Molecular Docking with Open Access Software: Development of an Online Laboratory Handbook and Remote Workflow for Chemistry and Pharmacy Master's Students to Undertake Computer-Aided Drug Design

被引:13
作者
Clent, Bethanie A. [1 ]
Wang, Yuhang [2 ]
Britton, Hugh C. [1 ]
Otto, Frank [1 ]
Swain, Christopher J. [3 ]
Todd, Matthew H. [2 ]
Wilden, Jonathan D. [1 ]
Tabor, Alethea B. [1 ]
机构
[1] UCL, Dept Chem, London WC1H 0AJ, England
[2] UCL, Sch Pharm, London WC1N 1AX, England
[3] Cambridge MedChem Consulting, Cambridge CB22 4RN, England
关键词
Graduate Education/Research; Chemoinformatics; Interdisciplinary/Multidisciplinary; Textbooks/Reference Books; Distance Learning/Self Instruction; Inquiry-Based/Discovery Learning; Medicinal Chemistry; Molecular Modeling; MEDICINAL CHEMISTRY; DISCOVERY;
D O I
10.1021/acs.jchemed.1c00289
中图分类号
O6 [化学];
学科分类号
0703 ;
摘要
In response to the closure of many university laboratories due to the Covid-19 pandemic in 2020, a handbook and remote webinar approach designed to support students in the use of software tools for computer-aided drug design has been developed. Specifically, the course has been designed for chemistry and pharmacy students who have little or no experience of computational techniques and can use open-source software on their own machines. In this way a flexible and relevant course, giving a rigorous academic experience, could be delivered even in the most challenging of circumstances. We believe that this laboratory protocol will help to "democratize" the scientific process in this field.
引用
收藏
页码:2899 / 2905
页数:7
相关论文
共 25 条
[1]   Computer-Aided Drug Design for the Organic Chemistry Laboratory Using Accessible Molecular Modeling Tools [J].
Acuna, Valeria V. ;
Hopper, Rachel M. ;
Yoder, Ryan J. .
JOURNAL OF CHEMICAL EDUCATION, 2020, 97 (03) :760-763
[2]  
[Anonymous], 2017, CONNECTED CURRICULUM, DOI DOI 10.14324/111.9781911576358
[3]   The ChEMBL bioactivity database: an update [J].
Bento, A. Patricia ;
Gaulton, Anna ;
Hersey, Anne ;
Bellis, Louisa J. ;
Chambers, Jon ;
Davies, Mark ;
Krueger, Felix A. ;
Light, Yvonne ;
Mak, Lora ;
McGlinchey, Shaun ;
Nowotka, Michal ;
Papadatos, George ;
Santos, Rita ;
Overington, John P. .
NUCLEIC ACIDS RESEARCH, 2014, 42 (D1) :D1083-D1090
[4]  
Covid Moonshot, TAK FRAGM IMP
[5]  
Davies J P., 2018, Teaching and learning in higher education: Perspectives from UCL
[6]   Crystallographic and electrophilic fragment screening of the SARS-CoV-2 main protease [J].
Douangamath, Alice ;
Fearon, Daren ;
Gehrtz, Paul ;
Krojer, Tobias ;
Lukacik, Petra ;
Owen, C. David ;
Resnick, Efrat ;
Strain-Damerell, Claire ;
Aimon, Anthony ;
Abranyi-Balogh, Peter ;
Brandao-Neto, Jose ;
Carbery, Anna ;
Davison, Gemma ;
Dias, Alexandre ;
Downes, Thomas D. ;
Dunnett, Louise ;
Fairhead, Michael ;
Firth, James D. ;
Jones, S. Paul ;
Keeley, Aaron ;
Keserue, Gyoergy M. ;
Klein, Hanna F. ;
Martin, Mathew P. ;
Noble, Martin E. M. ;
O'Brien, Peter ;
Powell, Ailsa ;
Reddi, Rambabu N. ;
Skyner, Rachael ;
Snee, Matthew ;
Waring, Michael J. ;
Wild, Conor ;
London, Nir ;
von Delft, Frank ;
Walsh, Martin A. .
NATURE COMMUNICATIONS, 2020, 11 (01)
[7]   Demonstration of AutoDock as an Educational Tool for Drug Discovery [J].
Helgren, Travis R. ;
Hagen, Timothy J. .
JOURNAL OF CHEMICAL EDUCATION, 2017, 94 (03) :345-349
[8]   Structure of Mpro from SARS-CoV-2 and discovery of its inhibitors [J].
Jin, Zhenming ;
Du, Xiaoyu ;
Xu, Yechun ;
Deng, Yongqiang ;
Liu, Meiqin ;
Zhao, Yao ;
Zhang, Bing ;
Li, Xiaofeng ;
Zhang, Leike ;
Peng, Chao ;
Duan, Yinkai ;
Yu, Jing ;
Wang, Lin ;
Yang, Kailin ;
Liu, Fengjiang ;
Jiang, Rendi ;
Yang, Xinglou ;
You, Tian ;
Liu, Xiaoce ;
Yang, Xiuna ;
Bai, Fang ;
Liu, Hong ;
Liu, Xiang ;
Guddat, Luke W. ;
Xu, Wenqing ;
Xiao, Gengfu ;
Qin, Chengfeng ;
Shi, Zhengli ;
Jiang, Hualiang ;
Rao, Zihe ;
Yang, Haitao .
NATURE, 2020, 582 (7811) :289-+
[9]   Computer-Aided Drug Discovery: Molecular Docking of Diminazene Ligands to DNA Minor Groove [J].
Kholod, Yana ;
Hoag, Erin ;
Muratore, Katlynn ;
Kosenkov, Dmytro .
JOURNAL OF CHEMICAL EDUCATION, 2018, 95 (05) :882-887
[10]   Refining the chemical toolbox to be fit for educational and practical purpose for drug discovery in the 21st Century [J].
Lolli, Marco ;
Narramore, Sarah ;
Fishwick, Colin W. G. ;
Pors, Klaus .
DRUG DISCOVERY TODAY, 2015, 20 (08) :1018-1026