Predicting Binding Affinities for GPCR Ligands Using Free-Energy Perturbation

The rapid growth of structural information for G-protein-coupled receptors (GPCRs) has led to a greater understanding of their structure, function, selectivity, and ligand binding. Although novel ligands have been identified using methods such as virtual screening, computationally driven lead optimization has been possible only in isolated cases because of challenges associated with predicting binding free energies for related compounds. Here, we provide a systematic characterization of the performance of free-energy perturbation (FEP) calculations to predict relative binding free energies of congeneric ligands binding to GPCR targets using a consistent protocol and no adjustable parameters. Using the FEP+ package, first we validated the protocol, which includes a full lipid bilayer and explicit solvent, by predicting the binding affinity for a total of 45 different ligands across four different GPCRs (adenosine A_2AAR, β₁ adrenergic, CXCR4 chemokine, and δ opioid receptors). Comparison with experimental binding affinity measurements revealed a highly predictive ranking correlation (average spearman ρ = 0.55) and low root-mean-square error (0.80 kcal/mol). Next, we applied FEP+ in a prospective project, where we predicted the affinity of novel, potent adenosine A_2A receptor (A_2AR) antagonists. Four novel compounds were synthesized and tested in a radioligand displacement assay, yielding affinity values in the nanomolar range. The affinity of two out of the four novel ligands (plus three previously reported compounds) was correctly predicted (within 1 kcal/mol), including one compound with approximately a tenfold increase in affinity compared to the starting compound. Detailed analyses of the simulations underlying the predictions provided insights into the structural basis for the two cases where the affinity was overpredicted. Taken together, these results establish a protocol for systematically applying FEP+ to GPCRs and provide guidelines for identifying potent molecules in drug discovery lead optimization projects.

Methodologies for the analysis of instantaneous lipid diffusion in MD simulations of large membrane systems

Interactions between lipids and membrane proteins play a key role in determining the nanoscale dynamic and structural properties of biological membranes. Molecular dynamics (MD) simulations provide a valuable tool for studying membrane models, complementing experimental approaches. It is now possible to simulate large membrane systems, such as simplified models of bacterial and viral envelope membranes. Consequently, there is a pressing need to develop tools to visualize and quantify the dynamics of these immense systems, which typically comprise millions of particles. To tackle this issue, we have developed visual and quantitative analyses of molecular positions and their velocity field using path line, vector field and streamline techniques. This allows us to highlight large, transient flow-like movements of lipids and to better understand crowding within the lipid bilayer. The current study focuses on visualization and analysis of lipid dynamics. However, the methods are flexible and can be readily applied to e.g. proteins and nanoparticles within large complex membranes. The protocols developed here are readily accessible both as a plugin for the molecular visualization program VMD and as a module for the MDAnalysis library.

The safety evaluation of bendiocarb, a residual insecticide for vector control

The safety evaluation of bendiocarb, a carbamate insecticide for vector control is described. During the course of field studies data were collected to relate dermal exposure, absorption, excretion of metabolites, whole blood cholinesterase inhibition and clinical signs and symptoms. Studies were also carried out on blood sampling techniques for cholinesterase assay and on the effects of temperature and humidity on the dermal absorption of bendiocarb. It was shown that inhibition of blood cholinesterase by bendiocarb is rapidly reversible and routine cholinesterase monitoring of operators is therefore not necessary. It was also shown that dermal absorption of bendiocarb and probably other insecticides is facilitated under hot and humid conditions and special care must be taken with insecticide application at these times. The importance of effective training, adequate protective clothing and good personal hygiene in achieving safe application of insecticides in house-spraying programmes is stressed. It is concluded from these studies that bendiocarb is a safe insecticide for vector control when used with normal safety precautions and this has been confirmed in subsequent large-scale operational programmes.

Killing of newly excysted juveniles of Fasciola hepatica in sensitized rats

Newly excysted juvenile Fasciola hepatica were injected intraperitoneally into previously sensitized rats. They were recovered at various intervals post-injection and examined by light and electron microscopy. The challenge flukes were rapidly coated with peritoneal cells which, in the early stages, were mainly eosinophils. The eosinophils adhered closely to the flukes and degranulated on to their surface releasing cytochemically detectable peroxidase. Vacuoles formed in the tegument of the flukes beneath the adherent eosinophils and these increased in size until they spanned the width of the tegument, thus destroying its continuity. From 4 h post-injection some of the flukes had lost their teguments and were surrounded by phagocytic cells, particularly neutrophils; at this stage they were judged to be dead. During the first five minutes post-injection degranulating mast cells were associated with the challenge flukes. Their role in eosinophil chemotaxis is discussed as are the possible mechanisms of eosinophil adherence and degranulation. Using an anti-C3 fluorescein conjugate, it was demonstrated that C3 was not bound to the surface of challenge flukes either in vivo or in vitro in immune serum.

Passive cutaneous anaphylaxis in the rat, induced with two homologous reagin-like antibodies and its specific inhibition with disodium cromoglycate

Rats immunized with egg albumin and Bordetella pertussis organisms produce a `mast cell sensitizing' antibody (MCSAb) which is thermolabile, a potent skin sensitizer and reagin in character. Similarly the immune response to Nippostrongylus brasiliensis in rats is closely associated with the formation of antibodies which also resembles human reagins. Homologous passive cutaneous anaphylactic (PCA) reactions induced by N. brasiliensis serum were found to be similar to those produced using the adjuvant induced antibody in that both were completely inhibited by, combined treatment with mepyramine and 2-bromo-D-lysergic acid diethylamide (BOL148), cyproheptadine or pretreatment with compound 48/80. In contrast, skin reactions involving passive sensitization of rats with rabbit hyperimmune antiserum were much less affected. Studies on mast cell disruption at the site of PCA reactions showed that such reactions using N. brasiliensis serum were accompanied by degranulation of mast cells, and confirmed that mast cell damage occurs in PCA induced with MCSAb. Both the PCA and the mast cell disruption were maximal 5 minutes after antigen challenge in both rat reagin systems. The skin reaction produced using rabbit hyperimmune antiserum was not primarily dependent on, or associated with, mast cell disruption, since it was still possible to induce skin reactions when the mast cells had been disrupted by compound 48/80, and skin reactions could be obtained without significant mast cell disruption.

Disodium cromoglycate, a new compound introduced for the treatment of asthma, was shown to inhibit both the PCA and mast cell disruption induced using both rat reagin antibodies but not the skin reactions produced with rabbit anti-serum. It was possible to obtain substantial inhibition of mast cell disruption induced by rat reagin, even when the PCA was inhibited only slightly. At higher doses the discharge of the mediators from mast cells was also prevented. This interference with mast cell permeability was not unspecific since disodium cromoglycate did not prevent the skin reaction or mast cell disruption produced by compound 48/80. As expected mepyramine was able to partially inhibit the skin reaction without affecting mast cell disruption induced by rat reagin or compound 48/80. It is suggested that disodium cromoglycate acts at some critical pathway in the events after the union of antigen with reagin antibody and that this critical pathway might be common to both the human and rat reagin systems.