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Application of Semiempirical Quantum Mechanical Methods To Accurately Estimate Ligand-Binding Structure in Biological
Charles-Alexandre Mattelaer1, Roberto Fino2, Christian Permann3,4
1Department of Chemistry, KU Leuven, Celestijnenlaan, 200F, Leuven 3001, Belgium.
Abstract:
This study presents a quantum mechanical (QM)-based workflow utilizing semiempirical methods for estimating ligand binding poses in protein-ligand complexes, focusing on kinases of pharmaceutical relevance: CDK2, CK2, p38α, and CAMK1DA. The protocol integrates xTB-based docking with PM6-D3H4X rescoring within a QM/MM framework, aiming to enhance the structural accuracy over traditional docking methods. Drug-like and fragment-like ligands were tested across different receptor structures to assess robustness for CDK2 and CK2. Results show that for drug-like ligands the QM approach reproduces experimental poses. However, performance is less consistent for the fragment-like ligands we have considered, perhaps due to structural ambiguity and weak binding interactions limiting accuracy.
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