A computer-based approach to the rational discovery of new trichomonacidal drugs by atom-type linear indices

Antileishmanial activity of 5-nitroindazole derivatives

Background

Currently, there is no safe and effective vaccine against leishmaniasis and existing therapies are inadequate due to high toxicity, cost and decreased efficacy caused by the emergence of resistant parasite strains. Some indazole derivatives have shown in vitro and in vivo activity against Trichomonas vaginalis and Trypanosoma cruzi. On that basis, 20 indazole derivatives were tested in vitro against Leishmania amazonensis.

Objective

To evaluate the in vitro activity of twenty 2-benzyl-5-nitroindazolin-3-one derivatives against L. amazonensis.

Design

For the selection of promising compounds, it is necessary to evaluate the indicators for in vitro activity. For this aim, a battery of studies for antileishmanial activity and cytotoxicity were implemented. These results enabled the determination of the substituents in the indazole derivatives responsible for activity and selectivity, through the analysis of the structure-activity relationship (SAR).

Methods

In vitro cytotoxicity against mouse peritoneal macrophages and growth inhibitory activity in promastigotes were evaluated for 20 compounds. Compounds that showed adequate selectivity were tested against intracellular amastigotes. The SAR from the results in promastigotes was represented using the SARANEA software.

Results

Eight compounds showed selectivity index >10% and 50% inhibitory concentration <1 µM against the promastigote stage. Against intracellular amastigotes, four were as active as Amphotericin B. The best results were obtained for 2-(benzyl-2,3-dihydro-5-nitro-3-oxoindazol-1-yl) ethyl acetate, with 50% inhibitory concentration of 0.46 ± 0.01 µM against amastigotes and a selectivity index of 875. The SAR study showed the positive effect on the selectivity of the hydrophilic fragments substituted in position 1 of 2-benzyl-5- nitroindazolin-3-one, which played a key role in improving the selectivity profile of this series of compounds.

Conclusion

2-bencyl-5-nitroindazolin-3-one derivatives showed selective and potent in vitro activity, supporting further investigations on this family of compounds as potential antileishmanial hits.

Computational discovery of novel anthelmintic natural compounds from Agave Brittoniana trel. Spp. Brachypus

Helminth infections are a medical problem in the world nowadays. This report used bond-based 2D quadratic indices, a bond-level QuBiLs-MAS molecular descriptor family, and Linear Discriminant Analysis (LDA) to obtain a quantitative linear model that discriminates between anthelmintic and non-anthelmintic drug-like organic-compounds. The model obtained correctly classified 87.46% and 81.82% of the training and external data sets, respectively. The developed model was used in a virtual screening to predict the biological activity of all chemicals (19) previously obtained and chemically characterized by some authors of this report from Agave brittoniana Trel. spp. Brachypus. The model identified several metabolites (12) as possible anthelmintics, and a group of 5 novel natural products was tested in an in vitro assay against Fasciola hepatica (100% effectivity at 500 µg/mL). Finally, the two best hits were evaluated in vivo in bald/c mice and the same helminth parasite using a 25 mg/kg dose. Compound 8 (Karatavinoside A) showed an efficacy of 92.2% in vivo. It is important to remark that this natural compound exhibits similar-to-superior activity as triclabendazole, the best human fasciolicide available in the market against Fasciola hepatica, resulting in a novel lead scaffold with anti-helminthic activity. Keywords: TOMOCOMD-CARDD Software; QuBiLs-MAS, nonstochastic and stochastic bond-based quadratic indices; LDA-based QSAR model; Computational Screening, Anthelmintic Agent; Agave brittoniana Trel. spp. Brachypus, Fasciola hepatica.

Promising hit compounds against resistant trichomoniasis: Synthesis and antiparasitic activity of 3-(ω-aminoalkoxy)-1-benzyl-5-nitroindazoles

A series of 11 3-(ω-aminoalkoxy)-1-benzyl-5-nitroindazoles (2-12) has been prepared starting from 1-benzyl-5-nitroindazol-3-ol 13, and evaluated against sensitive and resistant isolates of the sexually transmitted protozoan Trichomonas vaginalis. Compounds 2, 3, 6, 9, 10 and 11 showed trichomonacidal profiles with IC₅₀ < 20 µM against the metronidazole-sensitive isolate. Moreover, all these compounds submitted to cytotoxicity assays against mammalian cells exhibited low non-specific cytotoxic effects, except compounds 3 and 9 which displayed moderate cytotoxicity (CC₅₀ = 74.7 and 59.1 µM, respectively). Those compounds with trichomonacidal effect were also evaluated against a metronidazole-resistant culture. Special mention deserve compounds 6 and 10, which displayed better IC₅₀ values (1.3 and 0.5 µM respectively) than that of the reference drug (IC₅₀ MTZ = 3.0 µM). The high activity of these compounds against the resistant isolate reinforces the absence of cross-resistance with the reference drug. The remarkable trichomonacidal results against resistant T. vaginalis isolates suggest the interest of 3-(ω-aminoalkoxy)-1-benzyl-5-nitroindazoles to be considered as good prototypes to continue in the development of new drugs with enhanced trichomonacidal activity, aiming to increase the non-existent drugs to face clinical resistance efficiently for those patients in whom therapy with 5-nitroimidazoles is contraindicated.

Antichagasic and trichomonacidal activity of 1-substituted 2-benzyl-5-nitroindazolin-3-ones and 3-alkoxy-2-benzyl-5-nitro-2H-indazoles

Two series of new 5-nitroindazole derivatives, 1-substituted 2-benzylindazolin-3-ones (6-29, series A) and 3-alkoxy-2-benzyl-2H-indazoles (30-37, series B), containing differently functionalized chains at position 1 and 3, respectively, have been synthesized starting from 2-benzyl-5-nitroindazolin-3-one 5, and evaluated against the protozoan parasites Trypanosoma cruzi and Trichomonas vaginalis, etiological agents of Chagas disease and trichomonosis, respectively. Many indazolinones of series A were efficient against different morphological forms of T. cruzi CL Brener strain (compounds 6, 7, 9, 10 and 19-21: IC50 = 1.58-4.19 μM for epimastigotes; compounds 6, 19-21 and 24: IC50 = 0.22-0.54 μM for amastigotes) being as potent as the reference drug benznidazole. SAR analysis suggests that electron-donating groups at position 1 of indazolinone ring are associated with an improved antichagasic activity. Moreover, compounds of series A displayed low unspecific toxicities against an in vitro model of mammalian cells (fibroblasts), which were reflected in high values of the selectivity indexes (SI). Compound 20 was also very efficient against amastigotes from Tulahuen and Y strains of T. cruzi (IC50 = 0.81 and 0.60 μM, respectively), showing low toxicity towards cardiac cells (LC50 > 100 μM). In what concerns compounds of series B, some of them displayed moderate activity against trophozoites of a metronidazole-sensitive isolate of T. vaginalis (35 and 36: IC50 = 9.82 and 7.25 μM, respectively), with low unspecific toxicity towards Vero cells. Compound 36 was also active against a metronidazole-resistant isolate (IC50 = 9.11 μM) and can thus be considered a good prototype for the development of drugs directed to T. vaginalis resistant to 5-nitroimidazoles.

In vitro trichomonacidal activity and preliminary in silico chemometric studies of 5-nitroindazolin-3-one and 3-alkoxy-5-nitroindazole derivatives

A selection of 1,2-disubstituted 5-nitroindazolin-3-ones (1–19) and 3-alkoxy-5-nitroindazoles substituted at positions 1 (20–24) or 2 (25–39) from our in-house compound library were screened in vitro against the most common curable sexually transmitted pathogen, Trichomonas vaginalis. A total of 41% of the studied molecules (16/39) achieved a significant activity of more than 85% growth inhibition at the highest concentration assayed (100 µg mL−1). Among these compounds, 3-alkoxy-5-nitroindazole derivatives 23, 24, 25 and 27 inhibited parasite growth by more than 50% at 10 µg mL−1. In addition, the first two compounds (23, 24) still showed remarkable activity at the lowest dose tested (1 µg mL−1), inhibiting parasite growth by nearly 40%. Their specific activity towards the parasite was corroborated by the determination of their non-specific cytotoxicity against mammalian cells. The four mentioned compounds exhibited non-cytotoxic profiles at all of the concentrations assayed, showing a fair antiparasitic selectivity index (SI > 7·5). In silico studies were performed to predict pharmacokinetic properties, toxicity and drug-score using Molinspiration and OSIRIS computational tools. The current in vitro results supported by the virtual screening suggest 2-substituted and, especially, 1-substituted 3-alkoxy-5-nitroindazoles as promising starting scaffolds for further development of novel chemical compounds with the main aim of promoting highly selective trichomonacidal lead-like drugs with adequate pharmacokinetic and toxicological profiles.

QuBiLs-MAS method in early drug discovery and rational drug identification of antifungal agents

The QuBiLs-MAS approach is used for the in silico modelling of the antifungal activity of organic molecules. To this effect, non-stochastic (NS) and simple-stochastic (SS) atom-based quadratic indices are used to codify chemical information for a comprehensive dataset of 2478 compounds having a great structural variability, with 1087 of them being antifungal agents, covering the broadest antifungal mechanisms of action known so far. The NS and SS index-based antifungal activity classification models obtained using linear discriminant analysis (LDA) yield correct classification percentages of 90.73% and 92.47%, respectively, for the training set. Additionally, these models are able to correctly classify 92.16% and 87.56% of 706 compounds in an external test set. A comparison of the statistical parameters of the QuBiLs-MAS LDA-based models with those for models reported in the literature reveals comparable to superior performance, although the latter were built over much smaller and less diverse datasets, representing fewer mechanisms of action. It may therefore be inferred that the QuBiLs-MAS method constitutes a valuable tool useful in the design and/or selection of new and broad spectrum agents against life-threatening fungal infections.

Integration of ligand and structure-based virtual screening for identification of leading anabolic steroids

Parallel ligand- and structure-based virtual screenings of 269 steroids with anabolic activity evaluated in vivo were performed. The quantitative structure-activity relationship (QSAR) model expressed by selected descriptors as the octanol-water partition coefficient, the molar volume and the quantum mechanical calculated charge values on atoms C1, C2, C5, C9, C10, C14 and C17 of the steroid skeleton, expresses structural features of anabolic steroids (AS) contributing to the transport and steroid-receptor interaction. On the other hand, computational simulations of a candidate ligand binding to a receptor study (a "docking" procedure) predict the association of these AS with the human androgen receptor (AR). Fourteen compounds were identified as lead; the most potent was the 7α-methylestr-4-en-3, 17-dione. It was concluded that a good anabolic activity requires hydrogen bonding interactions between both Arg752 and Gln711 residues in the cycles A with O3 atom of the steroid and either Asn705 and Thr877 residues in the cycles D of steroid with O17 atom.

S. Cordeiro MN, Yañez M, González-Díaz H, García-Mera X. Model for high-throughput screening of multitarget drugs in chemical neurosciences: synthesis, assay, and theoretic study of rasagiline carbamates

The disappointing results obtained in recent clinical trials renew the interest in experimental/computational techniques for the discovery of neuroprotective drugs. In this context, multitarget or multiplexing QSAR models (mt-QSAR/mx-QSAR) may help to predict neurotoxicity/neuroprotective effects of drugs in multiple assays, on drug targets, and in model organisms. In this work, we study a data set downloaded from CHEMBL; each data point (>8000) contains the values of one out of 37 possible measures of activity, 493 assays, 169 molecular or cellular targets, and 11 different organisms (including human) for a given compound. In this work, we introduce the first mx-QSAR model for neurotoxicity/neuroprotective effects of drugs based on the MARCH-INSIDE (MI) method. First, we used MI to calculate the stochastic spectral moments (structural descriptors) of all compounds. Next, we found a model that classified correctly 2955 out of 3548 total cases in the training and validation series with Accuracy, Sensitivity, and Specificity values>80%. The model also showed excellent results in Computational-Chemistry simulations of High-Throughput Screening (CCHTS) experiments, with accuracy=90.6% for 4671 positive cases. Next, we reported the synthesis, characterization, and experimental assays of new rasagiline derivatives. We carried out three different experimental tests: assay (1) in the absence of neurotoxic agents, assay (2) in the presence of glutamate, and assay (3) in the presence of H2O2. Compounds 11 with 27.4%, 8 with 11.6%, and 9 with 15.4% showed the highest neuroprotective effects in assays (1), (2), and (3), respectively. After that, we used the mx-QSAR model to carry out a CCHTS of the new compounds in >400 unique pharmacological tests not carried out experimentally. Consequently, this model may become a promising auxiliary tool for the discovery of new drugs for the treatment of neurodegenerative diseases.

In vitro assessment of the acaricidal activity of computer-selected analogues of carvacrol and salicylic acid on Rhipicephalus (Boophilus) microplus

Rhipicephalus (Boophilus) microplus is a tick that causes huge economic losses in cattle. The indiscriminate use of acaricides has generated resistance to most compounds present on the market. This makes further investigation on other potential acaricides necessary, the in silico assay being an alternative to the design of new compounds. In the present study a biosilico assay was performed using TOMOCOMD-CARDD (TOpological MOlecular COMputer Design-Computer-Aided Rational Drug Design) and WEKA (Waikato Environment for Knowledge Analysis) software. Two carvacrol and four salicylic acid derivatives, synthesized by conventional methods and evaluated with the larval packet test on larvae of R. (B.) microplus were selected. All evaluated compounds presented acaricidal activity; however, ethyl 2-methoxybenzoate (91.8 ± 1.7 % mortality) and ethyl 2,5-dihydroxybenzoate (89.1 ± 1.6 % mortality) showed greater activity than salicylic acid. With regard to the carvacrol analogues, carvacrol acetate (67.8 ± 2.1 % mortality) and carvacrol methyl ether (71.7 ± 1.6 % mortality) also showed greater activity than carvacrol (35.9 ± 3.2 % mortality). TOMOCOMD-CARDD and WEKA software were helpful tools in the search for alternative structures with potential acaricidal activity on R. (B.) microplus.

Nucleotide's bilinear indices: novel bio-macromolecular descriptors for bioinformatics studies of nucleic acids. I. Prediction of paromomycin's affinity constant with HIV-1 Psi-RNA packaging region

A new set of nucleotide-based bio-macromolecular descriptors are presented. This novel approach to bio-macromolecular design from a linear algebra point of view is relevant to nucleic acids quantitative structure-activity relationship (QSAR) studies. These bio-macromolecular indices are based on the calculus of bilinear maps on Re(n)[b(mk)(x (m),y (m)):Re(n) x Re(n)-->Re] in canonical basis. Nucleic acid's bilinear indices are calculated from kth power of non-stochastic and stochastic nucleotide's graph-theoretic electronic-contact matrices, M(m)(k) and (s)M(m)(k), respectively. That is to say, the kth non-stochastic and stochastic nucleic acid's bilinear indices are calculated using M(m)(k) and (s)M(m)(k) as matrix operators of bilinear transformations. Moreover, biochemical information is codified by using different pair combinations of nucleotide-base properties as weightings (experimental molar absorption coefficient epsilon(260) at 260 nm and pH=7.0, first (Delta E(1)) and second (Delta E(2)) single excitation energies in eV, and first (f(1)) and second (f(2)) oscillator strength values (of the first singlet excitation energies) of the nucleotide DNA-RNA bases. As example of this approach, an interaction study of the antibiotic paromomycin with the packaging region of the HIV-1 Psi-RNA have been performed and it have been obtained several linear models in order to predict the interaction strength. The best linear model obtained by using non-stochastic bilinear indices explains about 91% of the variance of the experimental Log K (R=0.95 and s=0.08 x 10(-4)M(-1)) as long as the best stochastic bilinear indices-based equation account for 93% of the Log K variance (R=0.97 and s=0.07 x 10(-4)M(-1)). The leave-one-out (LOO) press statistics, evidenced high predictive ability of both models (q(2)=0.86 and s(cv)=0.09 x 10(-4)M(-1) for non-stochastic and q(2)=0.91 and s(cv)=0.08 x 10(-4)M(-1) for stochastic bilinear indices). The nucleic acid's bilinear indices-based models compared favorably with other nucleic acid's indices-based approaches reported nowadays. These models also permit the interpretation of the driving forces of the interaction process. In this sense, developed equations involve short-reaching (k<or=3), middle-reaching (4<k<9), and far-reaching (k=10 or greater) nucleotide's bilinear indices. This situation points to electronic and topologic nucleotide's backbone interactions control of the stability profile of paromomycin-RNA complexes. Consequently, the present approach represents a novel and rather promising way to theoretical-biology studies.

Application quantum and physico chemical molecular descriptors utilizing principal components to study mode of anticoagulant activity of pyridyl chromen-2-one derivatives

Factors II, V, VII and Xa have materialized as a key enzymes for the intervention of blood coagulation cascade and for the development of new anti thrombotic agents. The combined density functional quantum mechanical/molecular mechanical (QM/MM) approach has been used to access inhibition of prothrombin and thrombin production. The biological activities of coumarin derivatives as clotting factor inhibitors was quantitatively analyzed in terms of physicochemical parameters utilizing the principal component analysis. Structural requirements for maximal potency were derived from the results of a quantitative structure activity relationship analysis.

Estimation of ADME Properties in Drug Discovery: Predicting Caco-2 Cell Permeability Using Atom-Based Stochastic and Non-stochastic Linear Indices

The in vitro determination of the permeability through cultured Caco-2 cells is the most often-used in vitro model for drug absorption. In this report, we use the largest data set of measured P(Caco-2), consisting of 157 structurally diverse compounds. Linear discriminant analysis (LDA) was used to obtain quantitative models that discriminate higher absorption compounds from those with moderate-poorer absorption. The best LDA model has an accuracy of 90.58% and 84.21% for training and test set. The percentage of good correlation, in the virtual screening of 241 drugs with the reported values of the percentage of human intestinal absorption (HIA), was greater than 81%. In addition, multiple linear regression models were developed to predict Caco-2 permeability with determination coefficients of 0.71 and 0.72. Our method compares favorably with other approaches implemented in the Dragon software, as well as other methods from the international literature. These results suggest that the proposed method is a good tool for studying the oral absorption of drug candidates.

Discovery of anticonvulsant activity of abietic acid through application of linear discriminant analysis

Linear discriminant analysis was performed to derive discriminant functions based on 2D descriptors and capable of classifying anticonvulsant from non-anticonvulsant compounds. Through application in virtual screening of the discriminant function which performed best in the validation steps, abietic acid was identified as a potential new anticonvulsant agent. The anticonvulsant activity of abietic acid at 30 and 100mg/kg was confirmed in the Maximal Electroshock Test, both orally and intraperitoneally.

Applying pattern recognition methods plus quantum and physico-chemical molecular descriptors to analyze the anabolic activity of structurally diverse steroids

The great cost associated with the development of new anabolic-androgenic steroid (AASs) makes necessary the development of computational methods that shorten the drug discovery pipeline. Toward this end, quantum, and physicochemical molecular descriptors, plus linear discriminant analysis (LDA) were used to analyze the anabolic/androgenic activity of structurally diverse steroids and to discover novel AASs, as well as also to give a structural interpretation of their anabolic-androgenic ratio (AAR). The obtained models are able to correctly classify 91.67% (86.27%) of the AASs in the training (test) sets, respectively. The results of predictions on the 10% full-out cross-validation test also evidence the robustness of the obtained model. Moreover, these classification functions are applied to an "in house" library of chemicals, to find novel AASs. Two new AASs are synthesized and tested for in vivo activity. Although both AASs are less active than some commercially AASs, this result leaves a door open to a virtual variational study of the structure of the two compounds, to improve their biological activity. The LDA-assisted QSAR models presented here, could significantly reduce the number of synthesized and tested AASs, as well as could increase the chance of finding new chemical entities with higher AAR.

Predicting antitrichomonal activity: A computational screening using atom-based bilinear indices and experimental proofs

Existing Trichomonas vaginalis therapies are out of reach for most trichomoniasis people in developing countries and, where available, they are limited by their toxicity (mainly in pregnant women) and their cost. New antitrichomonal agents are needed to combat emerging metronidazole-resistant trichomoniasis and reduce the side effects associated with currently available drugs. Toward this end, atom-based bilinear indices, a new TOMOCOMD-CARDD molecular descriptor, and linear discriminant analysis (LDA) were used to discover novel, potent, and non-toxic lead trichomonacidal chemicals. Two discriminant functions were obtained with the use of non-stochastic and stochastic atom-type bilinear indices for heteroatoms and H-bonding of heteroatoms. These atomic-level molecular descriptors were calculated using a weighting scheme that includes four atomic labels, namely atomic masses, van der Waals volumes, atomic polarizabilities, and atomic electronegativities in Pauling scale. The obtained LDA-based QSAR models, using non-stochastic and stochastic indices, were able to classify correctly 94.51% (90.63%) and 93.41% (93.75%) of the chemicals in training (test) sets, respectively. They showed large Matthews' correlation coefficients (C); 0.89 (0.79) and 0.87 (0.85), for the training (test) sets, correspondingly. The result of predictions on the 15% full-out cross-validation test also evidenced the robustness and predictive power of the obtained models. In addition, canonical regression analyses corroborated the statistical quality of these models (R(can) of 0.749 and of 0.845, correspondingly); they were also used to compute biological activity canonical scores for each compound. On the other hand, a close inspection of the molecular descriptors included in both equations showed that several of these molecular fingerprints are strongly interrelated with each other. Therefore, these models were orthogonalized using the Randić orthogonalization procedure. These classification functions were then applied to find new lead antitrichomonal agents and six compounds were selected as possible active compounds by computational screening. The designed compounds were synthesized and tested for in vitro activity against T. vaginalis. Out of the six compounds that were designed, and synthesized, three molecules (chemicals VA5-5a, VA5-5c, and VA5-12b) showed high to moderate cytocidal activity at the concentration of 10 microg/ml, other two compounds (VA5-8pre and VA5-8) showed high cytocidal and cytostatic activity at the concentration of 100 microg/ml and 10 microg/ml, correspondingly, and the remaining chemical (compound VA5-5e) was inactive at these assayed concentrations. Nonetheless, these compounds possess structural features not seen in known trichomonacidal compounds and thus can serve as excellent leads for further optimization of antitrichomonal activity. The LDA-based QSAR models presented here can be considered as a computer-assisted system that could potentially significantly reduce the number of synthesized and tested compounds and increase the chance of finding new chemical entities with antitrichomonal activity.