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The current state of validated small molecules inhibiting SARS-CoV-2 nonstructural proteins. 经验证的抑制SARS-CoV-2非结构蛋白小分子的现状。
Pub Date : 2021-08-30 eCollection Date: 2021-01-01 DOI: 10.3906/biy-2106-42
Fatih Kocabaş, Merve Uslu

The current COVID-19 outbreak has had a profound influence on public health and daily life. Despite all restrictions and vaccination programs, COVID-19 still can lead to fatality due to a lack of COVID-19-specific treatments. A number of studies have demonstrated the feasibility to develop therapeutics by targeting underlying components of the viral proteome. Here we reviewed recently developed and validated small molecule inhibitors of SARS-CoV-2's nonstructural proteins. We described the validation level of identified compounds specific for SARS-CoV-2 in the presence of in vitro and in vivo supporting data. The mechanisms of pharmacological activity, as well as approaches for developing improved SARS-CoV-2 NSP inhibitors have been emphasized.

当前新冠肺炎疫情对公共卫生和日常生活产生了深远影响。尽管有所有限制和疫苗接种计划,但由于缺乏新冠肺炎特异性治疗,新冠肺炎仍可能导致死亡。许多研究已经证明了通过靶向病毒蛋白质组的潜在成分来开发治疗方法的可行性。在这里,我们回顾了最近开发和验证的严重急性呼吸系统综合征冠状病毒2型非结构蛋白的小分子抑制剂。我们描述了在体外和体内支持数据存在的情况下,已鉴定的严重急性呼吸系统综合征冠状病毒2型特异性化合物的验证水平。强调了药理学活性的机制,以及开发改进的严重急性呼吸系统综合征冠状病毒2型NSP抑制剂的方法。
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引用次数: 1
Determination of the interaction between the receptor binding domain of 2019-nCoV spike protein, TMPRSS2, cathepsin B and cathepsin L, and glycosidic and aglycon forms of some flavonols. 确定 2019-nCoV 穗状病毒蛋白、TMPRSS2、酪蛋白酶 B 和酪蛋白酶 L 的受体结合域与某些黄酮醇的糖苷和苷元形式之间的相互作用。
Pub Date : 2021-08-30 eCollection Date: 2021-01-01 DOI: 10.3906/biy-2104-51
Erman Salih Istifli, Arzuhan Şihoğlu Tepe, Paulo A Netz, Cengiz Sarikürkcü, İbrahim Halil Kiliç, Bektaş Tepe

The novel coronavirus (COVID-19, SARS-CoV-2) is a rapidly spreading disease with a high mortality. In this research, the interactions between specific flavonols and the 2019-nCoV receptor binding domain (RBD), transmembrane protease, serine 2 (TMPRSS2), and cathepsins (CatB and CatL) were analyzed. According to the relative binding capacity index (RBCI) calculated based on the free energy of binding and calculated inhibition constants, it was determined that robinin (ROB) and gossypetin (GOS) were the most effective flavonols on all targets. While the binding free energy of ROB with the spike glycoprotein RBD, TMPRSS2, CatB, and CatL were -5.02, -7.57, -10.10, and -6.11 kcal/mol, the values for GOS were -4.67, -5.24, -8.31, and -6.76, respectively. Furthermore, both compounds maintained their stability for at least 170 ns on respective targets in molecular dynamics simulations. The molecular mechanics Poisson-Boltzmann surface area (MM/PBSA) calculations also corroborated these data. Considering Lipinski's rule of five, ROB and GOS exhibited 3 (MW>500, N or O>10, NH or OH>5), and 1 (NH or OH>5) violations, respectively. Neither ROB nor GOS showed AMES toxicity or hepatotoxicity. The LD50 of these compounds in rats were 2.482 and 2.527 mol/kg, respectively. Therefore, we conclude that these compounds could be considered as alternative therapeutic agents in the treatment of COVID-19. However, the possible inhibitory effects of these compounds on cytochromes (CYPs) should be verified by in vitro or in vivo tests and their adverse effects on cellular energy metabolism should be minimized by performing molecular modifications if necessary.

新型冠状病毒(COVID-19,SARS-CoV-2)是一种传播迅速、死亡率极高的疾病。本研究分析了特定黄酮类化合物与 2019-nCoV 受体结合域(RBD)、跨膜蛋白酶丝氨酸 2(TMPRSS2)和胰蛋白酶(CatB 和 CatL)之间的相互作用。根据结合自由能和计算出的抑制常数计算出的相对结合能力指数(RBCI),可以确定知更鸟素(ROB)和格桑吡坦(GOS)是对所有靶标最有效的黄酮醇。ROB 与穗糖蛋白 RBD、TMPRSS2、CatB 和 CatL 的结合自由能分别为 -5.02、-7.57、-10.10 和 -6.11 kcal/mol,而 GOS 的结合自由能值分别为 -4.67、-5.24、-8.31 和 -6.76。此外,在分子动力学模拟中,这两种化合物在各自的靶标上都保持了至少 170 ns 的稳定性。分子力学泊松-玻尔兹曼表面积(MM/PBSA)计算也证实了这些数据。根据利宾斯基的五项规则,ROB 和 GOS 分别表现出 3 项(MW>500、N 或 O>10、NH 或 OH>5)和 1 项(NH 或 OH>5)违反规则。ROB 和 GOS 均未显示出 AMES 毒性或肝毒性。这些化合物对大鼠的半数致死剂量分别为 2.482 和 2.527 mol/kg。因此,我们认为这些化合物可被视为治疗 COVID-19 的替代疗法。不过,这些化合物对细胞色素(CYPs)可能产生的抑制作用应通过体外或体内试验进行验证,如有必要,应通过分子改造将其对细胞能量代谢的不利影响降至最低。
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引用次数: 0
The effect of weekend curfews on epidemics: a Monte Carlo simulation. 周末宵禁对流行病的影响:蒙特卡罗模拟。
Pub Date : 2021-08-30 eCollection Date: 2021-01-01 DOI: 10.3906/biy-2105-69
Hakan Kaygusuz, A Nihat Berker

The ongoing COVID-19 pandemic is being responded with various methods, applying vaccines, experimental treatment options, total lockdowns or partial curfews. Weekend curfews are among the methods for reducing the number of infected persons, and this method is practically applied in some countries such as Turkey. In this study, the effect of weekend curfews on reducing the spread of a contagious disease, such as COVID-19, is modeled using a Monte Carlo algorithm with a hybrid lattice model. In the simulation setup, a fictional country with three towns and 26,610 citizens were used as a model. Results indicate that applying a weekend curfew reduces the ratio of ill cases from 0.23 to 0.15. The results also show that applying personal precautions such as social distancing is important for reducing the number of cases and deaths. If the probability of disease spread can be reduced to 0.1, in that case, the death ratio can be minimized down to 0.

目前正在采用各种方法应对 COVID-19 大流行,包括应用疫苗、实验性治疗方案、全面封锁或部分宵禁。周末宵禁是减少感染人数的方法之一,土耳其等一些国家实际采用了这种方法。在本研究中,采用蒙特卡罗算法和混合网格模型,模拟了周末宵禁对减少 COVID-19 等传染病传播的影响。在模拟设置中,使用了一个拥有三个城镇和 26 610 名公民的虚构国家作为模型。结果表明,实行周末宵禁可将病例比率从 0.23 降至 0.15。结果还表明,采取个人预防措施(如拉开社交距离)对于减少病例和死亡人数非常重要。如果疾病传播的概率可以降低到 0.1,那么死亡比率就可以降到 0。
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引用次数: 0
An update comprehensive review on the status of COVID-19: vaccines, drugs, variants and neurological symptoms. 关于COVID-19现状的最新综合综述:疫苗、药物、变体和神经系统症状。
Pub Date : 2021-08-30 eCollection Date: 2021-01-01 DOI: 10.3906/biy-2106-23
Ebru Özkan Oktay, Salih Tuncay, Tuğba Kaman, Ömer Faruk Karasakal, Öznur Özge Özcan, Tuğçe Soylamiş, Mesut Karahan, Muhsin Konuk

Various recently reported mutant variants, candidate and urgently approved current vaccines against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), many current situations with severe neurological damage and symptoms as well as respiratory tract disorders have begun to be reported. In particular, drug, vaccine, and neutralizing monoclonal antibodies (mAbs) have been developed and are currently being evaluated in clinical trials. Here, we review lessons learned from the use of novel mutant variants of the COVID-19 virus, immunization, new drug solutions, and antibody therapies for infections. Next, we focus on the B 1.1.7, B 1.351, P.1, and B.1.617 lineages or variants of concern that have been reported worldwide, the new manifestations of neurological manifestations, the current therapeutic drug targets for its treatment, vaccine candidates and their efficacy, implantation of convalescent plasma, and neutralization of mAbs. We review specific clinical questions, including many emerging neurological effects and respiratory tract injuries, as well as new potential biomarkers, new studies in addition to known therapeutics, and chronic diseases of vaccines that have received immediate approval. To answer these questions, further understanding of the burden kinetics of COVID-19 and its correlation with neurological clinical outcomes, endogenous antibody responses to vaccines, pharmacokinetics of neutralizing mAbs, and action against emerging viral mutant variants is needed.

最近报道的各种变异株,针对严重急性呼吸综合征冠状病毒2型(SARS-CoV-2)的候选疫苗和紧急批准的当前疫苗,许多严重神经损伤和症状以及呼吸道疾病的当前情况已经开始报道。特别是,药物、疫苗和中和单克隆抗体(mAb)已经开发出来,目前正在临床试验中进行评估。在此,我们回顾了从新冠肺炎病毒新变异株的使用、免疫接种、新药解决方案和感染抗体疗法中吸取的经验教训。接下来,我们将重点关注世界各地报道的B 1.1.7、B 1.351、P.1和B.1.617谱系或变异毒株、神经系统表现的新表现、当前治疗药物的靶点、候选疫苗及其疗效、恢复期血浆的植入和mAbs的中和。我们回顾了具体的临床问题,包括许多新出现的神经系统影响和呼吸道损伤,以及新的潜在生物标志物、除已知疗法外的新研究,以及已立即获得批准的疫苗的慢性病。为了回答这些问题,需要进一步了解新冠肺炎的负担动力学及其与神经临床结果、对疫苗的内源性抗体反应、中和mAb的药代动力学以及对抗新出现的病毒变异株的作用的相关性。
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引用次数: 4
Targeting CoV-2 spike RBD and ACE-2 interaction with flavonoids of Anatolian propolis by in silico and in vitro studies in terms of possible COVID-19 therapeutics. 针对CoV-2刺突RBD和ACE-2与安纳托利亚蜂胶类黄酮相互作用的新冠肺炎治疗方法的硅和体外研究
Pub Date : 2021-08-30 eCollection Date: 2021-01-01 DOI: 10.3906/biy-2104-5
Halil İbrahim Güler, Fulya Ay Şal, Zehra Can, Yakup Kara, Oktay Yildiz, Ali Osman Beldüz, Sabriye Çanakçi, Sevgi Kolayli

Propolis is a multi-functional bee product rich in polyphenols. In this study, the inhibitory effect of Anatolian propolis against SARS-coronavirus-2 (SARS-CoV-2) was investigated in vitro and in silico. Raw and commercial propolis samples were used, and both samples were found to be rich in caffeic acid, p-coumaric acid, ferulic acid, t-cinnamic acid, hesperetin, chrysin, pinocembrin, and caffeic acid phenethyl ester (CAPE) at HPLC-UV analysis. Ethanolic propolis extracts (EPE) were used in the ELISA screening test against the spike S1 protein (SARS-CoV-2): ACE-2 interaction for in vitro study. The binding energy values of these polyphenols to the SARS-CoV-2 spike and ACE-2 protein were calculated separately with a molecular docking study using the AutoDock 4.2.6 program. In addition, the pharmacokinetics and drug-likeness properties of these eight polyphenols were calculated according to the SwissADME tool. The binding energy value of pinocembrin was highest in both receptors, followed by chrysin, CAPE, and hesperetin. Based on the in silico modeling and ADME (absorption, distribution, metabolism, and excretion) behaviors of the eight polyphenols, the compounds exhibited the potential ability to act effectively as novel drugs. The findings of both studies showed that propolis has a high inhibitory potential against the Covid-19 virus. However, further studies are now needed.

蜂胶是一种富含多酚的多功能蜂产品。本研究在体外和计算机上研究了安纳托利亚蜂胶对严重急性呼吸系统综合征冠状病毒2型(SARS-CoV-2)的抑制作用。使用原料和商业蜂胶样品,在HPLC-UV分析中发现这两个样品都富含咖啡酸、对香豆酸、阿魏酸、叔肉桂酸、橙皮素、白杨素、皮诺菌素和咖啡酸苯乙酯(CAPE)。乙醇蜂胶提取物(EPE)用于针对刺突S1蛋白(严重急性呼吸系统综合征冠状病毒2型)的ELISA筛选试验:用于体外研究的ACE-2相互作用。使用AutoDock 4.2.6程序进行分子对接研究,分别计算这些多酚与严重急性呼吸系统综合征冠状病毒2型刺突和ACE-2蛋白的结合能值。此外,根据SwissADME工具计算了这八种多酚的药代动力学和药物相似性。pinocembrin在两种受体中的结合能值最高,其次是白杨素、CAPE和橙皮素。基于八种多酚的计算机模拟和ADME(吸收、分布、代谢和排泄)行为,这些化合物显示出作为新药有效发挥作用的潜在能力。这两项研究的结果都表明,蜂胶对新冠肺炎病毒具有很高的抑制潜力。然而,现在还需要进一步的研究。
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引用次数: 22
CoronaVac (Sinovac) COVID-19 vaccine-induced molecular changes in healthy human serum by infrared spectroscopy coupled with chemometrics. 新冠肺炎疫苗诱导健康人血清分子变化的红外光谱联合化学计量学研究
Pub Date : 2021-08-30 eCollection Date: 2021-01-01 DOI: 10.3906/biy-2105-65
Ayca Dogan, Rafig Gurbanov, Mete Severcan, Feride Severcan

From the beginning of the COVID-19 coronavirus pandemic in December of 2019, the disease has infected millions of people worldwide and caused hundreds of thousands of deaths. Since then, several vaccines have been developed. One of those vaccines is inactivated CoronaVac-Sinovac COVID-19 vaccine. In this proof of concept study, we first aimed to determine CoronaVac-induced biomolecular changes in healthy human serum using infrared spectroscopy. Our second aim was to see whether the vaccinated group can be separated or not from the non-vaccinated group by applying chemometric techniques to spectral data. The results revealed that the vaccine administration induced significant changes in some functional groups belonging to lipids, proteins and nucleic acids. In addition, the non-vaccinated and vaccinated groups were successfully separated from each other by principal component analysis (PCA) and linear discriminant analysis (LDA). This proof-of-concept study will encourage future studies on CoronaVac as well as other vaccines and will lead to make a comparison between different vaccines to establish a better understanding of the vaccination outcomes on serum biomolecules.

自2019年12月COVID-19冠状病毒大流行开始以来,该疾病已在全球感染了数百万人,造成数十万人死亡。从那时起,已经开发了几种疫苗。其中一种疫苗是灭活疫苗。在这项概念验证研究中,我们首先旨在利用红外光谱技术确定冠状动脉炎引起的健康人血清中的生物分子变化。我们的第二个目标是通过对光谱数据应用化学计量学技术,看看是否可以将接种疫苗组与未接种疫苗组分开。结果显示,接种疫苗引起了脂质、蛋白质和核酸等功能基团的显著变化。此外,通过主成分分析(PCA)和线性判别分析(LDA)成功地分离了未接种疫苗组和接种疫苗组。这项概念验证研究将鼓励未来对CoronaVac和其他疫苗进行研究,并将导致对不同疫苗进行比较,以更好地了解疫苗接种对血清生物分子的影响。
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引用次数: 12
The potential use of Drosophila as an in vivo model organism for COVID-19-related research: a review. 果蝇作为体内模型生物在covid -19相关研究中的潜在应用综述
Pub Date : 2021-08-30 eCollection Date: 2021-01-01 DOI: 10.3906/biy-2104-26
Eşref Demir

The world urgently needs effective antiviral approaches against emerging viruses, as shown by the coronavirus disease 2019 (COVID-19) pandemic, which has become an exponentially growing health crisis. Scientists from diverse backgrounds have directed their efforts towards identifying key features of SARS-CoV-2 and clinical manifestations of COVID-19 infection. Reports of more transmissible variants of SARS-CoV-2 also raise concerns over the possibility of an explosive trajectory of the pandemic, so scientific attention should focus on developing new weapons to help win the fight against coronaviruses that may undergo further mutations in the future. Drosophila melanogaster offers a powerful and potential in vivo model that can significantly increase the efficiency of drug screening for viral and bacterial infections. Thanks to its genes with functional human homologs, Drosophila could play a significant role in such gene-editing studies geared towards designing vaccines and antiviral drugs for COVID-19. It can also help rectify current drawbacks of CRISPR-based therapeutics like off-target effects and delivery issues, representing another momentous step forward in healthcare. Here I present an overview of recent literature and the current state of knowledge, explaining how it can open up new avenues for Drosophila in our battle against infectious diseases.

世界迫切需要有效的抗病毒方法来对付新出现的病毒,正如2019年冠状病毒病(COVID-19)大流行所表明的那样,该疾病已成为一场呈指数级增长的健康危机。来自不同背景的科学家一直致力于确定SARS-CoV-2的关键特征和COVID-19感染的临床表现。关于SARS-CoV-2更具传染性变体的报道也引发了人们对大流行可能出现爆炸性轨迹的担忧,因此科学注意力应集中在开发新武器上,以帮助赢得与未来可能发生进一步突变的冠状病毒的斗争。黑腹果蝇提供了一种强大而有潜力的体内模型,可以显著提高病毒和细菌感染药物筛选的效率。由于果蝇具有功能性人类同源基因,它可以在旨在设计COVID-19疫苗和抗病毒药物的基因编辑研究中发挥重要作用。它还可以帮助纠正目前基于crispr的治疗方法的缺点,如脱靶效应和递送问题,代表着医疗保健领域的又一重大进步。在这里,我将概述最近的文献和当前的知识状态,解释它如何为果蝇在我们与传染病的斗争中开辟新的途径。
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引用次数: 4
Pathogenesis and treatment of cytokine storm in COVID-19. COVID-19细胞因子风暴的发病机制及治疗。
Pub Date : 2021-08-30 eCollection Date: 2021-01-01 DOI: 10.3906/biy-2105-37
Mehmet Soy, Gökhan Keser, Pamir Atagündüz

COVID-19 is a viral infection caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that killed a large number of patients around the world. A hyperinflammatory state resulting in a cytokine storm and adult respiratory distress syndrome seems to be the major cause of the death. Many mechanisms have been suggested in the pathogenesis of COVID-19 associated cytokine storm (COVID-CS). Insufficient viral clearance and persistence of a strong cytokine response despite inadequate antiviral immunity seem to be the main mechanisms underlying the pathogenesis. The diagnosis of COVID-19 is based on relatively constant clinical symptoms, clinical findings, laboratory tests, and imaging techniques, while the diagnosis of COVID-CS is a rather dynamic process, based on evolving or newly emerging findings during the clinical course. Management of COVID-19 consists of using antiviral agents to inhibit SARS-CoV-2 replication and treating potential complications including the cytokine storm together with general supportive measures. COVID-CS may be treated using appropriate immunosuppressive and immunomodulatory drugs that reduce the level of inappropriate systemic inflammation, which has the potential to cause organ damage. Currently corticosteroids, IL-6 blockers, or IL-1 blockers are most widely used for treating COVID-CS.

COVID-19是由严重急性呼吸综合征冠状病毒2 (SARS-CoV-2)引起的病毒感染,在世界各地造成大量患者死亡。导致细胞因子风暴和成人呼吸窘迫综合征的高炎症状态似乎是死亡的主要原因。关于COVID-19相关细胞因子风暴(COVID-CS)的发病机制,人们提出了多种机制。尽管抗病毒免疫不足,但病毒清除不足和强烈细胞因子反应的持久性似乎是发病机制的主要机制。COVID-19的诊断基于相对稳定的临床症状、临床表现、实验室检查和影像学技术,而COVID-CS的诊断是一个相当动态的过程,基于临床过程中不断发展或新出现的发现。COVID-19的管理包括使用抗病毒药物抑制SARS-CoV-2复制和治疗潜在并发症,包括细胞因子风暴以及一般支持措施。COVID-CS可以使用适当的免疫抑制和免疫调节药物进行治疗,以降低可能导致器官损伤的不适当全身炎症的水平。目前,治疗COVID-CS最广泛使用的是皮质类固醇、IL-6阻断剂或IL-1阻断剂。
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引用次数: 14
Genomic chronicle of SARS-CoV-2: a mutational analysis with over 1 million genome sequences. SARS-CoV-2的基因组编年史:超过100万个基因组序列的突变分析
Pub Date : 2021-08-30 eCollection Date: 2021-01-01 DOI: 10.3906/biy-2106-8
Osman Mutluhan Uğurel, Oğuz Ata, Dilek Turgut-Balik

Use of information technologies to analyse big data on SARS-CoV-2 genome provides an insight for tracking variations and examining the evolution of the virus. Nevertheless, storing, processing, alignment and analyses of these numerous genomes are still a challenge. In this study, over 1 million SARS-CoV-2 genomes have been analysed to show distribution and relationship of variations that could enlighten development and evolution of the virus. In all genomes analysed in this study, a total of over 215M SNVs have been detected and average number of SNV per isolate was found to be 21.83. Single nucleotide variant (SNV) average is observed to reach 31.25 just in March 2021. The average variation number of isolates is increasing and compromising with total case numbers around the world. Remarkably, cytosine deamination, which is one of the most important biochemical processes in the evolutionary development of coronaviruses, accounts for 46% of all SNVs seen in SARS-CoV-2 genomes within 16 months. This study is one of the most comprehensive SARS-CoV-2 genomic analysis study in terms of number of genomes analysed in an academic publication so far, and reported results could be useful in monitoring the development of SARS-CoV-2.

利用信息技术分析严重急性呼吸系统综合征冠状病毒2型基因组的大数据,可以深入了解病毒的变异和进化。然而,对这些众多基因组的存储、处理、比对和分析仍然是一个挑战。在这项研究中,已经分析了超过100万个严重急性呼吸系统综合征冠状病毒2型基因组,以显示变异的分布和关系,这可能会启发病毒的发展和进化。在本研究分析的所有基因组中,共检测到超过2.15亿个SNV,每个分离株的平均SNV数量为21.83。2021年3月,观察到单核苷酸变异株(SNV)的平均值达到31.25。分离株的平均变异数正在增加,并与世界各地的总病例数相妥协。值得注意的是,胞嘧啶脱氨作用是冠状病毒进化过程中最重要的生化过程之一,在16个月内占严重急性呼吸系统综合征冠状病毒2型基因组中所有SNV的46%。就学术出版物中分析的基因组数量而言,这项研究是迄今为止最全面的严重急性呼吸系统综合征冠状病毒2型基因组分析研究之一,报告的结果可能有助于监测严重急性呼吸综合征冠状病毒的发展。
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引用次数: 0
β-Carboline alkaloids induce structural plasticity and inhibition of SARS-CoV-2 nsp3 macrodomain more potently than remdesivir metabolite GS-441524: computational approach. β-咔啉生物碱诱导结构可塑性和抑制SARS-CoV-2 nsp3大域的作用比雷米替韦代谢物GS-441524更强:计算方法。
Pub Date : 2021-08-30 eCollection Date: 2021-01-01 DOI: 10.3906/biy-2106-64
Yusuf Oloruntoyin Ayipo, Sani Najib Yahaya, Halimah Funmilayo Babamale, Iqrar Ahmad, Harun Patel, Mohd Nizam Mordi

The nsp3 macrodomain is implicated in the viral replication, pathogenesis and host immune responses through the removal of ADP-ribosylation sites during infections of coronaviruses including the SARS-CoV-2. It has ever been modulated by macromolecules including the ADP-ribose until Ni and co-workers recently reported its inhibition and plasticity enhancement unprecedentedly by remdesivir metabolite, GS-441524, creating an opportunity for investigating other biodiverse small molecules such as β-Carboline (βC) alkaloids. In this study, 1497 βC analogues from the HiT2LEAD chemical database were screened, using computational approaches of Glide XP docking, molecular dynamics simulation and pk-CSM ADMET predictions. Selectively, βC ligands, 129, 584, 1303 and 1323 demonstrated higher binding affinities to the receptor, indicated by XP docking scores of -10.72, -10.01, -9.63 and -9.48 kcal/mol respectively than remdesivir and GS-441524 with -4.68 and -9.41 kcal/mol respectively. Consistently, their binding free energies were -36.07, -23.77, -24.07 and -17.76 kcal/mol respectively, while remdesivir and GS-441524 showed -21.22 and -24.20 kcal/mol respectively. Interestingly, the selected βC ligands displayed better stability and flexibility for enhancing the plasticity of the receptor than GS-441524, especially 129 and 1303. Their predicted ADMET parameters favour druggability and low expressions for toxicity. Thus, they are recommended as promising adjuvant/standalone anti-SARS-CoV-2 candidates for further study.Key words: SARS-CoV-2, nsp3 macrodomain, ADP-ribose, β-carboline, bioinformatics, drug design.

在包括 SARS-CoV-2 在内的冠状病毒感染过程中,nsp3 大域通过去除 ADP 核糖基化位点参与病毒复制、致病和宿主免疫反应。它一直受到包括 ADP 核糖在内的大分子的调控,直到 Ni 及其合作者最近报道雷米地韦代 谢物 GS-441524 史无前例地抑制了它并增强了它的可塑性,这为研究其他生物多样性小分子(如 β-咔啉(βC)生物碱)创造了机会。本研究采用 Glide XP docking、分子动力学模拟和 pk-CSM ADMET 预测等计算方法,从 HiT2LEAD 化学数据库中筛选出 1497 种 βC 类似物。与雷米替韦和 GS-441524 分别为 -4.68 和 -9.41 kcal/mol 的 XP docking 分数相比,βC 配体 129、584、1303 和 1323 与受体的选择性结合亲和力分别为 -10.72、-10.01、-9.63 和 -9.48 kcal/mol。同样,它们的结合自由能分别为-36.07、-23.77、-24.07和-17.76 kcal/mol,而雷米替韦和GS-441524分别为-21.22和-24.20 kcal/mol。有趣的是,与 GS-441524 相比,所选的βC 配体在增强受体的可塑性方面表现出更好的稳定性和灵活性,尤其是 129 和 1303。它们的 ADMET 预测参数有利于药物的可药性,而毒性表达较低。因此,建议将它们作为有前途的佐剂/独立抗 SARS-CoV-2 候选药物进行进一步研究:SARS-CoV-2、nsp3 大域、ADP-核糖、β-咔啉、生物信息学、药物设计。
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引用次数: 0
期刊
Turkish journal of biology = Turk biyoloji dergisi
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