Predictive Global Models of Cruzain Inhibitors with Large Chemical Coverage.

Chagas disease affects 8-11 million people worldwide, most of them living in Latin America. Moreover, migratory phenomena have spread the infection beyond endemic areas. Efforts for the development of new pharmacological therapies are paramount as the pharmacological profile of the two marketed drugs currently available, nifurtimox and benznidazole, needs to be improved. Cruzain, a parasitic cysteine protease, is one of the most attractive biological targets due to its roles in parasite survival and immune evasion. In this work, we compiled and curated a database of diverse cruzain inhibitors previously reported in the literature. From this data set, quantitative structure-activity relationship (QSAR) models for the prediction of their pIC50 values were generated using k-nearest neighbors and random forest algorithms. Local and global models were calculated and compared. The statistical parameters for internal and external validation indicate a significant predictability, with q loo 2 values around 0.66 and 0.61 and external R 2 coefficients of 0.725 and 0.766. The applicability domain is quantitatively defined, according to QSAR good practices, using the leverage and similarity methods. The models described in this work are readily available in a Python script for the discovery of novel cruzain inhibitors.

The impact of chemoinformatics on drug discovery in the pharmaceutical industry.

Introduction: Even though there have been substantial advances in our understanding of biological systems, research in drug discovery is only just now beginning to utilize this type of information. The single-target paradigm, which exemplifies the reductionist approach, remains a mainstay of drug research today. A deeper view of the complexity involved in drug discovery is necessary to advance on this field.Areas covered: This perspective provides a summary of research areas where cheminformatics has played a key role in drug discovery, including of the available resources as well as a personal perspective of the challenges still faced in the field.Expert opinion: Although great strides have been made in the handling and analysis of biological and pharmacological data, more must be done to link the data to biological pathways. This is crucial if one is to understand how drugs modify disease phenotypes, although this will involve a shift from the single drug/single target paradigm that remains a mainstay of drug research. Moreover, such a shift would require an increased awareness of the role of physiology in the mechanism of drug action, which will require the introduction of new mathematical, computer, and biological methods for chemoinformaticians to be trained in.

Distribution of toxicity values across different species and modes of action of pesticides from PESTIMEP and PPDB databases.

The continuous use of compounds contained in commodities such as processed food, medicines, and pesticides, demands safety measures, in particular, for those in direct contact with humans and the environment. Safety measures have evolved and regulations are now in place around the globe. In the case of pesticides, attempts have been made to use toxicological data to inform of potentially harmful compounds either across species, on different routes of exposure, or entirely new chemicals. The generation of models, based on statistical and molecular modeling studies, allows for such predictions. However, the use of these models is framed by the available data, the experimental errors, the complexity of the measurement, and the available computational algorithms, among other factors. In this work, we present the methodologies used for extrapolation across different species and routes of administration and show the appropriateness of developing predictive models of pesticides based on their type and mode of action. The analyses include comparisons based on structural characteristics and physicochemical properties. Whenever possible, the scope and limitations of the methodologies are discussed. We expect that this work will serve as a useful introductory guide of the tools employed in the toxicity assessment of agrochemical compounds.

Targeting cancer-specific glycans by cyclic peptide lectinomimics.

The transformation from normal to malignant phenotype in human cancers is associated with aberrant cell-surface glycosylation. Thus, targeting glycosylation changes in cancer is likely to provide not only better insight into the roles of carbohydrates in biological systems, but also facilitate the development of new molecular probes for bioanalytical and biomedical applications. In the reported study, we have synthesized lectinomimics based on odorranalectin 1; the smallest lectin-like cyclic peptide isolated from the frog Odorrana grahami skin, and assessed the ability of these peptides to bind specific carbohydrates on molecular and cellular levels. In addition, we have shown that the disulfide bond found in 1 can be replaced with a lactam bridge. However, the orientation of the lactam bridge, peptides 2 and 3, influenced cyclic peptide's conformation and thus these peptides' ability to bind carbohydrates. Naturally occurring 1 and its analog 3 that adopt similar conformation in water bind preferentially L-fucose, and to a lesser degree D-galactose and N-acetyl-D-galactosamine, typically found within the mucin O-glycan core structures. In cell-based assays, peptides 1 and 3 showed a similar binding profile to Aleuria aurantia lectin and these two peptides inhibited the migration of metastatic breast cancer cell lines in a Transwell assay. Altogether, the reported data demonstrate the feasibility of designing lectinomimics based on cyclic peptides.

Identification of potent and compartment-selective small molecule furin inhibitors using cell-based assays.

The proprotein convertase furin is implicated in a variety of pathogenic processes such as bacterial toxin activation, viral propagation, and cancer. Several groups have identified non-peptide compounds with high inhibitory potency against furin in vitro, although their efficacy in various cell-based assays is largely unknown. In this study we show that certain guanidinylated 2,5-dideoxystreptamine derivatives exhibit interesting ex vivo properties. Compound 1b (1,1'-(4-((2,4-diguanidino-5-(4-guanidinophenoxy)cyclohexyl)oxy)-1,3-phenylene)diguanidine) is a potent and cell-permeable inhibitor of cellular furin, since it was able to retard tumor cell migration, block release of a Golgi reporter, and protect cells against Bacillus anthracis (anthrax) and Pseudomonas aeruginosa intoxication, with no evident cell toxicity. Other compounds based on the 2,5-dideoxystreptamine scaffold, such as compound 1g (1,1'-(4,6-bis(4-guanidinophenoxy)cyclohexane-1,3-diyl)diguanidine) also efficiently protected cells against anthrax, but displayed only moderate protection against Pseudomonas exotoxin A and did not inhibit cell migration, suggesting poor cell permeability. Certain bis-guanidinophenyl ether derivatives such as 2f (1,3-bis(2,4-diguanidinophenoxy) benzene) exhibited micromolar potency against furin in vitro, low cell toxicity, and highly efficient protection against anthrax toxin; this compound only slightly inhibited intracellular furin. Thus, compounds 1g and 2f both represent potent furin inhibitors at the cell surface with low intracellular inhibitory action, and these particular compounds might therefore be of preferred therapeutic interest in the treatment of certain bacterial and viral infections.

Cruzain inhibitors: efforts made, current leads and a structural outlook of new hits.

Human African trypanosomiasis and Chagas disease are the main causes of heart failure in developing countries. The disadvantages of current therapy include: undesirable side-effects, resistance, lack of efficacy on late-stage disease and lack of pediatric formulations. Efforts to find new compound hits have spanned SAR studies to very high-throughput and virtual screens and drug repurposing. The integrated analysis of these strategies on the discovery of anti-Chagas agents is timely. This work accounts for the progress on the development of cruzain inhibitors following these avenues, with emphasis on structural aspects of the ligand-cruzain recognition process.

Synthesis, anti-inflammatory activity and modeling studies of cycloartane-type terpenes derivatives isolated from Parthenium argentatum.

The 12-O-tetradecanoylphorbol-13-acetate (TPA)-induced edema model in mice determined the anti-inflammatory activities in vivo of argentatins A, B and D, the main cycloartenol-type triterpenes present in Parthenium argentatum. Our results showed that argentatin B (ED50=1.5×10(-4)mmol/ear) and argentatin A (ED50=2.8×10(-4)mmol/ear) were more potent anti-inflammatory agents than indomethacin (ED50=4.5×10(-4)mmol/ear), the reference drug. Based on these findings, we decided to evaluate 13 derivatives of argentatins A and B. All the derivatives showed anti-inflammatory activity in the TPA-induced edema model in mice. The most active compound was 25-nor-cycloart-3, 16-dione-17-en-24-oic acid, obtained from argentatin A (ED50=1.4×10(-4)mmol/ear). Argentatin B was assayed as inhibitor of COX-2 activity one of the key enzymes involved in the TPA assay. The results showed that argentatin B at 15µM doses inhibited 77% COX-2 activity. Docking studies suggest that argentatin B interacts with Arg 120, a key residue for COX-2 activity.

The role of imidazole in peptide cyclization by transesterification: parallels to the catalytic triads of serine proteases.

The improved bioavailability, stability and selectivity of cyclic peptides over their linear counterparts make them attractive structures in the design and discovery of novel therapeutics. In our previous work, we developed an imidazole-promoted preparation of cyclic depsipeptides in which we observed that increasing the concentration of imidazole resulted in the concomitant increase in the yield of cyclic product and reduction in dimerization, but also resulted in the generation of an acyl-substituted side product. In this work, we used transition state analysis to explore the mechanism of the imidazole-catalyzed esterification of one such peptide, Ac-SAFYG-SCH2φ, and determined the acyl substitution product to be an intermediate in a competing reaction pathway involving acyl substitution of the thioester by imidazole. Our findings indicate that imidazole plays an essential role in this side-chain to C-terminal coupling, and by extension, in transesterifications in general, through a concerted mechanism wherein imidazole deprotonates the nucleophile as the nucleophile attacks the carbonyl. The system under study is identical to the histidine-serine portion of the catalytic triads in serine proteases and it is likely that these enzymes employ the same concerted mechanism in the first step of peptide cleavage. Additionally, relatively high concentrations of imidazole must be used to effectively catalyze reactions in aprotic solvents since the overall reaction involves imidazole acting both as an acid and as a base, existing in solution as an equilibrium distribution between the neutral form and its conjugate acid.

Molecular recognition of the Thomsen-Friedenreich antigen-threonine conjugate by adhesion/growth regulatory galectin-3: nuclear magnetic resonance studies and molecular dynamics simulations.

Nuclear magnetic resonance (NMR) spectroscopy and molecular modeling methods have been strategically combined to elucidate the molecular recognition features of the binding of threonine O-linked Thomsen-Friedenreich (TF) antigen to chimera-type avian galectin-3 (CG-3). Saturation transfer difference (STD) NMR experiments revealed the highest intensities for the H4 protons of both the ß-D-Galp and α-D-GalpNAc moieties, with 100 and 71% of relative STD, respectively. The methyl protons of the threonine residue exhibited a small STD effect, <15%, indicating that the interaction of the amino acid with the protein is rather transient. Two-dimensional transferred nuclear Overhauser effect spectroscopy NMR experiments and molecular modeling suggested some differences in conformer populations between the free and bound states. A dynamic binding mode for the TF antigen-CG-3 complex consisting of two poses has been deduced. In one pose, intermolecular interactions were formed between the terminal threonine residue and the receptor. In the second pose, intermolecular interactions involved the internal GalpNAc. The difference in the trend of some shifts in the heteronuclear single-quantum coherence titration spectra indicates some disparities in the binding interactions of CG-3 with lactose and TF antigen. The results obtained from this model of the avian orthologue of human galectin-3 will allow detailed interspecies comparison to give sequence deviations in phylogeny a structural and functional meaning. Moreover, the results indicate that the peptide scaffold presenting TF antigen could be relevant for binding and thus provides a possible route for the design of galectin-3 inhibitors with improved affinity and selectivity.

Furin inhibitors: importance of the positive formal charge and beyond.

Furin is the prototype member of the proprotein convertases superfamily. Proprotein convertases are associated with hormonal response, neural degeneration, viral and bacterial activation, and cancer. Several studies over the last decade have examined small molecules, natural products, peptides and peptide derivatives as furin inhibitors. Currently, subnanomolar inhibition of furin is possible. Herein, we report the analysis of 115 furin inhibitors reported in the literature. Analysis of the physicochemical properties of these compounds highlights the dependence of the inhibitory potency with the total formal charge and also shows how the most potent (peptide-based) furin inhibitors have physicochemical properties similar to drugs. In addition, we report docking studies of 26 furin inhibitors using Glide XP. Inspection of binding interactions shows that the two putative binding modes derived from our study are reasonable. Analysis of the binding modes and protein-ligand interaction fingerprints, used here as postdocking procedure, shows that electrostatic interactions predominate on S1, S2 and S4 subsites but are seldom in S3. Our models also show that the benzimidamide group, present in the most active inhibitors, can be accommodated in the S1 subsite. These results are valuable for the design of new furin inhibitors.

Consensus models of activity landscapes with multiple chemical, conformer, and property representations.

We report consensus Structure-Activity Similarity (SAS) maps that address the dependence of activity landscapes on molecular representation. As a case study, we characterized the activity landscape of 54 compounds with activities against human cathepsin B (hCatB), human cathepsin L (hCatL), and Trypanosoma brucei cathepsin B (TbCatB). Starting from an initial set of 28 descriptors we selected ten representations that capture different aspects of the chemical structures. These included four 2D (MACCS keys, GpiDAPH3, pairwise, and radial fingerprints) and six 3D (4p and piDAPH4 fingerprints with each including three conformers) representations. Multiple conformers are used for the first time in consensus activity landscape modeling. The results emphasize the feasibility of identifying consensus data points that are consistently formed in different reference spaces generated with several fingerprint models, including multiple 3D conformers. Consensus data points are not meant to eliminate data, disregarding, for example, "true" activity cliffs that are not identified by some molecular representations. Instead, consensus models are designed to prioritize the SAR analysis of activity cliffs and other consistent regions in the activity landscape that are captured by several molecular representations. Systematic description of the SARs of two targets give rise to the identification of pairs of compounds located in the same region of the activity landscape of hCatL and TbCatB suggesting similar mechanisms of action for the pairs involved. We also explored the relationship between property similarity and activity similarity and found that property similarities are suitable to characterize SARs. We also introduce the concept of structure-property-activity (SPA) similarity in SAR studies.

Integrating virtual screening and combinatorial chemistry for accelerated drug discovery.

Virtual screening is increasingly being used in drug discovery programs with a growing number of successful applications. Experimental methodologies developed to speed up the drug discovery processes include high-throughput screening and combinatorial chemistry. The complementarities between computational and experimental screenings have been recognized and reviewed in the literature. Computational methods have also been used in the combinatorial chemistry field, in particular in library design. However, the integration of computational and combinatorial chemistry screenings has been attempted only recently. Combinatorial libraries (experimental or virtual) represent a notable source of chemically related compounds. Advances in combinatorial chemistry and deconvolution strategies, have enabled the rapid exploration of novel and dense regions in the chemical space. The present review is focused on the integration of virtual and experimental screening of combinatorial libraries. Applications of virtual screening to discover novel anticancer agents and our ongoing efforts towards the integration of virtual screening and combinatorial chemistry are also discussed.