Drug discovery targeting NS2B-NS3 proteases from dengue and Zika viruses
The advancements in algorithms and tools for virtual screening have greatly expedited the process of virtual screening. Recent studies have focused on a prospective group of Zika Virus (ZIKV) proteases to circumvent the proliferation of the microcephaly-causing virus. In this research, a structure based virtual screening approach on the ZIKV NS2B-NS3 protease was adopted in order to identify ligands which could potentially inhibit the protease activity. Multiple Receptor Conformation screening workflow was applied through the sampling of initial crystal structure at different random initial velocities by molecular dynamics simulation to account for receptor flexibility. Conformations of the protein were clustered by binding pocket conformations. Molecules from virtual screening libraries such as ChemBridge and Enamine were docked to clustering representative structures using GOLD docking software, and a list of the most common top ranked 100 molecules were shortlisted for molecular simulations. A selected ligand subjected to protein-ligand complex molecular dynamics simulations revealed that the molecule remained stable in NS2B-NS3 binding cleft. Further experimental studies can be performed to validate the inhibitors identified.
Author: Chan KF et al <<< Published on: 30 August 2018
Automated submission script to AlloSigMA webserver: a viable approach for allosteric effects scanning
Online computational tools, e.g. webservers, have been used extensively for research analysis. Many of such webservers require user manual inputs that can be laborious. In such cases, it is possible to automate some tasks using scripts, especially when performing similar tasks with multiple inputs. This article describes one such script, using Python programming language, for the webserver AlloSigMA for the analysis of allosteric communications in proteins. Our Python script can minimize human inputs and reduces human errors in the use of the AlloSigMA server.
Author: Phua SX et al <<< Published on: 20 December 2018
Application Notes on APD Areametric App: Automated area quantification for both Android and iOS
Area measurements have a wide range of uses from the monitoring of skin features in healthcare, celestial bodies in astronomy, to determining furniture sizes in everyday indoor uses. Current measurement methods utilize some form of measuring tool and unless performed by skilled and trained professionals, human errors leading to inaccurate measurements can often arise. This is especially so for irregularly shaped objects with complex dimensions. To alleviate such inaccuracies, we created the APD Areametric native Android and Apple mobile application that leveraged upon image processing to more accurately determine areas of the defined object in images by using pixel ratios. This not only makes such measurement more convenient, but also greatly improves the accuracy and speed of area determination.
Author: Wu WL et al <<< Published on: 08 February 2019