Activity Of Novel Inhibitors Research Articles

Reconstitution of the alternative pathway of the complement system enables rapid delineation of the mechanism of action of novel inhibitors

The complement system plays a critical role in the innate immune response, acting as a first line of defense against invading pathogens. However, dysregulation of the complement system is implicated in the pathogenesis of numerous diseases, ranging from Alzheimer's to age-related macular degeneration and rare blood disorders. As such, complement inhibitors have enormous potential to alleviate disease burden. While a few complement inhibitors are in clinical use, there is still a significant unmet medical need for the discovery and development of novel inhibitors to treat patients suffering from disorders of the complement system. A key hurdle in the development of complement inhibitors has been the determination of their mechanism of action. Progression along the complement cascade involves the formation of numerous multimeric protein complexes, creating the potential for inhibitors to act at multiple nodes in the pathway. This is especially true for molecules that target the central component C3 and its fragment C3b, which serve a dual role as a substrate for the C3 convertases and as a scaffolding protein in both the C3 and C5 convertases. Here, we report a step-by-step invitro reconstitution of the complement alternative pathway using bio-layer interferometry. By physically uncoupling each step in the pathway, we were able to determine the kinetic signature of inhibitors that act at single steps in the pathway and delineate the full mechanism of action of known and novel C3 inhibitors. The method could have utility in drug discovery and further elucidating the biochemistry of the complement system.

Structural characterization of plasmodial aminopeptidase: a combined molecular docking and QSAR-based in silico approaches

Aminopeptidase M1 (PfAM1) is one of the key enzymes involved in the development of new antimalarials. To accelerate the discovery of inhibitors with selective activity against PfAM1 and microsomal neutral aminopeptidase (pAPN), in the present work, the optimum comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) models were built based on PfAM1 and pAPN inhibitors. The results of the developed 3D-QSAR models were as follows: PfAM1/CoMFA: [Formula: see text] = 0.740, [Formula: see text] = 0.7781; PfAM1/CoMSIA: [Formula: see text] = 0.740, [Formula: see text] = 0.7354; pAPN/CoMFA: [Formula: see text] = 0.612, [Formula: see text] = 0.7318; pAPN/CoMSIA: [Formula: see text] = 0.609, [Formula: see text] = 0.7480, and the models derived from MLR, PLSR and SVR methods provided high R2 values of 0.6960, 0.6965, 0.7971 for PfAM1, 0.7700, 0.7697, 0.8228 for pAPN and Q2 of 0.7004, 0.7004, 0.5632 for PfAM1, 0.7551, 0.7566 and 0.8394 for pAPN, respectively, indicating that the developed 3D-QSAR and 2D-QSAR models possess good ability for prediction of the relative compound activities. Furthermore, all inhibitors were docked into the active site of the PfAM1 and pAPN receptors, the hydrogen-bond interactions between the compound 33 with Glu497, Glu463 and Arg489 of the PfAM1, and the compound 4 with Ala348, Glu384 and Phe467 of the receptor pAPN are able to help to stabilize the conformation. The above results would provide helpful clues to predicting the binding activity of novel inhibitors and the foundation for understanding the interaction mechanism between the inhibitors and the receptors.

3D-QSAR studies on indole and 7-azoindole derivatives as ROCK-2 inhibitors: An integrative computational approach

Rho Kinases (ROCK) has been found to regulate a wide range of fundamental cell functions such as contraction, motility, proliferation, and apoptosis. Recent experiments have defined new functions of ROCKs in cells, including centrosome positioning and cell-size regulation, which might contribute to various physiological and pathological states. In this study, we have performed pharmacophore modeling and 3D QSAR studies on a series of 36 indoles and 7-azoindoles derivatives as ROCK2 inhibitors to elucidate the structural variations with their inhibitory activities. Ligand based CoMFA and CoMSIA models were generated based on three different alignment methods such as systematic search, simulated annealing and pharmacophore. A total of 15 CoMFA models and 27 CoMSIA were generated using different alignments. One model from each alignment is selected based on the statistical values. Contour maps of the selected models were compared, analysed and reported. The 3D QSAR study revealed that electro positive group linked to the methoxy-benzene ring position of the structure will enhance the biological activity and bulkier substitutions are preferred in the methyl dihydroindole region. Also, it is found that the hydrogen bond donor substituted at the R1 position enhances the inhibitory activity. In future, this study would give proper guidelines to further enhance the activity of novel inhibitors for ROCK2.

Activity of novel inhibitors of Staphylococcus aureus biofilms.

Staphylococcus aureus is one of the most important pathogens causing chronic biofilm infections. These are becoming more difficult to treat owing to drug resistance, particularly because S. aureus biofilms limit the efficacy of antimicrobial agents, leading to high morbidity and mortality. In the present study, we screened for inhibitors of S. aureus biofilm formation using a natural product library from the Korea Chemical Bank (KCB). Screening by crystal violet-based biomass staining assay identified hit compounds. Further examination of antibiofilm properties of these compounds was conducted and led to the identification of celastrol and telithromycin. In vitro, both celastrol and telithromycin were toxic to planktonic S. aureus and also active against a clinical methicillin-resistant S. aureus (MRSA) isolate. The effect of the compounds on preformed biofilms of clinical MRSA isolates was evaluated by confocal laser scanning microscopy (CLSM), which revealed the absence of typical biofilm architecture. In addition, celastrol and telithromycin inhibited the production of extracellular protein at selected sub-MIC concentrations, which revealed the reduced extracellular polymeric substance (EPS) secretion. Celastrol exhibited greater cytotoxicity than telithromycin. These data suggest that the hit compounds, especially telithromycin, could be considered novel inhibitors of S. aureus biofilm. Although the mechanisms of the effects on S. aureus biofilms are not fully understood, our data suggest that telithromycin could be a useful adjuvant therapeutic agent for S. aureus biofilm-related infections.

Design, synthesis, and in vivo activity of novel inhibitors of delta-5 desaturase for the treatment of metabolic syndrome.

The synthesis, SAR, and in vivo activity of inhibitors of delta-5 desaturase are described. Ring-constraint of the initial series provided access to a variety of in vitro active chemotypes, from which the indazole was selected. Examples from the indazole series displayed in vivo activity in reducing the enzymatic activity of liver delta-5 desaturase.

Pharmacological inhibitors of exocytosis and endocytosis: novel bullets for old targets.

Pharmacological inhibitors of vesicle trafficking possess great promise as valuable analytical tools for the study of a variety of biological processes and as potential therapeutic agents to fight microbial infections and cancer. However, many commonly used trafficking inhibitors are characterized by poor selectivity that diminishes their use in solving basic problems of cell biology or drug development. Recent high-throughput chemical screens intensified the search for novel modulators of vesicle trafficking, and successfully identified a number of small molecules that inhibit exocytosis and endocytosis in different types of mammalian cells. This chapter provides a systematic overview of recently discovered inhibitors of vesicle trafficking. It describes cellular effects and mechanisms of action of novel inhibitors of exocytosis and endocytosis. Furthermore, it pays special attention to the selectivity and possible off-target effects of these inhibitors.

Molecular modeling study of HIV-1 gp120 attachment inhibitors

The viral glycoprotein 120 (gp120) is a glycoprotein exposed on viral surface. The gp120 is essential for virus entry into cells as it plays a vital role in seeking out specific cell surface receptors for entry. In this article, we performed docking and three-dimensional quantitative structure activity relationship (3D-QSAR) study on a series of 48 indole glyoxamide derivatives as gp120 inhibitors. Docking study revealed that the inhibitor docked deeply into the gp120 cavity rather than Phe43 of cluster of differentiation 4 (CD4). 3D-QSAR methodologies, comparative molecular field analysis (CoMFA), and comparative molecular similarity indices analysis (CoMSIA) were utilized to rationalize the structural variations with their inhibitory activities. The docked pose of the most potent molecule (43) was used to determine the structures of other molecules. The CoMFA yielded a model with cross-validated correlation coefficient of (q 2) 0.73 and non-cross-validated correlation coefficient of (r 2) 0.89 with optimum number of components (N = 3). The CoMSIA models were obtained with the combination of various parameters. Final model was computed with steric, hydrophobic- and hydrogen-bond acceptor (SHA) parameters with reasonable statistics (q 2 = 0.80, r 2 = 0.94 and N = 5). The predictive power of developed CoMFA and CoMSIA models were assessed by test set (nine molecules). The predictive r pred 2 for CoMFA and CoMSIA model was found to be 0.93 and 0.74, respectively. The generated contour maps were plotted onto the gp120 active site to correlate structural variations with their biological activity in protein environment. Contour map analyses showed the importance of 4-F substitution of indole ring, which made essential electronic interaction with the crucial residue (Trp427). The 3D models could explain nicely the structure–activity relationships of indole glyoxamide analogs. This would give proper guidelines to further enhance the activity of novel inhibitors.

Docking and Molecular Dynamics Study on the Inhibitory Activity of Novel Inhibitors on Epidermal Growth Factor Receptor (EGFR)

EGFR is the cell-surface receptor. Its overexpression or overactivity has been associated with a number of cancers, including breast, lung, ovarian, and anal cancers. Many therapeutic approaches are aimed at the EGFR. A series of 2, 7-diamino-thiazolo [4,5-d] pyrimidine analogues are among the most highly potent and selective inhibitors of EGFR described to date. For in-depth investigation into the structural and chemical features responsible for the binding recognition mechanism concerned, as well as for exploring the binding pocket of these compounds, we performed a series of automated molecular docking operations. It was revealed that the binding site consisted of three main areas (P1, P2 and P3) composed of most of the hydrophobic amino acids able to accommodate the lipophilic arms of the compounds investigated. However, the solvent interface did not make much contribution to the binding of the inhibitors. The presence of residues Met793 and Asp855 may also be responsible for the binding recognition through H-bond interactions, with Phe856 through a T-shape π-π stacking interaction. The interaction model and pharmacophore of EGFR inhibitors were derived that can be successfully used to explain the different biologic activities of these inhibitors. Moreover, the docking results were quite robust as further validated by molecular dynamics. It is anticipated that the findings reported here may provide very useful information or clue for designing effective drugs for the therapeutic treatment of EGFR-related cancer.

Synthesis and biological activity of novel inhibitors of topoisomerase I: 2-Aryl-substituted 2-bis-1H-benzimidazoles

Inhibitors of topoisomerase I constitute a novel family of antitumor agents. The class of benzimidazole derivatives contains compounds possessing affinity to DNA. For example, fluorescent stains Hoechst 33342 and Hoechst 33258 interact with DNA as ligand and produce nonspecific inhibition of the catalytic activity of many enzymes involved in DNA synthesis, including DNA topoisomerase and DNA helicase. Several 2-aryl-5-substituted-2,5-bisbenzimidazole derivatives were synthesized and ability of these derivatives to induce DNA cleavage in the presence of topoisomerase I was evaluated in vitro. These analogs were also assayed for their cytotoxicity against U87, MCF7 and HeLa human tumor cells. All the four compounds showed a potent growth inhibitory effect on all the cell lines, with IC 50 in the μM range.

Synthesis of Novel β-Lactone Inhibitors of Fatty Acid Synthase

Fatty acid synthase (FAS) is necessary for growth and survival of tumor cells and is a promising drug target for oncology. Here, we report on the syntheses and activity of novel inhibitors of the thioesterase domain of FAS. Using the structure of orlistat as a starting point, which contains a beta-lactone as the central pharmacophore, 28 novel congeners were synthesized and examined. Structural features such as the length of the alpha- and beta-alkyl chains, their chemical composition, and amino ester substitutions were altered and the resulting compounds explored for inhibitory activity toward the thioesterase domain of FAS. Nineteen congeners show improved potency for FAS in biochemical assays relative to orlistat. Three of that subset, including the natural product valilactone, also display an increased potency in inducing tumor cell death and improved solubility compared to orlistat. These findings support the idea that an orlistat congener can be optimized for use in a preclinical drug design and for clinical drug development.

Structure-based design, synthesis, and study of pyrazolo[1,5-a][1,3,5]triazine derivatives as potent inhibitors of protein kinase CK2

The structure-based design, synthesis, and anticancer activity of novel inhibitors of protein kinase CK2 are described. Using pyrazolo[1,5-a][1,3,5]triazine as the core scaffold, a structure-guided series of modifications provided pM inhibitors with μM-level cytotoxic activity in cell-based assays with prostate and colon cancer cell lines.

Binding-Site Identification and Genotypic Profiling of Hepatitis C Virus Polymerase Inhibitors

The search for hepatitis C virus polymerase inhibitors has resulted in the identification of several nonnucleoside binding pockets. The shape and nature of these binding sites differ across and even within diverse hepatitis C virus genotypes. These differences confront antiviral drug discovery with the challenge of finding compounds that are capable of inhibition in variable binding pockets. To address this, we have established a hepatitis C virus mutant and genotypic recombinant polymerase panel as a means of guiding medicinal chemistry through the elucidation of the site of action of novel inhibitors and profiling against genotypes. Using a genotype 1b backbone, we demonstrate that the recombinant P495L, M423T, M414T, and S282T mutant enzymes can be used to identify the binding site of an acyl pyrrolidine analog. We assess the inhibitory activity of this analog and other nonnucleoside inhibitors with our panel of enzyme isolates generated from clinical sera representing genotypes 1a, 1b, 2a, 2b, 3a, 4a, 5a, and 6a.

The carboxyterminal processing protease of D1 protein: Herbicidal activity of novel inhibitors of the recombinant and native spinach enzymes

The carboxyterminal processing protease of D1 protein (CtpA) is predicted to be an excellent target for the discovery of a general broad-spectrum herbicide. Directed and random screening of compounds against recombinant spinach CtpA (rCtpA) has led to the discovery of five different chemical classes of inhibitors. Lead compounds from each inhibitor class were investigated for their in vitro effects on the activities of both recombinant and native spinach CtpA. All of the lead compounds have K i values of less than 50 μM when tested against rCtpA, and all except one showed competitive inhibition. Results from partially purified native CtpA from spinach were similar to those from the recombinant form of the enzyme, thus validating the use of rCtpA in the inhibitor screen. Compounds from three of the classes of CtpA inhibitors show in vivo herbicidal activity against Arabidopsis thaliana when applied either by addition to growth media or by spraying the leaves. Transgenic Arabidopsis plants which over-express CtpA showed greater resistance to the compounds than wild-type plants providing evidence that these inhibitors are directly acting against CtpA.

Structure‐Based Design, Synthesis, and Antimicrobial Activity of Purine Derived SAH/MTA Nucleosidase Inhibitors.

AbstractFor Abstract see ChemInform Abstract in Full Text.

Structure-based design, synthesis, and antimicrobial activity of purine derived SAH/MTA nucleosidase inhibitors

The structure-based design, synthesis, and biological activity of novel inhibitors of S-adenosyl homocysteine/methylthioadenosine (SAH/MTA) nucleosidase are described. Using 6-substituted purine and deaza purines as the core scaffolds, a systematic and structure guided series of modifications provided low nM inhibitors with broad-spectrum antimicrobial activity.

Evaluation of chemokine- and phlogistin-mediated leukocyte chemotaxis using an in vivo sponge model.

We have directly compared the in vivo activity of a number of chemokines and phlogistins using a modified murine in vivo sponge model in which gelatin sponges are soaked with chemoattractant and implanted in the peritoneal cavity. Sponges soaked with murine JE/MCP-1 (monocyte chemoattractant protein-1) or zymosan promoted the chemotaxis of specific leukocyte populations in a time-dependent manner, as judged by multiparameter flow cytometry, with granulocytes predominating in zymosan-soaked sponges and granulocytes and macrophages present in JE/MCP-1-soaked sponges. Smaller numbers of B, T and dendritic cells were identified as well. Eotaxin selectively chemoattracted eosinophils in this model, while MIG induced significant T cell migration relative to other chemokines. Cell migration was inhibited by administration of methotrexate, piroxicam or dexamethasone, and JE/MCP-1-mediated trafficking was impaired by treatment with anti-JE antibody or with IL-10, suggesting a role for pro-inflammatory factors in amplifying the JE/MCP-1-induced response. This amplification phase involves the production of the chemokine KC, since anti-KC antibody significantly attenuated JE/MCP-1-induced chemotaxis. These results indicate that intraperitoneally implanted chemoattractant-soaked gelatin sponges are capable of inducing a pronounced inflammatory response characterized by the selective migration of leukocyte populations, and suggest that this model may be useful for delineating the activity of novel inhibitors of leukocyte chemotaxis.

Structure-Based Drug Design: Combinatorial Chemistry and Molecular Modeling

Drug discovery efforts are shifting to include the rapid synthetic procedures of combinatorial chemistry and the elegance of rational library design. The wealth of computational methods which explore both the receptor structure and the ultimate pharmacophore complementarity, provide novel avenues for chemists to discover new lead compounds or design virtual libraries for screening prior to the synthetic stage. This mini-review provides an overview of a few current methodologies of library generation, highlighting docking procedures which have utility in both the discovery and optimization stages of drug development. Three specific examples of different approaches to the use of docking are provided. These describe the development of inhibitors to the human A3 adenosine receptor and HIV-1 protease, and the evaluation of the activity of novel inhibitors of the redox regulator protein, human thioredoxin.