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Quijano-Barraza JM, Zúñiga G, Cano-Ramírez C, López MF, Ramírez-Salinas GL, Becerril M. Evolution and functional role prediction of the CYP6DE and CYP6DJ subfamilies in Dendroctonus (Curculionidae: Scolytinae) bark beetles. Front Mol Biosci 2023; 10:1274838. [PMID: 37877122 PMCID: PMC10593416 DOI: 10.3389/fmolb.2023.1274838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 09/26/2023] [Indexed: 10/26/2023] Open
Abstract
Dendroctonus-bark beetles are natural components and key ecological agents of coniferous forests. They spend most of their lives under the bark, where they are exposed to highly toxic terpenes present in the oleoresin. Cytochrome P450 (CYP) is a multigene family involved in the detoxification of these compounds. It has been demonstrated that CYP6DE and CYP6DJ subfamilies hydroxylate monoterpenes, whose derivatives can act as pheromone synergist compounds or be pheromones themselves in these insects. Given the diversity and functional role of CYPs, we investigated whether these cytochromes have retained their function throughout the evolution of these insects. To test this hypothesis, we performed a Bayesian phylogenetic analysis to determine phylogenetic subgroups of cytochromes in these subfamilies. Subgroups were mapped and reconciled with the Dendroctonus phylogeny. Molecular docking analyses were performed with the cytochromes of each subgroup and enantiomers of α-pinene and β-pinene, (+)-3-carene, β-myrcene and R-(+)-limonene. In addition, functional divergence analysis was performed to identify critical amino acid sites that influence changes in catalytic site conformation and/or protein folding. Three and two phylogenetic subgroups were recovered for the CYP6DE and CYP6DJ subfamilies, respectively. Mapping and reconciliation analysis showed different gain and loss patterns for cytochromes of each subgroup. Functional predictions indicated that the cytochromes analyzed are able to hydroxylate all monoterpenes; however, they showed preferential affinities to different monoterpenes. Functional divergence analyses indicated that the CYP6DE subfamily has experimented type I and II divergence, whereas the CYP6DJ subfamily has evolved under strong functional constraints. Results suggest cytochromes of the CYP6DE subfamily evolve to reinforce their detoxifying capacity hydroxylating mainly α- and β-pinene to (+) and (-)-trans-verbenol, being the negative enantiomer used as a pheromone by several Dendroctonus species; whereas cytochromes of the CYP6DJ subfamily appear to retain their original function related to the detoxification of these compounds.
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Affiliation(s)
- J. Manuel Quijano-Barraza
- Laboratorio de Variación Biológica y Evolución, Departamento de Zoología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala s/n, Mexico City, Mexico
| | - Gerardo Zúñiga
- Laboratorio de Variación Biológica y Evolución, Departamento de Zoología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala s/n, Mexico City, Mexico
| | - Claudia Cano-Ramírez
- Laboratorio de Variación Biológica y Evolución, Departamento de Zoología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala s/n, Mexico City, Mexico
| | - María Fernanda López
- Laboratorio de Variación Biológica y Evolución, Departamento de Zoología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala s/n, Mexico City, Mexico
| | - Gema L. Ramírez-Salinas
- Laboratorio de Modelado Molecular y Diseño de Fármacos, Departamento de Bioquímica, Escuela Superior de Medicina, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Moises Becerril
- Laboratorio de Variación Biológica y Evolución, Departamento de Zoología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala s/n, Mexico City, Mexico
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Ramírez-Salinas GL, García-Machorro J, Quiliano M, Zimic M, Briz V, Rojas-Hernández S, Correa-Basurto J. Molecular modeling studies demonstrate key mutations that could affect the ligand recognition by influenza AH1N1 neuraminidase. J Mol Model 2015; 21:292. [PMID: 26499499 DOI: 10.1007/s00894-015-2835-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 10/09/2015] [Indexed: 01/23/2023]
Abstract
The goal of this study was to identify neuraminidase (NA) residue mutants from human influenza AH1N1 using sequences from 1918 to 2012. Multiple alignment studies of complete NA sequences (5732) were performed. Subsequently, the crystallographic structure of the 1918 influenza (PDB ID: 3BEQ-A) was used as a wild-type structure and three-dimensional (3-D) template for homology modeling of the mutated selected NA sequences. The 3-D mutated NAs were refined using molecular dynamics (MD) simulations (50 ns). The refined 3-D models were used to perform docking studies using oseltamivir. Multiple sequence alignment studies showed seven representative mutations (A232V, K262R, V263I, T264V, S367L, S369N, and S369K). MD simulations applied to 3-D NAs showed that each NA had different active-site shapes according to structural surface visualization and docking results. Moreover, Cartesian principal component analyses (cPCA) show structural differences among these NA structures caused by mutations. These theoretical results suggest that the selected mutations that are located outside of the active site of NA could affect oseltamivir recognition and could be associated with resistance to oseltamivir.
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Affiliation(s)
- Gema L Ramírez-Salinas
- Laboratorio de Modelado Molecular y Bioinformática, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón, 11340, México City, Mexico
| | - J García-Machorro
- Laboratorio de Medicina de Conservación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón, Mexico, DF, 11340, México
| | - Miguel Quiliano
- Unidad de Bioinformática y Biología Molecular, Laboratorios de Investigación y Desarrollo, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Mirko Zimic
- Unidad de Bioinformática y Biología Molecular, Laboratorios de Investigación y Desarrollo, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Verónica Briz
- Unidad de Infección Viral e Inmunidad, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, España
| | - Saul Rojas-Hernández
- Laboratory of Immunology, School of Medicine, National Polytechnic Institute, Mexico, DF, Mexico
| | - J Correa-Basurto
- Laboratorio de Modelado Molecular y Bioinformática, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón, 11340, México City, Mexico.
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Correa-Basurto J, Cuevas-Hernández RI, Phillips-Farfán BV, Martínez-Archundia M, Romo-Mancillas A, Ramírez-Salinas GL, Pérez-González ÓA, Trujillo-Ferrara J, Mendoza-Torreblanca JG. Identification of the antiepileptic racetam binding site in the synaptic vesicle protein 2A by molecular dynamics and docking simulations. Front Cell Neurosci 2015; 9:125. [PMID: 25914622 PMCID: PMC4392693 DOI: 10.3389/fncel.2015.00125] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Accepted: 03/17/2015] [Indexed: 01/21/2023] Open
Abstract
Synaptic vesicle protein 2A (SV2A) is an integral membrane protein necessary for the proper function of the central nervous system and is associated to the physiopathology of epilepsy. SV2A is the molecular target of the anti-epileptic drug levetiracetam and its racetam analogs. The racetam binding site in SV2A and the non-covalent interactions between racetams and SV2A are currently unknown; therefore, an in silico study was performed to explore these issues. Since SV2A has not been structurally characterized with X-ray crystallography or nuclear magnetic resonance, a three-dimensional (3D) model was built. The model was refined by performing a molecular dynamics simulation (MDS) and the interactions of SV2A with the racetams were determined by docking studies. A reliable 3D model of SV2A was obtained; it reached structural equilibrium during the last 15 ns of the MDS (50 ns) with remaining structural motions in the N-terminus and long cytoplasmic loop. The docking studies revealed that hydrophobic interactions and hydrogen bonds participate importantly in ligand recognition within the binding site. Residues T456, S665, W666, D670 and L689 were important for racetam binding within the trans-membrane hydrophilic core of SV2A. Identifying the racetam binding site within SV2A should facilitate the synthesis of suitable radio-ligands to study treatment response and possibly epilepsy progression.
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Affiliation(s)
- José Correa-Basurto
- Laboratorio de Modelado Molecular y Diseño de fármacos, Departamento de Bioquímica de la Escuela Superior de Medicina del Instituto Politécnico Nacional, México City Mexico
| | - Roberto I Cuevas-Hernández
- Laboratorio de Modelado Molecular y Diseño de fármacos, Departamento de Bioquímica de la Escuela Superior de Medicina del Instituto Politécnico Nacional, México City Mexico
| | - Bryan V Phillips-Farfán
- Laboratorio de Nutrición Experimental, Laboratorio de Oncología Experimental and Laboratorio de Neuroquímica, Instituto Nacional de Pediatría, México City Mexico
| | - Marlet Martínez-Archundia
- Laboratorio de Modelado Molecular y Diseño de fármacos, Departamento de Bioquímica de la Escuela Superior de Medicina del Instituto Politécnico Nacional, México City Mexico
| | - Antonio Romo-Mancillas
- División de Estudios de Posgrado, Facultad de Química, Universidad Autónoma de Querétaro, Santiago de Querétaro Mexico
| | - Gema L Ramírez-Salinas
- Laboratorio de Modelado Molecular y Diseño de fármacos, Departamento de Bioquímica de la Escuela Superior de Medicina del Instituto Politécnico Nacional, México City Mexico
| | - Óscar A Pérez-González
- Laboratorio de Nutrición Experimental, Laboratorio de Oncología Experimental and Laboratorio de Neuroquímica, Instituto Nacional de Pediatría, México City Mexico
| | - José Trujillo-Ferrara
- Laboratorio de Modelado Molecular y Diseño de fármacos, Departamento de Bioquímica de la Escuela Superior de Medicina del Instituto Politécnico Nacional, México City Mexico
| | - Julieta G Mendoza-Torreblanca
- Laboratorio de Nutrición Experimental, Laboratorio de Oncología Experimental and Laboratorio de Neuroquímica, Instituto Nacional de Pediatría, México City Mexico
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