Predictions in Clinical Efficiency of SARS-CoV-2 RNA-Dependent RNA Polymerase (RdRp) Inhibitors by Molecular Docking

This study utilizes the enzyme-substrate complex theory to predict the clinical efficacy of COVID-19 treatments at the biological systems level, using molecular docking stability indicators. Experimental data from the Protein Data Bank and molecular structures generated by AlphaFold 3 were used to create macromolecular complex templates. Six templates were developed, including the holo nsp7-nsp8-nsp12 (RNA-dependent RNA polymerase) complex with dsRNA primers (holo-RdRp-RNA). The study evaluated several ligands—Favipiravir-RTP, Remdesivir, Abacavir, Ribavirin, and Oseltamivir—as potential viral RNA polymerase inhibitors. Notably, the first four of these ligands have been clinically employed in the treatment of COVID-19, allowing for comparative analysis. Molecular docking simulations were performed using AutoDock 4, and statistical differences were assessed through t-tests and Mann-Whitney U tests. A review of the literature on COVID-19 treatment outcomes and inhibitors targeting RNA polymerase enzymes was conducted, and the inhibitors were ranked according to their clinical efficacy: Remdesivir > Favipiravir-RTP > Oseltamivir. Docking results obtained from the second and third templates aligned with clinical observations. Furthermore, Abacavir demonstrated a predicted efficacy comparable to Favipiravir-RTP, while Ribavirin exhibited a predicted efficacy similar to that of Remdesivir. This research, focused on inhibitors of SARS-CoV-2 RNA-dependent RNA polymerase, establishes a framework for screening AI-generated drug templates based on clinical outcomes. Additionally, it develops a drug screening platform based on molecular docking binding energy, enabling the evaluation of novel or repurposed drugs and potentially accelerating the drug development process.

Analysis of RNA-Dependent RNA Polymerase Sequence of Infectious Flacherie Virus Isolated in China and Its Expression in BmN Cells

Full gene sequence of RNA-dependent RNA polymerase （RdRp） from Bombyx mori infectious flacherie virus isolated in Zhejiang Province, China （Zhejiang01/CHN/2002） was cloned. The sequence was 1 920 nucleotides in length coding 639 amino acid residues. Sequences comparison of RdRp showed Zhejiang01/CHN/2002 was 99.7% nucleotide sequence and 99.1% amino acids sequence homology with Japanese strain. The RdRp sequence was aligned with 8 representative picorna（-like） viruses and 8 highly conserved regions were detected. The result indicated their relevance function. Phylogenetic tree of 14 picorna（-like） viruses which RdRp presumed protein sequences revealed that the viruses from Iflavirus genus formed an independent clade. The RdRp was successfully expressed in BmN cells using Bac-to-Bac expression system.

Crystal structures of RNA-dependent RNA polymerases from Jingmen tick virus and Alongshan virus

Jingmenviruses are a group of flavi-like viruses with segmented genome and have been found in various types of hosts,including humans,cattle,monkeys,bats,rodents,sheep,ticks,mosquitoes and nematodes.Jingmenviruses,including the Jingmen tick virus(JMTV)and Alongshan virus(ALSV),have been associated with febrile illness and flu-like symptoms in humans.Viral polymerase plays critical roles in genome replication and transcription and is an ideal target for antiviral drugs.Here,we determined the crystal structures of RNA-dependent RNA polymerase(RdRp)domains of JMTV and ALSV at 2.6Åand 3.2Åresolutions,respectively.The overall structures of JMTV and ALSV RdRp domains are similar to those from the typical unsegmented viruses in Flaviviridae family,especially the Flavivirus genus.JMTV and ALSV RdRps can be divided into three subdomains and the catalytical Motif A-G are conserved like the typical flaviviruses,whereas the zinc-binding pockets are absent from the JMTV and ALSV RdRps.The 50-ends of jingmenvirus genomes are varied in length and sequence,and a highly conserved 8-nucleotide element located on the tip of stem loop A was identified and shown to be required for binding with RdRp and performing de novo replication activity.These findings provide important structural insights into RdRp of segmented flavivirus and reveal the key region of virus genome responsible for replication initiation,which would promote molecular understanding of segmented flavivirus replication and the structure-based design of antiviral drugs against flaviviruses.

Unusual substructure conformations observed in crystal structures of a dicistrovirus RNA-dependent RNA polymerase suggest contribution of the N-terminal extension in proper folding

The Dicistroviridae is a virus family that includes many insect pathogens.These viruses contain a positive-sense RNA genome that is replicated by the virally encoded RNA-dependent RNA polymerase(RdRP)also named 3D^(pol).Compared with the Picornaviridae RdRPs such as poliovirus(PV)3D^(pol),the Dicistroviridae representative Israeli acute paralysis virus(IAPV)3D^(pol) has an additional N-terminal extension(NE)region that is about 40-residue in length.To date,both the structure and catalytic mechanism of the Dicistroviridae RdRP have remain elusive.Here we reported crystal structures of two truncated forms of IAPV 3D^(pol),namelyΔ85 andΔ40,both missing the NE region,and the 3D^(pol) protein in these structures exhibited three conformational states.The palm and thumb domains of these IAPV 3D^(pol) structures are largely consistent with those of the PV 3D^(pol) structures.However,in all structures,the RdRP fingers domain is partially disordered,while different conformations of RdRP substructures and interactions between them are also present.In particular,a large-scale conformational change occurred in the motif B-middle finger region in one protein chain of theΔ40 structure,while a previously documented alternative conformation of motif A was observed in all IAPV structures.These experimental data on one hand show intrinsic conformational variances of RdRP substructures,and on the other hand suggest possible contribution of the NE region in proper RdRP folding in IAPV.

Structures of EV71 RNA-dependent RNA polymerase in complex with substrate and analogue provide a drug target against the hand-foot-and-mouth disease pandemic in China

Enterovirus 71(EV71),one of the major causative agents for hand-foot-and-mouth disease(HFMD),has caused more than 100 deaths among Chinese children since March 2008.The EV71 genome encodes an RNAdependent RNA polymerase(RdRp),denoted 3D^(pol),which is central for viral genome replication and is a key target for the discovery of specific antiviral therapeutics.Here we report the crystal structures of EV71 RdRp(3D^(pol))and in complex with substrate guanosine-5'-triphosphate and analog 5-bromouridine-5'-triphosphate best to 2.4Åresolution.The structure of EV71 RdRp(3D^(pol))has a wider open thumb domain compared with the most closely related crystal structure of poliovirus RdRp.And the EV71 RdRp(3D^(pol))complex with GTP or Br-UTP bounded shows two distinct movements of the polymerase by substrate or analogue binding.The model of the complex with the template:primer derived by superimposition with foot-and-mouth disease virus(FMDV)3D/RNA complex reveals the likely recognition and binding of template:primer RNA by the polymerase.These results together provide a molecular basis for EV71 RNA replication and reveal a potential target for anti-EV71 drug discovery.

Crystal structure of the coxsackievirus A16 RNA-dependent RNA polymerase elongation complex reveals novel features in motif A dynamics

Dear Editor, Coxsackievirus A16 （CV A16） and enterovirus 71 （EV71） are currently the two primary causative agents of hand- foot-and-mouth disease （HFMD） （Solomon et al., 2010; Mao et al., 2014）, threatening health of children world- wide. They both belong to the Enterovirus genus of the Picornaviridae family, and have single-stranded positive- sense RNA genomes of about 7.5 kilobases （kb） in length. As with other positive-strand RNA viruses, the genome rep- lication process ofCV A16 is carried out by a membrane- associated replication complex with the virally encoded RNA-dependent RNA polymerase （RdRP） as the essential catalytic enzyme.

RNA-DEPENDENT RNA POLYMERASE ASSOCIATED WITH WHEAT ROSETTE STUNT VIRIONS

Wheat rosette stunt virus (WRSV) contains an RNA-dependent RNA polymerase. The RNA polymerase activity is associated with the viral nucleocapsid (NP).In vitro transcription of purified NP required all of the four nucleoside triphosphates and Mg^(2+).There was a need of a proper salt concentration and some reducing reagents in the system for increasing the RNA polymerase activity.The optimum temperature for in vitro transcription was around 25℃.Within the first 90 min of in vitro reaction, incorporation rose linearly with the time course of incubation. The experiments of ribonuclease and deoxyribonuclease treatments showed that single-stranded RNAs were synthesized in vitro by the RNA polymerase.Two fractions of WRSV-NP could be separated by SDS-dissociation and ultracentrifugation.The supernatant fraction contained three structural proteins of NP: L, N and NS;and the pellet fraction contained the viral RNA.When the supernatant proteins and the viral RNA were mixed together, RNA polymerase activity could be reconstituted.When the ratio between the amounts of the supernatant proteins and the viral RNA in the mixture was about 100:7.7, the reconstituted RNA polymerase activity reached the maximum.

Alternative Role of Motif B in Template Dependent Polymerase Inhibition

Severe acute respiratory syndrome coronavirus 2(SARS-Co V-2) relies on the central molecular machine RNA-dependent RNA polymerase(Rd Rp) for the viral replication and transcription. Remdesivir at the template strand has been shown to effectively inhibit the RNA synthesis in SARS-Co V-2 Rd Rp by deactivating not only the complementary UTP incorporation but also the next nucleotide addition. However, the underlying molecular mechanism of the second inhibitory point remains unclear. In this work, we have performed molecular dynamics simulations and demonstrated that such inhibition has not directly acted on the nucleotide addition at the active site. Instead, the translocation of Remdesivir from +1 to-1 site is hindered thermodynamically as the posttranslocation state is less stable than the pre-translocation state due to the motif B residue G683. Moreover, another conserved residue S682 on motif B further hinders the dynamic translocation of Remdesivir due to the steric clash with the 1′-cyano substitution. Overall,our study has unveiled an alternative role of motif B in mediating the translocation when Remdesivir is present in the template strand and complemented our understanding about the inhibitory mechanisms exerted by Remdesivir on the RNA synthesis in SARS-Co V-2 Rd Rp.

polo样激酶1、RNA聚合酶Ⅱ亚基A在人脑胶质瘤中的表达及与预后的关系

目的 探讨polo样激酶1(PLK1)、RNA聚合酶Ⅱ亚基A(POLR2A)在人脑胶质瘤(BG)中的表达及与预后的关系。方法 选取86例BG患者作为观察组,另选取30例非肿瘤脑疾病患者作为参照组,收集观察组患者的BG组织和参照组患者的非肿瘤脑组织。比较两组患者PLK1、POLR2A表达情况和不同临床特征BG患者的BG组织中PLK1、POLR2A的阳性表达情况;比较不同PLK1、POLR2A表达情况BG患者的生存情况;采用Cox回归模型分析BG患者预后的影响因素。结果 观察组患者PLK1、POLR2A阳性表达率分别高于参照组,差异均有统计学意义(P﹤0.05)。低分化BG患者的BG组织中PLK1、POLR2A阳性表达率均高于中高分化患者,差异均有统计学意义(P﹤0.05)。PLK1、POLR2A阳性表达患者的中位生存时间均明显短于PLK1、POLR2A阴性表达患者,差异均有统计学意义(P﹤0.01)。Cox多因素回归分析结果显示,低分化、PLK1阳性表达、POLR2A阳性表达均为BG患者预后的独立危险因素(P﹤0.05)。结论 BG患者PLK1、POLR2A呈高表达,PLK1、POLR2A高表达BG患者中位生存时间缩短,低分化、PLK1阳性表达、POLR2A阳性表达均为BG患者预后的独立危险因素。

重要人感染RNA病毒复制机制和靶向聚合酶药物开发研究进展

近年来,拉沙热、埃博拉、新冠和尼帕等多种病毒性传染病在世界范围内频繁暴发,给人类健康和社会经济发展带来了巨大威胁。广谱抗病毒药物是主动应对新发突发病毒性传染病的重要手段之一,而其研发的关键是发现病毒特有的保守药物靶点。病毒聚合酶负责病毒基因组的复制和转录过程,蛋白序列相对保守,是理想的药物靶点。本文以重要人感染RNA病毒聚合酶的工作机制和靶向病毒聚合酶的药物开发展开综述,为未来新发突发传染性疾病防控提供新思路和新策略。

Systematic identification of endogenous RNA polymeraseⅢpromoters for efficient RNA guidebased genome editing technologies in maize

Single-guide RNA(sg RNA) is one of the two core components of the CRISPR(clustered regularly interspaced short palindromic repeat)/Cas(CRISPR-associated) genome-editing technology. We established an in vitro Traffic Light Reporter(TLR) system, which is designated as the same colors as traffic lights such as green, red and yellow were produced in cells. The TLR can be readily used in maize mesophyll protoplast for a quick test of promoter activity. The TLR assay indicates the variation in transcription activities of the seven Pol III promoters, from 3.4%(U6-1) to over 21.0%(U6-6). The U6-2 promoter, which was constructed to drive sg RNA expression targeting the Zm Wx1 gene, yielded mutation efficiencies ranging from 48.5% to 97.1%. Based on the reported and unpublished data, the in vitro TLR assay results were confirmed to be a readily system and may be extended to other plant species amenable to efficient genome editing via CRISPR/Cas. Our efforts provide an efficient method of identifying native Pol III-recognized promoters for RNA guide-based genome-editing systems in maize.

The VP2 protein of grass carp reovirus(GCRV) expressed in a baculovirus exhibits RNA polymerase activity

The double-shelled grass carp reovirus （GCRV） is capable of endogenous RNA transcription and processing.Genome sequence analysis has revealed that the protein VP2,encoded by gene segment 2 （S2）,is the putative RNA-dependent RNA polymerase （RdRp）.In previous work,we have ex-pressed the functional region of VP2 that is associated with RNA polymerase activity （denoted as rVP2390-900） in E.coil and have prepared a polyclonal antibody against VP2.To characterize the GCRV RNA polymerase,a recombinant full-length VP2 （rVP2） was first constructed and expressed in a baculovirus system,as a fusion protein with an attached His-tag.Immunofluorescence （IF） assays,together with immunoblot （IB） analyses from both expressed cell extracts and purified Histagged rVP2,showed that rVP2 was successfully expressed in Sf9 cells.Further characterization of the replicase activity showed that purified rVP2 and GCRV particles exhibited poly（C）-dependent poly（G） polymerase activity.The RNA enzymatic activity required the divalent cation Mg2＋,and was optimal at 28 ℃.The results provide a foundation for further studies on the RNA polymerases of aquareoviruses during viral transcription and replication.

新型冠状病毒亚基因组RNA检测方法的建立及性能评估

目的建立检测新型冠状病毒(新冠病毒)亚基因组RNA(subgenomic RNA,sgRNA)的方法,并对所建立的方法进行性能评估。方法根据新型冠状病毒sgRNA序列设计引物和探针,建立检测sgRNA的实时荧光逆转录PCR(reverse transcription polymerase chain reaction,RT-PCR)方法,对所建立的方法进行优化,包括引物、探针的浓度及比例、延伸温度、反应体积和模板量。并对所建立的方法进行性能评估,包括最低检测限、灵敏度、特异性和重复性。对临床样本进行新冠病毒sgRNA和基因组RNA(genomic RNA,gRNA)检测,并对检测结果进行分析。结果建立了检测新冠病毒sgRNA的RT-PCR方法。所建方法的最低检测限为100 copies/mL,对常见病原体的检测结果均为阴性。对高、中、低浓度样本sgRNA进行检测,CV均<5%。115例疑似新冠病毒感染者的咽拭子样本sgRNA为阳性(115/330,阳性率为34.85%)。gRNA-N Ct值<30时,sgRNA-N的阳性率为100.00%;gRNA-N的Ct值介于30~32时,sgRNA-N的阳性率为68.75%;gRNA-N的Ct值介于32~35时,sgRNA-N的阳性率为44.44%;gRNA-N的Ct值>35时,sgRNA-N均为阴性。结论建立了新冠病毒sgRNA的RT-PCR检测方法,方法灵敏、特异、重复性好。

Small Amplicons Mutation Library for Vaccine Screening by Error-Prone Polymerase Chain Reaction

Library construction is a common method used to screen target genes in molecular biology.Most library constructions are not suitable for a small DNA library(<100 base pair(bp))and low RNA library output.To maximize the library’s complexity,error-prone polymerase chain reaction(PCR)was used to increase the base mutation rate.After introducing the DNA fragments into the competent cell,the library complexity could reach 109.Library mutation rate increased exponentially with the dilution and amplification of error-prone PCR.The error-prone PCR conditions were optimized including deoxyribonucleotide triphosphate(dNTP)concentration,Mn^(2+)concentration,Mg^(2+)concentration,PCR cycle number,and primer length.Then,a RNA library with high complexity can be obtained by in vitro transcription to meet most molecular biological screening requirements,and can also be used for mRNA vaccine screening.

Hordatines as a Potential Inhibitor of COVID-19 Main Protease and RNA Polymerase: An In-Silico Approach

Total 40 natural compounds were selected to perform the molecular docking studies to screen and identify the potent antiviral agents specifically for Severe Acute Respiratory Syndrome Coronavirus 2 that causes coronavirus disease 2019(COVID-19).The key targets of COVID-19,protease(PDB ID:7BQY)and RNA polymerase(PDB ID:7bV2)were used to dock our target compounds by Molecular Operating Environment(MOE)version 2014.09.We used 3 different conformations of protease target(6M0K,6Y2F and 7BQY)and two different score functions to strengthen the probability of inhibitors discovery.After an extensive screening analysis,20 compounds exhibit good binding affinities to one or both COVID-19 targets.7 out of 20 compounds were predicted to overcome the activity of both targets.The top 7 hits are,flacourticin(3),sagerinic acid(16),hordatine A(23),hordatine B(24),N-feruloyl tyramine dimer(25),bisavenanthramides B-5(29)and vulnibactins(40).According to our results,all these top hits was found to have a better binding scores than remdesivir,the native ligand in RNA polymerase target(PDB ID:7bV2).Hordatines are phenolic compounds present in barley,were found to exhibit the highest binding affinity to both protease and polymerase through forming strong hydrogen bonds with the catalytic residues,as well as significant interactions with other receptor-binding residues.These results probably provided an excellent lead candidate for the development of therapeutic drugs against COVID-19.Eventually,animal experiment and accurate clinical trials are needed to confirm the preventive potentials of these compounds.

流感病毒RNA碱性聚合酶-2抑制剂研究进展

季节流行性感冒是一种易在人际传播的急性病毒感染,是目前对人类健康构成威胁的主要呼吸道传染病之一。迄今为止,流感的预防和治疗主要采用接种疫苗预防和开发抗病毒药物防治并重的应对手段。目前临床应用的抗流感病毒药物包括基质蛋白-2抑制剂(如金刚烷胺)、神经氨酸酶抑制剂(如奥司他韦)、内切酶抑制剂(如巴洛沙韦酯)和聚合酶抑制剂(如法匹拉韦)等,均已产生广泛耐药性。研究开发机制新颖的、与现有药物没有交叉耐药的抗流感病毒药物是解决季节流行性感冒治疗这一尚未完全解决的医学问题,以及应对流感大规模爆发的有效手段。流感病毒RNA碱性聚合酶-2(PB2),由于其在不同流感病毒间的高度保守性而不易产生耐药性,使其成为一个非常有吸引力的药物靶点。目前PB2抑制剂的研究开发已成为抗流感病毒药物的一个热点,特别是围绕明星分子吡莫地韦及其类似物的研究吸引了极大的关注,虽然吡莫地韦因疗效不理想最终止步于Ⅲ期临床试验,但是在其研究过程中所揭示出的PB2蛋白与小分子结合模式及构效关系,为进一步开发该类药物奠定了扎实的基础。本文主要针对PB2抑制剂近10年相关药物化学的研究进展进行综述,并对该药物研究领域的前景提出展望。

Brownian ratchet mechanism of translocation in T7 RNA polymerase facilitated by a post-translocation energy bias arising from the conformational change of the enzyme

T7 RNA polymerase can transcribe DNA to RNA by translocating along the DNA. Structural studies suggest that the pivoting rotation of the O helix in the fingers domain may drive the movement of the O helix C-terminal Tyr639 from pre- to post-translocation positions. In a series of all-atom molecular dynamics simulations, we show that the movement of Tyr639 is not tightly coupled to the rotation of the O helix, and that the two processes are only weakly dependent on each other. We also show that the internal potential of the enzyme itself generates a small difference in free energy （△E） between the post- and pre-translocation positions of Tyr639. The calculated value of △E is consistent with that obtained from single-molecule experimental data. These findings lend support to a model in which the translocation takes place via a Brownian ratchet mechanism, with the small free energy bias △E arising from the conformational change of the enzyme itself.

An intermediate state of T7 RNA polymerase provides another pathway of nucleotide selection

Phage T7 RNA polymerase is a single-subunit transcription enzyme, transcribing template DNA to RNA. Nucleoside triphosphate （NTP） selection and translocation are two critical steps of the transcription elongation. Here, using all-atom molecular dynamics simulations, we found that between pre- and post-translocation states of T7 RNA polymerase an intermediate state exists, where the O helix C-terminal residue tyrosine 639, which plays important roles in translocation, locates between its pre- and post-translocation positions and the side chain of the next template DNA nucleotide has moved into the active site. NTP selection in this intermediate state was studied, revealing that the selection in the intermediate state can be achieved relying on the effect of Watson-Crick interaction between NTP and template DNA nucleotide, effect of stability of the components near the active site such as the nascent DNA-RNA hybrid and role of tyrosine 639. This indicates that another NTP-selection pathway can also exist besides the main pathway where NTP selection begins at the post-translocation state upon the entry of NTE

Probing conformational change of T7 RNA polymerase and DNA complex by solid-state nanopores

Proteins are crucial to most biological processes, such as enzymes, and in various catalytic processes a dynamic motion is required. The dynamics of protein are embodied as a conformational change, which is closely related to the flexibility of protein. Recently, nanopore sensors have become accepted as a low cost and high throughput method to study the features of proteins. In this article, we used a SiN nanopore device to study the flexibility of T7 RNA polymerase（RNAP） and its complex with DNA promoter. By calculating full-width at half-maximum（FWHM） of Gaussian fits to the blockade histograms, we found that T7 RNAP becomes more flexible after binding DNA promoter. Moreover, the distribution of fractional current blockade suggests that flexibility alters due to a breath-like change of the volume.

lncRNA Gm44981抑制心脏衰老的作用和机制研究

目的分析小鼠心脏衰老过程中长链非编码(lnc)RNA Gm44981的表达水平,探索其抑制心脏衰老的机制。方法选取3月龄年轻和24月龄年老小鼠各5只,提取心肌组织RNA后,采用实时定量聚合酶链式反应(qRT-PCR)检测Gm44981的表达水平。另选取4月龄快速老化小鼠10只,分为对照组和Gm44981过表达组(构建Gm44981过表达快速老化小鼠模型),各5只。采用qRT-PCR检测对照组和Gm44981过表达组小鼠Gm44981和衰老相关分泌表型(SASP)表达水平,β-半乳糖苷酶(SA-β-gal)染色检测SA-β-gal活性,蛋白质免疫印迹试验检测p53和Sirt1衰老相关蛋白表达水平。采用qRT-PCR检测miRNA-34a表达水平。结果Gm44981在年老小鼠的心肌组织中表达水平较年轻小鼠低,差异有统计学意义(P<0.05)。与对照组比较,Gm44981过表达组小鼠Gm44981表达上调,白细胞介素(IL)-1α和IL-6等SASP和SA-β-gal表达下调,p53表达下调,Sirt1表达上调,miRNA-34a表达下调,差异均有统计学意义(P<0.05)。结论lncRNA Gm44981在心脏衰老过程中表达下调,其可能通过作用于miRNA-34a/Sirt1抑制心脏衰老。