Improving virtual screening of G protein-coupled receptors via ligand-directed modeling

G protein-coupled receptors (GPCRs) play crucial roles in cell physiology and pathophysiology. There is increasing interest in using structural information for virtual screening (VS) of libraries and for structure-based drug design to identify novel agonist or antagonist leads. However, the sparse availability of experimentally determined GPCR/ligand complex structures with diverse ligands impedes the application of structure-based drug design (SBDD) programs directed to identifying new molecules with a select pharmacology. In this study, we apply ligand-directed modeling (LDM) to available GPCR X-ray structures to improve VS performance and selectivity towards molecules of specific pharmacological profile. The described method refines a GPCR binding pocket conformation using a single known ligand for that GPCR. The LDM method is a computationally efficient, iterative workflow consisting of protein sampling and ligand docking. We developed an extensive benchmark comparing LDM-refined binding pockets to GPCR X-ray crystal structures across seven different GPCRs bound to a range of ligands of different chemotypes and pharmacological profiles. LDM-refined models showed improvement in VS performance over origin X-ray crystal structures in 21 out of 24 cases. In all cases, the LDM-refined models had superior performance in enriching for the chemotype of the refinement ligand. This likely contributes to the LDM success in all cases of inhibitor-bound to agonist-bound binding pocket refinement, a key task for GPCR SBDD programs. Indeed, agonist ligands are required for a plethora of GPCRs for therapeutic intervention, however GPCR X-ray structures are mostly restricted to their inactive inhibitor-bound state

Seasonal demography of the threatened Montevideo redbelly toad (melanophryniscus montevidensis) in a protected area of Uruguay

Estimates of demographic parameters are scarce for Neotropical amphibians, a concerning fact because this region has the highest proportion of threatened amphibians in the world. We conducted a 3-year study where we applied a robust capture-mark-recapture design to assess the importance of breeding and non-breeding activity patterns over the survival rates, detection probabilities, and abundances of the Montevideo Redbelly Toad (Melanophryniscus montevidensis (Philippi, 1902)), a threatened anuran from Uruguay. The best models grouped seasons into hot and cold periods cyclically, were state-dependent in transition probabilities, and were time-dependent in detection probabilities for adults, but had constant detection probabilities for juveniles. Averaged estimates suggest a high survivorship rate during cold seasons (above 80%), but lower probabilities (below 60%) during hot seasons, especially for males. Analogously, the non-breeding activity had a seasonal pattern, with higher activity during spring and higher sheltering rates during autumn. These activity rates negatively influenced the averaged survivorship rates of adult males and females. Long-term (matrix) projections of seasonal survivorships, along with assessments of the causes of these patterns, should be carried out to determine extinction probabilities and possible threats for the conservation of the genus Melanophryniscus972131141CONSELHO NACIONAL DE DESENVOLVIMENTO CIENTÍFICO E TECNOLÓGICO - CNPQFUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULO - FAPESP300896/2016-62014/23388-7; 2016/25358-