Targeting simian retrovirus type 1 RNA pseudoknot with small molecules

• Main Author: Lau, Qing Yi
• Other Authors: Mu Yuguang
• Format: Final Year Project
• Language: English
• Published: 2019
• Subjects: Science::Biological sciences::Molecular biology
• Online Access: http://hdl.handle.net/10356/79014
• Institution: Nanyang Technological University

RNA might not be a popular choice of drug targets as compared to proteins, however, much remains unknown of its potential. In this study, Simian retrovirus type 1 (SRV-1) RNA pseudoknot was focused as a target for small molecules for its complex structure and numerous possibilities as a drug target. The objective of this study was to utilise Computational Biology methods to process and analyse SRV-1 RNA pseudoknot through molecular dynamics simulations to verify the stability of the RNA, as well as to dock small molecules onto the RNA, where Linux was used as the platform for all processes. Results have shown successful docking of small molecules onto SRV-1 RNA pseudoknot with ligands from OTAVA PrimScreen1 library, with the help of AutoDock Vina and PyMOL for viewing the consolidated results. The top 3 ligands with the highest binding affinities were selected as the results of this study as relatively high binding affinities translates into successful docking and binding stability of small molecules onto the RNA. Mason-Pfizer monkey virus caused by Simian retroviruses could highly possibly be prevented with the computational results supported by experimental data, in which further research would be required to determine the accuracy of the computational results.