Discovery of Novel and Cardioselective Diltiazem-like Calcium Channel Blockers via Virtual Screening

A Multifield Study on Dimethyl Acetylenedicarboxylate: A Reagent Able to Build a New Cycle on Diaminoimidazoles

A new effective method for the synthesis of imidazo[1,5-b]pyridazines derivatives (yields = 68–89%) by the interaction of 1,2-diamino-4-phenylimidazole with DMAD, in methanol and in the presence of a catalytic amount of acetic acid, is proposed. The course of reaction has been examined by classical organic methods, HPLC-MS analysis, and quantum-chemical calculations.

Advances in L-Type Calcium Channel Structures, Functions and Molecular Modeling

L-type Calcium Channels (LTCCs), also termed as Ca_v1, belong to voltage-gated calcium channels (VGCCs/Ca_vs), which play a critical role in a wide spectrum of physiological processes, including neurotransmission, cell cycle, muscular contraction, cardiac action potential and gene expression. Aberrant regulation of calcium channels is involved in neurological, cardiovascular, muscular and psychiatric disorders. Accordingly, LTCCs have been regarded as important drug targets, and a number of LTCC drugs are in clinical use. In this review, the recent development of structures and biological functions of LTCCs are introduced. Moreover, the representative modulators and ligand binding sites of LTCCs are discussed. Finally, molecular modeling and Computer-aided Drug Design (CADD) methods for understanding structure-function relations of LTCCs are summarized.

Design, synthesis and biological evaluation of isochroman-4-one hybrids bearing piperazine moiety as antihypertensive agent candidates

7,8-Dihydroxy-3-methyl-isochromanone-4 (XJP), is a polyphenolic natural product with moderate antihypertensive activity. To obtain new agents with stronger potency and safer profile, we employed XJP and naftopidil as the lead compounds to design and synthesize a novel class of hybrids as antihypertensive agent candidates. In the present study, a series of hybrids (6a-r) of XJP bearing arylpiperazine moiety, which is identified as the pharmacophore of naftopidil, were designed and synthesized as novel α₁-adrenergic receptor antagonists. The biological evaluation showed that target compounds 6c, 6e, 6f, 6g, 6h, 6m and 6q possessed potent in vitro vasodilation potency and α₁-adrenergic receptor antagonistic activity. Furthermore, the most potent compound 6e significantly reduced the systolic and diastolic blood pressure in spontaneously hypertensive rats (SHRs), which was comparable to that of naftopidil, and it had no observable effects on the basal heart rate, suggesting that 6e deserves to be further investigated as a potential clinical candidate for the treatment of hypertension.

Mononuclear Rearrangement of the Z-Phenylhydrazones of Some 3-Acyl-1,2,4-oxadiazoles: Effect of Substituents on the Nucleophilic Character of the >C═N-NH-C6 H5 Chain and on the Charge Density of N-2 of the 1,2,4-Oxadiazole Ring (Electrophilic Counterpart)

The reaction rates for the mononuclear rearrangement of the Z-phenylhydrazones of 3-acyl-1,2,4-oxadiazoles 3a-c into the relevant 2-phenyl-2 H-1,2,3-triazoles (4a-c) have been measured in dioxane/water at different temperatures in a large range of proton concentrations. The occurrence of two different reaction pathways (one uncatalyzed, water assisted, and the other general base catalyzed) has- been observed. The obtained results have been able to furnish information about the effects of the nature of the 3-acyl structure and of the 5-substituents in the 1,2,4-oxadiazole ring on the reactivity of the examined rearrangements: they are well in line with the previsions carried out considering some our previous computational results as well as experimental kinetic ones.

Discovery of Novel, Potent, and Specific Cell-Death Inducers in the Jurkat Acute Lymphoblastic Leukemia Cell Line

The limited clinical efficacy of many cancer therapeutics has initiated intense research efforts toward the discovery of novel chemical entities in this field. In this study, 31 hit candidates were selected from nearly 800,000 database compounds in a ligand-based virtual screening campaign. In turn, three of these hits were found to have (sub)micromolar potencies in proliferation assays with the Jurkat acute lymphatic leukemic cell line. In this assay, the three hits were found to exhibit higher potency than clinically tested cell-death inducers (GDC-0152, AT-406, and birinapant). Importantly, antiproliferative activity toward non-cancer peripheral blood mononuclear cells (PBMCs) was found to be marginal. Further biological characterization demonstrated the cell-death-inducing properties of these compounds. Biological testing of hit congeners excluded a nonspecific, toxic effect of the novel structures. Altogether, these findings may have profound relevance for the development of clinical candidates in tumor therapy.

Isozyme-specific ligands for O-acetylserine sulfhydrylase, a novel antibiotic target

The last step of cysteine biosynthesis in bacteria and plants is catalyzed by O-acetylserine sulfhydrylase. In bacteria, two isozymes, O-acetylserine sulfhydrylase-A and O-acetylserine sulfhydrylase-B, have been identified that share similar binding sites, although the respective specific functions are still debated. O-acetylserine sulfhydrylase plays a key role in the adaptation of bacteria to the host environment, in the defense mechanisms to oxidative stress and in antibiotic resistance. Because mammals synthesize cysteine from methionine and lack O-acetylserine sulfhydrylase, the enzyme is a potential target for antimicrobials. With this aim, we first identified potential inhibitors of the two isozymes via a ligand- and structure-based in silico screening of a subset of the ZINC library using FLAP. The binding affinities of the most promising candidates were measured in vitro on purified O-acetylserine sulfhydrylase-A and O-acetylserine sulfhydrylase-B from Salmonella typhimurium by a direct method that exploits the change in the cofactor fluorescence. Two molecules were identified with dissociation constants of 3.7 and 33 µM for O-acetylserine sulfhydrylase-A and O-acetylserine sulfhydrylase-B, respectively. Because GRID analysis of the two isoenzymes indicates the presence of a few common pharmacophoric features, cross binding titrations were carried out. It was found that the best binder for O-acetylserine sulfhydrylase-B exhibits a dissociation constant of 29 µM for O-acetylserine sulfhydrylase-A, thus displaying a limited selectivity, whereas the best binder for O-acetylserine sulfhydrylase-A exhibits a dissociation constant of 50 µM for O-acetylserine sulfhydrylase-B and is thus 8-fold selective towards the former isozyme. Therefore, isoform-specific and isoform-independent ligands allow to either selectively target the isozyme that predominantly supports bacteria during infection and long-term survival or to completely block bacterial cysteine biosynthesis.

Hit identification and optimization in virtual screening: practical recommendations based on a critical literature analysis

A critical analysis of virtual screening results published between 2007 and 2011 was performed. The activity of reported hit compounds from over 400 studies was compared to their hit identification criteria. Hit rates and ligand efficiencies were calculated to assist in these analyses, and the results were compared with factors such as the size of the virtual library and the number of compounds tested. A series of promiscuity, druglike, and ADMET filters were applied to the reported hits to assess the quality of compounds reported, and a careful analysis of a subset of the studies that presented hit optimization was performed. These data allowed us to make several practical recommendations with respect to selection of compounds for experimental testing, definition of hit identification criteria, and general virtual screening hit criteria to allow for realistic hit optimization. A key recommendation is the use of size-targeted ligand efficiency values as hit identification criteria.

Molecular docking methodologies

Molecular docking represents an important technology for structure-based drug design. Docking is a computational technique aimed at the prediction of the most favorable ligand-target spatial configuration and an estimate of the corresponding complex free energy, although as stated at the beginning accurate scoring methods remain still elusive. In this chapter, the state of art of molecular docking methodologies and their applications in drug discovery is summarized.

A novel approach for predicting P-glycoprotein (ABCB1) inhibition using molecular interaction fields

P-glycoprotein (Pgp or ABCB1) is an ABC transporter protein involved in intestinal absorption, drug metabolism, and brain penetration, and its inhibition can seriously alter a drug's bioavailability and safety. In addition, inhibitors of Pgp can be used to overcome multidrug resistance. Given this dual purpose, reliable in silico procedures to predict Pgp inhibition are of great interest. A large and accurate literature collection yielded more than 1200 structures; a model was then constructed using various molecular interaction field-based technologies, considering pharmacophoric features and those physicochemical properties related to membrane partitioning. High accuracy was demonstrated internally with two different validation sets and, moreover, using a number of molecules, for which Pgp inhibition was not experimentally available but was evaluated in-house. All of the validations confirmed the robustness of the model and its suitability to help medicinal chemists in drug discovery. The information derived from the model was rationalized as a pharmacophore for competitive Pgp inhibition.

FLAP: GRID molecular interaction fields in virtual screening. validation using the DUD data set

The performance of FLAP (Fingerprints for Ligands and Proteins) in virtual screening is assessed using a subset of the DUD (Directory of Useful Decoys) benchmarking data set containing 13 targets each with more than 15 different chemotype classes. A variety of ligand and receptor-based virtual screening approaches are examined, using combinations of individual templates 2D structures of known actives, a cocrystallized ligand, a receptor structure, or a cocrystallized ligand-biased receptor structure. We examine several data fusion approaches to combine the results of the individual virtual screens. In doing so, we show that excellent chemotype enrichment is achieved in both single target ligand-based and receptor-based approaches, of approximately 17-fold over random on average at a false positive rate of 1%. We also show that using as much starting knowledge as possible improves chemotype enrichment, and that data fusion using Pareto ranking is an effective method to do this giving up to 50% improvement in enrichment over the single methods. Finally we show that if inactivity or decoy data is incorporated, automatically training the scoring function in FLAP improves recovery still further, with almost 2-fold improvement over the enrichments shown by the single methods. The results clearly demonstrate the utility of FLAP for virtual screening when either a limited or wide range of prior knowledge is available.

Discovery of novel inhibitors of the NorA multidrug transporter of Staphylococcus aureus

Four novel inhibitors of the NorA efflux pump of Staphylococcus aureus, discovered through a virtual screening process, are reported. The four compounds belong to different chemical classes and were tested for their in vitro ability to block the efflux of a well-known NorA substrate, as well as for their ability to potentiate the effect of ciprofloxacin (CPX) on several strains of S. aureus, including a NorA overexpressing strain. Additionally, the MIC values of each of the compounds individually are reported. A structure-activity relationship study was also performed on these novel chemotypes, revealing three new compounds that are also potent NorA inhibitors. The virtual screening procedure employed FLAP, a new methodology based on GRID force field descriptors.

Lead Discovery Using Virtual Screening

The practice of virtual screening (VS) to identify chemical leads to known or novel targets is becoming a core function of the computational chemist within industry. By employing a range of techniques, when attempting to identify compounds with activity against a biological target, a small focused subset of a larger collection of compounds can be identified and tested, often with results much better than selecting a similar number of compounds at random. We will review the key methods available, their relative success, and provide practical insights into best practices and key gaps. We will also argue that the capability of VS methods has grown to a point where fuller integration with experimental methods, including HTS, could increase the effectiveness of both.