Alchemical Free Energy Calculations on Membrane-Associated Proteins

Abstract

Membrane proteins have diverse functions within cells and are well-established drug targets. The advances in membrane protein structural biology have revealed drug and lipid binding sites on membrane proteins, while computational methods such as molecular simulations can resolve the thermodynamic basis of these interactions. Particularly, alchemical free energy calculations have shown promise in the calculation of reliable and reproducible binding free energies of protein–ligand and protein–lipid complexes in membrane-associated systems. In this review, we present an overview of representative alchemical free energy studies on G-protein-coupled receptors, ion channels, transporters as well as protein–lipid interactions, with emphasis on best practices and critical aspects of running these simulations. Additionally, we analyze challenges and successes when running alchemical free energy calculations on membrane-associated proteins. Finally, we highlight the value of alchemical free energy calculations calculations in drug discovery and their applicability in the pharmaceutical industry.

Adsorption of Flavonoids in a Transcriptional Regulator TtgR: Relative Binding Free Energies and Intermolecular Interactions

“…We have conducted AFE simulations in aqueous solutions and TtgR-ligand complexes to calculate the relative binding free energies of the seven flavonoids. Among the recent advancements in AFE methods, − we have invoked the ACES approach to enhance conformational and alchemical sampling and produce reliable free energy estimates . As illustrated in Figure , the common cores incorporate the basic skeleton of the flavonoids, while the softcore regions undergo transformation between two ligands in each AFE simulation.…”

“…AFE simulations have been used extensively in drug discovery for the prediction of ligand–protein binding, and have been the subject of several reviews. − We conducted AFE simulations to compute the relative binding free energies of the flavonoids using the Amber 2022 package and AMBER Drug Discovery Boost Tools that leverage high-performance GPU acceleration. , The version differences in the Amber program for standard MD simulations and AFE simulations are expected to have minimal impact on the prediction results. The relative binding free energy between ligands 1 and 2 in TtgR is defined as the difference between their absolute binding free energies, ΔΔ G bind = Δ G bind,2 – Δ G bind,1 .…”

Alchemical Enhanced Sampling with Optimized Phase Space Overlap

“…Alchemical free energy (AFE) simulations − play an important role in computer-aided drug discovery. − They are used in lead refinement to predict target binding affinity and selectivity in order to prioritize proposed compound synthesis and testing. AFE simulations use an artificial “alchemical” coordinate (referred to as “λ”) to transform one ligand into another in a relative binding free energy (RBFE) calculation. , Alternatively, absolute binding free energy calculations , “annihilate” the ligand by transforming it into a noninteracting “dummy” state. − The reliability of AFE simulations depends critically on the ability to robustly sample the important regions of phase space along the entire alchemical pathway.…”

Correlation of Experimental and Calculated Inhibition Constants of Protease Inhibitor Complexes

“…There are numerous software packages and web servers that can be utilized to calculate the interaction energies and equilibrium constants of all biological molecule and ligand types [1][2][3]. For instance, the sophisticated screening for computer generated inhibitors of a galactofuranosyl-transferase highlights the connection between the free binding energy ∆G (Gibbs free energy) in the complex and the corresponding inhibition constant K i [4].…”