• MÁRCIA MACHADO MARINHO Department of Clinical and Toxicological Analysis, Federal University of Ceara, Ceara, Brazil.
  • RICARDO PIRES DOS SANTOS Department of Computer Engineering/Biotechnology, Federal University of Ceara, Ceara, Brazil.
  • EVELINE MATIAS BEZERRA Department of Exact and Natural Sciences, Federal Rural University of Semiarid (UFERSA), Mossoró, Rio Grande do Norte, Brazil.
  • RONER FERREIRA COSTA Department of Exact and Natural Sciences, Federal Rural University of Semiarid (UFERSA), Mossoró, Rio Grande do Norte, Brazil.
  • CIRO SIQUEIRA FIGUEIRA Department of Computer Engineering/Biotechnology, Federal University of Ceara, Ceara, Brazil.
  • ALICE MARIA COSTA MARTINS Department of Clinical and Toxicological Analysis, Federal University of Ceara, Ceara, Brazil.
  • PEDRO LIMA NETO Department of Analytical Chemistry and Physical-Chemistry, Federal University of Ceara, Ceara, Brazil.
  • EMMANUEL SILVA MARINHO Dom Aureliano Matos Faculty of Philosophy, Ceara State University, Ceara, Brazil.
  • VALDER NOGUEIRA FREIRE Department of Physics, Federal University of Ceara, Ceara, Brazil.
  • EUDENILSON LINS ALBUQUERQUE Department of Biophysics and Pharmacology, Federal University of Rio Grande do Norte, Rio Grande do Norte, Brazil.


Objective: The objective of this study was to use the molecular fractionation with conjugate caps (MFCC) method to elucidate the possible interaction mechanism of anacardic acid (AA) with the saturated alkyl chain (AA0) in the Trypanosoma cruzi glyceraldehyde-3-phosphate dehydrogenase (TcGAPHD) enzyme.

Methods: Initially, the geometry optimization of the AA three-dimensional structure (with the pentadecyl chain) was performed using density functional theory (B3LYP) calculations. With the AA0 optimization data, it was possible to plot the molecular electrostatic potential (MESP) surface. Molecular docking simulation was performed using automated coupling with the AutoDock Vina program. The best-fit conformation in the docking simulation of AA0 is the binding site used for the construction of the TcGAPHD-AA0 complex. Interaction energies between the AA0 molecule and the amino acid residues of the TcGAPHD enzyme were estimated using the MFCC strategy.

Results: To obtain more reliable quantitative information on the interaction of AA with the active site of the TcGAPHD enzyme, the fragmentation method was combined with conjugated layers (MFCC) and molecular docking. It can be observed that the AA0 molecule occupies a region near the active site of the chalepin molecule in the TcGAPHD enzyme, and the Ile13 residue has the strongest binding energy of approximately 25 kcal/mol with AA0, through a strong Van der Waals interaction.

Conclusion: The paper presents an improved quantitative analysis approach for assessing the contribution of individual amino acids to the free energy of interaction between AA and TcGAPHD. Specifically, the paper illustrates the advantageous approach of combining molecular docking with the MFCC method.

Keywords: Anacardic acid, Chagas disease, Density functional theory, Glyceraldehyde-3-phosphate dehydrogenase, Trypanosoma cruzi, Molecular electrostatic potential, Molecular fractionation with conjugate caps, molecular docking


1. Rassi A, Rassi A, Marin-Neto JA. Chagas disease. Lancet 2010;375:1388-402. Available from: science/article/pii/S014067361060061X.
2. Schmunis GA. Epidemiology of Chagas disease in non-endemic countries: The role of international migration. Mem Inst Oswaldo Cruz 2007;102:75-85.
3. Bern C, Kjos S, Yabsley MJ, Montgomery SP. Trypanosoma cruzi and Chagas’ disease in the united states. Clin Microbiol Rev 2011;24:655-81.
4. Jackson Y, Gétaz L, Wolff H, Holst M, Mauris A, Tardin A, et al. Prevalence, clinical staging and risk for blood-borne transmission of Chagas disease among latin American migrants in Geneva, Switzerland. PLoS Negl Trop Dis 2010;4:1-7.
5. Coura JR, de Castro SL. A critical review on Chagas disease chemotherapy. Mem Inst Oswaldo Cruz 2002;97:3-24.
6. Nagajyothi F, Machado FS, Burleigh BA, Jelicks LA, Scherer E, Mukherjee S, et al. Mechanisms of Trypanosoma cruzi persistence in Chagas disease. Cell Microbiol 2013;14:634-43.
7. Morillo CA, Marin-Neto JA, Avezum A, Sosa-Estani S, Rassi A, Rosas F, et al. Randomized Trial of benznidazole for chronic Chagas’ cardiomyopathy. N Engl J Med 2015;373:1295-306.
8. Sosa-Estani S, Viotti R, Leonor ES. Therapy, diagnosis and prognosis of chronic Chagas disease: Insight gained in Argentina. Mem Inst Oswaldo Cruz 2009;104:167.
9. Bakker BM, Westerhoff HV, Opperdoes FR, Michels PA. Metabolic control analysis of glycolysis in trypanosomes as an approach to improve selectivity and effectiveness of drugs. Mol Biochem Parasitol 2000;106:1-10.
10. Ladame S, Castilho MS, Silva CH, Denier C, Hannaert V, Périé J, et al. Crystal structure of Trypanosoma cruzi glyceraldehyde-3-phosphate dehydrogenase complexed with an analogue of 1,3-bisphospho-D-glyceric acid: Selective inhibition by structure-based design. Eur J Biochem 2003;270:4574-86.
11. Prokopczyk IM, Ribeiro JF, Sartori GR, Sesti-Costa R, Silva JS, Freitas RF, et al. Integration of methods in cheminformatics and biocalorimetry for the design of trypanosomatid enzyme inhibitors. Future Med Chem 2013;6:17-33.
12. Harris JI., Waters M. In: Boyer P, editor. The Enzymes. 3rd ed. New York: Academic Press; 1976. p. 1-49.
13. Zinsser VL, Hoey EM, Trudgett A, Timson DJ. Biochemical characterisation of glyceraldehyde 3-phosphate dehydrogenase (GAPDH) from the liver fluke, Fasciola hepatica. Biochim Biophys Acta 2014;1844:744-9.
14. Nowicki MW, Tulloch LB, Worralll L, McNae IW, Hannaert V, Michels PA, et al. Design, synthesis and trypanocidal activity of lead compounds based on inhibitors of parasite glycolysis. Bioorg Med Chem 2008;16:5050-61.
15. Yang S, Pannecouque C, Daelemans D, Ma XD, Liu Y, Chen FE, et al. Molecular design, synthesis and biological evaluation of BP-O-DAPY and O-DAPY derivatives as non-nucleoside HIV-1 reverse transcriptase inhibitors. Eur J Med Chem 2013;65:134-43.
16. Nicholls C, Li H, Liu JP. GAPDH: A common enzyme with uncommon functions. Clin Exp Pharmacol Physiol 2012;39:674-9.
17. Tarze A, Deniaud A, Le Bras M, Maillier E, Molle D, Larochette N, et al. GAPDH, a novel regulator of the pro-apoptotic mitochondrial membrane permeabilization. Oncogene 2007;26:2606-20.
18. Menezes IR, Lopes JC, Montanari CA, Oliva G, Pavão F, Castilho MS, et al. 3D QSAR studies on binding affinities of coumarin natural products for glycosomal GAPDH of Trypanosoma cruzi. J Comput Aided Mol Des 2003;17:277-90.
19. Hanau S, Rinaldi E, Dallocchio F, Gilbert IH, Dardonville C, Adams MJ, et al. 6-phosphogluconate dehydrogenase: A target for drugs in African trypanosomes. Curr Med Chem 2004;11:2639-50.
20. De Marchi AA, Castilho MS, Nascimento PG, Archanjo FC, Del Ponte G, Oliva G, et al. New 3-piperonylcoumarins as inhibitors of glycosomal glyceraldehyde-3- phosphate dehydrogenase (gGAPDH) from Trypanosoma cruzi. Bioorg Med Chem 2004;12:4823-33.
21. Schmelzer GH, Gurib-Fakim R, Ameenah B. Plant Resources of Tropical Africa 11(1) : Medicinal Plants 1. Vol. 11. Wageningen: PROTA Foundation; 2008.
22. Vieira PC, Mafezoli J, Pupo MT, Fernandes JB, da Silva MF, de Albuquerque S, et al. Strategies for the isolation and identification of trypanocidal compounds from the rutales. Pure Appl Chem 2001;73:617-22.
23. Pereira JM, Severino RP, Vieira PC, Fernandes JB, da Silva MF, Zottis A, et al. Anacardic acid derivatives as inhibitors of glyceraldehyde-3- phosphate dehydrogenase from Trypanosoma cruzi. Bioorg Med Chem 2008;16:8889-95.
24. Santos RP, Santiago AA, Gadelha CA, Cajazeiras JB, Cavada BS, Martins JL, et al. Production and characterization of the cashew (Anacardium occidentale L.) peduncle bagasse ashes. J Food Eng 2007;79:1432-7.
25. Hemshekhar M, Santhosh MS, Kemparaju K, Girish KS. Emerging roles of anacardic acid and its derivatives: A pharmacological overview. Basic Clin Pharmacol Toxicol 2012;110:122-32.
26. Kubo I, Masuoka N, Ha TJ, Tsujimoto K. Antioxidant activity of anacardic acids. Food Chem 2006;99:555-62.
27. Mendes N, Oliveira A. Atividade moluscicida da mistura de ácidos 6-n-alquil salicílicos (ácido anacárdico) e dos seus complexos com cobre (II) e chumbo (II). Rev Soc Bras Med 1990;23:217-24. Available from:
28. Oliveira MS, Morais SM, Magalhães DV, Batista WP, Vieira ÍG, Craveiro AA, et al. Antioxidant, larvicidal and antiacetylcholinesterase activities of cashew nut shell liquid constituents. Acta Trop 2011;117:165-70.
29. Tan J, Chen B, He L, Tang Y, Jiang Z, Yin G, et al. Anacardic acid (6-pentadecylsalicylic acid) induces apoptosis of prostate cancer cells through inhibition of androgen receptor and activation of p53 signaling. Chin J Cancer Res 2012;24:275-83.
30. Tyman JH. Long-chain phenols. Part Ill identification of the components of a novel phenolic fraction in Anacardium occidentale (cashew nut-shell liquid) and synthesis of the saturated member. J Chem Soc Perkin 1973;1:1639-47.
31. Freitas RF, Prokopczyk IM, Zottis A, Oliva G, Andricopulo AD, Trevisan MT, et al. Discovery of novel Trypanosoma cruzi glyceraldehyde-3-phosphate dehydrogenase inhibitors. Bioorganic Med Chem 2009;17:2476-82.
32. Dahl SG, Sylte I. Molecular modelling of drug targets: The past, the present and the future. Basic Clin Pharmacol Toxicol 2005;96:151-5.
33. Roberto CA, Marinho ES, Campos OS. Neo-chlorogenic acid : Conformatinal and molecular analysis by semi-empirical methods. Int J Recent Res Rev 2019;12:21-6.
34. Ziegler T, Autschbach J. Theoretical methods of potential use for studies of inorganic reaction mechanisms. Chem Rev 2005;105:2695-722.
35. Bezerra EM, Flores MZ, Caetano EW, Freire VN, Lemos V, Cavada BS, et al. Quantum mechanical ab initio calculations of the Raman scattering from psoralens. J Phys Condens Matter 2006;18:8325- 36. Available from: a=017?key=crossref.7a39631f55a558529eb9a2b0f6680af9.
36. Devipriya B, Kumaradhas P. Charge density distribution and the electrostatic moments of CTPB in the active site of p300 enzyme: A DFT and charge density study. J Theor Biol 2013;335:119-29.
37. Pires R, Marinho MM, Sá RA, Martins JL, Teixeira EH, Chagas F, et al. Compositional analysis of cashew (Anacardium occidentale L.) peduncle bagasse ash and its in vitro antifungal activity against Fusarium species. 2011;9:200-5.
38. Brooijmans N, Kuntz ID. Molecular recognition and docking algorithms. Annu Rev Biophys Biomol Struct 2003;32:335-73. Available from:
39. Sousa SF, Fernandes PA, Ramos MJ. Protein-ligand docking: Current status and future challenges. Proteins Struct Funct Bioinf 2006;65:15-26.
40. Kitchen DB, Decornez H, Furr JR, Bajorath J. Docking and scoring in virtual screening for drug discovery: Methods and applications. Nat Rev Drug Discov 2004;3:935-49.
41. Sooderhjelm SG, Ryde U. Protein-ligand interactions. In: Gohlke H, editor. Wiley-VCH Verlag GmbH and Co.; 2012. p. 121-44.
42. Zanatta G, Barroso-Neto IL, Junior VB. Quantum biochemistry description of the human dopamine D3 receptor in complex with the selective antagonist eticlopride. J Proteomics Bioinform 2012;5:155-62. Available from:
43. Da Costa RF, Freire VN, Bezerra EM, Cavada BS, Caetano EW, De Lima Filho JL, et al. Explaining statin inhibition effectiveness of HMG-CoA reductase by quantum biochemistry computations. Phys Chem Phys 2012;14:1389-98.
44. Zhang DW, Zhang JZ. Molecular fractionation with conjugate caps for full quantum mechanical calculation of protein-molecule interaction energy. J Chem Phys 2003;119:3599-605.
45. Devipriya B, Kumaradhas P. Probing the effect of intermolecular interaction and understanding the electrostatic moments of anacardic acid in the active site of p300 enzyme via DFT and charge density analysis. J Mol Graph Model 2012;34:57-66.
46. Da Silva JG, Souza IA, Higino JS, Siqueira JP, Pereira JV, Pereira MD. Atividade antimicrobiana do extrato de Anacardium occidentale Linn. em amostras multiresistentes de Staphylococcus aureus. Braz J Pharmacogn 2007;17:572-7.
47. Irwin JJ, Sterling T, Mysinger MM, Bolstad ES, Coleman RG. ZINC: A free tool to discover chemistry for biology. J Chem Inf Model 2012;52:1757-68.
48. Trott O, Olson A. NIH public access. J Comput Chem 2010;31:455-61.
49. Pavão F, Castilho MS, Pupo MT, Dias RL, Correa AG, Fernandes JB, et al. Structure of Trypanosoma cruzi glycosomal glyceraldehyde-3- phosphate dehydrogenase complexed with chalepin, a natural product inhibitor, at 1.95 AÅ resolution. FEBS Lett 2002;520:13-7.
50. Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, et al. UCSF chimera a visualization system for exploratory research and analysis. J Comput Chem 2004;25:1605-12.
51. Barroso-Neto IL, Marques JP, Da Costa RF, Caetano EW, Cavada BS, Gottfried C, et al. Inactivation of ovine cyclooxygenase-1 by bromoaspirin and aspirin: A quantum chemistry description. J Phys Chem B 2012;116:3270-9.
52. Momany FA, Rone R. Validation of the general purpose QUANTA ®3.2/CHARMm® force field. J Comput Chem 1992;13:888-900.
53. Delley B. An all-electron numerical method for solving the local density functional for polyatomic molecules. J Chem Phys 1990;92:508-17.
54. Delley B. From molecules to solids with the DMol3 approach. J Chem Phys 2000;113:7756-64.
55. Inada Y, Orita H. Efficiency of numerical basis sets for predicting the binding energies of hydrogen bonded complexes: Evidence of small basis set superposition error compared to gaussian basis sets. J Comput Chem 2008;29:225-32.
56. Reed AE, Weinhold F. Natural localized molecular orbitals. J Chem Phys 1985;83:1736-40.
57. Politzer P, Murray JS. The fundamental nature and role of the electrostatic potential in atoms and molecules. Theor Chem Acc 2002;108:134-42.
58. Yearley EJ, Zhurova EA, Zhurov VV, Pinkerton AA. Experimental electron density studies of non-steroidal synthetic estrogens: Diethylstilbestrol and dienestrol. J Mol Struct 2008;890:240-8.
59. Hibbs DE, Overgaard J, Platts JA, Waller MP, Hursthouse MB. Experimental and theoretical charge density studies of tetrafluorophthalonitrile and tetrafluoroisophthalonitrile. J Phys Chem B 2004;108:3663-72.
60. Politzer P, Murray JS, Peralta-Inga Z. Molecular surface electrostatic potentials in relation to noncovalent interactions in biological systems. Int J Quantum Chem 2001;684:676-84.
61. Ophardt CE. Virtual ChemBook. Elmhurst College; 2003. Available from: [Last accessed on 2018 Jan 25].
62. Prabavathi N, Nilufer A, Krishnakumar V. Vibrational spectroscopic (FT-iR and FT-Raman) studies, natural bon orbital analysis and molecular electrostatic potential surface of isoxanthopterin. Spectrochim Acta Part A Mol Biomol Spectrosc 2013;114:101-13.
63. Herring GE, Petrucci RH, Harwood WS, Madura J. General Chemistry: Principles and Modern Applications. 9th ed. New Jersey: Pearson Education Inc.; 2007.
64. Seminario J, editor. Recent Developments and Applications of Modern Density Functional Theory. 1st ed. Amsterdam, The Netherland: Elsevier; 1996. p. 3-838. Available from: https://www.sciencedirect. com/bookseries/theoretical-and-computational-chemistry/vol/4.
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