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Navarro M, Justo RMS, Delgado GYS, Visbal G. Metallodrugs for the Treatment of Trypanosomatid Diseases: Recent Advances and New Insights. Curr Pharm Des 2021; 27:1763-1789. [PMID: 33185155 DOI: 10.2174/1381612826666201113104633] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 08/23/2020] [Accepted: 08/31/2020] [Indexed: 11/22/2022]
Abstract
Trypanosomatid parasites are responsible for many Neglected Tropical Diseases (NTDs). NTDs are a group of illnesses that prevail in low-income populations, such as in tropical and subtropical areas of Africa, Asia, and the Americas. The three major human diseases caused by trypanosomatids are African trypanosomiasis, Chagas disease and leishmaniasis. There are known drugs for the treatment of these diseases that are used extensively and are affordable; however, the use of these medicines is limited by several drawbacks such as the development of chemo-resistance, side effects such as cardiotoxicity, low selectivity, and others. Therefore, there is a need to develop new chemotherapeutic against these tropical parasitic diseases. Metal-based drugs against NTDs have been discussed over the years as alternative ways to overcome the difficulties presented by approved antiparasitic agents. The study of late transition metal-based drugs as chemotherapeutics is an exciting research field in chemistry, biology, and medicine due to the ability to develop multitarget antiparasitic agents. The evaluation of the late transition metal complexes for the treatment of trypanosomatid diseases is provided here, as well as some insights about their mechanism of action.
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Affiliation(s)
- Maribel Navarro
- Departamento de Quimica, Instituto de Ciencias Exatas, Universidade Federal de Juiz de Fora, Juiz de Fora, Brazil
| | - Rodrigo M S Justo
- Departamento de Química, Instituto de Ciências Exatas, Universidade Federal de Juiz de Fora, Juiz de Fora, Brazil
| | - Giset Y Sánchez Delgado
- Departamento de Química, Instituto de Ciências Exatas, Universidade Federal de Juiz de Fora, Juiz de Fora, Brazil
| | - Gonzalo Visbal
- Instituto Nacional de Metrologia, Qualidade e Tecnologia (INMETRO), Brazil
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2
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Alves KMA, Cardoso FJB, Honorio KM, de Molfetta FA. Design of Inhibitors for Glyceraldehyde-3-phosphate Dehydrogenase (GAPDH) Enzyme of <i>Leishmania mexicana</i>. Med Chem 2021; 16:784-795. [PMID: 31309897 DOI: 10.2174/1573406415666190712111139] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 06/24/2019] [Accepted: 06/24/2019] [Indexed: 01/04/2023]
Abstract
BACKGROUND Leishmaniosis is a neglected tropical disease and glyceraldehyde 3- phosphate dehydrogenase (GAPDH) is a key enzyme in the design of new drugs to fight this disease. OBJECTIVE The present study aimed to evaluate potential inhibitors of GAPDH enzyme found in Leishmania mexicana (L. mexicana). METHODS A search for novel antileishmanial molecules was carried out based on similarities from the pharmacophoric point of view related to the binding site of the crystallographic enzyme using the ZINCPharmer server. The molecules selected in this screening were subjected to molecular docking and molecular dynamics simulations. RESULTS Consensual analysis of the docking energy values was performed, resulting in the selection of ten compounds. These ligand-receptor complexes were visually inspected in order to analyze the main interactions and subjected to toxicophoric evaluation, culminating in the selection of three compounds, which were subsequently submitted to molecular dynamics simulations. The docking results showed that the selected compounds interacted with GAPDH from L. mexicana, especially by hydrogen bonds with Cys166, Arg249, His194, Thr167, and Thr226. From the results obtained from molecular dynamics, it was observed that one of the loop regions, corresponding to the residues 195-222, can be related to the fitting of the substrate at the binding site, assisting in the positioning and the molecular recognition via residues responsible for the catalytic activity. CONCLUSION The use of molecular modeling techniques enabled the identification of promising compounds as inhibitors of the GAPDH enzyme from L. mexicana, and the results obtained here can serve as a starting point to design new and more effective compounds than those currently available.
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Affiliation(s)
- Krisnna M A Alves
- Laboratorio de Modelagem Molecular, Instituto de Ciencias Exatas e Naturais, Universidade Federal do Para, CP 11101, 60075-110, Belem, PA, Brazil
| | - Fábio José Bonfim Cardoso
- Laboratorio de Modelagem Molecular, Instituto de Ciencias Exatas e Naturais, Universidade Federal do Para, CP 11101, 60075-110, Belem, PA, Brazil
| | - Kathia M Honorio
- Escola de Artes, Ciencias e Humanidades, Universidade de Sao Paulo (USP), 03828-000, Sao Paulo, SP, Brazil.,Universidade Federal do ABC (UFABC), Santo André, SP, Brazil
| | - Fábio A de Molfetta
- Laboratorio de Modelagem Molecular, Instituto de Ciencias Exatas e Naturais, Universidade Federal do Para, CP 11101, 60075-110, Belem, PA, Brazil
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Aguiar AC, de Sousa LR, Garcia CR, Oliva G, Guido RV. New Molecular Targets and Strategies for Antimalarial Discovery. Curr Med Chem 2019; 26:4380-4402. [DOI: 10.2174/0929867324666170830103003] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 07/24/2017] [Accepted: 07/24/2017] [Indexed: 02/07/2023]
Abstract
Malaria remains a major health problem, especially because of the emergence
of resistant P. falciparum strains to artemisinin derivatives. In this context, safe and affordable
antimalarial drugs are desperately needed. New proteins have been investigated
as molecular targets for research and development of innovative compounds with welldefined
mechanism of action. In this review, we highlight genetically and clinically validated
plasmodial proteins as drug targets for the next generation of therapeutics. The enzymes
described herein are involved in hemoglobin hydrolysis, the invasion process,
elongation factors for protein synthesis, pyrimidine biosynthesis, post-translational modifications
such as prenylation, phosphorylation and histone acetylation, generation of ATP
in mitochondrial metabolism and aminoacylation of RNAs. Significant advances on proteomics,
genetics, structural biology, computational and biophysical methods provided
invaluable molecular and structural information about these drug targets. Based on this,
several strategies and models have been applied to identify and improve lead compounds.
This review presents the recent progresses in the discovery of antimalarial drug candidates,
highlighting the approaches, challenges, and perspectives to deliver affordable, safe
and low single-dose medicines to treat malaria.
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Affiliation(s)
- Anna Caroline Aguiar
- Sao Carlos Institute of Physics, University of Sao Paulo, PO Box 369, 13560-970, Sao Carlos, SP, Brazil
| | - Lorena R.F. de Sousa
- Sao Carlos Institute of Physics, University of Sao Paulo, PO Box 369, 13560-970, Sao Carlos, SP, Brazil
| | - Celia R.S. Garcia
- Physiology Department, Bioscience Institute, University of Sao Paulo, Sao Paulo, SP, Brazil
| | - Glaucius Oliva
- Sao Carlos Institute of Physics, University of Sao Paulo, PO Box 369, 13560-970, Sao Carlos, SP, Brazil
| | - Rafael V.C. Guido
- Sao Carlos Institute of Physics, University of Sao Paulo, PO Box 369, 13560-970, Sao Carlos, SP, Brazil
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Bruno S, Uliassi E, Zaffagnini M, Prati F, Bergamini C, Amorati R, Paredi G, Margiotta M, Conti P, Costi MP, Kaiser M, Cavalli A, Fato R, Bolognesi ML. Molecular basis for covalent inhibition of glyceraldehyde-3-phosphate dehydrogenase by a 2-phenoxy-1,4-naphthoquinone small molecule. Chem Biol Drug Des 2017; 90:225-235. [DOI: 10.1111/cbdd.12941] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2016] [Revised: 01/05/2017] [Accepted: 01/05/2017] [Indexed: 12/16/2022]
Affiliation(s)
- Stefano Bruno
- Department of Pharmacy; University of Parma; Parma Italy
| | - Elisa Uliassi
- Department of Pharmacy and Biotechnology; Alma Mater Studiorum - University of Bologna; Bologna Italy
| | - Mirko Zaffagnini
- Department of Pharmacy and Biotechnology; Alma Mater Studiorum - University of Bologna; Bologna Italy
| | - Federica Prati
- Department of Pharmacy and Biotechnology; Alma Mater Studiorum - University of Bologna; Bologna Italy
| | - Christian Bergamini
- Department of Pharmacy and Biotechnology; Alma Mater Studiorum - University of Bologna; Bologna Italy
| | - Riccardo Amorati
- Department of Chemistry “G. Ciamician”; Alma Mater Studiorum - University of Bologna; Bologna Italy
| | | | | | - Paola Conti
- Department of Pharmaceutical Sciences; University of Milan; Milan Italy
| | - Maria Paola Costi
- Department of Life Sciences; University of Modena and Reggio Emilia; Modena Italy
| | - Marcel Kaiser
- Swiss Tropical & Public Health Institute; Basel Switzerland
- University of Basel; Basel Switzerland
| | - Andrea Cavalli
- Department of Pharmacy and Biotechnology; Alma Mater Studiorum - University of Bologna; Bologna Italy
- CompuNet; Istituto Italiano di Tecnologia; Genova Italy
| | - Romana Fato
- Department of Pharmacy and Biotechnology; Alma Mater Studiorum - University of Bologna; Bologna Italy
| | - Maria Laura Bolognesi
- Department of Pharmacy and Biotechnology; Alma Mater Studiorum - University of Bologna; Bologna Italy
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5
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de Souza AS, Ferreira LG, Andricopulo AD. 2D and 3D QSAR Studies on a Series of Antichagasic Fenarimol Derivatives. PHARMACEUTICAL SCIENCES 2017. [DOI: 10.4018/978-1-5225-1762-7.ch037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Chagas disease is one of the most important neglected tropical diseases. Endemic in Latin America, the disease is a global public health problem, affecting several countries in North America, Europe, Asia and Oceania. The disease affects around 8-10 million people worldwide and the limited treatments available present low efficacy and severe side effects, highlighting the urgent need for new therapeutic options. In this work, the authors developed QSAR models for a series of fenarimol derivatives exhibiting anti-T. cruzi activity. The models were constructed using the Hologram QSAR (HQSAR), Comparative Molecular Field Analysis (CoMFA) and Comparative Molecular Similarity Indices Analysis (CoMSIA) methods. The QSAR models presented substantial predictive ability for a series of test set compounds (HQSAR, r2pred = 0.66; CoMFA, r2pred = 0.82; and CoMSIA, r2pred = 0.76), and were valuable to identify key structural features related to the observed trypanocidal activity. The results reported herein are useful for the design of novel derivatives having improved antichagasic properties.
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Affiliation(s)
- Anacleto S. de Souza
- Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, Brazil
| | - Leonardo G. Ferreira
- Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, Brazil
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A pharmacophore-based virtual screening approach for the discovery of Trypanosoma cruzi GAPDH inhibitors. Future Med Chem 2014; 5:2019-35. [PMID: 24215344 DOI: 10.4155/fmc.13.166] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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.
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Kumar M, Makhal B, Gupta VK, Sharma A. In silico investigation of medicinal spectrum of imidazo-azines from the perspective of multitarget screening against malaria, tuberculosis and Chagas disease. J Mol Graph Model 2014; 50:1-9. [DOI: 10.1016/j.jmgm.2014.02.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2013] [Revised: 02/14/2014] [Accepted: 02/21/2014] [Indexed: 11/29/2022]
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8
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Lozano NBH, Oliveira RF, Weber KC, Honorio KM, Guido RVC, Andricopulo AD, de Sousa AG, da Silva ABF. Pattern recognition techniques applied to the study of leishmanial glyceraldehyde-3-phosphate dehydrogenase inhibition. Int J Mol Sci 2014; 15:3186-203. [PMID: 24566143 PMCID: PMC3958905 DOI: 10.3390/ijms15023186] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Revised: 01/21/2014] [Accepted: 01/24/2014] [Indexed: 11/16/2022] Open
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.
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Affiliation(s)
- Norka B H Lozano
- Instituto de Química de São Carlos, USP, São Carlos (SP), 13566-590, Brazil.
| | - Rafael F Oliveira
- Universidade Federal da Paraíba, João Pessoa (PB), 58051-900, Brazil.
| | - Karen C Weber
- Universidade Federal da Paraíba, João Pessoa (PB), 58051-900, Brazil.
| | - Kathia M Honorio
- Escola de Artes Ciências e Humanidades, USP, São Paulo (SP), 03828-000, Brazil.
| | - Rafael V C Guido
- Instituto de Física de São Carlos, USP, São Carlos (SP), 13566-590, Brazil.
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9
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Interactions of antiparasitic alkaloids with Leishmania protein targets: a molecular docking analysis. Future Med Chem 2013; 5:1777-99. [DOI: 10.4155/fmc.13.114] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Background: Leishmaniasis is a collection of chronic diseases caused by protozoa of the genus Leishmania. Current antileishmanial chemotherapeutics have demonstrated adverse side effects and therefore R&D into new safer alternative treatments are needed. Methods: A molecular docking analysis has been carried out to assess possible Leishmania biochemical targets of antiparasitic alkaloids. A total of 209 antiparasitic alkaloids were docked with 24 Leishmania protein targets. Results: The strongest docking alkaloid ligands were flinderoles A and B and juliflorine with Leishmania major methionyl-tRNA synthetase; juliflorine, juliprosine, prosopilosidine and prosopilosine with Leishmania mexicana glycerol-3-phosphate dehydrogenase; and ancistrogriffithine A with L. major N-myristoyl transferase. Conclusion: This molecular docking study has provided evidence for what classes and structural types of alkaloids may be targeting specific Leishmania protein targets.
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10
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In-silico Leishmania target selectivity of antiparasitic terpenoids. Molecules 2013; 18:7761-847. [PMID: 23823876 PMCID: PMC6270436 DOI: 10.3390/molecules18077761] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Revised: 06/23/2013] [Accepted: 06/26/2013] [Indexed: 01/21/2023] Open
Abstract
Neglected Tropical Diseases (NTDs), like leishmaniasis, are major causes of mortality in resource-limited countries. The mortality associated with these diseases is largely due to fragile healthcare systems, lack of access to medicines, and resistance by the parasites to the few available drugs. Many antiparasitic plant-derived isoprenoids have been reported, and many of them have good in vitro activity against various forms of Leishmania spp. In this work, potential Leishmania biochemical targets of antiparasitic isoprenoids were studied in silico. Antiparasitic monoterpenoids selectively docked to L. infantum nicotinamidase, L. major uridine diphosphate-glucose pyrophosphorylase and methionyl t-RNA synthetase. The two protein targets selectively targeted by germacranolide sesquiterpenoids were L. major methionyl t-RNA synthetase and dihydroorotate dehydrogenase. Diterpenoids generally favored docking to L. mexicana glycerol-3-phosphate dehydrogenase. Limonoids also showed some selectivity for L. mexicana glycerol-3-phosphate dehydrogenase and L. major dihydroorotate dehydrogenase while withanolides docked more selectively with L. major uridine diphosphate-glucose pyrophosphorylase. The selectivity of the different classes of antiparasitic compounds for the protein targets considered in this work can be explored in fragment- and/or structure-based drug design towards the development of leads for new antileishmanial drugs.
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11
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Lozano NBH, Oliveira RF, Weber KC, Honorio KM, Guido RV, Andricopulo AD, Da Silva ABF. Identification of electronic and structural descriptors of adenosine analogues related to inhibition of leishmanial glyceraldehyde-3-phosphate dehydrogenase. Molecules 2013; 18:5032-50. [PMID: 23629757 PMCID: PMC6269754 DOI: 10.3390/molecules18055032] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2012] [Revised: 04/27/2013] [Accepted: 04/28/2013] [Indexed: 11/24/2022] Open
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.
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Affiliation(s)
- Norka B. H. Lozano
- Instituto de Química de São Carlos, Universidade de São Paulo, São Carlos, SP 13566-590, Brazil; E-Mail:
| | - Rafael F. Oliveira
- Departamento de Química, Universidade Federal da Paraiba, João Pessoa, PB 13083-970, Brazil; E-Mails: (R.F.O.); (K.W.C.)
| | - Karen C. Weber
- Departamento de Química, Universidade Federal da Paraiba, João Pessoa, PB 13083-970, Brazil; E-Mails: (R.F.O.); (K.W.C.)
| | - Kathia M. Honorio
- Centro de Ciência Naturais e Humanas, Universidade Federal do ABC, Santo Andre, SP 09210-170, Brazil; E-Mail:
- Escola de Artes, Ciências e Humanidades, Universidade de São Paulo, São Paulo, SP 03828-000, Brazil; E-Mail:
| | - Rafael V. Guido
- Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, SP 13560-590, Brazil; E-Mails: (R.V.G.); (A.D.A.)
| | - Adriano D. Andricopulo
- Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, SP 13560-590, Brazil; E-Mails: (R.V.G.); (A.D.A.)
| | - Albérico B. F. Da Silva
- Instituto de Química de São Carlos, Universidade de São Paulo, São Carlos, SP 13566-590, Brazil; E-Mail:
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Abstract
Drug discovery has moved toward more rational strategies based on our increasing understanding of the fundamental principles of protein–ligand interactions. Structure- (SBDD) and ligand-based drug design (LBDD) approaches bring together the most powerful concepts in modern chemistry and biology, linking medicinal chemistry with structural biology. The definition and assessment of both chemical and biological space have revitalized the importance of exploring the intrinsic complementary nature of experimental and computational methods in drug design. Major challenges in this field include the identification of promising hits and the development of high-quality leads for further development into clinical candidates. It becomes particularly important in the case of neglected tropical diseases (NTDs) that affect disproportionately poor people living in rural and remote regions worldwide, and for which there is an insufficient number of new chemical entities being evaluated owing to the lack of innovation and R&D investment by the pharmaceutical industry. This perspective paper outlines the utility and applications of SBDD and LBDD approaches for the identification and design of new small-molecule agents for NTDs.
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Ameta KL, Rathore NS, Kumar B, Malaga M ES, P MV, Gilman RH, Verma BL. Synthesis and Trypanocidal Evaluation of Some Novel 2-(Substituted Benzylidene)-5, 7-Dibromo-6-Hydroxy-1-Benzofuran-3(2<i>H</i>)-Ones. ACTA ACUST UNITED AC 2012. [DOI: 10.4236/ijoc.2012.223040] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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14
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Drug discovery and the use of computational approaches for infectious diseases. Future Med Chem 2011; 3:1011-25. [DOI: 10.4155/fmc.11.60] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
For centuries infectious diseases were the scourge of humanity, overcome only by the discovery of vaccination and penicillin. With an armamentarium of effective antibiotics, vaccines and drugs at hand, infectious diseases for many years were considered to be negligible. With the onset of the AIDS pandemic, the return of tuberculosis and influenza (e.g., swine influenza) this notion has changed in recent years. Drug discovery for infectious diseases, therefore, is again gaining increasing interest. This article discusses the drug-discovery process in this area and introduces major computational approaches used to identify suitable drug targets and to discover and optimize chemical lead compounds towards drug candidates using examples from antiparasitic drug discovery.
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Clark RD, Norinder U. Two personal perspectives on a key issue in contemporary 3D QSAR. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2011. [DOI: 10.1002/wcms.69] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | - Ulf Norinder
- AstraZeneca Research and Development, Södertälje, Sweden
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16
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Ferreira RS, Guido RVC, Andricopulo AD, Oliva G. In silicoscreening strategies for novel inhibitors of parasitic diseases. Expert Opin Drug Discov 2011; 6:481-9. [DOI: 10.1517/17460441.2011.563297] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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17
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Postigo MP, Guido RVC, Oliva G, Castilho MS, da R Pitta I, de Albuquerque JFC, Andricopulo AD. Discovery of new inhibitors of Schistosoma mansoni PNP by pharmacophore-based virtual screening. J Chem Inf Model 2011; 50:1693-705. [PMID: 20695479 DOI: 10.1021/ci100128k] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Schistosomiasis is considered the second most important tropical parasitic disease, with severe socioeconomic consequences for millions of people worldwide. Schistosoma mansoni , one of the causative agents of human schistosomiasis, is unable to synthesize purine nucleotides de novo, which makes the enzymes of the purine salvage pathway important targets for antischistosomal drug development. In the present work, we describe the development of a pharmacophore model for ligands of S. mansoni purine nucleoside phosphorylase (SmPNP) as well as a pharmacophore-based virtual screening approach, which resulted in the identification of three thioxothiazolidinones (1-3) with substantial in vitro inhibitory activity against SmPNP. Synthesis, biochemical evaluation, and structure-activity relationship investigations led to the successful development of a small set of thioxothiazolidinone derivatives harboring a novel chemical scaffold as new competitive inhibitors of SmPNP at the low-micromolar range. Seven compounds were identified with IC(50) values below 100 μM. The most potent inhibitors 7, 10, and 17 with IC(50) of 2, 18, and 38 μM, respectively, could represent new potential lead compounds for further development of the therapy of schistosomiasis.
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Affiliation(s)
- Matheus P Postigo
- Laboratório de Química Medicinal e Computacional, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos-SP, Brazil
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Machado FS, Tanowitz HB, Teixeira MM. New drugs for neglected infectious diseases: Chagas' disease. Br J Pharmacol 2010; 160:258-9. [PMID: 20423339 DOI: 10.1111/j.1476-5381.2010.00662.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Chagas' disease (CD) is caused by the protozoan Trypanosoma cruzi (Tc) and remains an important cause of morbidity and mortality. Most researchers in the field now agree that chronic low grade parasite persistence in tissue drives tissue damage and the autoimmune component of CD. Current therapy relies on two compounds: benznidazole and nifurtimox. Despite their long history in the treatment of CD, both compounds induce significant side-effects. In the current issue of the BJP, two contributions demonstrate that NO-donors are active, especially in combination with benznidazole, against Tc in vitro and in experimental models in vivo. The basic concept used by the authors to develop novel anti-Tc compounds relied on the demonstrated ability of nitric oxide to kill the parasite. There are several issues still to be resolved but the reported studies are a clear advance to the field and should be considered for further pre-clinical development.
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Affiliation(s)
- Fabiana S Machado
- Department of Biochemistry and Immunology, Federal University of Minas Gerais, Belo Horizonte, Brazil
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19
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Structural basis for selective inhibition of purine nucleoside phosphorylase from Schistosoma mansoni: Kinetic and structural studies. Bioorg Med Chem 2010; 18:1421-7. [DOI: 10.1016/j.bmc.2010.01.022] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2009] [Revised: 01/07/2010] [Accepted: 01/09/2010] [Indexed: 11/18/2022]
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Novel ruthenium complexes as potential drugs for Chagas's disease: enzyme inhibition and in vitro/in vivo trypanocidal activity. Br J Pharmacol 2010; 160:260-9. [PMID: 20105182 DOI: 10.1111/j.1476-5381.2009.00524.x] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND AND PURPOSE The discovery of the pharmacological functions of nitric oxide has led to the development of NO donor compounds as therapeutic agents. A new generation of ruthenium NO donors, cis-[Ru(NO)(bpy)(2)L]X(n), has been developed, and our aim was to show that these complexes are able to lyse Trypanosoma cruzi in vitro and in vivo. EXPERIMENTAL APPROACH NO donors were incubated with T. cruzi and their anti-T. cruzi activities evaluated as the percentage of lysed parasites compared to the negative control. In vivo, trypanocidal activity was evaluated by observing the levels of parasitaemia, survival rate and elimination of amastigotes in mouse myocardial tissue. The inhibition of GAPDH was monitored by the biochemical reduction of NAD(+) to NADH. KEY RESULTS The NO donors cis-[Ru(NO)(bpy)(2)L]X(n) presented inhibitory effects on T. cruzi GAPDH (IC(50) ranging from 89 to 153 microM). The crystal structure of the enzyme shows that the inhibitory mechanism is compatible with S-nitrosylation of the active cysteine (cys166) site. Compounds cis-[Ru(NO)(bpy)(2)imN](PF(6))(3) and cis-[Ru(NO)(bpy)(2)SO(3)]PF(6), at a dose of 385 nmol.kg(-1), yielded survival rates of 80 and 60%, respectively, in infected mice, and eradicated any amastigotes from their myocardial tissue. CONCLUSIONS AND IMPLICATIONS The ruthenium compounds exhibited potent in vitro and in vivo trypanocidal activities at doses up to 1000-fold lower than the clinical dose for benznidazole. Furthermore, one mechanism of action of these compounds is via the S-nitrosylation of Cys166 of T. cruzi GAPDH. Thus, these compounds show huge potential as candidates for the development of new drugs for the treatment of Chagas's disease.
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Pharmacophore-based 3D QSAR studies on a series of high affinity 5-HT1A receptor ligands. Eur J Med Chem 2010; 45:1508-14. [PMID: 20133028 DOI: 10.1016/j.ejmech.2009.12.059] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2009] [Accepted: 12/18/2009] [Indexed: 11/21/2022]
Abstract
5-HT(1A) receptor antagonists have been employed to treat depression, but the lack of structural information on this receptor hampers the design of specific and selective ligands. In this study, we have performed CoMFA studies on a training set of arylpiperazines (high affinity 5-HT(1A) receptor ligands) and to produce an effective alignment of the data set, a pharmacophore model was produced using Galahad. A statistically significant model was obtained, indicating a good internal consistency and predictive ability for untested compounds. The information gathered from our receptor-independent pharmacophore hypothesis is in good agreement with results from independent studies using different approaches. Therefore, this work provides important insights on the chemical and structural basis involved in the molecular recognition of these compounds.
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Valadares NF, Salum LB, Polikarpov I, Andricopulo AD, Garratt RC. Role of Halogen Bonds in Thyroid Hormone Receptor Selectivity: Pharmacophore-Based 3D-QSSR Studies. J Chem Inf Model 2009; 49:2606-16. [DOI: 10.1021/ci900316e] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Napoleão F. Valadares
- Centro de Biotecnologia Molecular Estrutural, Departamento de Física e Informática, Instituto de Física de São Carlos, Universidade de São Paulo, Av. Trabalhador São-Carlense 400, 13560-970 São Carlos-SP, Brazil
| | - Lívia B. Salum
- Centro de Biotecnologia Molecular Estrutural, Departamento de Física e Informática, Instituto de Física de São Carlos, Universidade de São Paulo, Av. Trabalhador São-Carlense 400, 13560-970 São Carlos-SP, Brazil
| | - Igor Polikarpov
- Centro de Biotecnologia Molecular Estrutural, Departamento de Física e Informática, Instituto de Física de São Carlos, Universidade de São Paulo, Av. Trabalhador São-Carlense 400, 13560-970 São Carlos-SP, Brazil
| | - Adriano D. Andricopulo
- Centro de Biotecnologia Molecular Estrutural, Departamento de Física e Informática, Instituto de Física de São Carlos, Universidade de São Paulo, Av. Trabalhador São-Carlense 400, 13560-970 São Carlos-SP, Brazil
| | - Richard C. Garratt
- Centro de Biotecnologia Molecular Estrutural, Departamento de Física e Informática, Instituto de Física de São Carlos, Universidade de São Paulo, Av. Trabalhador São-Carlense 400, 13560-970 São Carlos-SP, Brazil
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Cáceres AJ, Michels PAM, Hannaert V. Genetic validation of aldolase and glyceraldehyde-3-phosphate dehydrogenase as drug targets in Trypanosoma brucei. Mol Biochem Parasitol 2009; 169:50-4. [PMID: 19748525 DOI: 10.1016/j.molbiopara.2009.09.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2009] [Revised: 09/01/2009] [Accepted: 09/02/2009] [Indexed: 10/20/2022]
Abstract
Aldolase (ALD) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) of Trypanosoma brucei are considered to be promising targets for chemotherapeutic treatment of African sleeping sickness, because glycolysis is the single source of ATP for the parasite when living in the human bloodstream. Moreover, these enzymes appeared to possess distinct kinetic and structural properties that have already been exploited for the discovery of effective and selective inhibitors with trypanocidal activity. Here we present an experimental, quantitative assessment of the importance of these enzymes for the glycolytic pathway. This was achieved by decreasing the concentrations of ALD and GAPDH by RNA interference. The effects of these knockdowns on parasite growth, levels of various enzymes and transcripts, enzyme activities and glucose consumption were studied. A partial depletion of ALD and GAPDH was already sufficient to rapidly kill the trypanosomes. An effect was also observed on the activity of some other glycolytic enzymes.
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Affiliation(s)
- Ana Judith Cáceres
- Centro de Ingeniería Genética, Universidad de Los Andes, Mérida, Venezuela
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Salum LB, Polikarpov I, Andricopulo AD. Structure-based approach for the study of estrogen receptor binding affinity and subtype selectivity. J Chem Inf Model 2009; 48:2243-53. [PMID: 18937440 DOI: 10.1021/ci8002182] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Estrogens exert important physiological effects through the modulation of two human estrogen receptor (hER) subtypes, alpha (hERalpha) and beta (hERbeta). Because the levels and relative proportion of hERalpha and hERbeta differ significantly in different target cells, selective hER ligands could target specific tissues or pathways regulated by one receptor subtype without affecting the other. To understand the structural and chemical basis by which small molecule modulators are able to discriminate between the two subtypes, we have applied three-dimensional target-based approaches employing a series of potent hER-ligands. Comparative molecular field analysis (CoMFA) studies were applied to a data set of 81 hER modulators, for which binding affinity values were collected for both hERalpha and hERbeta. Significant statistical coefficients were obtained (hERalpha, q(2) = 0.76; hERbeta, q(2) = 0.70), indicating the internal consistency of the models. The generated models were validated using external test sets, and the predicted values were in good agreement with the experimental results. Five hER crystal structures were used in GRID/PCA investigations to generate molecular interaction fields (MIF) maps. hERalpha and hERbeta were separated using one factor. The resulting 3D information was integrated with the aim of revealing the most relevant structural features involved in hER subtype selectivity. The final QSAR and GRID/PCA models and the information gathered from 3D contour maps should be useful for the design of novel hER modulators with improved selectivity.
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Affiliation(s)
- Lívia B Salum
- Laboratorio de Quimica Medicinal e Computacional, Centro de Biotecnologia Molecular Estrutural, Instituto de Fisica de Sao Carlos, Universidade de Sao Paulo, Av Trabalhador Sao-Carlense 400, 13560-970 Sao Carlos-SP, Brazil
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Trossini GHG, Guido RVC, Oliva G, Ferreira EI, Andricopulo AD. Quantitative structure-activity relationships for a series of inhibitors of cruzain from Trypanosoma cruzi: molecular modeling, CoMFA and CoMSIA studies. J Mol Graph Model 2009; 28:3-11. [PMID: 19376735 DOI: 10.1016/j.jmgm.2009.03.001] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2008] [Revised: 02/27/2009] [Accepted: 03/02/2009] [Indexed: 11/28/2022]
Abstract
Human parasitic diseases are the foremost threat to human health and welfare around the world. Trypanosomiasis is a very serious infectious disease against which the currently available drugs are limited and not effective. Therefore, there is an urgent need for new chemotherapeutic agents. One attractive drug target is the major cysteine protease from Trypanosoma cruzi, cruzain. In the present work, comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) studies were conducted on a series of thiosemicarbazone and semicarbazone derivatives as inhibitors of cruzain. Molecular modeling studies were performed in order to identify the preferred binding mode of the inhibitors into the enzyme active site, and to generate structural alignments for the three-dimensional quantitative structure-activity relationship (3D QSAR) investigations. Statistically significant models were obtained (CoMFA, r2=0.96 and q2=0.78; CoMSIA, r2=0.91 and q2=0.73), indicating their predictive ability for untested compounds. The models were externally validated employing a test set, and the predicted values were in good agreement with the experimental results. The final QSAR models and the information gathered from the 3D CoMFA and CoMSIA contour maps provided important insights into the chemical and structural basis involved in the molecular recognition process of this family of cruzain inhibitors, and should be useful for the design of new structurally related analogs with improved potency.
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Affiliation(s)
- Gustavo H G Trossini
- Laboratório de Planejamento e Síntese de Quimioterápicos Potenciais Contra Endemias Tropicais, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, Av. Professor Lineu Prestes 580, 05508-900, São Paulo, SP, Brazil
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Salum L, Dias L, Andricopulo A. Fragment-Based QSAR and Molecular Modeling Studies on a Series of Discodermolide Analogs as Microtubule-Stabilizing Anticancer Agents. ACTA ACUST UNITED AC 2009. [DOI: 10.1002/qsar.200860109] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Fragment-based QSAR: perspectives in drug design. Mol Divers 2009; 13:277-85. [PMID: 19184499 DOI: 10.1007/s11030-009-9112-5] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2008] [Accepted: 01/11/2009] [Indexed: 12/25/2022]
Abstract
Drug design is a process driven by innovation and technological breakthroughs involving a combination of advanced experimental and computational methods. A broad variety of medicinal chemistry approaches can be used for the identification of hits, generation of leads, as well as to accelerate the optimization of leads into drug candidates. Quantitative structure-activity relationship (QSAR) methods are among the most important strategies that can be applied for the successful design of small molecule modulators having clinical utility. Hologram QSAR (HQSAR) is a modern 2D fragment-based QSAR method that employs specialized molecular fingerprints. HQSAR can be applied to large data sets of compounds, as well as traditional-size sets, being a versatile tool in drug design. The HQSAR approach has evolved from a classical use in the generation of standard QSAR models for data correlation and prediction into advanced drug design tools for virtual screening and pharmacokinetic property prediction. This paper provides a brief perspective on the evolution and current status of HQSAR, highlighting present challenges and new opportunities in drug design.
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Andrade CH, Salum LDB, Castilho MS, Pasqualoto KFM, Ferreira EI, Andricopulo AD. Fragment-based and classical quantitative structure–activity relationships for a series of hydrazides as antituberculosis agents. Mol Divers 2008; 12:47-59. [DOI: 10.1007/s11030-008-9074-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2007] [Accepted: 02/24/2008] [Indexed: 11/29/2022]
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