Small molecules, big targets: drug discovery faces the protein–protein interaction challenge

DE Scott, AR Bayly, C Abell, J Skidmore - Nature Reviews Drug …, 2016 - nature.com
Protein–protein interactions (PPIs) are of pivotal importance in the regulation of biological
systems and are consequently implicated in the development of disease states. Recent work …

Stapled peptide design: principles and roles of computation

YS Tan, DP Lane, CS Verma - Drug Discovery Today, 2016 - Elsevier
Highlights•One of the most widely adopted strategies for α-helix stabilisation is peptide
stapling.•Stapled peptides are highly promising therapeutic agents.•General design …

Driving structure-based drug discovery through cosolvent molecular dynamics: Miniperspective

P Ghanakota, HA Carlson - Journal of medicinal chemistry, 2016 - ACS Publications
Identifying binding hotspots on protein surfaces is of prime interest in structure-based drug
discovery, either to assess the tractability of pursuing a protein target or to drive improved …

Optimization and evaluation of site-identification by ligand competitive saturation (SILCS) as a tool for target-based ligand optimization

VD Ustach, SK Lakkaraju, S Jo, W Yu… - Journal of chemical …, 2019 - ACS Publications
Chemical fragment cosolvent sampling techniques have become a versatile tool in ligand-
protein binding prediction. Site-identification by ligand competitive saturation (SILCS) is one …

Mapping the binding sites of challenging drug targets

AE Wakefield, D Kozakov, S Vajda - Current opinion in structural biology, 2022 - Elsevier
An increasing number of medically important proteins are challenging drug targets because
their binding sites are too shallow or too polar, are cryptic and thus not detectable without a …

Deciphering cryptic binding sites on proteins by mixed-solvent molecular dynamics

SR Kimura, HP Hu, AM Ruvinsky… - Journal of chemical …, 2017 - ACS Publications
In recent years, molecular dynamics simulations of proteins in explicit mixed solvents have
been applied to various problems in protein biophysics and drug discovery, including …

Discovery of small-molecule enzyme activators by activity-based protein profiling

BP Kok, S Ghimire, W Kim, S Chatterjee… - Nature chemical …, 2020 - nature.com
Activity-based protein profiling (ABPP) has been used extensively to discover and optimize
selective inhibitors of enzymes. Here, we show that ABPP can also be implemented to …

Partially Saturated Bicyclic Heteroaromatics as an sp3‐Enriched Fragment Collection

DG Twigg, N Kondo, SL Mitchell… - Angewandte …, 2016 - Wiley Online Library
Fragment‐based lead generation has proven to be an effective means of identifying high‐
quality lead compounds for drug discovery programs. However, the fragment screening sets …

Halogen bonding in halocarbon-protein complexes and computational tools for rational drug design

PJ Costa, R Nunes, D Vila-Viçosa - Expert Opinion on Drug …, 2019 - Taylor & Francis
Introduction: Halogens have a prominent role in drug design. Often used as a mean to
improve ADME properties, they are also becoming a tool in protein–ligand recognition given …

Application of site-identification by ligand competitive saturation in computer-aided drug design

H Goel, A Hazel, W Yu, S Jo… - New Journal of Chemistry, 2022 - pubs.rsc.org
Site Identification by Ligand Competitive Saturation (SILCS) is a molecular simulation
approach that uses diverse small solutes in aqueous solution to obtain functional group …