Predicting protein druggability is a key interest in the target identification phase of drug discovery. Here, we assess the pocket estimation methods' influence on druggability predictions by comparing statistical models constructed from pockets estimated using different pocket estimation methods: a proximity of either 4 or 5.5 Å to a cocrystallized ligand or DoGSite and fpocket estimation methods. We developed PockDrug, a robust pocket druggability model that copes with uncertainties in pocket boundaries. It is based on a linear discriminant analysis from a pool of 52 descriptors combined with a selection of the most stable and efficient models using different pocket estimation methods. PockDrug retains the best combinations of three pocket properties which impact druggability: geometry, hydrophobicity, and aromaticity. It results in an average accuracy of 87.9% ± 4.7% using a test set and exhibits higher accuracy (∼5-10%) than previous studies that used an identical apo set. In conclusion, this study confirms the influence of pocket estimation on pocket druggability prediction and proposes PockDrug as a new model that overcomes pocket estimation variability.

Membrane-bound pyrophosphatases are homodimeric integral membrane proteins that hydrolyze pyrophosphate into orthophosphates, coupled to the active transport of protons or sodium ions across membranes. They are important in the life cycle of bacteria, archaea, plants, and parasitic protists, but no homologous proteins exist in vertebrates, making them a promising drug target. Here, we report the first nonphosphorus allosteric inhibitor of the thermophilic bacterium Thermotoga maritima membrane-bound pyrophosphatase and its bound structure together with the substrate analog imidodiphosphate. The unit cell contains two protein homodimers, each binding a single inhibitor dimer near the exit channel, creating a hydrophobic clamp that inhibits the movement of β-strand 1–2 during pumping, and thus prevents the hydrophobic gate from opening. This asymmetry of inhibitor binding with respect to each homodimer provides the first clear structural demonstration of asymmetry in the catalytic cycle of membrane-bound pyrophosphatases.

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The alpha(2)-adrenergic receptors (alpha(2)-ARs) belong to the large family of rhodopsinlike G-protein-coupled receptors that share a common structure of seven transmembrane (TM) alpha-helices. The aims of this study were (1) to determine the number of alpha(2)-AR genes in a teleost fish, the zebrafish (Danio rerio), (2) to study the gene duplication events that generated the alpha(2)-AR subtypes, and (3) to study changes in receptor structure that have occurred since the divergence of the mammalian and fish lineages. Here, we report the cloning and chromosomal mapping of fish orthologs for all three mammalian alpha(2)-ARs. In addition, we identified a fourth alpha(2)-AR subtype with two duplicates in zebrafish. Chromosomal mapping showed that the zebrafish alpha(2)-AR genes are located within conserved chromosomal segments, consistent with the origin of the four alpha(2)-AR subtypes by two rounds of chromosome or block duplication before the divergence of the ray fin fish and tetrapod lineages. Thus, the fourth subtype has apparently been present in the common ancestor of vertebrates but has been deleted or is yet to be identified in mammals. The overall percentage identity between the fish and mammalian orthologs is 53% to 67%, and in the TM regions 80% to 87%. These values are clearly lower than what is observed between mammalian orthologs. Still, all of the residues thought to be important for alpha(2)-adrenergic ligand binding are conserved across species and subtypes, and even the most divergent regions of the fish receptors show clear "molecular fingerprints" typical for orthologs of a given subtype.

1 Zebrafish has five distinct a 2 -adrenoceptors. Two of these, a 2Da and a 2Db , represent a duplicated, fourth a 2 -adrenoceptor subtype, while the others are orthologue of the human a 2A -, a 2B -and a 2C -adrenoceptors. Here, we have compared the pharmacological properties of these receptors to infer structural determinants of ligand interactions. 2 The zebrafish a 2 -adrenoceptors were expressed in Chinese hamster ovary cells and tested in competitive ligand binding assays and in a functional assay (agonist-stimulated [ 35 S]GTPgS binding). The affinity results were used to cluster the receptors and, separately, the ligands using both principal component analysis and binary trees. 3 The overall ligand binding characteristics, the order of potency and efficacy of the tested agonists and the G-protein coupling of the zebrafish and human a 2 -adrenoceptors, separated by B350 million years of evolution, were found to be highly conserved. The binding affinities of the 20 tested ligands towards the zebrafish a 2 -adrenoceptors are generally comparable to those of their human counterparts, with a few compounds showing up to 40-fold affinity differences. 4 The a 2A orthologues and the zebrafish a 2D duplicates clustered as close pairs, but the relationships between the orthologues of a 2B and a 2C were not clearly defined. Applied to the ligands, our clustering methods segregated the ligands based on their chemical structures and functional properties. As the ligand binding pockets formed by the transmembrane helices show only minor differences among the a 2 -adrenoceptors, we suggest that the second extracellular loop -where significant sequence variability is located -might contribute significantly to the observed affinity differences.

We derived homology models for all human catecholamine-binding GPCRs (CABRs; the alpha-1, alpha-2, and beta-adrenoceptors and the D1-type and D2-type dopamine receptor) using the bovine rhodopsin-11-cis-retinal X-ray structure. Interactions were predicted from the endogenous ligands norepinephrine or dopamine and from the binding site and were used to optimize receptor-ligand interactions. Similar binding modes in the complexes agree with a large "binding core" conserved across the CABRs, that is, D3.32, V(I)3.33, T3.37, S5.42, S(A/C)5.43, S5.46, F6.51, F6.52, and W6.48. Model structures and docking simulations suggest that extracellular loop 2 could provide a common attachment point for the ligands' beta-hydroxyl via a hydrogen bond donated by the main-chain NH group of residue xl2.52. The modeled CABRs and docking modes are in good agreement with published experimental studies. Complementarity between the ligand and the binding site suggests that the bovine rhodopsin structure is a suitable template for modeling agonist-bound CABRs.

Two new trypsin inhibitors, nostosin A (1) and B (2), were isolated from a hydrophilic extract of Nostoc sp. strain FSN, which was collected from a paddy field in the Golestan Province of Iran. Nostosins A (1) and B (2) are composed of three subunits, 2-hydroxy-4-(4-hydroxyphenyl)butanoic acid (Hhpba), L-Ile, and L-argininal (1) or argininol (2). Nostosins A (1) and B (2) exhibited IC50 values of 0.35 and 55 μM against porcine trypsin, respectively, suggesting that the argininal aldehyde group plays a crucial role in the efficient inhibition of trypsin. Molecular docking of nostosin A (1) (449 Da), leupeptin (426 Da, IC50 0.5 μM), and spumigin E (610 Da, IC50 < 0.1 μM) with trypsin suggested prominent binding similarity between nostosin A (1) and leupeptin but only partial binding similarity with spumigin E. The number of hydrogen bonds between ligands and trypsin increased according to the length and size of the ligand molecule, and the docking affinity values followed the measured IC50 values. Nostosin A (1) is the first highly potent three-subunit trypsin inhibitor with potency comparable to the known commercial trypsin inhibitor leupeptin. These findings expand the known diversity of short-chain linear peptide protease inhibitors produced by cyanobacteria.

1 The structural determinants of catechol hydroxyl interactions with adrenergic receptors were examined using 12 a 2 -adrenergic agonists and a panel of mutated human a 2A -adrenoceptors. The a 2A Ser201 mutant had a Cys-Ser201 (position 5.43) amino-acid substitution, and a 2A Ser201Cys200 and a 2A Ser201Cys204 had Ser-Cys200 (5.42) and Ser-Cys204 (5.46) substitutions, respectively, in addition to the Cys-Ser201 substitution. 2 Automated docking methods were used to predict the receptor interactions of the ligands. Radioligand-binding assays and functional [35 S]GTPgS-binding assays were performed using transfected Chinese hamster ovary cells to experimentally corroborate the predicted binding modes. 3 The hydroxyl groups of phenethylamines were found to have different effects on ligand affinity towards the activated and resting forms of the wild-type a 2A -adrenoceptor. Substitution of Ser200 or Ser204 with cysteine caused a deterioration in the capability of catecholamines to activate the a 2A -adrenoceptor. The findings indicate that (i) Cys201 plays a significant role in the binding of catecholamine ligands and UK14,304 (for the latter, by a hydrophobic interaction), but Cys201 is not essential for receptor activation; (ii) Ser200 interacts with the meta-hydroxyl group of phenethylamine ligands, affecting both catecholamine binding and receptor activation; while (iii) substituting Ser204 with a cysteine interferes both with the binding of catecholamine ligands and with receptor activation, due to an interaction between Ser204 and the para-hydroxyl group of the catecholic ring.