Chasing molecular glue degraders: screening approaches

A Domostegui, L Nieto-Barrado… - Chemical Society …, 2022 - pubs.rsc.org
Protein–protein interactions (PPIs) govern all biological processes. Some small molecules
modulate PPIs through induced protein proximity. In particular, molecular glue degraders …

Standard Binding Free-Energy Calculations: How Far Are We from Automation?

H Fu, C Chipot, X Shao, W Cai - The Journal of Physical Chemistry …, 2023 - ACS Publications
Recent success stories suggest that in silico protein–ligand binding free-energy calculations
are approaching chemical accuracy. However, their widespread application remains limited …

Protein–protein interfaces in molecular glue-induced ternary complexes: classification, characterization, and prediction

H Rui, KS Ashton, J Min, C Wang, PR Potts - RSC Chemical Biology, 2023 - pubs.rsc.org
Molecular glues are a class of small molecules that stabilize the interactions between
proteins. Naturally occurring molecular glues are present in many areas of biology where …

Computational Approaches to Predict Protein–Protein Interactions in Crowded Cellular Environments

G Grassmann, M Miotto, F Desantis… - Chemical …, 2024 - ACS Publications
Investigating protein–protein interactions is crucial for understanding cellular biological
processes because proteins often function within molecular complexes rather than in …

Hazardous shortcuts in standard binding free energy calculations

M Blazhynska… - The Journal of …, 2022 - ACS Publications
Calculating the standard binding free energies of protein–protein and protein–ligand
complexes from atomistic molecular dynamics simulations in explicit solvent is a problem of …

Developing an implicit solvation machine learning model for molecular simulations of ionic media

A Coste, E Slejko, J Zavadlav… - Journal of chemical …, 2023 - ACS Publications
Molecular dynamics (MD) simulations of biophysical systems require accurate modeling of
their native environment, ie, aqueous ionic solution, as it critically impacts the structure and …

Design of novel coumarin derivatives as NUDT5 antagonists that act by restricting ATP synthesis in breast cancer cells

V Niranjan, S Jayaprasad, A Uttarkar, R Kusanur… - Molecules, 2022 - mdpi.com
Breast cancer, a heterogeneous disease, is among the most frequently diagnosed diseases
and is the second leading cause of death due to cancer among women after lung cancer …

De novo design of anti-COVID drugs using machine learning-based equivariant diffusion model targeting the spike protein

V Niranjan, A Uttarkar, A Ramakrishnan… - Current Issues in …, 2023 - mdpi.com
The drug discovery and research for an anti-COVID-19 drug has been ongoing despite
repurposed drugs in the market. Over time, these drugs were discontinued due to side …

Computational generation and characterization of IsdA‐binding aptamers with single‐molecule FRET analysis

GO Sabbih, KM Wijesinghe, C Algama… - Biotechnology …, 2023 - Wiley Online Library
Staphylococcus aureus is a major foodborne bacterial pathogen. Early detection of S.
aureus is crucial to prevent infections and ensure food quality. The iron‐regulated surface …

Mycobacterium time-series genome analysis identifies AAC2′ as a potential drug target with naloxone showing potential bait drug synergism

V Niranjan, A Uttarkar, K Murali, S Niranjan, J Gopal… - Molecules, 2022 - mdpi.com
The World Health Organization has put drug resistance in tuberculosis on its list of
significant threats, with a critical emphasis on resolving the genetic differences in …