Computational approaches for the design of modulators targeting protein-protein interactions
ABSTRACT Background Protein-protein interactions (PPIs) are intriguing targets for
designing novel small-molecule inhibitors. The role of PPIs in various infectious and …
designing novel small-molecule inhibitors. The role of PPIs in various infectious and …
Peptide-based inhibitors of protein–protein interactions: biophysical, structural and cellular consequences of introducing a constraint
H Wang, RS Dawber, P Zhang, M Walko, AJ Wilson… - Chemical …, 2021 - pubs.rsc.org
Protein–protein interactions (PPIs) are implicated in the majority of cellular processes by
enabling and regulating the function of individual proteins. Thus, PPIs represent high-value …
enabling and regulating the function of individual proteins. Thus, PPIs represent high-value …
Application of variational graph encoders as an effective generalist algorithm in computer-aided drug design
Although there has been considerable progress in molecular property prediction in
computer-aided drug design, there is a critical need to have fast and accurate models. Many …
computer-aided drug design, there is a critical need to have fast and accurate models. Many …
Anchor extension: a structure-guided approach to design cyclic peptides targeting enzyme active sites
Despite recent success in computational design of structured cyclic peptides, de novo
design of cyclic peptides that bind to any protein functional site remains difficult. To address …
design of cyclic peptides that bind to any protein functional site remains difficult. To address …
Free energy methods in drug discovery—introduction
Complete understanding of most, if not all chemical processes requires at its very core the
knowledge of the underlying free-energy change. In computer-aided drug design, for …
knowledge of the underlying free-energy change. In computer-aided drug design, for …
Designing stapled peptides to inhibit protein‐protein interactions: an analysis of successes in a rapidly changing field
MTJ Bluntzer, J O'Connell, TS Baker, J Michel… - Peptide …, 2021 - Wiley Online Library
Two decades after their discovery, stapled peptide methodologies have evolved to a point
where they can be used with confidence to generate therapeutic leads. Research groups …
where they can be used with confidence to generate therapeutic leads. Research groups …
Computational molecular interaction between SARS-CoV-2 main protease and theaflavin digallate using free energy perturbation and molecular dynamics
Our objective was to identify the molecule which can inhibit SARS-CoV-2 main protease and
can be easily procured. Natural products may provide such molecules and can supplement …
can be easily procured. Natural products may provide such molecules and can supplement …
Free energy perturbation guided Synthesis with Biological Evaluation of Substituted Quinoline derivatives as small molecule L858R/T790M/C797S mutant EGFR …
KS Karnik, AP Sarkate, SV Tiwari, R Azad… - Bioorganic Chemistry, 2021 - Elsevier
Two different schemes of novel substituted quinoline derivatives were designed and
synthesized via simple reaction steps and conditions. A comparative molecular docking …
synthesized via simple reaction steps and conditions. A comparative molecular docking …
Computational modeling as a tool to investigate PPI: from drug design to tissue engineering
Protein-protein interactions (PPIs) mediate a large number of important regulatory pathways.
Their modulation represents an important strategy for discovering novel therapeutic agents …
Their modulation represents an important strategy for discovering novel therapeutic agents …
Unlocking novel therapies: Cyclic peptide design for amyloidogenic targets through synergies of experiments, simulations, and machine learning
D de Raffele, IM Ilie - Chemical Communications, 2024 - pubs.rsc.org
Existing therapies for neurodegenerative diseases like Parkinson's and Alzheimer's address
only their symptoms and do not prevent disease onset. Common therapeutic agents, such as …
only their symptoms and do not prevent disease onset. Common therapeutic agents, such as …