Water-based pharmacophore modeling in kinase inhibitor design : a case study on Fyn and Lyn protein kinases

Ljubič, Martin (author), Sollner Dolenc, Marija (author), Borišek, Jure (author), Perdih, Andrej (author)

Water-based pharmacophore modeling is an emerging approach in inhibitor design that leverages the dynamics of explicit water molecules within ligand-free, water-filled binding sites to derive 3D pharmacophores for virtual screening. In this study, we assess the potential of this strategy through a case study targeting the ATP binding sites of Fyn and Lyn protein kinases─members of the Src family that have been less explored in anticancer drug discovery compared to other family members. Molecular dynamics simulations of multiple kinase structures were used to generate and validate several water-derived pharmacophores, which were subsequently employed to screen chemically diverse libraries of compounds. Two active compounds were identified in biochemical assays: a flavonoid-like molecule with low-micromolar inhibitory activity and a weaker inhibitor from the library of nature-inspired synthetic compounds. Structural analysis via molecular docking and simulations revealed that key predicted interactions, particularly with the hinge region and the ATP binding pocket, were retained in the bound states of these hits. However, interactions with more flexible regions, such as the N-terminal lobe and activation loop, were less consistently captured. These findings outline both the strengths and challenges of using water-based pharmacophores: while effective at modeling conserved core interactions, they may miss peripheral contacts governed by protein flexibility. Incorporating ligand information where available may help address this challenge. Overall, water-based pharmacophore modeling presents a promising ligand-independent strategy for identifying novel chemotypes and exploring undercharged chemical and conformational space in kinases as well as other therapeutically relevant targets.

• Language: English
• Keywords: drug discovery, inhibitors, ligands, peptides, proteins, pharmacophores
• Work type: Article
• Typology: 1.01 - Original Scientific Article
• Organization: FFA - Faculty of Pharmacy
• Publication status: Published
• Publication version: Version of Record
• Year: 2025
• Number of pages: Str. 9747−9761
• Numbering: Vol. 65, iss. 18
• PID: 20.500.12556/RUL-176572
• UDC: 66.011:615
• ISSN on article: 1549-960X
• DOI: 10.1021/acs.jcim.5c01478
• COBISS.SI-ID: 247223299
• Publication date in RUL: 04.12.2025

Record is a part of a journal

• Title: Journal of chemical information and modeling
• Publisher: American Chemical Society
• ISSN: 1549-960X
• COBISS.SI-ID: 3037204

Licences

• License: CC BY 4.0, Creative Commons Attribution 4.0 International
• Link: http://creativecommons.org/licenses/by/4.0/
• Description: This is the standard Creative Commons license that gives others maximum freedom to do what they want with the work as long as they credit the author.

Secondary language

• Language: Slovenian
• Keywords: odkrivanje zdravil, inhibitorji, ligandi, peptidi, proteini, farmakofori, modeliranje procesov, zdravila