Discovery of selective small-molecule HDAC6 inhibitor for overcoming proteasome inhibitor resistance in multiple myeloma.

Multiple myeloma (MM) has proven clinically susceptible to modulation of pathways of protein homeostasis. Blockade of proteasomal degradation of polyubiquitinated misfolded proteins by the proteasome inhibitor bortezomib (BTZ) achieves responses and prolongs survival in MM, but long-term treatment with BTZ leads to drug-resistant relapse in most patients. In a proof-of-concept study, we previously demonstrated that blocking aggresomal breakdown of polyubiquitinated misfolded proteins with the histone deacetylase 6 (HDAC6) inhibitor tubacin enhances BTZ-induced cytotoxicity in MM cells in vitro.

The cytoplasmic prolyl-tRNA synthetase of the malaria parasite is a dual-stage target of febrifugine and its analogs.

The emergence of drug resistance is a major limitation of current antimalarials. The discovery of new druggable targets and pathways including those that are critical for multiple life cycle stages of the malaria parasite is a major goal for developing next-generation antimalarial drugs. Using an integrated chemogenomics approach that combined drug resistance selection, whole-genome sequencing, and an orthogonal yeast model, we demonstrate that the cytoplasmic prolyl-tRNA (transfer RNA) synthetase (PfcPRS) of the malaria parasite Plasmodium falciparum is a biochemical and functional target of febrifugine and its synthetic derivative halofuginone.

Design and synthesis of a crosslinker for studying intracellular steroid trafficking pathways.

A crosslinker was designed and synthesized as a molecular tool for potential use in probing the intracellular trafficking pathways of steroids. The design was guided by computational modeling based upon a model for the transfer of cholesterol between two proteins, NPC1 and NPC2. These proteins play critical roles in the transport of low-density lipoprotein-derived cholesterol from the lumen of lysosomes to other subcellular compartments.

A molecular mechanism of artemisinin resistance in Plasmodium falciparum malaria.

Artemisinins are the cornerstone of anti-malarial drugs. Emergence and spread of resistance to them raises risk of wiping out recent gains achieved in reducing worldwide malaria burden and threatens future malaria control and elimination on a global level. Genome-wide association studies (GWAS) have revealed parasite genetic loci associated with artemisinin resistance.

Characterization of the Anopheles gambiae octopamine receptor and discovery of potential agonists and antagonists using a combined computational-experimental approach.

Background: Octopamine receptors (OARs) perform key functions in the biological pathways of primarily invertebrates, making this class of G-protein coupled receptors (GPCRs) a potentially good target for insecticides. However, the lack of structural and experimental data for this insect-essential GPCR family has promoted the development of homology models that are good representations of their biological equivalents for in silico screening of small molecules.

Methods: Two Anopheles gambiae OARs were cloned, analysed and functionally characterized using a heterologous cell reporter system.

Docking applied to the prediction of the affinity of compounds to P-glycoprotein.

P-glycoprotein (P-gp) is involved in the transport of xenobiotic compounds and responsible for the decrease of the drug accumulation in multi-drug-resistant cells. In this investigation we compare several docking algorithms in order to find the conditions that are able to discriminate between P-gp binders and nonbinders. We built a comprehensive dataset of binders and nonbinders based on a careful analysis of the experimental data available in the literature, trying to overcome the discrepancy noticeable in the experimental results.

Synthesis and HDAC inhibitory activity of isosteric thiazoline-oxazole largazole analogs.

The synthesis of an isosteric analog of the natural product and HDAC inhibitor largazole is described. The sulfur atom in the thizaole ring of the natural product has been replaced with an oxygen atom, constituting an oxazole ring. The biochemical activity and cytotoxicity of this species is described.

Computational studies of the cholesterol transport between NPC2 and the N-terminal domain of NPC1 (NPC1(NTD)).

The transport of cholesterol from NPC2 to NPC1 is essential for the maintenance of cholesterol homeostasis in late endosomes. On the basis of a rigid docking model of the crystal structures of the N-terminal cholesterol binding domain of NPC1(NTD) and the soluble NPC2 protein, models of the NPC1(NTD)-NPC2-cholesterol complexes at the beginning and the end of the transport as well as the unligated NPC1(NTD)-NPC2 complex were studied using 86 ns MD simulations. Significant differences in the cholesterol binding mode and the overall structure of the two proteins compared to the crystal structures of the cholesterol binding separate units were obtained.

Identifying ligand binding conformations of the β2-adrenergic receptor by using its agonists as computational probes.

Recently available G-protein coupled receptor (GPCR) structures and biophysical studies suggest that the difference between the effects of various agonists and antagonists cannot be explained by single structures alone, but rather that the conformational ensembles of the proteins need to be considered. Here we use an elastic network model-guided molecular dynamics simulation protocol to generate an ensemble of conformers of a prototypical GPCR, β(2)-adrenergic receptor (β(2)AR). The resulting conformers are clustered into groups based on the conformations of the ligand binding site, and distinct conformers from each group are assessed for their binding to known agonists of β(2)AR.

Inhibition pattern of sulfamide-related compounds in binding to carbonic anhydrase isoforms I, II, VII, XII and XIV.

A set of sulfamides and sulfamates were synthesized and tested against several isoforms of carbonic anhydrase: CA I, CA II, CA VII, CA XII and CA XIV. The biological assays showed a broad range of inhibitory activity, and interesting results were found for several compounds in terms of activity (Ki <1μm) and selectivity: some aromatic sulfamides are active against CA I, CA II and/or CA VII; while they are less active in CA XII and CA XIV. On the other hand, bulky sulfamides are selective to CA VII.

Catalytic site remodelling of the DOT1L methyltransferase by selective inhibitors.

Selective inhibition of protein methyltransferases is a promising new approach to drug discovery. An attractive strategy towards this goal is the development of compounds that selectively inhibit binding of the cofactor, S-adenosylmethionine, within specific protein methyltransferases. Here we report the three-dimensional structure of the protein methyltransferase DOT1L bound to EPZ004777, the first S-adenosylmethionine-competitive inhibitor of a protein methyltransferase with in vivo efficacy.

Identification of novel bacterial histidine biosynthesis inhibitors using docking, ensemble rescoring, and whole-cell assays.

The rapid spread on multidrug-resistant strains of Staphylococcus aureus requires not just novel treatment options, but the development of faster methods for the identification of new hits for drug development. The exponentially increasing speed of computational methods makes a more extensive use in the early stages of drug discovery attractive if sufficient accuracy can be achieved. Computational target identification using systems-level methods suggested the histidine biosynthesis pathway as an attractive target against S.

Affinity of sulfamates and sulfamides to carbonic anhydrase II isoform: experimental and molecular modeling approaches.

Sixteen aromatic and aliphatic sulfamides and sulfamates were synthesized and tested in their inhibition to carbonic anhydrase CAII activity. The weaker inhibition pattern shown by sulfamides as compared to sulfamates is interpreted in this research by means of molecular modeling techniques, including known inhibitors (topiramate and its sulfamide cognate) in the analysis. The results nicely explain the origin of the inhibitory activity, which is not only related to positive interactions of the ligand with the active site residues but also to the solvation pattern characteristic of each ligand.

On the inhibition of histone deacetylase 8.

Histone deacetylases are key regulators of gene expression and have recently emerged as important therapeutic targets for cancer and a growing number of non-malignant diseases. Many widely studied inhibitors of HDACs such as SAHA are thought to have low selectivity within or between the human HDAC isoform classes. Using an isoform-selective assay, we have shown that a number of the known inhibitors have in fact a low activity against HDAC8.

Thermal behavior, powder X-ray diffraction, DFT calculations and vibrational spectra of barium bis(pentacyanonitrosylchromate) octahydrate, Ba3[Cr(CN)5NO]2.8H2O(D2O).

The cell parameters of Ba3[Cr(CN)5NO]2.8H2O were determined from powder X-ray diffraction using the autoindexing program TREOR, and refined by the Le Bail methods with the FULLPROF program. An orthorhombic cell was determined with cell parameters a = 15.

Unfolding of the [Cu2(1,3-bis(9-methyl-1,10-phenanthrolin-2-yl)propane)2]2+ helicate. Coupling of the chlorocarbon dehalogenation to the unfolding process.

A new helical dimeric copper(I) complex [Cu(2)(mphenpr)(2)](ClO(4))(2) where mphenpr is 1,3-bis(9-methyl-1,10-phenanthrolin-2-yl)propane has been prepared and characterized by X-ray crystallography and NMR. In the solid state, the metal centers are 6.42 A apart, and the electronic structure has been investigated with use of density functional theory (DFT) calculations.

Blueprint for antimicrobial hit discovery targeting metabolic networks.

Advances in genome analysis, network biology, and computational chemistry have the potential to revolutionize drug discovery by combining system-level identification of drug targets with the atomistic modeling of small molecules capable of modulating their activity. To demonstrate the effectiveness of such a discovery pipeline, we deduced common antibiotic targets in Escherichia coli and Staphylococcus aureus by identifying shared tissue-specific or uniformly essential metabolic reactions in their metabolic networks. We then predicted through virtual screening dozens of potential inhibitors for several enzymes of these reactions and showed experimentally that a subset of these inhibited both enzyme activities in vitro and bacterial cell viability.

Synthesis and modeling of new benzofuranone histone deacetylase inhibitors that stimulate tumor suppressor gene expression.

New benzofuranones were synthesized and evaluated toward NCI-H661 non-small cell lung cancer cells. Benzamide derivatives possessed micromolar antiproliferative and histone deacetylase inhibitory activities and modulate histone H4 acetylation. Hydroxamic acids were found to be potent nanomolar antiproliferative agents and HDAC inhibitors.

Synthesis and conformation-activity relationships of the peptide isosteres of FK228 and largazole.

The peptide isosteres (10 and 11) of the naturally occurring and potent histone deacetylase (HDAC) inhibitors FK228 and largazole have been synthesized and evaluated side-by-side with FK228, largazole, and SAHA for inhibition of the class I HDACs 1, 2, 3, and 6.

Residues in the 11 A channel of histone deacetylase 1 promote catalytic activity: implications for designing isoform-selective histone deacetylase inhibitors.

Histone deacetylase 1 (HDAC1) has been linked to cell growth and cell cycle regulation, which makes it a widely recognized target for anticancer drugs. Whereas variations of the metal-binding and capping groups of HDAC inhibitors have been studied extensively, the role of the linker region is less well known, despite the potency of inhibitors with diverse linkers, such as MS-275. To facilitate a drug design that targets HDAC1, we assessed the influence of residues in the 11 A channel of the HDAC1 active site on activity by using an alanine scan.

Structural origin of selectivity in class II-selective histone deacetylase inhibitors.

The development of class- and isoform-selective histone deacetylase (HDAC) inhibitors is highly desirable for the study of the complex interactions of these proteins central to transcription regulation as well as for the development of selective HDAC inhibitors as drugs in epigenetics. To provide a structural basis for the rational design of such inhibitors, a combined computational and experimental study of inhibition of three different histone deacetylase isoforms, HDAC1, -6, and -8, with three different hydroxamate inhibitors is reported. While SAHA was found to be unselective for the inhibition of class I and class II HDACs, the other inhibitors were found to be selective toward class II HDACs.

Nucleophilic activity of a linked bis{guanidine} leading to formation of a dicationic C4N4-heterocycle.

The methylene-linked bis{guanidine}, H(2)C{hpp}(2) (hppH = 1,3,4,6,7,8-hexahydro-2H-pyrimido[1,2-a]pyrimidine), displays nucleophilic activity towards organic halides, including the activation of dichloromethane under ambient conditions affording the cyclic dication, [H(2)C{hpp}(2)CH(2)](2+)[Cl](2).

Competitive hydrolytic and elimination mechanisms in the urease catalyzed decomposition of urea.

We present a high-level quantum chemical study of possible elimination reaction mechanisms associated with the catalytic decomposition of urea at the binuclear nickel active site cluster of urease. Stable intermediates and transition state structures have been identified along several possible reaction pathways. The computed results are compared with those reported by Suarez et al.

The hydrolysis of amides and the proficiency of amidohydrolases. The burden borne by kw.

The hydrolysis of small amides has garnered major attention due to its relevance to peptide hydrolysis, one of the most fundamental reactions of biology. Both experimental and theoretical research efforts have studied the reaction in different media, and a consensus has been reached regarding the specific acid- and base-catalyzed reaction pathways. Nevertheless, for the water reaction, large discrepancies between theoretical and experimental results are found in the literature.