=================
计算机辅助药物设计
=================
====
论文
==== |
====
软件
==== |
====
数据
==== |
========
视频教程
======== |
========
重要链接
======== |
|
===========
小组成员进入
=========== |
|
====
Back
==== |
第一批文献：
1..Network-based drug repurposing for novel coronavirus 2019-nCoV/SARS-CoV-2
2. Design, synthesis and molecular docking of novel triazole derivatives as potential CoV helicase inhibitors （ACTA PHARMACEUTICA， 2020）
3. Fast Identification of Possible Drug Treatment of Coronavirus Disease -19 (COVID-19) Through Computational Drug Repurposing Study. （Journal of chemical information and modeling， 2020）
4. Identification of chymotrypsin-like protease inhibitors of SARS-CoV-2 via integrated computational approach. （Journal of biomolecular structure & dynamics，2020）
5. Structure of Mpro from COVID-19 virus and discovery of its inhibitors. (Nature, 2020, 饶子和，蒋华良)
6. In-silico homology assisted identification of inhibitor of RNA binding against 2019-nCoV N-protein (N terminal domain） （Journal of biomolecular structure & dynamics， 2020）
7. Structural and molecular modelling studies reveal a new mechanism of action of chloroquine and hydroxychloroquine against SARS-CoV-2 infection. （International journal of antimicrobial agents， 2020）
8. Potential covalent drugs targeting the main protease of the SARS-CoV-2 coronavirus. （Bioinformatics， 2020）
9. A guideline for homology modeling of the proteins from newly discovered betacoronavirus, 2019 novel coronavirus (2019-nCoV) （JOURNAL OF MEDICAL VIROLOGY，2020）
10. Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved alpha-ketoamide inhibitors. （Science， 2020）
11. Molecular docking analysis of selected natural products from plants for inhibition of SARS-CoV-2 main protease. （CURRENT SCIENCE， 2020）
12. The potential chemical structure of anti-SARS-CoV-2 RNA-dependent RNA polymerase. （JOURNAL OF MEDICAL VIROLOGY，2020）
13. Therapeutic options for the 2019 novel coronavirus (2019-nCoV). （NATURE REVIEWS DRUG DISCOVERY， 2020）
14. Drug targets for corona virus: A systematic review. （INDIAN JOURNAL OF PHARMACOLOGY， 2020）
15. Molecular docking and dynamics simulation of FDA approved drugs with the main protease from 2019 novel coronavirus. （Bioinformation， 2020）
16. Predicting commercially available antiviral drugs that may act on the novel coronavirus (SARS-CoV-2) through a drug-target interaction deep learning model. （Computational and structural biotechnology journal， 2020）
17. MERS-CoV spike protein: a key target for antivirals. （EXPERT OPINION ON THERAPEUTIC TARGETS0， 2017）
18. Small molecules targeting viral RNA. （WILEY INTERDISCIPLINARY REVIEWS-RNA， 2016）
19. R-BIND: An Interactive Database for Exploring and Developing RNA Targeted Chemical Probes. （ACS CHEMICAL BIOLOGY， 2019）
20. Principles for targeting RNA with drug-like small molecules. （NATURE REVIEWS DRUG DISCOVERY， 2018）
21. Coronavirus main proteinase (3CL(pro)) structure: Basis for design of anti-SARS drugs. （SCIENCE，2003）
22. Binding mechanism of coronavirus main proteinase with ligands and its implication to drug design against SARS. （BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS，2003）
23. Design of wide-spectrum inhibitors targeting coronavirus main proteases. (PLOS BIOLOGY, 2005)
24. Virtual screening for SARS-CoV protease based on KZ7088 pharmacophore pointst. (JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES, 2004)
25. Progress in computational approach to drug development against SARS. (CURRENT MEDICINAL CHEMISTRY, 2006)
26. TargetCPP: accurate prediction of cell-penetrating peptides from optimized multi-scale features using gradient boost decision tree. (JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 2020)
27. iDrug-Target: predicting the interactions between drug compounds and target proteins in cellular networking via benchmark dataset optimization approach. (JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 2015)
28. A 3D model of SARS_CoV 3CL proteinase and its inhibitors design by virtual screening. (ACTA PHARMACOLOGICA SINICA, 2003)
29. Molecular model of SARS coronavirus polymerase: Implications for biochemical functions and drug design. (NUCLEIC ACIDS RESEARCH, 2003)
30. iNR-Drug: Predicting the Interaction of Drugs with Nuclear Receptors in Cellular Networking. (INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, 2014)
31. Broad-Spectrum Antivirals against 3C or 3C-Like Proteases of Picornaviruses, Noroviruses, and Coronaviruses. (JOURNAL OF VIROLOGY, 2012)
32. AVPpred: collection and prediction of highly effective antiviral peptides. (NUCLEIC ACIDS RESEARCH, 2012)
33. Anti-SARS drug screening by molecular docking. (Amino Acids , 2006)
34. Computational identification of inhibitors of protein-protein interactions. (CURRENT TOPICS IN MEDICINAL CHEMISTRY, 2007)
35. AVPdb: a database of experimentally validated antiviral peptides targeting medically important viruses. (NUCLEIC ACIDS RESEARCH, 2014)
36. From SARS to MERS, Thrusting Coronaviruses into the Spotlight (VIRUSES-BASEL, 2019)
37. Computer-Assisted and Data Driven Approaches for Surveillance, Drug Discovery, and Vaccine Design for the Zika Virus ( 2019, PHARMACEUTICALS)
第二批文献：
1. End-Point Binding Free Energy Calculation with MM/PBSA and MM/GBSA: Strategies and Applications in Drug Design . CHEMICAL REVIEWS，2019
2. The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities. EXPERT OPINION ON DRUG DISCOVERY. MAY 2015
3. Recent Advances in Free Energy Calculations with a Combination of Molecular Mechanics and Continuum Models. Current Computer-Aided Drug Design, 2006, 2, 95-103
4. Develop and Test a Solvent Accessible Surface Area-Based Model in Conformational Entropy Calculations .J Chem Inf Model. 2012 May 25; 52(5): 1199–1212
5. An overview of the Amber biomolecular simulation package. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE. MAR-APR 2013： DOI: 10.1002/wcms.1121
6.The Amber biomolecular simulation programs. JOURNAL OF COMPUTATIONAL CHEMISTRY. 2005.12
7. Identification of potential inhibitors of three key enzymes of SARS-CoV2 using computational approach. COMPUTERS IN BIOLOGY AND MEDICINE. 2020.7 重复
8. Fast Identification of Possible Drug Treatment of Coronavirus Disease-19 (COVID-19) Through Computational Drug Repurposing Study. Journal of Chemical Information and Modeling. 2020.4
9. Large-scale comparison of machine learning methods for drug target prediction on ChEMBL. Chemical Science.2018
10. LigPlot+: Multiple Ligand–Protein Interaction Diagrams for Drug Discovery. J. Chem. Inf. Model. 2011, 51, 10, 2778–2786
11. Recent discovery and development of inhibitors targeting coronaviruses DRUG DISCOVERY TODAY. 2020.4
12.A rational roadmap for SARS-CoV-2/COVID-19 pharmacotherapeutic research and development . BRITISH JOURNAL OF PHARMACOLOGY .2020.7
13. Potential therapeutic targets and promising drugs for combating SARS-CoV-2. BRITISH JOURNAL OF PHARMACOLOGY. 2020.6
14. Drug targets for COVID-19 therapeutics: Ongoing global efforts. JOURNAL OF BIOSCIENCES 2020.6
15 SARS-CoV-2 RNA Dependent RNA polymerase (RdRp)–A drug repurposing study. 2020.7
2019年12月在中国爆发SARS-CoV-2导致大流行。疫苗和特定抗病毒药物的缺乏引发了全球性的健康灾难。为了持续控制和保护，开发潜在的抗病毒药物是目标方法之一。虽然总是鼓励设计和开发一组新药物分子。但是，在当前的紧急情况下，药物再利用研究是最有效，最快捷的选择之一。最近已经通过X射线晶体学破译了SARS-CoV-2（严重急性呼吸系统综合症冠状病毒2）RNA依赖性RNA聚合酶（RdRp）的晶体结构。
核心RNA依赖性RNA聚合酶的单链依赖于病毒编码的辅助因子nsp7和nsp8的两个单元，以发挥其最佳功能。这项研究探索了FDA批准的7922个分子的数据库，并针对核心聚合酶和辅因子进行了筛选。在这里，我们报告了一组FDA批准的药物，这些药物显示出与活性部位关键氨基酸残基的实质性相互作用。有趣的是，某些鉴定出的药物（降压素，Lypressin，Examorelin，Polymyxin B1）在两种形式的RdRp的结合口袋中都具有很强的结合力。此外，我们还发现了复杂形式的强候选者，其中包括纳科霉素，西斯替辛，西沙曲库铵（以及其他）。这些药物在寻求治疗选择时有可能被考虑。
16. Should We Try SARS-CoV-2 Helicase Inhibitors for COVID-19 Therapy? ！！
通过了解病毒复制周期和致病性，可以发现用于治疗新冠状病毒（SARS-CoV-2）或重新利用已经用于其他病毒感染的新药的发现。 本文强调了靶向非结构蛋白之一解旋酶（nsp13）优于其他SARS-CoV-2蛋白的优势。 强调在类似冠状病毒（SARS-CoV和MERS）和已知抑制剂中靶向Nsp13的经验，这篇文章呼吁研究将解旋酶抑制剂作为潜在的COVID-19治疗方法。
17. Origin and Evolution of RNA-Dependent RNA Polymerase. Front Genet. 2017; 8: 125.
18. Emerging coronaviruses: Genome structure, replication, and pathogenesis. JOURNAL OF MEDICAL VIROLOGY. 2020.2: DOI: 10.1002/jmv.25681
19. State-of-the-art tools unveil potent drug targets amongst clinically approved drugs to inhibit helicase in SARS-CoV-2. ARCHIVES OF MEDICAL SCIENCE. 2020.4:
20. SARS-CoV ORF1b-encoded nonstructural proteins 12-16: Replicative enzymes as antiviral targets. ANTIVIRAL RESEARCH. 2014.1
21. Nature|中国攻关联盟解析新冠“要害”，筛选出多种病毒抑制小分子
22. Structure of Mpro from SARS-CoV-2 and discovery of its inhibitors.Nature.：582, pages289–293(2020)
23. Comprehensive in silico Study of GLUT10: Prediction of Possible Substrate Binding Sites and Interacting Molecules. CURRENT PHARMACEUTICAL BIOTECHNOLOGY.2020
JBSD papers：
1. Identification of potential molecules against COVID-19 main protease through structure-guided virtual screening approach. JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS. 2020. 5
2. Pharmacoinformatics and molecular dynamics simulation studies reveal potential covalent and FDA-approved inhibitors of SARS-CoV-2 main protease 3CL(pro). JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS 2020.6
3. In-silico investigation of phytochemicals fromAsparagus racemosusas plausible antiviral agent in COVID-19. JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS. 2020.6
4. Sars-cov-2 host entry and replication inhibitors from Indian ginseng: anin-silicoapproach. JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS. 2020.6
5. Identification of bioactive compounds fromGlycyrrhiza glabraas possible inhibitor of SARS-CoV-2 spike glycoprotein and non-structural protein-15: a pharmacoinformatics study. JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS.2020.6
6. SARS-CoV-2 RNA dependent RNA polymerase (RdRp) targeting: an in silico perspective. Journal of Biomolecular Structure and Dynamics . 2020.4
7. Identification of a potential SARS-CoV2 inhibitor via molecular dynamics simulations and amino acid decomposition analysis. JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS.2020.7
8. Cyanobacterial metabolites as promising drug leads against the M(pro)and PL(pro)of SARS-CoV-2: anin silicoanalysis.JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS.2020.6
9. Targeting virus-host interaction by novel pyrimidine derivative: anin silicoapproach towards discovery of potential drug against COVID-19. JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS.2020.7
10. Bacterial protein azurin and derived peptides as potential anti-SARS-CoV-2 agents: insights from molecular docking and molecular dynamics simulations. JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS. 2020.7
11. In silicoidentification of potential inhibitors fromCinnamonagainst main protease and spike glycoprotein of SARS CoV-2. JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS. 2020.6
12. Targeting SARS-COV-2 non-structural protein 16: a virtual drug repurposing study. JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS.2020.6
13. Natural compounds from Clerodendrum spp. as possible therapeutic candidates against SARS-CoV-2: An in silico investigation. JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS. 2020.6
14. Chemical-informatics approach to COVID-19 drug discovery: Monte Carlo based QSAR, virtual screening and molecular docking study of somein-housemolecules as papain-like protease (PLpro) inhibitors. JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS.2020.6.
15. Virtual screening-driven drug discovery of SARS-CoV2 enzyme inhibitors targeting viral attachment, replication, post-translational modification and host immunity evasion infection mechanisms. JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS. 2020.6
16. Drug repurposing studies targeting SARS-CoV-2: an ensemble docking approach on drug target 3C-like protease (3CL(pro)). JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS.2020.7
17.Molecular docking, simulation and MM-PBSA studies ofnigella sativacompounds: a computational quest to identify potential natural antiviral for COVID-19 treatment. JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS.2020.6
18. In-silico strategies for probing chloroquine based inhibitors against SARS-CoV-2. JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS.2020.6
19. Structural and simulation analysis of hotspot residues interactions of SARS-CoV 2 with human ACE2 receptor. JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS.2020.6
20. Identification of phytochemical inhibitors against main protease of COVID-19 using molecular modeling approaches.JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS.2020.6
21. Marine natural compounds as potents inhibitors against the main protease of SARS-CoV-2-a molecular dynamic study. JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS. 2020.5
22. Tackling COVID-19: identification of potential main protease inhibitors via structural analysis, virtual screening, molecular docking and MM-PBSA calculations. JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS.2020.7: DOI: 10.1080/07391102.2020.1800514
23. Computational investigation of potential inhibitors of novel coronavirus 2019 through structure-based virtual screening, molecular dynamics and density functional theory studies.JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS. 2020.7
24. Potential anti-viral activity of approved repurposed drug against main protease of SARS-CoV-2: anin silicobased approach. JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS. 2020.5: DOI: 10.1080/07391102.2020.1768902
25. Identification of potential molecules against COVID-19 main protease through structure-guided virtual screening approach. JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS.2020.5
26 Using integrated computational approaches to identify safe and rapid treatment for SARS-CoV-2. JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS.2020.5
27. Investigating the binding affinity, interaction, and structure-activity-relationship of 76 prescription antiviral drugs targeting RdRp and Mpro of SARS-CoV-2. JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS.2020.7 : DOI: 10.1080/07391102.2020.1796804
28. Virtual screening, ADMET prediction and dynamics simulation of potential compounds targeting the main protease of SARS-CoV-2. JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS. 2020.7: DOI: 10.1080/07391102.2020.1796812
29. Computational discovery of small drug-like compounds as potential inhibitors of SARS-CoV-2 main protease. JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS. 2020.7
30 SARS-CoV-2 RNA dependent RNA polymerase (RdRp) targeting: an in silico perspective. JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS.2020.5
第四批文献：
1. Ligand and structure-based virtual screening applied to the SARS-CoV-2 main protease: anin silicorepurposing study. FUTURE MEDICINAL CHEMISTRY.2020.8
目的：鉴定治疗冠状病毒病-19大流行的药物仍然很紧迫。通过这种方式，药物再利用是一个合适的策略，可以节省在常规药物发现框架中通常花费的资源和时间。对病毒复制至关重要，主要的蛋白酶已被探索作为一个有希望的目标药物发现工艺.材料& 方法：我们的虚拟筛选管道依赖于已知的非共价配体的3D性质和结晶配合物的特征，在每一项中应用一致性分析步骤.结果两种口服药物（贝达奎林和格列本脲）和一种口腔药物（咪康唑）与已知配体具有三维相似性，合理的预测结合模式和微摩尔预测的结合亲和力价值观。结论：我们确定了三种被批准的药物作为主要病毒蛋白酶抑制剂和为未来研究开发新型选择性抑制剂提出了设计见解。
2. Potential inhibitors of the interaction between ACE2 and SARS-CoV-2 (RBD), to develop a drug. LIFE SCIENCES 2020.9
目的：由SARS-CoV-2引起的COVID-19疾病已经成为一种大流行，目前还没有有效的治疗方法来减少传染。迫切需要提出新的治疗方案，在病毒与细胞的相互作用中更有效。本研究旨在寻找新的抗血管紧张素转换酶2（ACE2）的药理化合物，以抑制与SARS-CoV-2的相互作用。
材料和方法：对接，虚拟筛选，使用近500000种化合物在ACE2中的残基（Gln24、Asp30、His34、Tyr41、Gln42、Met82、Lys353和Arg357）之间相互作用。分析了化合物的δG平均值、标准差和理论毒性。
主要发现：20种最佳化合物在ACE2中以很高的概率在人体内安全地相互作用，经ADME和毒性预测网络服务器（ProTox II和PreADMET）的验证，使ACE2与SARS-CoV-2的区域结合域（RBD）之间难以相互作用。
意义：本研究以SARS-CoV-2的ACE2与RBD的相互作用区域为重点，通过对接的方法确定了20个化合物。这些化合物在体外试验中被公开用于验证效果。
3. Structural and functional properties of SARS-CoV-2 spike protein: potential antivirus drug development for COVID-19. Acta Pharmacologica Sinica 2020.8.
2019年冠状病毒病是一种新出现的传染病，目前正在世界各地蔓延。它是由一种新型冠状病毒，严重急性呼吸综合征冠状病毒2（SARS-CoV-2）引起的。SARS-CoV-2的棘突蛋白由S1和S2两个亚基组成，在受体识别和细胞膜融合过程中起关键作用。S1亚单位包含一个受体结合域，识别并结合宿主受体血管紧张素转换酶2，而S2亚单位通过两个七肽重复结构域形成六个螺旋束来介导病毒细胞膜融合。本文综述了近年来针对S蛋白的抗病毒药物的结构、功能和研究进展。