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.

Bioimaging techniques require development of a wide variety of fluorescent probes that absorb and emit red light. One way to shift absorption and emission of a chromophore to longer wavelengths is to modify its chemical structure by adding polycyclic aromatic hydrocarbon (PAH) fragments, thus increasing the conjugation length of a molecule while maintaining its rigidity. Here, we consider four novel classes of conformationally locked Green Fluorescent Protein (GFP) chromophore derivatives obtained by extending their aromatic systems in different directions. Using high-level ab initio quantum chemistry calculations, we show that the alteration of their electronic structure upon annulation may unexpectedly result in a drastic change of their fluorescent properties. A flip of optically bright and dark electronic states is most prominent in the symmetric fluorene-based derivative. The presence of a completely dark lowest-lying excited state is supported by the experimentally measured extremely low fluorescence quantum yield of the newly synthesized compound. Importantly, one of the asymmetric modes of annulation provides a very promising strategy for developing red-shifted molecular emitters with an absorption wavelength of ∼600 nm, having no significant impact on the character of the bright S-S₁ transition.

Conception rationnelle des agonistes, antagonistes et modulateurs allostériques des récepteurs synaptiques: Les canaux ioniques pentamériques ligand-dépendants (pLGIC) assurent la transmission synaptique ; leur dysfonctionnement est à l'origine de troubles neurologiques, ce qui en fait des cibles thérapeutiques intéressantes. Cette thèse propose une preuve de principe in silico du cadre Monod-Wyman-Changeux (MWC) de la pharmacologie des modulateurs pLGIC. Grâce à la dynamique moléculaire QM/MM, nous montrons que les champs de force standards reproduisent la position du neurotransmetteur dans le récepteur de la glycine (GlyR). Ensuite, sur le substitut du récepteur nicotinique de l'acétylcholine, nous testons les calculs d'énergie libre de liaison, obtenant une bonne concordance avec l'expérience. Sur cette base, nous classons les modulateurs GlyR par force agoniste via des calculs d'énergie libre de liaison. Enfin, nous présentons un processus de criblage virtuel couplant l'apprentissage actif aux calculs d'énergie libre, ouvrant la voie à la conception rationnelle de modulateurs pLGIC.

Summary: AI foundational models for predicting protein-ligand interactions and binding affinities have started to emerge. We challenged Boltz-2 on a difficult dataset constructed on ten ultra-large virtual screening hit lists of pharmacologically relevant targets with in vitro binding assays. We show that Boltz-2 is the best classifier, with a success rate twice that of any other rescoring strategy. Ligand classifications by Boltz-2 are straightforward, accurate, efficient and robust, opening to million-compound accurate rankings on commodity resources.