, Kirchdoerfer RN, Russo JJ. Nucleotide analogues as inhibitors of SARS-CoV Polymerase. Pharmacol Res Perspect 2020; 8:e00674. [PMID: 33124786 PMCID: PMC7596664 DOI: 10.1002/prp2.674] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/14/2020] [Accepted: 09/21/2020] [Indexed: 01/18/2023] Open
Abstract
SARS-CoV-2, a member of the coronavirus family, has caused a global public health emergency. Based on our analysis of hepatitis C virus and coronavirus replication, and the molecular structures and activities of viral inhibitors, we previously reasoned that the FDA-approved hepatitis C drug EPCLUSA (Sofosbuvir/Velpatasvir) should inhibit coronaviruses, including SARS-CoV-2. Here, using model polymerase extension experiments, we demonstrate that the active triphosphate form of Sofosbuvir is incorporated by low-fidelity polymerases and SARS-CoV RNA-dependent RNA polymerase (RdRp), and blocks further incorporation by these polymerases; the active triphosphate form of Sofosbuvir is not incorporated by a host-like high-fidelity DNA polymerase. Using the same molecular insight, we selected 3'-fluoro-3'-deoxythymidine triphosphate and 3'-azido-3'-deoxythymidine triphosphate, which are the active forms of two other anti-viral agents, Alovudine and AZT (an FDA-approved HIV/AIDS drug) for evaluation as inhibitors of SARS-CoV RdRp. We demonstrate the ability of two of these HIV reverse transcriptase inhibitors to be incorporated by SARS-CoV RdRp where they also terminate further polymerase extension. Given the 98% amino acid similarity of the SARS-CoV and SARS-CoV-2 RdRps, we expect these nucleotide analogues would also inhibit the SARS-CoV-2 polymerase. These results offer guidance to further modify these nucleotide analogues to generate more potent broad-spectrum anti-coronavirus agents.
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Affiliation(s)
- Jingyue Ju
- Center for Genome Technology and Biomolecular EngineeringColumbia UniversityNew YorkNew YorkUSA
- Department of Chemical EngineeringColumbia UniversityNew YorkNYUSA
- Department of Molecular Pharmacology and TherapeuticsColumbia UniversityNew YorkNYUSA
| | - Xiaoxu Li
- Center for Genome Technology and Biomolecular EngineeringColumbia UniversityNew YorkNew YorkUSA
- Department of Chemical EngineeringColumbia UniversityNew YorkNYUSA
| | - Shiv Kumar
- Center for Genome Technology and Biomolecular EngineeringColumbia UniversityNew YorkNew YorkUSA
- Department of Chemical EngineeringColumbia UniversityNew YorkNYUSA
| | - Steffen Jockusch
- Center for Genome Technology and Biomolecular EngineeringColumbia UniversityNew YorkNew YorkUSA
- Department of ChemistryColumbia UniversityNew YorkNYUSA
| | - Minchen Chien
- Center for Genome Technology and Biomolecular EngineeringColumbia UniversityNew YorkNew YorkUSA
- Department of Chemical EngineeringColumbia UniversityNew YorkNYUSA
| | - Chuanjuan Tao
- Center for Genome Technology and Biomolecular EngineeringColumbia UniversityNew YorkNew YorkUSA
- Department of Chemical EngineeringColumbia UniversityNew YorkNYUSA
| | - Irina Morozova
- Center for Genome Technology and Biomolecular EngineeringColumbia UniversityNew YorkNew YorkUSA
- Department of Chemical EngineeringColumbia UniversityNew YorkNYUSA
| | - Sergey Kalachikov
- Center for Genome Technology and Biomolecular EngineeringColumbia UniversityNew YorkNew YorkUSA
- Department of Chemical EngineeringColumbia UniversityNew YorkNYUSA
| | - Robert N. Kirchdoerfer
- Department of BiochemistryUniversity of Wisconsin‐MadisonMadisonWisconsinUSA
- Institute of Molecular VirologyUniversity of Wisconsin‐MadisonMadisonWisconsinUSA
| | - James J. Russo
- Center for Genome Technology and Biomolecular EngineeringColumbia UniversityNew YorkNew YorkUSA
- Department of Chemical EngineeringColumbia UniversityNew YorkNYUSA
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25
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Chien M, Anderson TK, Jockusch S, Tao C, Li X, Kumar S, Russo JJ, Kirchdoerfer RN, Ju J. Nucleotide Analogues as Inhibitors of SARS-CoV-2 Polymerase, a Key Drug Target for COVID-19. J Proteome Res 2020; 19:4690-4697. [PMID: 32692185 PMCID: PMC7640960 DOI: 10.1021/acs.jproteome.0c00392] [Citation(s) in RCA: 190] [Impact Index Per Article: 47.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Indexed: 12/18/2022]
Abstract
SARS-CoV-2 is responsible for the current COVID-19 pandemic. On the basis of our analysis of hepatitis C virus and coronavirus replication, and the molecular structures and activities of viral inhibitors, we previously demonstrated that three nucleotide analogues (the triphosphates of Sofosbuvir, Alovudine, and AZT) inhibit the SARS-CoV RNA-dependent RNA polymerase (RdRp). We also demonstrated that a library of additional nucleotide analogues terminate RNA synthesis catalyzed by the SARS-CoV-2 RdRp, a well-established drug target for COVID-19. Here, we used polymerase extension experiments to demonstrate that the active triphosphate form of Sofosbuvir (an FDA-approved hepatitis C drug) is incorporated by SARS-CoV-2 RdRp and blocks further incorporation. Using the molecular insight gained from the previous studies, we selected the active triphosphate forms of six other antiviral agents, Alovudine, Tenofovir alafenamide, AZT, Abacavir, Lamivudine, and Emtricitabine, for evaluation as inhibitors of the SARS-CoV-2 RdRp and demonstrated the ability of these viral polymerase inhibitors to be incorporated by SARS-CoV-2 RdRp, where they terminate further polymerase extension with varying efficiency. These results provide a molecular basis for inhibition of the SARS-CoV-2 RdRp by these nucleotide analogues. If sufficient efficacy of some of these FDA-approved drugs in inhibiting viral replication in cell culture is established, they may be explored as potential COVID-19 therapeutics.
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Affiliation(s)
- Minchen Chien
- Center
for Genome Technology and Biomolecular Engineering, Departments of Chemical
Engineering, Pharmacology, and Chemistry, Columbia University, New York, New York 10027, United States
| | - Thomas K. Anderson
- Department of Biochemistry and Institute of Molecular Virology, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Steffen Jockusch
- Center
for Genome Technology and Biomolecular Engineering, Departments of Chemical
Engineering, Pharmacology, and Chemistry, Columbia University, New York, New York 10027, United States
| | - Chuanjuan Tao
- Center
for Genome Technology and Biomolecular Engineering, Departments of Chemical
Engineering, Pharmacology, and Chemistry, Columbia University, New York, New York 10027, United States
| | - Xiaoxu Li
- Center
for Genome Technology and Biomolecular Engineering, Departments of Chemical
Engineering, Pharmacology, and Chemistry, Columbia University, New York, New York 10027, United States
| | - Shiv Kumar
- Center
for Genome Technology and Biomolecular Engineering, Departments of Chemical
Engineering, Pharmacology, and Chemistry, Columbia University, New York, New York 10027, United States
| | - James J. Russo
- Center
for Genome Technology and Biomolecular Engineering, Departments of Chemical
Engineering, Pharmacology, and Chemistry, Columbia University, New York, New York 10027, United States
| | - Robert N. Kirchdoerfer
- Department of Biochemistry and Institute of Molecular Virology, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Jingyue Ju
- Center
for Genome Technology and Biomolecular Engineering, Departments of Chemical
Engineering, Pharmacology, and Chemistry, Columbia University, New York, New York 10027, United States
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26
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Jockusch S, Tao C, Li X, Chien M, Kumar S, Morozova I, Kalachikov S, Russo JJ, Ju J. Sofosbuvir terminated RNA is more resistant to SARS-CoV-2 proofreader than RNA terminated by Remdesivir. Sci Rep 2020; 10:16577. [PMID: 33024223 PMCID: PMC7538426 DOI: 10.1038/s41598-020-73641-9] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 09/17/2020] [Indexed: 12/11/2022] Open
Abstract
SARS-CoV-2 is responsible for COVID-19, resulting in the largest pandemic in over a hundred years. After examining the molecular structures and activities of hepatitis C viral inhibitors and comparing hepatitis C virus and coronavirus replication, we previously postulated that the FDA-approved hepatitis C drug EPCLUSA (Sofosbuvir/Velpatasvir) might inhibit SARS-CoV-2. We subsequently demonstrated that Sofosbuvir triphosphate is incorporated by the relatively low fidelity SARS-CoV and SARS-CoV-2 RNA-dependent RNA polymerases (RdRps), serving as an immediate polymerase reaction terminator, but not by a host-like high fidelity DNA polymerase. Other investigators have since demonstrated the ability of Sofosbuvir to inhibit SARS-CoV-2 replication in lung and brain cells; additionally, COVID-19 clinical trials with EPCLUSA and with Sofosbuvir plus Daclatasvir have been initiated in several countries. SARS-CoV-2 has an exonuclease-based proofreader to maintain the viral genome integrity. Any effective antiviral targeting the SARS-CoV-2 RdRp must display a certain level of resistance to this proofreading activity. We report here that Sofosbuvir terminated RNA resists removal by the exonuclease to a substantially higher extent than RNA terminated by Remdesivir, another drug being used as a COVID-19 therapeutic. These results offer a molecular basis supporting the current use of Sofosbuvir in combination with other drugs in COVID-19 clinical trials.
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Affiliation(s)
- Steffen Jockusch
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY, 10027, USA
- Department of Chemistry, Columbia University, New York, NY, 10027, USA
| | - Chuanjuan Tao
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY, 10027, USA
- Department of Chemical Engineering, Columbia University, New York, NY, 10027, USA
| | - Xiaoxu Li
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY, 10027, USA
- Department of Chemical Engineering, Columbia University, New York, NY, 10027, USA
| | - Minchen Chien
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY, 10027, USA
- Department of Chemical Engineering, Columbia University, New York, NY, 10027, USA
| | - Shiv Kumar
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY, 10027, USA
- Department of Chemical Engineering, Columbia University, New York, NY, 10027, USA
| | - Irina Morozova
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY, 10027, USA
- Department of Chemical Engineering, Columbia University, New York, NY, 10027, USA
| | - Sergey Kalachikov
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY, 10027, USA
- Department of Chemical Engineering, Columbia University, New York, NY, 10027, USA
| | - James J Russo
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY, 10027, USA
- Department of Chemical Engineering, Columbia University, New York, NY, 10027, USA
| | - Jingyue Ju
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY, 10027, USA.
- Department of Chemical Engineering, Columbia University, New York, NY, 10027, USA.
- Department of Molecular Pharmacology and Therapeutics, Columbia University, New York, NY, 10032, USA.
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27
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Coggins SA, Mahboubi B, Schinazi RF, Kim B. Mechanistic cross-talk between DNA/RNA polymerase enzyme kinetics and nucleotide substrate availability in cells: Implications for polymerase inhibitor discovery. J Biol Chem 2020; 295:13432-13443. [PMID: 32737197 PMCID: PMC7521635 DOI: 10.1074/jbc.rev120.013746] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 07/31/2020] [Indexed: 01/01/2023] Open
Abstract
Enzyme kinetic analysis reveals a dynamic relationship between enzymes and their substrates. Overall enzyme activity can be controlled by both protein expression and various cellular regulatory systems. Interestingly, the availability and concentrations of intracellular substrates can constantly change, depending on conditions and cell types. Here, we review previously reported enzyme kinetic parameters of cellular and viral DNA and RNA polymerases with respect to cellular levels of their nucleotide substrates. This broad perspective exposes a remarkable co-evolution scenario of DNA polymerase enzyme kinetics with dNTP levels that can vastly change, depending on cell proliferation profiles. Similarly, RNA polymerases display much higher Km values than DNA polymerases, possibly due to millimolar range rNTP concentrations found in cells (compared with micromolar range dNTP levels). Polymerases are commonly targeted by nucleotide analog inhibitors for the treatments of various human diseases, such as cancers and viral pathogens. Because these inhibitors compete against natural cellular nucleotides, the efficacy of each inhibitor can be affected by varying cellular nucleotide levels in their target cells. Overall, both kinetic discrepancy between DNA and RNA polymerases and cellular concentration discrepancy between dNTPs and rNTPs present pharmacological and mechanistic considerations for therapeutic discovery.
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Affiliation(s)
- Si'Ana A Coggins
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia, USA
| | - Bijan Mahboubi
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia, USA
| | - Raymond F Schinazi
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia, USA
| | - Baek Kim
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia, USA; Center for Drug Discovery, Children's Healthcare of Atlanta, Atlanta, Georgia, USA.
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28
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Villalba B, Johnson KA. Rate-limiting pyrophosphate release by hepatitis C virus polymerase NS5B improves fidelity. J Biol Chem 2020; 295:16436-16444. [PMID: 32938715 DOI: 10.1074/jbc.ra120.015394] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Revised: 09/04/2020] [Indexed: 01/02/2023] Open
Abstract
The hepatitis C virus RNA-dependent RNA polymerase NS5B is responsible for the replication of the viral genome. Previous studies have uncovered NTP-mediated excision mechanisms that may be responsible for aiding in maintaining fidelity (the frequency of incorrect incorporation events relative to correct), but little is known about the fidelity of NS5B. In this study, we used transient-state kinetics to examine the mechanistic basis for polymerase fidelity. We observe a wide range of efficiency for incorporation of various mismatched base pairs and have uncovered a mechanism in which the rate constant for pyrophosphate release is slowed for certain misincorporation events. This results in an increase in fidelity against these specific misincorporations. Furthermore, we discover that some mismatches are highly unfavorable and cannot be observed under the conditions used here. The calculated fidelity of NS5B ranges between 10-4-10-9 for different mismatches.
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Affiliation(s)
- Brian Villalba
- Institutes for Cell and Molecular Biology, University of Texas at Austin, Austin, Texas, USA
| | - Kenneth A Johnson
- Institutes for Cell and Molecular Biology, University of Texas at Austin, Austin, Texas, USA.
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29
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Jockusch S, Tao C, Li X, Anderson TK, Chien M, Kumar S, Russo JJ, Kirchdoerfer RN, Ju J. A library of nucleotide analogues terminate RNA synthesis catalyzed by polymerases of coronaviruses that cause SARS and COVID-19. Antiviral Res 2020; 180:104857. [PMID: 32562705 PMCID: PMC7299870 DOI: 10.1016/j.antiviral.2020.104857] [Citation(s) in RCA: 86] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 05/30/2020] [Accepted: 06/12/2020] [Indexed: 02/08/2023]
Abstract
SARS-CoV-2, a member of the coronavirus family, is responsible for the current COVID-19 worldwide pandemic. We previously demonstrated that five nucleotide analogues inhibit the SARS-CoV-2 RNA-dependent RNA polymerase (RdRp), including the active triphosphate forms of Sofosbuvir, Alovudine, Zidovudine, Tenofovir alafenamide and Emtricitabine. We report here the evaluation of a library of nucleoside triphosphate analogues with a variety of structural and chemical features as inhibitors of the RdRps of SARS-CoV and SARS-CoV-2. These features include modifications on the sugar (2′ or 3′ modifications, carbocyclic, acyclic, or dideoxynucleotides) or on the base. The goal is to identify nucleotide analogues that not only terminate RNA synthesis catalyzed by these coronavirus RdRps, but also have the potential to resist the viruses' exonuclease activity. We examined these nucleotide analogues for their ability to be incorporated by the RdRps in the polymerase reaction and to prevent further incorporation. While all 11 molecules tested displayed incorporation, 6 exhibited immediate termination of the polymerase reaction (triphosphates of Carbovir, Ganciclovir, Stavudine and Entecavir; 3′-OMe-UTP and Biotin-16-dUTP), 2 showed delayed termination (Cidofovir diphosphate and 2′-OMe-UTP), and 3 did not terminate the polymerase reaction (2′-F-dUTP, 2′–NH2–dUTP and Desthiobiotin-16-UTP). The coronaviruses possess an exonuclease that apparently requires a 2′-OH at the 3′-terminus of the growing RNA strand for proofreading. In this study, all nucleoside triphosphate analogues evaluated form Watson-Crick-like base pairs. The nucleotide analogues demonstrating termination either lack a 2′-OH, have a blocked 2′-OH, or show delayed termination. Thus, these nucleotide analogues are of interest for further investigation to evaluate whether they can evade the viral exonuclease activity. Prodrugs of five of these nucleotide analogues (Cidofovir, Abacavir, Valganciclovir/Ganciclovir, Stavudine and Entecavir) are FDA-approved medications for treatment of other viral infections, and their safety profiles are well established. After demonstrating potency in inhibiting viral replication in cell culture, candidate molecules can be rapidly evaluated as potential therapies for COVID-19. Cidofovir triphosphate is a delayed terminator for SARS-CoV-2 RNA polymerase. Abacavir, Ganciclovir, and Stavudine triphosphates inhibit SARS-CoV-2 polymerase. 2′-O-methylated UTP substantially terminates the SARS-CoV-2 polymerase reaction.
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Affiliation(s)
- Steffen Jockusch
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY, 10027, USA; Department of Chemistry, Columbia University, New York, NY, 10027, USA
| | - Chuanjuan Tao
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY, 10027, USA; Department of Chemical Engineering, Columbia University, New York, NY, 10027, USA
| | - Xiaoxu Li
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY, 10027, USA; Department of Chemical Engineering, Columbia University, New York, NY, 10027, USA
| | - Thomas K Anderson
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA; Institute of Molecular Virology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Minchen Chien
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY, 10027, USA; Department of Chemical Engineering, Columbia University, New York, NY, 10027, USA
| | - Shiv Kumar
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY, 10027, USA; Department of Chemical Engineering, Columbia University, New York, NY, 10027, USA
| | - James J Russo
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY, 10027, USA; Department of Chemical Engineering, Columbia University, New York, NY, 10027, USA
| | - Robert N Kirchdoerfer
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA; Institute of Molecular Virology, University of Wisconsin-Madison, Madison, WI, 53706, USA.
| | - Jingyue Ju
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY, 10027, USA; Department of Chemical Engineering, Columbia University, New York, NY, 10027, USA; Department of Pharmacology, Columbia University, New York, NY, 10027, USA.
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30
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Atkins WM. Mechanisms of promiscuity among drug metabolizing enzymes and drug transporters. FEBS J 2020; 287:1306-1322. [PMID: 31663687 PMCID: PMC7138722 DOI: 10.1111/febs.15116] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 10/04/2019] [Accepted: 10/29/2019] [Indexed: 12/11/2022]
Abstract
Detoxication, or 'drug-metabolizing', enzymes and drug transporters exhibit remarkable substrate promiscuity and catalytic promiscuity. In contrast to substrate-specific enzymes that participate in defined metabolic pathways, individual detoxication enzymes must cope with substrates of vast structural diversity, including previously unencountered environmental toxins. Presumably, evolution selects for a balance of 'adequate' kcat /KM values for a wide range of substrates, rather than optimizing kcat /KM for any individual substrate. However, the structural, energetic, and metabolic properties that achieve this balance, and hence optimize detoxication, are not well understood. Two features of detoxication enzymes that are frequently cited as contributions to promiscuity include the exploitation of highly reactive versatile cofactors, or cosubstrates, and a high degree of flexibility within the protein structure. This review examines these intuitive mechanisms in detail and clarifies the contributions of the classic ligand binding models 'induced fit' (IF) and 'conformational selection' (CS) to substrate promiscuity. The available literature data for drug metabolizing enzymes and transporters suggest that IF is exploited by these promiscuous detoxication enzymes, as it is with substrate-specific enzymes, but the detoxication enzymes uniquely exploit 'IFs' to retain a wide range of substrates at their active sites. In contrast, whereas CS provides no catalytic advantage to substrate-specific enzymes, promiscuous enzymes may uniquely exploit it to recruit a wide range of substrates. The combination of CS and IF, for recruitment and retention of substrates, can potentially optimize the promiscuity of drug metabolizing enzymes and drug transporters.
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Affiliation(s)
- William M. Atkins
- Department of Medicinal ChemistryUniversity of WashingtonSeattleWAUSA
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31
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Chien M, Anderson TK, Jockusch S, Tao C, Kumar S, Li X, Russo JJ, Kirchdoerfer RN, Ju J. Nucleotide Analogues as Inhibitors of SARS-CoV-2 Polymerase. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.03.18.997585. [PMID: 32511320 PMCID: PMC7239050 DOI: 10.1101/2020.03.18.997585] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
SARS-CoV-2, a member of the coronavirus family, is responsible for the current COVID-19 pandemic. Based on our analysis of hepatitis C virus and coronavirus replication, and the molecular structures and activities of viral inhibitors, we previously demonstrated that three nucleotide analogues inhibit the SARS-CoV RNA-dependent RNA polymerase (RdRp). Here, using polymerase extension experiments, we have demonstrated that the active triphosphate form of Sofosbuvir (a key component of the FDA approved hepatitis C drug EPCLUSA), is incorporated by SARS-CoV-2 RdRp, and blocks further incorporation. Using the same molecular insight, we selected the active triphosphate forms of three other anti-viral agents, Alovudine, AZT (an FDA approved HIV/AIDS drug) and Tenofovir alafenamide (TAF, an FDA approved drug for HIV and hepatitis B) for evaluation as inhibitors of SARS-CoV-2 RdRp. We demonstrated the ability of these three viral polymerase inhibitors, 3'-fluoro-3'-deoxythymidine triphosphate, 3'-azido-3'-deoxythymidine triphosphate and Tenofovir diphosphate (the active triphosphate forms of Alovudine, AZT and TAF, respectively) to be incorporated by SARS-CoV-2 RdRp, where they also terminate further polymerase extension. These results offer a strong molecular basis for these nucleotide analogues to be evaluated as potential therapeutics for COVID-19.
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Affiliation(s)
- Minchen Chien
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY 10027
- Department of Chemical Engineering, Columbia University, New York, NY 10027
| | - Thomas K. Anderson
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706
- Institute of Molecular Virology, University of Wisconsin-Madison, Madison, WI 53706
| | - Steffen Jockusch
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY 10027
- Department of Chemistry, Columbia University, New York, NY 10027
| | - Chuanjuan Tao
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY 10027
- Department of Chemical Engineering, Columbia University, New York, NY 10027
| | - Shiv Kumar
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY 10027
- Department of Chemical Engineering, Columbia University, New York, NY 10027
| | - Xiaoxu Li
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY 10027
- Department of Chemical Engineering, Columbia University, New York, NY 10027
| | - James J. Russo
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY 10027
- Department of Chemical Engineering, Columbia University, New York, NY 10027
| | - Robert N. Kirchdoerfer
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706
- Institute of Molecular Virology, University of Wisconsin-Madison, Madison, WI 53706
| | - Jingyue Ju
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY 10027
- Department of Chemical Engineering, Columbia University, New York, NY 10027
- Department of Pharmacology, Columbia University, New York, NY 10027
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32
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Caldwell HS, Ngo K, Pata JD, Kramer LD, Ciota AT. West Nile Virus fidelity modulates the capacity for host cycling and adaptation. J Gen Virol 2020; 101:410-419. [PMID: 32068528 DOI: 10.1099/jgv.0.001393] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The fidelity of flaviviruses is thought to be tightly regulated for optimal fitness within and between hosts. West Nile virus (WNV) high-fidelity (HiFi) mutations V793I and G806R within the RNA-dependent RNA polymerase, and low-fidelity (LoFi) mutation T248I within the methyltransferase, were previously shown to attenuate infectivity and replicative fitness in Culex mosquitoes and Culex tarsalis (CXT) cells but not in mammalian cells. We hypothesized that fidelity alterations would modify adaptation and maintenance in a host-specific manner. To test this hypothesis, wild-type (WT), HiFi (V793I/G806R) and LoFi (T248I) variants were sequentially passaged eight times in avian (PDE) or mosquito cells, or alternately between the two. Initial characterization confirmed that fidelity mutants are attenuated in mosquito, but not avian, cells. Deep sequencing revealed mutations unique to both cell lines and fidelity mutants, including ENV G1378A, a mutation associated with avian cell adaptation. To characterize maintenance and adaptation, viral outputs were monitored throughout passaging and viral fitness was assessed. The results indicate that fidelity mutants can at times recover fitness during mosquito cell passage, but remain attenuated relative to WT. Despite similar initial fitness, LoFi mutants were impaired during sequential passage in avian cells. Conversely, HiFi mutants passaged in avian cells showed increased adaptation, suggesting that increased fidelity may be advantageous in avian hosts. Although some adaptation occurred with individual mutants, the output titres of fidelity mutants were on average lower and were often lost during host switching. These data confirm that arbovirus fidelity is likely fine-tuned to maximize survival in disparate hosts.
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Affiliation(s)
- Haley S Caldwell
- The Arbovirus Laboratory, Wadsworth Center, New York State Department of Health, Slingerlands, NY, USA.,Department of Biomedical Sciences, State University of New York at Albany School of Public Health, Albany, NY, USA
| | - Kiet Ngo
- The Arbovirus Laboratory, Wadsworth Center, New York State Department of Health, Slingerlands, NY, USA
| | - Janice D Pata
- Department of Biomedical Sciences, State University of New York at Albany School of Public Health, Albany, NY, USA
| | - Laura D Kramer
- The Arbovirus Laboratory, Wadsworth Center, New York State Department of Health, Slingerlands, NY, USA.,Department of Biomedical Sciences, State University of New York at Albany School of Public Health, Albany, NY, USA
| | - Alexander T Ciota
- The Arbovirus Laboratory, Wadsworth Center, New York State Department of Health, Slingerlands, NY, USA.,Department of Biomedical Sciences, State University of New York at Albany School of Public Health, Albany, NY, USA
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33
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Du Pont KE, Davidson RB, McCullagh M, Geiss BJ. Motif V regulates energy transduction between the flavivirus NS3 ATPase and RNA-binding cleft. J Biol Chem 2020; 295:1551-1564. [PMID: 31914411 PMCID: PMC7008374 DOI: 10.1074/jbc.ra119.011922] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 12/22/2019] [Indexed: 01/01/2023] Open
Abstract
The unwinding of dsRNA intermediates is critical for the replication of flavivirus RNA genomes. This activity is provided by the C-terminal helicase domain of viral nonstructural protein 3 (NS3). As a member of the superfamily 2 (SF2) helicases, NS3 requires the binding and hydrolysis of ATP/NTP to translocate along and unwind double-stranded nucleic acids. However, the mechanism of energy transduction between the ATP- and RNA-binding pockets is not well-understood. Previous molecular dynamics simulations conducted by our group have identified Motif V as a potential "communication hub" for this energy transduction pathway. To investigate the role of Motif V in this process, here we combined molecular dynamics, biochemistry, and virology approaches. We tested Motif V mutations in both the replicon and recombinant protein systems to investigate viral genome replication, RNA-binding affinity, ATP hydrolysis activity, and helicase-mediated unwinding activity. We found that the T407A and S411A substitutions in NS3 reduce viral replication and increase the helicase-unwinding turnover rates by 1.7- and 3.5-fold, respectively, suggesting that flaviviruses may use suboptimal NS3 helicase activity for optimal genome replication. Additionally, we used simulations of each mutant to probe structural changes within NS3 caused by each mutation. These simulations indicate that Motif V controls communication between the ATP-binding pocket and the helical gate. These results help define the linkage between ATP hydrolysis and helicase activities within NS3 and provide insight into the biophysical mechanisms for ATPase-driven NS3 helicase function.
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Affiliation(s)
- Kelly E Du Pont
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523; Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado 80523
| | - Russell B Davidson
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523
| | - Martin McCullagh
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523.
| | - Brian J Geiss
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado 80523; School of Biomedical Engineering, Colorado State University, Fort Collins, Colorado 80523.
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Kamelian K, Montoya V, Olmstead A, Dong W, Harrigan R, Morshed M, Joy JB. Phylogenetic surveillance of travel-related Zika virus infections through whole-genome sequencing methods. Sci Rep 2019; 9:16433. [PMID: 31712570 PMCID: PMC6848190 DOI: 10.1038/s41598-019-52613-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 10/21/2019] [Indexed: 01/11/2023] Open
Abstract
In 2018, the World Health Organization identified the Zika virus (ZIKV) as a pathogen that should be prioritized for public health research due to its epidemic potential. In this study, whole-genome sequencing (WGS) of travel-acquired ZIKV infections was used to examine the limitations of phylogenetic analysis. WGS and phylogenetic analysis were performed to investigate geographic clustering of samples from five Canadians with travel-acquired ZIKV infections and to assess the limitations of phylogenetic analysis of ZIKV sequences using a phylogenetic cluster approach. Genomic variability of ZIKV samples was assessed and for context, compared with hepatitis C virus (HCV) samples. Phylogenetic analysis confirmed the suspected region of ZIKV infection for one of five samples and one sample failed to cluster with sequences from its suspected country of infection. Travel-acquired ZIKV samples depicted low genomic variability relative to HCV samples. A floating patristic distance threshold classified all pre-2000 ZIKV sequences into separate clusters, while only Cambodian, Peruvian, Malaysian, and South Korean sequences were similarly classifiable. While phylogenetic analysis of ZIKV data can identify the broad geographical region of ZIKV infection, ZIKV’s low genomic variability is likely to limit precise interpretations of phylogenetic analysis of the origins of travel-related cases.
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Affiliation(s)
- Kimia Kamelian
- University of British Columbia, Division of AIDS, Department of Medicine, Vancouver, BC, Canada.,BC Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | | | | | - Winnie Dong
- BC Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Richard Harrigan
- University of British Columbia, Division of AIDS, Department of Medicine, Vancouver, BC, Canada
| | - Muhammad Morshed
- BC Centre for Disease Control Public Health Laboratory, Vancouver, BC, Canada.,University of British Columbia, Department of Pathology and Laboratory Medicine, Vancouver, BC, Canada
| | - Jeffrey B Joy
- BC Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada. .,University of British Columbia, Division of Infectious Diseases, Department of Medicine, Vancouver, BC, Canada.
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35
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Peersen OB. A Comprehensive Superposition of Viral Polymerase Structures. Viruses 2019; 11:E745. [PMID: 31412589 PMCID: PMC6723251 DOI: 10.3390/v11080745] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 08/07/2019] [Accepted: 08/11/2019] [Indexed: 12/24/2022] Open
Abstract
Nucleic acid polymerases are essential enzymes that replicate the genomes of both RNA and DNA viruses. These enzymes are generally encoded by viruses themselves so as to provide biochemical functions and control elements that differ from those of the host cell polymerases. The core active site structure used by all replicative polymerases is highly conserved and composed of two key aspartate residues from the conserved motifs A and C, but beyond this there is significant divergence among structures. These differences can make it difficult to select which portions of structures to align for comparisons, yet there are extended structural similarities within different groups of viral polymerases that should clearly be considered to generate optimal alignments. This manuscript describes a comprehensive structure-based superposition of every viral polymerase structure solved thus far based on an alignment-tree approach wherein aligned regions grow in complexity as similarity among polymerases increases. The result is a set of 646 structures that have been aligned into a single common orientation. This provides a convenient resource for directly comparing viral polymerases and illustrating structural conservation among them. It also sets the stage for detailed bioinformatics analysis to further assess common structural features. The full set of protein data bank (PDB) formatted files is publicly available at http://www.zenodo.org/communities/pols/.
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Affiliation(s)
- Olve B Peersen
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, CO 80523-1870, USA.
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36
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Dubankova A, Boura E. Structure of the yellow fever NS5 protein reveals conserved drug targets shared among flaviviruses. Antiviral Res 2019; 169:104536. [PMID: 31202975 DOI: 10.1016/j.antiviral.2019.104536] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 06/07/2019] [Accepted: 06/12/2019] [Indexed: 12/23/2022]
Abstract
Yellow fever virus (YFV) is responsible for devastating outbreaks of Yellow fever (YF) in humans and is associated with high mortality rates. Recent large epidemics and epizootics and exponential increases in the numbers of YF cases in humans and non-human primates highlight the increasing threat YFV poses, despite the availability of an effective YFV vaccine. YFV is the first human virus discovered, but the structures of several of the viral proteins remain poorly understood. Here we report the structure of the full-length NS5 protein, a key enzyme for the replication of flaviviruses that contains both a methyltransferase domain and an RNA dependent RNA polymerase domain, at 3.1 Å resolution. The viral polymerase adopts right-hand fold, demonstrating the similarities of the Yellow fever, Dengue and Zika polymerases. Together this data suggests NS5 as a prime and ideal target for the design of pan-flavivirus inhibitors.
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Affiliation(s)
- Anna Dubankova
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Nam. 2, 166 10, Prague 6, Czech Republic
| | - Evzen Boura
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Nam. 2, 166 10, Prague 6, Czech Republic.
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37
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Smertina E, Urakova N, Strive T, Frese M. Calicivirus RNA-Dependent RNA Polymerases: Evolution, Structure, Protein Dynamics, and Function. Front Microbiol 2019; 10:1280. [PMID: 31244803 PMCID: PMC6563846 DOI: 10.3389/fmicb.2019.01280] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 05/22/2019] [Indexed: 12/11/2022] Open
Abstract
The Caliciviridae are viruses with a positive-sense, single-stranded RNA genome that is packaged into an icosahedral, environmentally stable protein capsid. The family contains five genera (Norovirus, Nebovirus, Sapovirus, Lagovirus, and Vesivirus) that infect vertebrates including amphibians, reptiles, birds, and mammals. The RNA-dependent RNA polymerase (RdRp) replicates the genome of RNA viruses and can speed up evolution due to its error-prone nature. Studying calicivirus RdRps in the context of genuine virus replication is often hampered by a lack of suitable model systems. Enteric caliciviruses and RHDV in particular are notoriously difficult to propagate in cell culture; therefore, molecular studies of replication mechanisms are challenging. Nevertheless, research on recombinant proteins has revealed several unexpected characteristics of calicivirus RdRps. For example, the RdRps of RHDV and related lagoviruses possess the ability to expose a hydrophobic motif, to rearrange Golgi membranes, and to copy RNA at unusually high temperatures. This review is focused on the structural dynamics, biochemical properties, kinetics, and putative interaction partners of these RdRps. In addition, we discuss the possible existence of a conserved but as yet undescribed structural element that is shared amongst the RdRps of all caliciviruses.
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Affiliation(s)
- Elena Smertina
- Commonwealth Scientific and Industrial Research Organisation, Health and Biosecurity, Canberra, ACT, Australia
- Faculty of Science and Technology, University of Canberra, Canberra, ACT, Australia
| | - Nadya Urakova
- Department of Entomology, Pennsylvania State University, University Park, PA, United States
| | - Tanja Strive
- Commonwealth Scientific and Industrial Research Organisation, Health and Biosecurity, Canberra, ACT, Australia
- Invasive Animals Cooperative Research Centre, University of Canberra, Canberra, ACT, Australia
| | - Michael Frese
- Faculty of Science and Technology, University of Canberra, Canberra, ACT, Australia
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38
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Zavyalova E, Kopylov A. Energy Transfer as A Driving Force in Nucleic Acid⁻Protein Interactions. Molecules 2019; 24:molecules24071443. [PMID: 30979095 PMCID: PMC6480146 DOI: 10.3390/molecules24071443] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 04/10/2019] [Accepted: 04/11/2019] [Indexed: 12/19/2022] Open
Abstract
Many nucleic acid–protein structures have been resolved, though quantitative structure-activity relationship remains unclear in many cases. Thrombin complexes with G-quadruplex aptamers are striking examples of a lack of any correlation between affinity, interface organization, and other common parameters. Here, we tested the hypothesis that affinity of the aptamer–protein complex is determined with the capacity of the interface to dissipate energy of binding. Description and detailed analysis of 63 nucleic acid–protein structures discriminated peculiarities of high-affinity nucleic acid–protein complexes. The size of the amino acid sidechain in the interface was demonstrated to be the most significant parameter that correlates with affinity of aptamers. This observation could be explained in terms of need of efficient energy transfer from interacting residues. Application of energy dissipation theory provided an illustrative tool for estimation of efficiency of aptamer–protein complexes. These results are of great importance for a design of efficient aptamers.
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Affiliation(s)
| | - Alexey Kopylov
- Chemistry Department, Lomonosov Moscow State University, 119991 Moscow, Russia.
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Ben Ouirane K, Boulard Y, Bressanelli S. The hepatitis C virus RNA-dependent RNA polymerase directs incoming nucleotides to its active site through magnesium-dependent dynamics within its F motif. J Biol Chem 2019; 294:7573-7587. [PMID: 30867194 DOI: 10.1074/jbc.ra118.005209] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Revised: 03/12/2019] [Indexed: 12/13/2022] Open
Abstract
RNA viruses synthesize new genomes in the infected host thanks to dedicated, virally-encoded RNA-dependent RNA polymerases (RdRps). As such, these enzymes are prime targets for antiviral therapy, as has recently been demonstrated for hepatitis C virus (HCV). However, peculiarities in the architecture and dynamics of RdRps raise fundamental questions about access to their active site during RNA polymerization. Here, we used molecular modeling and molecular dynamics simulations, starting from the available crystal structures of HCV NS5B in ternary complex with template-primer duplexes and nucleotides, to address the question of ribonucleotide entry into the active site of viral RdRp. Tracing the possible passage of incoming UTP or GTP through the RdRp-specific entry tunnel, we found two successive checkpoints that regulate nucleotide traffic to the active site. We observed that a magnesium-bound nucleotide first binds next to the tunnel entry, and interactions with the triphosphate moiety orient it such that its base moiety enters first. Dynamics of RdRp motifs F1 + F3 then allow the nucleotide to interrogate the RNA template base prior to nucleotide insertion into the active site. These dynamics are finely regulated by a second magnesium dication, thus coordinating the entry of a magnesium-bound nucleotide with shuttling of the second magnesium necessary for the two-metal ion catalysis. The findings of our work suggest that at least some of these features are general to viral RdRps and provide further details on the original nucleotide selection mechanism operating in RdRps of RNA viruses.
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Affiliation(s)
- Kaouther Ben Ouirane
- From the Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette cedex, France
| | - Yves Boulard
- From the Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette cedex, France
| | - Stéphane Bressanelli
- From the Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette cedex, France
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