Artificial intelligence in the prediction of protein–ligand interactions: recent advances and future directions

A Dhakal, C McKay, JJ Tanner… - Briefings in …, 2022 - academic.oup.com
New drug production, from target identification to marketing approval, takes over 12 years
and can cost around $2.6 billion. Furthermore, the COVID-19 pandemic has unveiled the …

Scoring functions for protein-ligand binding affinity prediction using structure-based deep learning: a review

R Meli, GM Morris, PC Biggin - Frontiers in bioinformatics, 2022 - frontiersin.org
The rapid and accurate in silico prediction of protein-ligand binding free energies or binding
affinities has the potential to transform drug discovery. In recent years, there has been a …

Theoretical studies on the molecular properties, toxicity, and biological efficacy of 21 new chemical entities

R Srivastava - ACS omega, 2021 - ACS Publications
New chemical entities (NCEs) such as small molecules and antibody–drug conjugates have
strong binding affinity for biological targets, which provide deep insights into structure …

Synthesis, vibrational analysis, molecular property investigation, and molecular docking of new benzenesulphonamide-based carboxamide derivatives against …

UD Izuchukwu, FC Asogwa, H Louis… - Journal of Molecular …, 2022 - Elsevier
Zinc chloride mediated synthesis, density functional theory (DFT) studies and molecular
docking of new carboxamide derivatives containing sulphonamide functionality is reported …

Machine learning enables prediction of Pyrrolysyl-tRNA synthetase substrate specificity

Q Zhang, W Zheng, Z Song, Q Zhang, L Yang… - ACS Synthetic …, 2023 - ACS Publications
Knowledge about the substrate scope for a given enzyme is informative for elucidating
biochemical pathways and also for expanding applications of the enzyme. However, no …

Building intuition for binding free energy calculations: Bound state definition, restraints, and symmetry

E Duboué-Dijon, J Hénin - The Journal of Chemical Physics, 2021 - pubs.aip.org
The theory behind computation of absolute binding free energies using explicit-solvent
molecular simulations is well-established, yet somewhat complex, with counter-intuitive …

Exploring Securigera securidaca Seeds as a Source of Potential CDK1 Inhibitors: Identification of Hippeastrine and Naringenin as Promising Hit Candidates

MEM Abdelbagi, GM Al-Mazaideh, AE Ahmed… - Processes, 2023 - mdpi.com
CDK1 (cyclin dependent kinase 1) is a key regulator of the cell cycle and is frequently
dysregulated in cancer, making it a promising target for anticancer therapy. Securigera …

[HTML][HTML] Machine learning small molecule properties in drug discovery

N Schapin, M Majewski, A Varela-Rial, C Arroniz… - Artificial Intelligence …, 2023 - Elsevier
Abstract Machine learning (ML) is a promising approach for predicting small molecule
properties in drug discovery. Here, we provide a comprehensive overview of various ML …

Quantifying functional-group-like structural fragments in molecules and its applications in drug design

G Mukherjee, A Braka, S Wu - Journal of Chemical Information …, 2023 - ACS Publications
A functional group in a molecule is a structural fragment consisting of a few atoms or a single
atom that imparts reactivity to a molecule. Hence, defining functional groups is crucial in …

Virtual screening of potential anticancer drugs based on microbial products

GP Pinto, NM Hendrikse, J Stourac… - Seminars in Cancer …, 2022 - Elsevier
The development of microbial products for cancer treatment has been in the spotlight in
recent years. In order to accelerate the lengthy and expensive drug development process, in …