Artificial intelligence (AI) is often presented as a new Industrial Revolution. Many domains use AI, including molecular simulation for drug discovery. In this review, we provide an overview of ligand-protein molecular docking and how machine learning (ML), especially deep learning (DL), a subset of ML, is transforming the field by tackling the associated challenges.
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http://dx.doi.org/10.1016/j.drudis.2021.09.007 | DOI Listing |
Nat Commun
January 2025
Crick-GSK Biomedical LinkLabs, GSK, Gunnels Wood Road, Stevenage, Hertfordshire, UK.
Identifying pharmacological probes for human proteins represents a key opportunity to accelerate the discovery of new therapeutics. High-content screening approaches to expand the ligandable proteome offer the potential to expedite the discovery of novel chemical probes to study protein function. Screening libraries of reactive fragments by chemoproteomics offers a compelling approach to ligand discovery, however, optimising sample throughput, proteomic depth, and data reproducibility remains a key challenge.
View Article and Find Full Text PDFPLoS One
December 2024
Department of Pharmacology, KLE College of Pharmacy KAHER, A Constituent Unit of KAHER-Belagavi University, Rajajinagar, Bengaluru, Karnataka, India.
Liver cancer is one of the most prevalent malignant diseases in humans and the second leading cause of cancer-related mortality globally. Angiopteris helferiana was mentioned as a possible anticancer herb according to ethnomedicinal applications. However, the molecular docking and chemical profiling of the bioactive phytoconstituents accountable for the reported anticancer action still require research.
View Article and Find Full Text PDFACS Pharmacol Transl Sci
December 2024
University of Münster, Institute of Pharmaceutical and Medicinal Chemistry, Pharma Campus, Corrensstr. 48, 48149 Münster, Germany.
Hyperpolarization-activated cyclic nucleotide-gated (HCN) ion channels play a critical role in regulating neuronal and cardiac rhythmicity, with their function being modulated by cyclic nucleotide binding. Dysfunction of HCN ion channels leads to the genesis of several diseases such as arrhythmia, bradycardia, or epilepsy. This study employs a multidisciplinary approach integrating mutagenesis, ligand binding assays, and molecular dynamics (MD) simulations combined with dynamic pharmacophore studies to investigate the impact of single residue mutations within the cyclic nucleotide-binding domain (CNBD) of HCN4 channels.
View Article and Find Full Text PDFJ Agric Food Chem
December 2024
Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P. R. China.
Mol Divers
December 2024
Deparment of Microbiology, Assam University, Silchar, 788011, Assam, India.
Leishmaniasis, a neglected tropical disease caused by various Leishmania species, poses a significant global health challenge, especially in resource-limited regions. Visceral Leishmaniasis (VL) stands out among its severe manifestations, and current drug therapies have limitations, necessitating the exploration of new, cost-effective treatments. This study utilized a comprehensive computational workflow, integrating traditional 2D-QSAR, q-RASAR, and molecular docking to identify novel anti-leishmanial compounds, with a focus on Glycyl-tRNA Synthetase (LdGlyRS) as a promising drug target.
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