eprintid: 223201 rev_number: 5 eprint_status: archive userid: 958 dir: disk0/00/22/32/01 datestamp: 2025-09-02 13:00:14 lastmod: 2025-09-02 13:00:14 status_changed: 2025-09-02 13:00:14 type: article metadata_visibility: show contact_email: tibor.szalai2718@gmail.com sword_depositor: 958 creators_name: Szalai, Tibor Viktor creators_name: Bajusz, Dávid creators_name: Börzsei, Rita creators_name: Zsidó, Balázs Zoltán creators_name: Ilaš, Janez creators_name: Ferenczy, György creators_name: Hetényi, Csaba creators_name: Keserű, György Miklós creators_orcid: creators_orcid: 0000-0003-4277-9481 creators_orcid: creators_orcid: creators_orcid: 0000-0002-0124-0474 creators_orcid: 0000-0002-5771-4616 creators_orcid: creators_orcid: corp_creators: Gyógyszerkémiai Kutatócsoport HRN TTK / SZKI GyKKCs [2014-] corp_creators: Farmakológiai és Farmakoterápiai Intézet PTE / ÁOK FFI corp_creators: Szerves Kémia és Technológia Tanszék BME / VBK SZKTT [2006-] title: Effect of Water Networks On Ligand Binding: Computational Predictions vs Experiments ispublished: pub subjects: QD full_text_status: public abstract: Rational drug design focuses on the explanation and prediction of complex formation between therapeutic targets and small-molecule ligands. As a third and often overlooked interacting partner, water molecules play a critical role in the thermodynamics of protein−ligand binding, impacting both the entropy and enthalpy components of the binding free energy and by extension, on-target affinity and bioactivity. The community has realized the importance of binding site waters, as evidenced by the number of computational tools to predict the structure and thermodynamics of their networks. However, quantitative experimental characterization of relevant protein−ligand−water systems, and consequently the validation of these modeling methods, remains challenging. Here, we investigated the impact of solvent exchange from light (H2O) to heavy water (D2O) to provide complete thermodynamic profiling of these ternary systems. Utilizing the solvent isotope effects, we gain a deeper understanding of the energetic contributions of various components. Specifically, we conducted isothermal titration calorimetry experiments on trypsin with a series of psubstituted benzamidines, as well as carbonic anhydrase II (CAII) with a series of aromatic sulfonamides. Significant differences in binding enthalpies found between light vs heavy water indicate a substantial role of the binding site water network in protein−ligand binding. Next, we challenged two conceptually distinct modeling methods, the grid-based WaterFLAP and the molecular dynamicsbased MobyWat, by predicting and scoring relevant water networks. The predicted water positions accurately reproduce those in available high-resolution X-ray and neutron diffraction structures of the relevant protein−ligand complexes. Estimated energetic contributions of the identified water networks were corroborated by the experimental thermodynamics data. Besides providing a direct validation for the predictive power of these methods, our findings confirmed the importance of considering binding site water networks in computational ligand design. date: 2024 date_type: published publication: JOURNAL OF CHEMICAL INFORMATION AND MODELING volume: 64 number: 23 pagerange: 8980-8998 id_number: MTMT:35597879 10.1021/acs.jcim.4c01291 refereed: TRUE issn: 1549-9596 official_url: https://doi.org/10.1021/acs.jcim.4c01291 funders: Bolyai János Kutatási Ösztöndíj fp7_project: no fp7_type: info:eu-repo/semantics/article citation: Szalai, Tibor Viktor and Bajusz, Dávid and Börzsei, Rita and Zsidó, Balázs Zoltán and Ilaš, Janez and Ferenczy, György and Hetényi, Csaba and Keserű, György Miklós (2024) Effect of Water Networks On Ligand Binding: Computational Predictions vs Experiments. JOURNAL OF CHEMICAL INFORMATION AND MODELING, 64 (23). pp. 8980-8998. ISSN 1549-9596 document_url: https://real.mtak.hu/223201/1/szalai2024.pdf