Enzymes Pub Date : 2021-01-01 Epub Date: 2021-07-24 DOI: 10.1016/bs.enz.2021.06.009

Yeonoh Shin, Katsuhiko S Murakami

引用次数: 1

HCV RdRp, sofosbuvir and beyond. HCV RdRp，索非布韦及其他。

Enzymes Pub Date : 2021-01-01 Epub Date: 2021-09-24 DOI: 10.1016/bs.enz.2021.06.003

Joy Y Feng, Adrian S Ray

{"title":"HCV RdRp, sofosbuvir and beyond.","authors":"Joy Y Feng, Adrian S Ray","doi":"10.1016/bs.enz.2021.06.003","DOIUrl":"https://doi.org/10.1016/bs.enz.2021.06.003","url":null,"abstract":"The therapeutic targeting of the nonstructural protein 5B (NS5B) RNA-dependent RNA polymerase (RdRp) of the Hepatitis C Virus (HCV) with nucleotide analogs led to a deep understanding of this enzymes structure, function and substrate specificity. Unlike previously studied DNA polymerases including the reverse transcriptase of Human Immunodeficiency Virus, development of biochemical assays for HCV RdRp proved challenging due to low solubility of the full-length protein and inefficient acceptance of exogenous primer/templates. Despite the poor apparent specific activity, HCV RdRp was found to support rapid and processive transcription once elongation is initiated in vitro consistent with its high level of viral replication in the livers of patients. Understanding of the substrate specificity of HCV RdRp led to the discovery of the active triphosphate of sofosbuvir as a nonobligate chain-terminator of viral RNA transcripts. The ternary crystal structure of HCV RdRp, primer/template, and incoming nucleotide showed the interaction between the nucleotide analog and the 2'-hydroxyl binding pocket and how an unfit mutation of serine 282 to threonine results in resistance by interacting with the uracil base and modified 2'-position of the analog. Host polymerases mediate off-target toxicity of nucleotide analogs and the active metabolite of sofosbuvir was found to not be efficiently incorporated by host polymerases including the mitochondrial RNA polymerase (POLRMT). Knowledge from studying inhibitors of HCV RdRp serves to advance antiviral drug discovery for other emerging RNA viruses including the discovery of remdesivir as an inhibitor of severe acute respiratory syndrome coronavirus 2 (SARS-CoV2), the virus that causes COVID-19.","PeriodicalId":39097,"journal":{"name":"Enzymes","volume":" ","pages":"63-82"},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39560062","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 5

Viral genome packaging machines: Structure and enzymology. 病毒基因组包装机：结构和酶学。

Enzymes Pub Date : 2021-01-01 Epub Date: 2021-11-10 DOI: 10.1016/bs.enz.2021.09.006

Carlos E Catalano, Marc C Morais

引用次数: 0

Mechanisms of inhibition of viral RNA replication by nucleotide analogs. 核苷酸类似物抑制病毒RNA复制的机制。

Enzymes Pub Date : 2021-01-01 Epub Date: 2021-09-27 DOI: 10.1016/bs.enz.2021.07.001

Kenneth A Johnson, Tyler Dangerfield

引用次数: 7

Allosteric and dynamic control of RNA-dependent RNA polymerase function and fidelity. RNA依赖性RNA聚合酶功能和保真度的变构和动态控制。

Enzymes Pub Date : 2021-01-01 Epub Date: 2021-07-19 DOI: 10.1016/bs.enz.2021.06.001

Dennis S Winston, David D Boehr

{"title":"Allosteric and dynamic control of RNA-dependent RNA polymerase function and fidelity.","authors":"Dennis S Winston, David D Boehr","doi":"10.1016/bs.enz.2021.06.001","DOIUrl":"https://doi.org/10.1016/bs.enz.2021.06.001","url":null,"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.","PeriodicalId":39097,"journal":{"name":"Enzymes","volume":" ","pages":"149-193"},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39569529","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Structural basis of viral RNA-dependent RNA polymerase nucleotide addition cycle in picornaviruses. 小核糖核酸病毒RNA依赖RNA聚合酶核苷酸加成周期的结构基础。

Enzymes Pub Date : 2021-01-01 Epub Date: 2021-07-19 DOI: 10.1016/bs.enz.2021.06.002

Peng Gong

引用次数: 6

Single-cell analysis for the study of viral inhibitors. 用于病毒抑制剂研究的单细胞分析。

Enzymes Pub Date : 2021-01-01 Epub Date: 2021-08-23 DOI: 10.1016/bs.enz.2021.07.004

Mohamad S Sotoudegan, Jamie J Arnold, Craig E Cameron

{"title":"Single-cell analysis for the study of viral inhibitors.","authors":"Mohamad S Sotoudegan, Jamie J Arnold, Craig E Cameron","doi":"10.1016/bs.enz.2021.07.004","DOIUrl":"https://doi.org/10.1016/bs.enz.2021.07.004","url":null,"abstract":"Stochastic outcomes of viral infections are attributed in large part to multiple layers of intrinsic and extrinsic heterogeneity that exist within a population of cells and viruses. Traditional methods in virology often lack the ability to demonstrate cell-to-cell variability in response to the invasion of viruses, and to decipher the sources of heterogeneities that are reflected in the variable infection dynamics. To overcome this challenge, the field of single-cell virology emerged less than a decade ago, enabling researchers to reveal the behavior of single, isolated, infected cells that has been masked in population-based assays. The use of microfluidics in single-cell virology, in particular, has resulted in the development of high-throughput devices that are capable of capturing, isolating, and monitoring single infected cells over the duration of an infection. Results from the studies of viral infection dynamics presented in this chapter indicate how single-cell data provide a more accurate prediction of the start time, replication rate, duration, and yield of infection when compared to population-based data. Additionally, single-cell analysis reveals striking differences between genetically distinct viruses that are almost indistinguishable in population methods. Importantly, both the efficacy and distinct mechanisms of action of antiviral compounds can be elucidated by using single-cell analysis.","PeriodicalId":39097,"journal":{"name":"Enzymes","volume":" ","pages":"195-213"},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39569530","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Picornaviral 2C proteins: A unique ATPase family critical in virus replication. 小核糖核酸病毒2C蛋白:一个独特的atp酶家族，在病毒复制中起关键作用。

Enzymes Pub Date : 2021-01-01 Epub Date: 2021-07-24 DOI: 10.1016/bs.enz.2021.06.008

Pu Chen, Zhijian Li, Sheng Cui

{"title":"Picornaviral 2C proteins: A unique ATPase family critical in virus replication.","authors":"Pu Chen, Zhijian Li, Sheng Cui","doi":"10.1016/bs.enz.2021.06.008","DOIUrl":"https://doi.org/10.1016/bs.enz.2021.06.008","url":null,"abstract":"The 2C proteins of Picornaviridae are unique members of AAA+ protein family. Although picornavirus 2C shares many conserved motifs with Super Family 3 DNA helicases, duplex unwinding activity of many 2C proteins remains undetected, and high-resolution structures of 2C hexamers are unavailable. All characterized 2C proteins exhibit ATPase activity, but the purpose of ATP hydrolysis is not fully understood. 2C is highly conserved among picornaviruses and plays crucial roles in nearly all steps of the virus lifecycle. It is therefore considered as an effective target for broad-spectrum antiviral drug development. Crystallographic investigation of enterovirus 2C proteins provide structural details important for the elucidation of 2C function and development of antiviral drugs. This chapter summarizes not only the findings of enzymatic activities, biochemical and structural characterizations of the 2C proteins, but also their role in virus replication, immune evasion and morphogenesis. The linkage between structure and function of the 2C proteins is discussed in detail. Inhibitors targeting the 2C proteins are also summarized to provide an overview of drug development. Finally, we raise several key questions to be addressed in this field and provide future research perspective on this unique class of ATPases.","PeriodicalId":39097,"journal":{"name":"Enzymes","volume":" ","pages":"235-264"},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39569532","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Retroviral integrase: Structure, mechanism, and inhibition. 逆转录病毒整合酶:结构、机制和抑制。

Enzymes Pub Date : 2021-01-01 Epub Date: 2021-08-23 DOI: 10.1016/bs.enz.2021.06.007

Dario Oliveira Passos, Min Li, Robert Craigie, Dmitry Lyumkis

引用次数: 5

DNA polymerases of herpesviruses and their inhibitors. 疱疹病毒的DNA聚合酶及其抑制剂。

Enzymes Pub Date : 2021-01-01 Epub Date: 2021-09-01 DOI: 10.1016/bs.enz.2021.07.003

Jocelyne Piret, Guy Boivin

{"title":"DNA polymerases of herpesviruses and their inhibitors.","authors":"Jocelyne Piret, Guy Boivin","doi":"10.1016/bs.enz.2021.07.003","DOIUrl":"https://doi.org/10.1016/bs.enz.2021.07.003","url":null,"abstract":"Human herpesviruses are large double-stranded DNA viruses belonging to the Herpesviridae family. The main characteristics of these viruses are their ability to establish a lifelong latency into the host with a potential to reactivate periodically. Primary infections and reactivations with herpesviruses are responsible for a large spectrum of diseases and may result in severe complications in immunocompromised patients. The viral DNA polymerase is a key enzyme in the replicative cycle of herpesviruses, and the target of most antiviral agents (i.e., nucleoside, nucleotide and pyrophosphate analogs). However, long-term prophylaxis and treatment with these antivirals may lead to the emergence of drug-resistant isolates harboring mutations in genes encoding viral enzymes that phosphorylate drugs (nucleoside analogs) and/or DNA polymerases, with potential cross-resistance between the different analogs. Drug resistance mutations mainly arise in conserved regions of the polymerase and exonuclease functional domains of these enzymes. In the polymerase domain, mutations associated with resistance to nucleoside/nucleotide analogs may directly or indirectly affect drug binding or incorporation into the primer strand, or increase the rate of extension of DNA to overcome chain termination. In the exonuclease domain, mutations conferring resistance to nucleoside/nucleotide analogs may reduce the rate of excision of incorporated drug, or continue DNA elongation after drug incorporation without excision. Mutations associated with resistance to pyrophosphate analogs may alter drug binding or the conformational changes of the polymerase domain required for an efficient activity of the enzyme. Novel herpesvirus inhibitors with a potent antiviral activity against drug-resistant isolates are thus needed urgently.","PeriodicalId":39097,"journal":{"name":"Enzymes","volume":" ","pages":"79-132"},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39958017","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 3

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