Performance and Analysis of the Alchemical Transfer Method for Binding Free Energy Predictions of Diverse Ligands

The Alchemical Transfer Method (ATM) is herein validated against the relative binding free energies of a diverse set of protein-ligand complexes. We employed a streamlined setup workflow, a bespoke force field, and the AToM-OpenMM software to compute the relative binding free energies (RBFE) of the benchmark set prepared by Schindler and collaborators at Merck KGaA. This benchmark set includes examples of standard small R-group ligand modifications as well as more challenging scenarios, such as large R-group changes, scaffold hopping, formal charge changes, and charge-shifting transformations. The novel coordinate perturbation scheme and a dual-topology approach of ATM address some of the challenges of single-topology alchemical relative binding free energy methods. Specifically, ATM eliminates the need for splitting electrostatic and Lennard-Jones interactions, atom mapping, defining ligand regions, and post-corrections for charge-changing perturbations. Thus, ATM is simpler and more broadly applicable than conventional alchemical methods, especially for scaffold-hopping and charge-changing transformations. Here, we performed well over 500 relative binding free energy calculations for eight protein targets and found that ATM achieves accuracy comparable to existing state-of-the-art methods, albeit with larger statistical fluctuations. We discuss insights into specific strengths and weaknesses of the ATM method that will inform future deployments. This study confirms that ATM is applicable as a production tool for relative binding free energy (RBFE) predictions across a wide range of perturbation types within a unified, open-source framework

Type II Kinase Inhibitors Show an Unexpected Inhibition Mode against Parkinson’s Disease-Linked LRRK2 Mutant G2019S

A number of well-known type II inhibitors (ATP-noncompetitive) that bind kinases in their DFG-out conformation were tested against wild-type LRRK2 and the most common Parkinson’s disease-linked mutation, G2019S. We found that traditional type II inhibitors exhibit surprising variability in their inhibition mechanism between the wild type (WT) and the G2019S mutant of LRRK2. The type II kinase inhibitors were found to work in an ATP-competitive fashion against the G2019S mutant, whereas they appear to follow the expected noncompetitive mechanism against WT. Because the G2019S mutation lies in the DXG motif (DYG in LRRK2 but DFG in most other kinases) of the activation loop, we explored the structural consequence of the mutation on loop dynamics using an enhanced sampling method called metadynamics. The simulations suggest that the G2019S mutation stabilizes the DYG-in state of LRRK2 through a series of hydrogen bonds, leading to an increase in the conformational barrier between the active and inactive forms of the enzyme and a relative stabilization of the active form. The conformational bias toward the active form of LRRK2 mutants has two primary consequences. (1) The mutant enzyme becomes hyperactive, a known contributor to the Parkinsonian phenotype, as a consequence of being “locked” into the activated state, and (2) the mutation creates an unusual allosteric pocket that can bind type II inhibitors but in an ATP-competitive fashion. Our results suggest that developing type II inhibitors, which are generally considered superior to type I inhibitors because of desirable selectivity profiles, might be especially challenging for the G2019S LRRK2 mutant

The Binding of Benzoarylsulfonamide Ligands to Human Carbonic Anhydrase is Insensitive to Formal Fluorination of the Ligand

Auf das Wasser kommt es an: Konservierte Bindungsgeometrie, enthalpiegetriebene Bindungsweise und nichtunterscheidbare Bindungsaffinitäten für fluorierte und nichtfluorierte Liganden von humaner Carbonsäureanhydrase (siehe Bild) stützen die Theorie, dass das Schlüssel-Schloss-Modell einen wichtigen Bestandteil des Bindungsvorgangs unbeachtet lässt: das Wasser, das die Bindungstasche des Proteins füllt und den Liganden umgibt.Chemistry and Chemical Biolog

Water-Restructuring Mutations Can Reverse the Thermodynamic Signature of Ligand Binding to Human Carbonic Anhydrase

This study uses mutants of human carbonic anhydrase (HCAII) to examine how changes in the organization of water within a binding pocket can alter the thermodynamics of protein–ligand association. Results from calorimetric, crystallographic, and theoretical analyses suggest that most mutations strengthen networks of water-mediated hydrogen bonds and reduce binding affinity by increasing the enthalpic cost and, to a lesser extent, the entropic benefit of rearranging those networks during binding. The organization of water within a binding pocket can thus determine whether the hydrophobic interactions in which it engages are enthalpy-driven or entropy driven. Our findings highlight a possible asymmetry in protein–ligand association by suggesting that, within the confines of the binding pocket of HCAII, binding events associated with enthalpically favorable rearrangements of water are stronger than those associated with entropically favorable ones.Chemistry and Chemical Biolog

Interactions between Hofmeister Anions and the Binding Pocket of a Protein

This paper uses the binding pocket of human carbonic anhydrase II (HCAII, EC 4.2.1.1) as a tool to examine the properties of Hofmeister anions that determine (i) where, and how strongly, they associate with concavities on the surfaces of proteins and (ii) how, upon binding, they alter the structure of water within those concavities. Results from X-ray crystallography and isothermal titration calorimetry show that most anions associate with the binding pocket of HCAII by forming inner-sphere ion pairs with the Zn2+ cofactor. In these ion pairs, the free energy of anion–Zn2+ association is inversely proportional to the free energetic cost of anion dehydration; this relationship is consistent with the mechanism of ion pair formation suggested by the “law of matching water affinities”. Iodide and bromide anions also associate with a hydrophobic declivity in the wall of the binding pocket. Molecular dynamics simulations suggest that anions, upon associating with Zn2+, trigger rearrangements of water that extend up to 8 Å away from their surfaces. These findings expand the range of interactions previously thought to occur between ions and proteins by suggesting that (i) weakly hydrated anions can bind complementarily shaped hydrophobic declivities, and that (ii) ion-induced rearrangements of water within protein concavities can (in contrast with similar rearrangements in bulk water) extend well beyond the first hydration shells of the ions that trigger them. This study paints a picture of Hofmeister anions as a set of structurally varied ligands that differ in size, shape, and affinity for water and, thus, in their ability to bind to—and to alter the charge and hydration structure of—polar, nonpolar, and topographically complex concavities on the surfaces of proteins.Chemistry and Chemical Biolog

Mechanism of biomolecular recognition of trimethyllysine by the fluorinated aromatic cage of KDM5A PHD3 finger

The understanding of biomolecular recognition of posttranslationally modified histone proteins is centrally important to the histone code hypothesis. Despite extensive binding and structural studies on the readout of histones, the molecular language by which posttranslational modifications on histone proteins are read remains poorly understood. Here we report physical-organic chemistry studies on the recognition of the positively charged trimethyllysine by the electron-rich aromatic cage containing PHD3 finger of KDM5A. The aromatic character of two tryptophan residues that solely constitute the aromatic cage of KDM5A was fine-tuned by the incorporation of fluorine substituents. Our thermodynamic analyses reveal that the wild-type and fluorinated KDM5A PHD3 fingers associate equally well with trimethyllysine. This work demonstrates that the biomolecular recognition of trimethyllysine by fluorinated aromatic cages is associated with weaker cation-π interactions that are compensated by the energetically more favourable trimethyllysine-mediated release of high-energy water molecules that occupy the aromatic cage

Deep Synoptic Array Science: First FRB and Host Galaxy Catalog

Fast Radio Bursts (FRBs) are a powerful and mysterious new class of transient that are luminous enough to be detected at cosmological distances. By associating FRBs to host galaxies, we can measure intrinsic and environmental properties that test FRB origin models, in addition to using them as precise probes of distant cosmic gas. The 110-antenna Deep Synoptic Array (DSA-110) is a radio interferometer built to maximize the rate at which it can simultaneously detect and localize FRBs. Here, we present the first sample of FRBs and host galaxies discovered by the DSA-110. This sample of 11 FRBs is the largest uniform sample of localized FRBs to date and is selected based on association to host galaxies identified in optical imaging by Pan-STARRS1 and follow-up spectroscopy at the Palomar and Keck observatories. These FRBs have not been observed to repeat and their radio properties (dispersion, temporal scattering, energy) are similar to that of the known non-repeating FRB population. Most host galaxies have ongoing star formation, as has been identified before for FRB hosts. In contrast to prior work, a large fraction (four of eleven) of the new sample are more massive than 10$^{11}$\ M$_{\odot}$ and most had elevated star formation rates more than 100 Myr in their past. The distribution of star-formation history across this host-galaxy sample shows that the delay-time distribution is wide, spanning from $\sim100$\,Myr to $\sim10$\,Gyr. This requires the existence of one or more progenitor formation channels associated with old stellar populations, such as the binary evolution of compact objects.Comment: 21 pages. Submitted to AAS Journal

Deep Synoptic Array Science: Implications of Faraday Rotation Measures of Localized Fast Radio Bursts

Faraday rotation measures (RMs) of fast radio bursts (FRBs) offer the prospect of directly measuring extragalactic magnetic fields. We present an analysis of the RMs of ten as yet non-repeating FRBs detected and localized to host galaxies by the 110-antenna Deep Synoptic Array (DSA-110). We combine this sample with published RMs of 15 localized FRBs, nine of which are repeating sources. For each FRB in the combined sample, we estimate the host-galaxy dispersion measure (DM) contributions and extragalactic RM. We find compelling evidence that the extragalactic components of FRB RMs are often dominated by contributions from the host-galaxy interstellar medium (ISM). Specifically, we find that both repeating and as yet non-repeating FRBs show a correlation between the host-DM and host-RM in the rest frame, and we find an anti-correlation between extragalactic RM (in the observer frame) and redshift for non-repeaters, as expected if the magnetized plasma is in the host galaxy. Important exceptions to the ISM origin include a dense, magnetized circum-burst medium in some repeating FRBs, and the intra-cluster medium (ICM) of host or intervening galaxy clusters. We find that the estimated ISM magnetic-field strengths, $B_{||}$, are characteristically larger than those inferred from Galactic radio pulsars. This suggests either increased ISM magnetization in FRB hosts in comparison with the Milky Way, or that FRBs preferentially reside in regions of increased magnetic-field strength within their hosts