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Our research

Current GMMSB/LNCC projects include the development of:

  • Own computational receptor-ligand docking methodologies using Genetic Algorithms, Generalized Simulated Annealing Algorithm and Artificial Neural Networks;
  • A web-based ligand data base program (LLDB - "LASSBio Ligand Data Base");
  • A biological workflow (MHOLline) for structural genomic projects;
  • Methodologies to investigate molecular targets associated to the TriTryps genomes (Trypanosoma cruzi, Trypanosoma brucei and Leishmania major parasites) with the aim to find new lead compounds for the development of drugs against Chagas' disease, sleeping sickness and leishmaniasis;
  • Own computational methodologies for the ab initio prediction of protein structures;
  • A polarizable force field based on quantum mechanical electronic structure calculations for a future use in receptor-ligand docking methodologies.

Publications

  • Design, synthesis and pharmacological evaluation of N -benzyl-piperidinyl-aryl-acylhydrazone derivatives as donepezil hybrids: Discovery of novel multi-target anti-alzheimer prototype drug candidates DOI: 10.1016/j.bmc.2018.10.003
  • Empirical Scoring Functions for Structure-Based Virtual Screening: Applications, Critical Aspects, and Challenges DOI: 10.3389/fphar.2018.01089
  • Design, synthesis and pharmacological evaluation of N -benzyl-piperidinyl-aryl-acylhydrazone derivatives as donepezil hybrids: Discovery of novel multi-target anti-alzheimer prototype drug candidates DOI: 10.1016/j.ejmech.2018.01.066
  • Chiral Bistacrine Analogues: Synthesis, Cholinesterase Inhibitory Activity and a Molecular Modeling Approach DOI: 10.21577/0103-5053.20170074
  • Discovery of naphthyl- N -acylhydrazone p38α MAPK inhibitors with in vivo anti-inflammatory and anti-TNF-α activity DOI: 10.1111/cbdd.13085
  • Design, synthesis and evaluation of novel feruloyl-donepezil hybrids as potential multitarget drugs for the treatment of Alzheimer's disease DOI: 10.1016/j.ejmech.2017.02.043
  • Novel series of tacrine-tianeptine hybrids: Synthesis, cholinesterase inhibitory activity, S100B secretion and a molecular modeling approach DOI: 10.1016/j.ejmech.2016.06.025
  • A unique SaeS allele overrides cell-density dependent expression of saeR and lukSF-PV in the ST30-SCCmecIV lineage of CA-MRSA DOI: 10.1016/j.ijmm.2016.05.001
  • LASSBio-1829 Hydrochloride: Development of a New Orally Active N-Acylhydrazone IKK2 Inhibitor with Anti-inflammatory Properties DOI: 10.1002/cmdc.201500266
  • Structural modeling and docking studies of ribose 5-phosphate isomerase from Leishmania major and Homo sapiens: A comparative analysis for Leishmaniasis treatment DOI: 10.1016/j.jmgm.2014.11.002
  • Trevizani, R., Custódio, F. L., dos Santos, K. B., & Dardenne, L. E. (2017). Critical features of fragment libraries for protein structure prediction. PloS one, 12(1), e0170131. DOI: 10.1371/journal.pone.0170131
  • Santos, K. B., Custódio, F. L., Barbosa, H. J., & Dardenne, L. E. (2015, August). Genetic operators based on backbone constraint angles for protein structure prediction. In Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), 2015 IEEE Conference on (pp. 1-8). IEEE. DOI: 10.1109/CIBCB.2015.7300285
  • Rocha, G. K., Angelo, J. S., Santos, K. B., Custódio, F. L., Dardenne, L. E., & Barbosa, H. J. (2017, August). Using an aggregation tree to arrange energy function terms for protein structure prediction. In Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), 2017 IEEE Conference on (pp. 1-7). IEEE. DOI: 10.1109/CIBCB.2017.8058533
  • Santos, K. B., Rocha, G. K., Custódio, F. L., Barbosa, H. J., & Dardenne, L. E. (2017, August). Improving de novo protein structure prediction using contact maps information. In Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), 2017 IEEE Conference on (pp. 1-6). IEEE. DOI: 10.1109/CIBCB.2017.8058535
  • Rocha, G. K., Dos Santos, K. B., Angelo, J. S., Custodio, F. L., Barbosa, H. J., & Dardenne, L. E. (2018, July). Inserting Co-Evolution Information from Contact Maps into a Multiobjective Genetic Algorithm for Protein Structure Prediction. In 2018 IEEE Congress on Evolutionary Computation (CEC) (pp. 1-8). IEEE DOI: 10.1109/CEC.2018.8477890
  • Santos, K. B., Trevizani, R., Custódio, F. L., & Dardenne, L. E. (2015, January). Profrager web server: Fragment libraries generation for protein structure prediction. In Proceedings of the International Conference on Bioinformatics & Computational Biology (BIOCOMP) (p. 38). The Steering Committee of The World Congress in Computer Science, Computer Engineering and Applied Computing (WorldComp). DOI: .
  • Custódio, F. L., Barbosa, H. J., & Dardenne, L. E. (2014). A multiple minima genetic algorithm for protein structure prediction. Applied Soft Computing, 15, 88-99. DOI: 10.1016/j.asoc.2013.10.029
  • Custódio, F. L., Barbosa, H. J., & Dardenne, L. E. (2010, July). Full-atom ab initio protein structure prediction with a genetic algorithm using a similarity-based surrogate model. In Evolutionary Computation (CEC), 2010 IEEE Congress on (pp. 1-8). IEEE. DOI: 10.1109/CEC.2010.5585959
  • Rocha, G. K., Custódio, F. L., Barbosa, H. J. C., & Dardenne, L. E. (2015, August). A multiobjective approach for protein structure prediction using a steady-state genetic algorithm with phenotypic crowding. In Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), 2015 IEEE Conference on (pp. 1-8). IEEE. DOI: 10.1109/CIBCB.2015.7300284
  • Priscila VSZ Capriles, Ana CR Guimarães, Thomas D Otto, Antonio B Miranda, Laurent E Dardenne and Wim M Degrave. Structural modelling and comparative analysis of homologous, analogous and specific proteins from Trypanosoma cruzi versus Homo sapiens: putative drug targets for Chagas' disease treatment. BMC Genomics, v.11, p. 610-619, 2010. DOI: 10.1186/1471-2164-11-610