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Carraro R, Iribarne F, Paulino M. Analysis of cyclosporin A and a set of analogs as inhibitors of a T. cruzi cyclophilin by docking and molecular dynamics. J Biomol Struct Dyn 2015; 34:399-413. [PMID: 26046477 DOI: 10.1080/07391102.2015.1038584] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Cyclophilins (CyPs) are enzymes involved in protein folding. In Trypanosoma cruzi (T. cruzi), the most abundantly expressed CyP is the isoform TcCyP19. It has been shown that TcCyP19 is inhibited by the immunosuppressive drug cyclosporin A (CsA) and analogs, which also proved to have potent trypanosomicidal activity in vitro. In this work, we continue and expand a previous study on the molecular interactions of CsA, and a set of analogs modeled in complexes with TcCyP19. The modeled complexes were used to evaluate binding free energies by molecular dynamics (MD), applying the Linear Interaction Energy (LIE) method. In addition, putative binding sites were identified by molecular docking. In our analysis, the binding free energy calculations did not correlate with experimental data. The heterogeneity of the non-bonded energies and the variation in the pattern of hydrogen bonds suggest that the systems may not be suitable for the application of the LIE method. Further, the docking calculations identified two other putative binding sites with comparable scoring energies to the active site, a fact that may also explain the lack of correlation found. Kinetic experiments are needed to confirm or reject the multiple binding sites hypothesis. In the meantime, MD simulations at the alternative sites, employing other methods to compute binding free energies, might be successful at finding good correlations with the experimental data.
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Affiliation(s)
- Roberto Carraro
- a Facultad de Química, Centro de Bioinformática Estructural, DETEMA , Universidad de la República , Gral. Flores 2124, C.P. 11800, C.C. 1157, Montevideo , Uruguay
| | - Federico Iribarne
- a Facultad de Química, Centro de Bioinformática Estructural, DETEMA , Universidad de la República , Gral. Flores 2124, C.P. 11800, C.C. 1157, Montevideo , Uruguay
| | - Margot Paulino
- a Facultad de Química, Centro de Bioinformática Estructural, DETEMA , Universidad de la República , Gral. Flores 2124, C.P. 11800, C.C. 1157, Montevideo , Uruguay
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Assaying phenothiazine derivatives as trypanothione reductase and glutathione reductase inhibitors by theoretical docking and Molecular Dynamics studies. J Mol Graph Model 2009; 28:371-81. [DOI: 10.1016/j.jmgm.2009.09.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2009] [Revised: 07/31/2009] [Accepted: 09/15/2009] [Indexed: 11/22/2022]
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Iribarne F, González M, Cerecetto H, Aguilera S, Tapia O, Paulino M. Interaction energies of nitrofurans with trypanothione reductase and glutathione reductase studied by molecular docking. ACTA ACUST UNITED AC 2007. [DOI: 10.1016/j.theochem.2007.04.035] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Paulino M, Iribarne F, Hansz M, Vega M, Seoane G, Cerecetto H, Di Maio R, Caracelli I, Zukerman-Schpector J, Olea C, Stoppani AO, Berriman M, Fairlamb AH, Tapia O. Computer assisted design of potentially active anti-trypanosomal compounds. ACTA ACUST UNITED AC 2002. [DOI: 10.1016/s0166-1280(02)00009-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Shimazaki K, Kakinuma H, Takahashi K, Niihata S, Takahashi N, Matsushita H, Nishi Y, Sakakibara K. Ab initio study toward designing transition-state analogues which elicit proteolytic catalytic antibodies. J PHYS ORG CHEM 2000. [DOI: 10.1002/(sici)1099-1395(200003)13:3<167::aid-poc215>3.0.co;2-m] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Oliva M, Safont VS, Andrés J, Tapia O. A Theoretical Study of the Molecular Mechanism for the Carboxylation Chemistry in Rubisco. J Phys Chem A 1999. [DOI: 10.1021/jp992052k] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- M. Oliva
- Departament de Ciències Experimentals, Universitat Jaume I, Box 224, 12080 Castelló, Spain
| | - V. S. Safont
- Departament de Ciències Experimentals, Universitat Jaume I, Box 224, 12080 Castelló, Spain
| | - J. Andrés
- Departament de Ciències Experimentals, Universitat Jaume I, Box 224, 12080 Castelló, Spain
| | - O. Tapia
- Department of Physical Chemistry, Uppsala University, Box 532,S-75121 Uppsala, Sweden
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Oliva M, Safont VS, Andrés J, Tapia O. Theoretical Study of the Molecular Mechanism for the Oxygenation Chemistry in Rubisco. J Phys Chem A 1999. [DOI: 10.1021/jp9907342] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- M. Oliva
- Departament de Ciències Experimentals, Universitat Jaume I, Box 224, 12080 Castelló, Spain, and Department of Physical Chemistry, Uppsala University, Box 532, S-85121 Uppsala, Sweden
| | - V. S. Safont
- Departament de Ciències Experimentals, Universitat Jaume I, Box 224, 12080 Castelló, Spain, and Department of Physical Chemistry, Uppsala University, Box 532, S-85121 Uppsala, Sweden
| | - J. Andrés
- Departament de Ciències Experimentals, Universitat Jaume I, Box 224, 12080 Castelló, Spain, and Department of Physical Chemistry, Uppsala University, Box 532, S-85121 Uppsala, Sweden
| | - O. Tapia
- Departament de Ciències Experimentals, Universitat Jaume I, Box 224, 12080 Castelló, Spain, and Department of Physical Chemistry, Uppsala University, Box 532, S-85121 Uppsala, Sweden
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Cerecetto H, Di Maio R, Ibarruri G, Seoane G, Denicola A, Peluffo G, Quijano C, Paulino M. Synthesis and anti-trypanosomal activity of novel 5-nitro-2-furaldehyde and 5-nitrothiophene-2-carboxaldehyde semicarbazone derivatives. FARMACO (SOCIETA CHIMICA ITALIANA : 1989) 1998; 53:89-94. [PMID: 9604315 DOI: 10.1016/s0014-827x(97)00011-6] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Several novel semicarbazones derivatives were prepared from 5-nitro-2-furaldehyde or 5-nitrothiophene-2-carboxaldehyde, and tested in vitro as potential anti-trypanosomal agents. The compounds were prepared in good to excellent yields in 2-3 steps from readily available starting materials. Some derivatives were found to be active against Trypanosoma cruzi with an activity similar to that of Nifurtimox.
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Affiliation(s)
- H Cerecetto
- Departamento de Química Orgánica, Facultad de Química, Universidad de la República, Montevideo, Uruguay
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Safont V, Oliva M, Andrés J, Tapia O. Transition structures of carbon dioxide fixation, hydration and C2 inversion for a model of Rubisco catalyzed reaction. Chem Phys Lett 1997. [DOI: 10.1016/s0009-2614(97)01001-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Transition structures for hydride transfer reactions in vacuo and their role in enzyme catalysis. ACTA ACUST UNITED AC 1996. [DOI: 10.1016/s0166-1280(96)04670-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Tapia O, Andrés J, Safont VS. Inactivation of Ribulose-1,5-bisphosphate Carboxylase/Oxygenase during Catalysis. A Theoretical Study of Related Transition Structures. ACTA ACUST UNITED AC 1996. [DOI: 10.1021/jp951661z] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- O. Tapia
- Department of Physical Chemistry, Uppsala University, Box 532, S-75121 Uppsala, Sweden
| | - J. Andrés
- Department of Experimental Sciences, University Jaume I, Box 242, 12080 Castelló, Spain
| | - V. S. Safont
- Department of Experimental Sciences, University Jaume I, Box 242, 12080 Castelló, Spain
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Diaz W, Aullo J, Paulino M, Tapia O. Transition structure and reactive complexes for hydride transfer in an isoalloxazine-nicotinamide complex. On the catalytic mechanism of glutathione reductase. An ab initio MO SCF study. Chem Phys 1996. [DOI: 10.1016/0301-0104(95)00425-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Tapia O, Andrés J, Safont V. Transition structures in vacuo and the theory of enzyme catalysis. Rubisco's catalytic mechanism: a paradigmatic case? ACTA ACUST UNITED AC 1995. [DOI: 10.1016/0166-1280(95)90101-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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