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计算机辅助新药设计相关筛选数据库的研究进展
作者:许彤  郭庚妮  蒋南 
单位:南京医科大学 药学院, 江苏 南京 211166
关键词:计算机辅助新药设计 药物虚拟筛选 UniProt数据库 RCSB蛋白质数据库 文献综述 
分类号:R918
出版年·卷·期(页码):2022·41·第六期(876-883)
摘要:

作者对计算机辅助新药设计与虚拟筛选相关的常用蛋白质、核酸、药效团数据库进行了总结,详细介绍了其构建内容(包括信息来源、数据内容、检索字段等)和使用方法等,并分析了数据库开发的问题和挑战,进而对其发展方向与对策提出见解。

参考文献:

[1] GURUNG A B,ALI M A,LEE J,et al.An updated review of computer-aided drug design and its application to COVID-19[J].Biomed Res Int,2021,2021:8853056.
[2] VOLKOV M,TURK J A,DRIZARD N,et al.On the frustration to predict binding affinities from protein-ligand structures with deep neural networks[J].J Med Chem,2022,65(11):7946-7958.
[3] LLOYD M D.High-throughput screening for the discovery of enzyme inhibitors[J].J Med Chem,2020,63(19):10742-10772.
[4] WU C,LIU Y,YANG Y,et al.Analysis of therapeutic targets for SARS-CoV-2 and discovery of potential drugs by computational methods[J].Actapharm Sin B,2020,10(5):766-788.
[5] WARSZYCKI D,STRUSKI L,SMIEJA M,et al.Pharmacoprint:a combination of a pharmacophore fingerprint and artificial intelligence as a tool for Computer-Aided Drug Design[J].J Chem Inf Model,2021,61(10):5054-5065.
[6] DAI Z,AN L Y,CHEN X Y,et al.Target fishing reveals a novel mechanism of 1,2,4-oxadiazole derivatives targeting rpn6,a subunit of 26s proteasome[J].J Med Chem,2022,65(6):5029-5043.
[7] GENTILE D,FLORESTA G,PATAMIA V,et al.An integrated pharmacophore/docking/3D-QSAR approach to screening a large library of products in search of future botulinum neurotoxin a inhibitors[J].Int J Mol Sci,2020,21(24):9470.
[8] UniProt Consortium.UniProt:the universal protein knowledgebase in 2021[J].Nucleic Acids Res,2021,49(D1):D480-D489.
[9] 罗静初.UniProt蛋白质数据库简介[J].生物信息学,2019,17(3):131-144.
[10] BARKER W C,GARAVELLI J S,MCGARVEY P B,et al.The PIR-international protein sequence database[J].Nucleic Acids Res,1999,27(1):39-43.
[11] BOUTET E,LIEBERHERR D,TOGNOLLI M,et al.UniProtKB/Swiss-Prot[J].Methods Mol Biol,2007,406:89-112.
[12] BOECKMANN B,BAIROCH A,APWEILER R,et al.The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003[J].Nucleic Acids Res,2003,31(1):365-370.
[13] WANG Y,WANG Q,HUANG H,et al.A crowdsourcing open platform for literature curation in UniProt[J].PLoS Biol,2021,19(12):e3001464.
[14] SUZEK B E,HUANG H,MCGARVEY P,et al.UniRef:comprehensive and non-redundant UniProt reference clusters[J].Bioinformatics,2007,23(10):1282-1288.
[15] MACDOUGALL A,VOLYNKIN V,SAIDI R,et al.UniRule:a unified rule resource for automatic annotation in the UniProt Knowledgebase[J].Bioinformatics,2021,36:22-23.
[16] BOUTET E,LIEBERHERR D,TOGNOLLI M,et al.UniProtKB/Swiss-Prot,the manually annotated section of the UniProt KnowledgeBase:how to use the entry view[J].Methods Mol Biol,2016,1374:23-54.
[17] BURLEY S K,BHIKADIYA C,BI C,et al.RCSB protein data bank:powerful new tools for exploring 3D structures of biological macromolecules for basic and applied research and education in fundamental biology,biomedicine,biotechnology,bioengineering and energy sciences[J].Nucleic Acids Res,2021,49(D1):D437-D451.
[18] WESTBROOK J D,YOUNG J Y,SHAO C,et al.PDBx/mmCIF ecosystem:foundational semantic tools for structural biology[J].J Mol Biol,2022,434(11):167599.
[19] VARADI M,ANYANGO S,DESHPANDE M,et al.AlphaFold protein structure database:massively expanding the structural coverage of protein-sequence space with high-accuracy models[J].Nucleic Acids Res,2022,50(D1):D439-D444.
[20] RUFF K M,PAPPU R V.AlphaFold and implications for intrinsically disordered proteins[J].J Mol Biol,2021,433(20):167208.
[21] KOES D R,CAMACHO C J.ZINCPharmer:pharmacophore search of the ZINC database[J].Nucleic Acids Res,2012,40(W1):W409-W414.
[22] WANG X,SHEN Y,WANG S,et al.PharmMapper 2017 update:a web server for potential drug target identification with a comprehensive target pharmacophore database[J].Nucleic Acids Res,2017,45(W1):W356-W360.
[23] KOES D R,CAMACHO C J.Pharmer:efficient and exact pharmacophore search[J].J Chem Inf Model,2011,51(6):1307-1314.
[24] UBA A I,YELEKCI K.Pharmacophore-based virtual screening for identification of potential selective inhibitors of human histone deacetylase 6[J].Comput Biol Chem,2018,77:318-330.
[25] GOGOI N,CHETIA D,GOGOI B,et al.Multiple-targets directed screening of flavonoid compounds from citrus species to find out antimalarial lead with predicted mode of action:an in silico and wholecell-based in vitro approach[J].Curr Comput Aided Drug Des,2021,17(1):69-82.
[26] ABE H,OKAZAWA M,OYAMA T,et al.A unique anti-cancer 3-styrylchromone suppresses inflammatory response via HMGB1-RAGE signaling[J].Medicines(Basel),2021,8(4):17.
[27] ELSEGINY S A.Virtual screening and structure-based 3D pharmacophore approach to identify small-molecule inhibitors of SARS-CoV-2 M(pro)[J].J Biomol Struct Dyn,2021,1-17.
[28] MOUMBOCK A F A,LI J,TRAN H T T,et al.ePharmaLib:A versatile library of e-pharmacophores to address small-molecule (poly-) pharmacology[J].J Chem Inf Model,2021,61(7):3659-3666.
[29] DESAPHY J,BRET G,ROGNAN D,et al.Sc-PDB:a 3D-database of ligandable binding sites-10 years on[J].Nucleic Acids Res,2015,43(Database issue):D399-D404.
[30] TAMINAU J,THIJS G,DE WINTER H.Pharao:pharmacophore alignment and optimization[J].J Chem Inf Model,2008,27(2):161-169.

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