[Show abstract][Hide abstract] ABSTRACT: The malaria parasite Plasmodium goes through two life stages in the human host, a non-symptomatic liver stage (LS) followed by a blood stage with all clinical manifestation of the disease. In this study, we investigated a series of 2-alkynoic fatty acids (2-AFAs) with chain lengths between 14 and 18 carbon atoms for dual in vitro activity against both life stages. 2-Octadecynoic acid (2-ODA) was identified as the best inhibitor of Plasmodium berghei parasites with ten times higher potency (IC50=0.34μg/ml) than the control drug. In target determination studies, the same compound inhibited three Plasmodium falciparum FAS-II (PfFAS-II) elongation enzymes PfFabI, PfFabZ, and PfFabG with the lowest IC50 values (0.28-0.80μg/ml, respectively). Molecular modeling studies provided insights into the molecular aspects underlying the inhibitory activity of this series of 2-AFAs and a likely explanation for the considerably different inhibition potentials. Blood stages of P. falciparum followed a similar trend where 2-ODA emerged as the most active compound, with 20 times less potency. The general toxicity and hepatotoxicity of 2-AFAs were evaluated by in vitro and in vivo methods in mammalian cell lines and zebrafish models, respectively. This study identifies 2-ODA as the most promising antiparasitic 2-AFA, particularly towards P. berghei parasites.
[Show abstract][Hide abstract] ABSTRACT: Hybrid bioisoster derivatives from N-acylhydrazones and furoxan groups were designed with the objective of obtaining at least a dual mechanism of action: cruzain inhibition and nitric oxide (NO) releasing activity. Fifteen designed compounds were synthesized varying the substitution in N-acylhydrazone and in furoxan group as well. They had its anti-Trypanosoma cruzi activity in amastigotes forms, NO releasing potential and inhibitory cruzain activity evaluated. The two most active compounds (6, 14) both in the parasite amastigotes and in the enzyme contain the nitro group in para position of the aromatic ring. The permeability screening in Caco-2 cell and cytotoxicity assay in human cells were performed for those most active compounds and both showed to be less cytotoxic than the reference drug, benznidazole. Compound 6 was the most promising, since besides activity it showed good permeability and selectivity index, higher than the reference drug. Thereby the compound 6 was considered as a possible candidate for additional studies.
European Journal of Medicinal Chemistry 06/2014; 82C:418-425. · 3.43 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: The development of cruzain inhibitors has been driven by the urgent need to develop novel and more effective drugs for the treatment of Chagasꞌ disease. Herein, we report the lead optimization of a class of noncovalent cruzain inhibitors, starting from an inhibitor previously co-crystallized with the enzyme (Ki = 0.8 µM). With the goal of achieving a better understanding of the structure-activity relationships (SARs), we have synthesized and evaluated a series of over 40 analogues, leading to the development of a very promising competitive inhibitor (8r, IC50 = 200 nM, Ki = 82 nM). Investigation of the in vitro trypanocidal activity and preliminary cytotoxicity revealed the potential of the most potent cruzain inhibitors in guiding further medicinal chemistry efforts to develop drug candidates for Chagasꞌ disease.
Journal of Medicinal Chemistry 02/2014; · 5.48 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Chemometric pattern recognition techniques were employed in order to obtain Structure-Activity Relationship (SAR) models relating the structures of a series of adenosine compounds to the affinity for glyceraldehyde 3-phosphate dehydrogenase of Leishmania mexicana (LmGAPDH). A training set of 49 compounds was used to build the models and the best ones were obtained with one geometrical and four electronic descriptors. Classification models were externally validated by predictions for a test set of 14 compounds not used in the model building process. Results of good quality were obtained, as verified by the correct classifications achieved. Moreover, the results are in good agreement with previous SAR studies on these molecules, to such an extent that we can suggest that these findings may help in further investigations on ligands of LmGAPDH capable of improving treatment of leishmaniasis.
International Journal of Molecular Sciences 02/2014; 15(2):3186-203. · 2.34 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Background: Chagas disease is a major cause of morbidity and death for millions of people in Latin America. The drugs currently available exhibit poor efficacy and severe side effects. Therefore, there is an urgent need for new, safe and effective drugs against Chagas disease. The vital dependence on glycolysis as energy source makes the glycolytic enzymes of Trypanosoma cruzi, the causative agent of Chagas disease, attractive targets for drug design. In this work, glyceraldehyde-3-phosphate dehydrogenase from T. cruzi (TcGAPDH) was employed as molecular target for the discovery of new inhibitors as hits. Results: Integrated protein-based pharmacophore and structure-based virtual screening approaches resulted in the identification of three hits from three chemical classes with moderate inhibitory activity against TcGAPDH. The inhibitors showed IC50 values in the high micromolar range. Conclusion: The new chemotypes are attractive molecules for future medicinal chemistry efforts aimed at developing new lead compounds for Chagas disease.
[Show abstract][Hide abstract] ABSTRACT: Background: Sleeping sickness is a major cause of death in Africa. Since no secure treatment is available, the development of novel therapeutic agents is urgent. In this context, the enzyme trypanothione reductase (TR) is a prominent molecular target that has been investigated in drug design for sleeping sickness. Results: In this study, comparative molecular field analysis models were generated for a series of Trypanosoma brucei TR inhibitors. Statistically significant results were obtained and the models were applied to predict the activity of external test sets, with good correlation between predicted and experimental results. We have also investigated the structural requirements for the selective inhibition of the parasite's enzyme over the human glutathione reductase. Conclusion: The quantitative structure-activity relationship models provided valuable information regarding the essential molecular requirements for the inhibitory activity upon the target protein, providing important insights into the design of more potent and selective TR inhibitors.
[Show abstract][Hide abstract] ABSTRACT: Medicinal chemistry is a multidisciplinary subject that integrates knowledge from a variety of fields of science, including, but not limited to, chemistry, biology, and physics. The area of drug design involves the cooperative work of scientists with a diverse range of backgrounds and technical skills, trying to tackle complex problems using an integration of approaches and methods. One important contribution to this field comes from physics through studies that attempt to identify and quantify the molecular interactions between small molecules (drugs) and biological targets (receptors), such as the forces that govern the interactions, the thermodynamics of the drug–receptor interactions, and so on. In this context, the interfaces of physics, medicinal chemistry, and drug design are of vital importance for the development of drugs that not only have the right chemistry but also the right intermolecular properties to interact at the macromolecular level, providing useful information about the principles and molecular mechanisms underlying the therapeutic action of drugs. This article highlights some of the most important connections between physics and medicinal chemistry in the design of new drugs.
Brazilian Journal of Physics 08/2013; 43(4). · 0.68 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Mycobacterium tuberculosis InhA (MtInhA) is an attractive enzyme to drug discovery efforts due to its validation as an effective biological target for tuberculosis therapy. In this work, two different virtual-ligand-screening approaches were applied in order to identify new InhA inhibitors' candidates from a library of ligands selected from the ZINC database. First, a 3-D pharmacophore model was built based on 36 available MtInhA crystal structures. By combining structure-based and ligand-based information, four pharmacophoric points were designed to select molecules able to satisfy the binding features of MtInhA substrate-binding cavity. The second approach consisted in using four well established docking programs, with different search algorithms, to compare the binding mode and score of the selected molecules from the aforementioned library. After detailed analyses of the results, six ligands were selected for in vitro analysis. Three of these molecules presented a satisfactory inhibitory activity with IC50 values ranging from 24 (± 2) μM to 83 (± 5) μM. The best compound presented an uncompetitive inhibition mode to NADH and 2-trans-dodecenoyl-CoA substrates, with Ki values of 24 (± 3) μM and 20 (± 2) μM, respectively. These molecules were not yet described as antituberculars or as InhA inhibitors, making its novelty interesting to start efforts on ligand optimization in order to identify new effective drugs against Tuberculosis having InhA as a target. More studies are underway to dissect the discovered uncompetitive inhibitor interactions with MtInhA.
Journal of Chemical Information and Modeling 07/2013; · 4.30 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Drug resistance is a common concern for the development of novel antiviral, antimicrobial and anticancer therapies. To overcome this problem, several strategies have been developed, many of which involving the theme of this review, the use of structure-based drug design (SBDD) approaches. These include the successful design of new compounds that target resistant mutant proteins, as well as the development of drugs that target multiple proteins involved in specific biochemical pathways. Finally, drug resistance can also be considered in the early stages of drug discovery, through the use of strategies to delay the development of resistance. The purpose of this brief review is to underline the usefulness of SBDD approaches based on case studies, highlighting present challenges and opportunities in drug design.
Current pharmaceutical design 05/2013; · 4.41 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Quantitative structure-activity relationship (QSAR) studies were performed in order to identify molecular features responsible for the antileishmanial activity of 61 adenosine analogues acting as inhibitors of the enzyme glyceraldehyde 3-phosphate dehydrogenase of Leishmania mexicana (LmGAPDH). Density functional theory (DFT) was employed to calculate quantum-chemical descriptors, while several structural descriptors were generated with Dragon 5.4. Variable selection was undertaken with the ordered predictor selection (OPS) algorithm, which provided a set with the most relevant descriptors to perform PLS, PCR and MLR regressions. Reliable and predictive models were obtained, as attested by their high correlation coefficients, as well as the agreement between predicted and experimental values for an external test set. Additional validation procedures were carried out, demonstrating that robust models were developed, providing helpful tools for the optimization of the antileishmanial activity of adenosine compounds.
[Show abstract][Hide abstract] ABSTRACT: YopH plays a relevant role in three pathogenic species of Yersinia. Due to its importance in the prevention of the inflammatory response of the host, this enzyme has become a valid target for the identification and development of new inhibitors. In this work, an in-house library of 283 synthetic compounds was assayed against recombinant YopH from Yersinia enterocolitica. From these, four chalcone derivatives and one sulfonamide were identified for the first time as competitive inhibitors of YopH with binding affinity in the low micromolar range. Molecular modeling investigations indicated that the new inhibitors showed similar binding modes, establishing polar and hydrophobic contacts with key residues of the YopH binding site.
European Journal of Medicinal Chemistry 04/2013; 64C:35-41. · 3.43 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Based on classical colchicine site ligands and a computational model of the colchicine binding site on beta tubulin, two classes of chalcone derivatives were designed, synthesized and evaluated for inhibition of tubulin assembly and toxicity in human cancer cell lines. Docking studies suggested that the chalcone scaffold could fit the colchicine site on tubulin in an orientation similar to that of the natural product. In particular, a 3,4,5-trimethoxyphenyl ring adjacent to the carbonyl group appeared to benefit the ligand-tubulin interaction, occupying the same subcavity as the corresponding moiety in colchicine. Consistent with modeling predictions, several 3,4,5-trimethoxychalcones showed improved cytotoxicity to murine acute lymphoblastic leukemia cells compared with a previously described parent compound, and inhibited tubulin assembly in vitro as potently as colchicine. The most potent chalcones inhibited the growth of human leukemia cell lines at nanomolar concentrations, caused microtubule destabilization and mitotic arrest in human cervical cancer cells, and inhibited human breast cancer cell migration in scratch wound and Boyden chamber assays.
European Journal of Medicinal Chemistry 03/2013; 63C:501-510. · 3.43 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Human African trypanosomiasis, also known as sleeping sickness, is a major cause of death in Africa, and for which there are no safe and effective treatments available. The enzyme aldolase from Trypanosoma brucei is an attractive, validated target for drug development. A series of alkyl-glycolamido and alkyl-monoglycolate derivatives was studied employing a combination of drug design approaches. Three-dimensional quantitative structure-activity relationships (3D QSAR) models were generated using the comparative molecular field analysis (CoMFA). Significant results were obtained for the best QSAR model (r2= 0.95, non-cross-validated correlation coefficient, and q2= 0.80, cross-validated correlation coefficient), indicating ts predictive ability for untested compounds. The model was then used to predict values of the dependent variables (pKi) of an external test set, and the predicted values were in good agreement with the experimental results. The integration of 3D QSAR, molecular docking and molecular dynamics simulations provided further insight into the structural basis for selective inhibition of the target enzyme.
Journal of the Brazilian Chemical Society 02/2013; 24(2):201-211. · 1.25 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Complexes [Ga(2Ac4pFPh)(2)]NO(3) (1), [Ga(2Ac4pClPh)(2)]NO(3) (2), [Ga(2Ac4pIPh)(2)]NO(3) (3), [Ga(2Ac4pNO(2)Ph)(2)]NO(3)·3H(2)O (4) and [Ga(2Ac4pT)(2)]NO(3) (5) were obtained with 2-acetylpyridine N(4)-para-fluorophenyl-(H2Ac4pFPh), 2-acetylpyridine N(4)-para-chlorophenyl-(H2Ac4pClPh), 2-acetylpyridine N(4)-para-iodophenyl-(H2Ac4pIPh), 2-acetylpyridine N(4)-para-nitrophenyl-(H2Ac4pNO(2)Ph) and 2-acetylpyridine N(4)-para-tolyl-(H2Ac4pT) thiosemicarbazone. 1-5 presented antimicrobial and cytotoxic properties. Coordination to gallium(III) proved to be an effective strategy for activity improvement against Pseudomonas aeruginosa and Candida albicans. The complexes were highly cytotoxic against malignant glioblastoma and breast cancer cells at nanomolar concentrations. The compounds induced morphological changes characteristic of apoptotic death in tumor cells and showed no toxicity against erythrocytes. 2 partially inhibited tubulin assembly at high concentrations and induced cellular microtubule disorganization, but this does not appear to be the main mechanism of cytotoxic activity.
[Show abstract][Hide abstract] ABSTRACT: We describe herein the design and development of an innovative tool called the NuBBE database (NuBBE(DB)), a new Web-based database, which incorporates several classes of secondary metabolites and derivatives from the biodiversity of Brazil. This natural product database incorporates botanical, chemical, pharmacological, and toxicological compound information. The NuBBE(DB) provides specialized information to the worldwide scientific community and can serve as a useful tool for studies on the multidisciplinary interfaces related to chemistry and biology, including virtual screening, dereplication, metabolomics, and medicinal chemistry. The NuBBE(DB) site is at http://nubbe.iq.unesp.br/nubbeDB.html .
Journal of Natural Products 01/2013; · 3.95 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: In an article recently published in Química Nova, entitled "Chemistry Without Borders" ("Química Sem Fronteiras") [Pinto, A. C.; Zucco, C.; Galembeck, F.; Andrade, J. B.; Vieira, P. C. Quim. Nova 2012, 35, 2092], the authors highlighted the important aspects of science and technology with special emphasis on the field of Chemistry and its contributions toward a more prosperous Brazil of future. As a second step in that direction, this article extends the discussion of a key issue for the country in the framework of the chemistry community through the so called position papers in strategic areas. This document is a part of the contribution of the Brazilian Chemical Society to the World Science Forum to be held in Rio de Janeiro in November 2013. In this context, the present paper provides a brief discussion on neglected tropical diseases (NTDs) with emphasis on the current challenges and opportunities towards the development and evolution of the field. NTDs leads to illness, long-term disability or death, and has severe social, economic and psychological consequences for millions of men, women, and children worldwide. In most cases, the available treatments are inadequate and extremely limited in terms of efficacy and safety, leading to an urgent demand for new drugs. In addition to the traditional challenges involved in any drug discovery process, it is widely recognized that there is an innovation gap and a lack of investment for research and development (R&D) in the area of NTDs. In the last few decades, methods toward combating, eradication, prevention, and treatment of NTDs have been repeatedly emphasized in the major international agendas. Developments in these strategies and alliances have continued to have an essential impact, particularly in the area of drug discovery, both in Brazil and globally and should be encouraged and supported. Several examples of international activities dedicated to the reduction of the devastating global impact of NTDs can be provided. Despite the beneficial developments in the past 30 years, NTDs continue to devastate poor communities in remote and vulnerable areas, in large part, due to market failures and public policies. Recent studies have shown that among 756 new drugs approved between 2000 and 2011, only four new chemical entities (NCEs) were identified for the treatment of malaria, while none were developed against NTDs or tuberculosis. Furthermore, only 1.4% of approximately 150,000 clinical trials were registered for neglected diseases, with a smaller number of trials for NCEs. Establishment and strengthening of global strategies involving the triad "governmentacademiaindustry" is fundamental to the success in R&D of new drugs for NTDs. National and international publicprivate initiatives that aim to create, encourage, and invest in R&D projects have been implemented and therefore are of utmost importance to successfully integrate Brazil into this new paradigm. It is essential to lay the foundation for mechanisms that will intensify investments in infrastructure, training, and qualification of personnel with an ultimate strategic vision that foresees continuity. Our research group has made significant contributions to the development of this field with the goal of forging new frontiers while tackling both current and future challenges that include indispensable elements such as innovation and integration.
Química Nova 12/2012; 36(10):1552-1556. · 0.66 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Blood-brain barrier (BBB) permeation is an essential property for drugs that act in the central nervous system (CNS) for the treatment of human diseases, such as epilepsy, depression, Alzheimer's disease, Parkinson disease, schizophrenia, among others. In the present work, quantitative structure-property relationship (QSPR) studies were conducted for the development and validation of in silico models for the prediction of BBB permeation. The data set used has substantial chemical diversity and a relatively wide distribution of property values. The generated QSPR models showed good statistical parameters and were successfully employed for the prediction of a test set containing 48 compounds. The predictive models presented herein are useful in the identification, selection and design of new drug candidates having improved pharmacokinetic properties.
Journal of the Brazilian Chemical Society 12/2012; 23(12):2191-2196. · 1.25 Impact Factor