Modern alchemical free energy methods for drug discovery explained

DM York - ACS Physical Chemistry Au, 2023 - ACS Publications
This Perspective provides a contextual explanation of the current state-of-the-art alchemical
free energy methods and their role in drug discovery as well as highlights select emerging …

Importance of tautomerism in drugs

PV Bharatam, OR Valanju, AA Wani, DK Dhaked - Drug Discovery Today, 2023 - Elsevier
Highlights•Tautomers significantly influence solid state properties of drugs and drug
delivery.•Many drugs exhibit tautomerism, the tautomers are important in drug action …

QDπ: A quantum deep potential interaction model for drug discovery

J Zeng, Y Tao, TJ Giese, DM York - Journal of chemical theory …, 2023 - ACS Publications
We report QDπ-v1. 0 for modeling the internal energy of drug molecules containing H, C, N,
and O atoms. The QDπ model is in the form of a quantum mechanical/machine learning …

Software Infrastructure for Next-Generation QM/MM− ΔMLP Force Fields

TJ Giese, J Zeng, L Lerew, E McCarthy… - The Journal of …, 2024 - ACS Publications
We present software infrastructure for the design and testing of new quantum
mechanical/molecular mechanical and machine-learning potential (QM/MM− ΔMLP) force …

Modern semiempirical electronic structure methods and machine learning potentials for drug discovery: Conformers, tautomers, and protonation states

J Zeng, Y Tao, TJ Giese, DM York - The Journal of chemical physics, 2023 - pubs.aip.org
Modern semiempirical electronic structure methods have considerable promise in drug
discovery as universal “force fields” that can reliably model biological and drug-like …

Revisiting the structure and chemistry of 3 (5)-substituted pyrazoles

A Secrieru, PM O'Neill, MLS Cristiano - Molecules, 2019 - mdpi.com
Pyrazoles are known as versatile scaffolds in organic synthesis and medicinal chemistry,
often used as starting materials for the preparation of more complex heterocyclic systems …

Recent advances in constraint and machine learning-based metabolic modeling by leveraging stoichiometric balances, thermodynamic feasibility and kinetic law …

PF Suthers, CJ Foster, D Sarkar, L Wang… - Metabolic …, 2021 - Elsevier
Understanding the governing principles behind organisms' metabolism and growth
underpins their effective deployment as bioproduction chassis. A central objective of …

Favipiravir tautomerism: a theoretical insight

L Antonov - Theoretical chemistry accounts, 2020 - Springer
There is no experimental information about the tautomerism of Favipiravir (T-705).
Therefore, its tautomeric state was predicted by using density functional theory in gas phase …

Computer Prediction of pKa Values in Small Molecules and Proteins

CD Navo, G Jiménez-Osés - ACS Medicinal Chemistry Letters, 2021 - ACS Publications
Accurately determining the acid dissociation constants (K a or their logarithmic form, p K a)
of small molecules and large biomolecules has proven to be pivotal for the study different …

MolTaut: A Tool for the Rapid Generation of Favorable Tautomer in Aqueous Solution

X Pan, F Zhao, Y Zhang, X Wang, X Xiao… - Journal of Chemical …, 2023 - ACS Publications
Fast and proper treatment of the tautomeric states for drug-like molecules is critical in
computer-aided drug discovery since the major tautomer of a molecule determines its …