[HTML][HTML] Computational methods in drug discovery

SP Leelananda, S Lindert - Beilstein journal of organic …, 2016 - beilstein-journals.org
The process for drug discovery and development is challenging, time consuming and
expensive. Computer-aided drug discovery (CADD) tools can act as a virtual shortcut …

Advances in molecular dynamics simulations and enhanced sampling methods for the study of protein systems

R Lazim, D Suh, S Choi - International journal of molecular sciences, 2020 - mdpi.com
Molecular dynamics (MD) simulation is a rigorous theoretical tool that when used efficiently
could provide reliable answers to questions pertaining to the structure-function relationship …

Computer-aided drug design methods

W Yu, AD MacKerell - Antibiotics: methods and protocols, 2017 - Springer
Computational approaches are useful tools to interpret and guide experiments to expedite
the antibiotic drug design process. Structure-based drug design (SBDD) and ligand-based …

Structural and thermodynamic framework for PIEZO1 modulation by small molecules

W Jiang, TD Wijerathne, H Zhang… - Proceedings of the …, 2023 - National Acad Sciences
Mechanosensitive PIEZO channels constitute potential pharmacological targets for multiple
clinical conditions, spurring the search for potent chemical PIEZO modulators. Among them …

Discovery of high-affinity small-molecule binders of the epigenetic reader YEATS4

AT Londregan, K Aitmakhanova, J Bennett… - Journal of medicinal …, 2022 - ACS Publications
A series of small-molecule YEATS4 binders have been discovered as part of an ongoing
research effort to generate high-quality probe molecules for emerging and/or challenging …

[HTML][HTML] The rise of molecular simulations in fragment-based drug design (FBDD): an overview

M Bissaro, M Sturlese, S Moro - Drug Discovery Today, 2020 - Elsevier
Highlights•Fragment-based drug design (FBDD) is revolutionizing the identification and
optimization of new drug candidates.•Molecular simulations-based approaches are …

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 …

Ligandability and druggability assessment via machine learning

F Di Palma, C Abate, S Decherchi… - Wiley Interdisciplinary …, 2023 - Wiley Online Library
Drug discovery is a daunting and failure‐prone task. A critical process in this research field
is represented by the biological target and pocket identification steps as they heavily …

Ranking reversible covalent drugs: from free energy perturbation to fragment docking

H Zhang, W Jiang, P Chatterjee… - Journal of chemical …, 2019 - ACS Publications
Reversible covalent inhibitors have drawn increasing attention in drug design, as they are
likely more potent than noncovalent inhibitors and less toxic than covalent inhibitors. Despite …

Intermolecular interactions in G protein-coupled receptor allosteric sites at the membrane interface from molecular dynamics simulations and quantum chemical …

T Ding, DS Karlov, A Pino-Angeles… - Journal of Chemical …, 2022 - ACS Publications
Allosteric modulators are called promising candidates in G protein-coupled receptor (GPCR)
drug development by displaying subtype selectivity and more specific receptor modulation …