1. Probing Factor Xa Protein–Ligand Interactions: Accurate Free Energy Calculations and Experimental Validations of Two Series of High-Affinity Ligands
- Author
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María Isabel Fernández-Bachiller, Songhwan Hwang, María Elena Schembri, Peter Lindemann, Mónica Guberman, Svenja Herziger, Edgar Specker, Hans Matter, David W. Will, Jörg Czech, Michael Wagner, Armin Bauer, Herman Schreuder, Kurt Ritter, Matthias Urmann, Volkmar Wehner, Han Sun, and Marc Nazaré
- Subjects
Halogens ,Indoles ,Alkynes ,Factor Xa ,Drug Discovery ,Proteins ,Thermodynamics ,Molecular Medicine ,Molecular Dynamics Simulation ,Ligands ,Protein Binding - Abstract
The accurate prediction of protein-ligand binding affinity belongs to one of the central goals in computer-based drug design. Molecular dynamics (MD)-based free energy calculations have become increasingly popular in this respect due to their accuracy and solid theoretical basis. Here, we present a combined study which encompasses experimental and computational studies on two series of factor Xa ligands, which enclose a broad chemical space including large modifications of the central scaffold. Using this integrated approach, we identified several new ligands with different heterocyclic scaffolds different from the previously identified indole-2-carboxamides that show superior or similar affinity. Furthermore, the so far underexplored terminal alkyne moiety proved to be a suitable non-classical bioisosteric replacement for the higher halogen-π aryl interactions. With this challenging example, we demonstrated the ability of the MD-based non-equilibrium free energy calculation approach for guiding crucial modifications in the lead optimization process, such as scaffold replacement and single-site modifications at molecular interaction hot spots.
- Published
- 2022