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Structural analysis and prediction of potent bioactive molecule for eNOS protein through molecular docking. In Silico Pharmacol 2021; 9:48. [PMID: 34422545 DOI: 10.1007/s40203-021-00106-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 07/12/2021] [Indexed: 10/20/2022] Open
Abstract
Reactive oxygen species by uncoupled eNOS is linked to endothelial dysfunction. Ellagic acid (EA), a polyphenol possesses numerous biological activities including radical scavenging. whether EA exerts a vasculo-protective effect via antioxidant mechanisms in blood vessels remains unknown. Molecular docking provides an initial model of protein and molecular interactions in various physiological and/or pathological functions. To identify a eNOS modulatory biomolecule through molecular docking as possible vascular protective agent. On the basis of binding affinities and other physicochemical features, a molecular docking-based approach was used to classify and evaluate eNOS binding micronutrients found in natural sources, Lipinski's rule was used taking into account their adsorption, delivery, metabolism, and excretion (ADME). An insilico approach focused on the ligand-protein interaction technique to determine the therapeutic potential of certain phytochemical-based drugs for the vascular remodelling.20 bioactive molecules were screened, docking analysis on human eNOS proteins was performed. The best poses for target protein was established based on binding energy and inhibition constant. EA and caffeine acid are the strongest candidates for eNOS protein functional norms. This provides a novel insight into the interaction properties of known human eNOS protein with EA and used as a therapeutic agent in various pathologies. Predicting interaction of ellagic acid with eNOS protein by molecular docking in endothelial dysfunction.
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Cavada BS, Pinto-Junior VR, Osterne VJS, Oliveira MV, Silva IB, Laranjeira EPP, Pires AF, Domingos JLC, Ferreira WP, Sousa JS, Assreuy AMS, Nascimento KS. In depth analysis on the carbohydrate-binding properties of a vasorelaxant lectin from Dioclea lasiophylla Mart Ex. Benth seeds. J Biomol Struct Dyn 2021; 40:6817-6830. [PMID: 33616012 DOI: 10.1080/07391102.2021.1890224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Lectins are a class of proteins or glycoproteins capable of recognizing and interacting with carbohydrates in a specific and reversible manner. Owing to this property, these proteins can interact with glycoconjugates present on the cell surface, making it possible to decipher the glycocode, as well as elicit biological effects, such as inflammation and vasorelaxation. Here, we report a structural and biological study of the mannose/glucose-specific lectin from Dioclea lasiophylla seeds, DlyL. The study aimed to evaluate in detail the interaction of DlyL with Xman and high-mannose N-glycans (MAN3, MAN5 and MAN9) by molecular dynamics (MD) and the resultant in vitro effect on vasorelaxation using rat aortic rings. In silico analysis of molecular docking was performed to obtain the initial coordinates of the DlyL complexes with the carbohydrates to apply as inputs in MD simulations. The MD trajectories demonstrated the stability of DlyL over time as well as different profiles of interaction with Xman and N-glycans. Furthermore, aortic rings assays demonstrated that the lectin could relax pre-contracted aortic rings with the participation of the carbohydrate recognition domain (CRD) and nitric oxide (NO) when endothelial tissue is preserved. These results confirm the ability of DlyL to interact with high-mannose N-glycans with its expanded CRD, supporting the hypothesis that DlyL vasorelaxant activity occurs primarily through its interaction with cell surface glycosylated receptors.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Benildo Sousa Cavada
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Fortaleza, Brazil
| | - Vanir Reis Pinto-Junior
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Fortaleza, Brazil.,Departamento de Física, Universidade Federal do Ceará, Fortaleza, Brazil
| | - Vinicius Jose Silva Osterne
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Fortaleza, Brazil.,Departamento de Nutrição, Universidade Estadual do Ceará, Fortaleza, Brazil
| | - Messias Vital Oliveira
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Fortaleza, Brazil
| | - Ivanice Bezerra Silva
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Fortaleza, Brazil
| | | | - Alana Freitas Pires
- Instituto Superior de Ciências Biomédicas, Universidade Estadual Do Ceará, Fortaleza, Brazil
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Cavada BS, Silva MTL, Osterne VJS, Pinto-Junior VR, Lossio CF, Madeira JC, Pereira MG, Leal RB, Ferreira WP, Nascimento KS, Assreuy AMS. Exploring the carbohydrate-binding ability of Canavalia bonariensis lectin in inflammation models. J Mol Recognit 2020; 33:e2870. [PMID: 32648306 DOI: 10.1002/jmr.2870] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 05/16/2020] [Accepted: 05/29/2020] [Indexed: 01/01/2023]
Abstract
Lectins are a group of proteins of non-immune origin recognized for their ability to bind reversibly to carbohydrates. Researchers have been intrigued by oligosaccharides and glycoconjugates for their involvement as mediators of complex cellular events and then many biotechnological applications of lectins are based on glycocode decoding and their activities. Here, we report a structural and biological study of a ConA-like mannose/glucose-specific lectin from Canavalia bonariensis seeds, CaBo. More specifically, we evaluate the binding of CaBo with α-methyl-D-mannoside (MMA) and mannose-1,3-α-D-mannose (M13) and the resultant in vivo effects on a rat model of acute inflammation. A virtual screening was also carried out to cover a larger number of possible bindings of CaBo. In silico analysis demonstrated the stability of CaBo interaction with mannose-type ligands, and the lectin was able to induce acute inflammation in rats with the participation of the carbohydrate recognition domain (CRD) and histamine release. These results confirm the ability of CaBo to interact with hybrid and high-mannose N-glycans, supporting the hypothesis that CaBo's biological activity occurs primarily through its interaction with cell surface glycosylated receptors.
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Affiliation(s)
- Benildo S Cavada
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Fortaleza, Brazil
| | - Mayara T L Silva
- Departamento de Bioquímica, Universidade Federal de Santa Catarina, Florianópolis, Brazil
| | - Vinicius J S Osterne
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Fortaleza, Brazil
| | | | - Claudia F Lossio
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Fortaleza, Brazil
| | - Juliana C Madeira
- Instituto Superior de Ciências Biomédicas, Universidade Estadual do Ceará, Fortaleza, Brazil
| | - Maria G Pereira
- Instituto Superior de Ciências Biomédicas, Universidade Estadual do Ceará, Fortaleza, Brazil
| | - Rodrigo B Leal
- Departamento de Bioquímica, Universidade Federal de Santa Catarina, Florianópolis, Brazil
| | | | - Kyria S Nascimento
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Fortaleza, Brazil
| | - Ana M S Assreuy
- Instituto Superior de Ciências Biomédicas, Universidade Estadual do Ceará, Fortaleza, Brazil
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Cavada BS, Pinto-Junior VR, Osterne VJS, Lossio CF, Silva MTL, Correia JLA, Correia SEG, Nagano CS, Oliveira MV, Lima LD, Vital APMS, Leal RB, Nascimento KS. A Diocleinae type II lectin from Dioclea lasiophylla Mart. Ex Benth seeds specific to α-lactose/GalNAc. Process Biochem 2020. [DOI: 10.1016/j.procbio.2020.03.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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dos Santos Silva PM, de Oliveira WF, Albuquerque PBS, dos Santos Correia MT, Coelho LCBB. Insights into anti-pathogenic activities of mannose lectins. Int J Biol Macromol 2019; 140:234-244. [DOI: 10.1016/j.ijbiomac.2019.08.059] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 07/14/2019] [Accepted: 08/07/2019] [Indexed: 02/07/2023]
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Cavada BS, Pinto-Junior VR, Osterne VJS, Nascimento KS. ConA-Like Lectins: High Similarity Proteins as Models to Study Structure/Biological Activities Relationships. Int J Mol Sci 2018; 20:ijms20010030. [PMID: 30577614 PMCID: PMC6337138 DOI: 10.3390/ijms20010030] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 12/17/2018] [Accepted: 12/19/2018] [Indexed: 01/03/2023] Open
Abstract
Lectins are a widely studied group of proteins capable of specific and reversible binding to carbohydrates. Undoubtedly, the best characterized are those extracted from plants of the Leguminosae family. Inside this group of proteins, those from the Diocleinae subtribe have attracted attention, in particular Concanavalin A (ConA), the best-studied lectin of the group. Diocleinae lectins, also called ConA-like lectins, present a high similarity of sequence and three-dimensional structure and are known to present inflammatory, vasoactive, antibiotic, immunomodulatory and antitumor activities, among others. This high similarity of lectins inside the ConA-like group makes it possible to use them to study structure/biological activity relationships by the variability of both carbohydrate specificity and biological activities results. It is in this context the following review aims to summarize the most recent data on the biochemical and structural properties, as well as biological activities, of ConA-like lectins and the use of these lectins as models to study structure/biological activity relationships.
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Affiliation(s)
- Benildo S Cavada
- BioMol-Lab, Department of Biochemistry and Molecular Biology, Federal University of Ceara, Fortaleza-CE 60440-970, Brazil.
| | - Vanir R Pinto-Junior
- BioMol-Lab, Department of Biochemistry and Molecular Biology, Federal University of Ceara, Fortaleza-CE 60440-970, Brazil.
| | - Vinicius J S Osterne
- BioMol-Lab, Department of Biochemistry and Molecular Biology, Federal University of Ceara, Fortaleza-CE 60440-970, Brazil.
| | - Kyria S Nascimento
- BioMol-Lab, Department of Biochemistry and Molecular Biology, Federal University of Ceara, Fortaleza-CE 60440-970, Brazil.
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Neco AHB, Pinto-Junior VR, Araripe DA, Santiago MQ, Osterne VJS, Lossio CF, Nobre CAS, Oliveira MV, Silva MTL, Martins MGQ, Cajazeiras JB, Marques GFO, Costa DR, Nascimento KS, Assreuy AMS, Cavada BS. Structural analysis, molecular docking and molecular dynamics of an edematogenic lectin from Centrolobium microchaete seeds. Int J Biol Macromol 2018; 117:124-133. [DOI: 10.1016/j.ijbiomac.2018.05.166] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 05/11/2018] [Accepted: 05/23/2018] [Indexed: 12/30/2022]
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Homology modeling, molecular docking, and dynamics of two α-methyl-d-mannoside-specific lectins from Arachis genus. J Mol Model 2018; 24:251. [DOI: 10.1007/s00894-018-3800-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 08/16/2018] [Indexed: 02/04/2023]
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Crystal structure of DlyL, a mannose-specific lectin from Dioclea lasiophylla Mart. Ex Benth seeds that display cytotoxic effects against C6 glioma cells. Int J Biol Macromol 2018; 114:64-76. [DOI: 10.1016/j.ijbiomac.2018.03.080] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 02/28/2018] [Accepted: 03/16/2018] [Indexed: 12/27/2022]
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Crystal structure of Pisum arvense seed lectin (PAL) and characterization of its interaction with carbohydrates by molecular docking and dynamics. Arch Biochem Biophys 2017; 630:27-37. [DOI: 10.1016/j.abb.2017.07.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Revised: 07/19/2017] [Accepted: 07/23/2017] [Indexed: 02/07/2023]
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Structural studies and nociceptive activity of a native lectin from Platypodium elegans seeds (nPELa). Int J Biol Macromol 2017; 107:236-246. [PMID: 28867234 DOI: 10.1016/j.ijbiomac.2017.08.174] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 08/29/2017] [Accepted: 08/30/2017] [Indexed: 12/14/2022]
Abstract
A native lectin (nPELa), purified from seeds of the species Platypodium elegans, Dalbergieae tribe, was crystallized and structurally characterized by X-ray diffraction crystallography and bioinformatics tools. The obtained crystals diffracted to 1.6Å resolution, and nPELa structure were solved through molecular substitution. In addition, nPELa has a metal binding site and a conserved carbohydrate recognition domain (CRD) similar to other Dalbergieae tribe lectins, such as PAL (Pterocarpus angolensis) and CTL (Centrolobium tomentosum). Molecular docking analysis indicated high affinity of this lectin for different mannosides, mainly trimannosides, formed by α-1,3 or α-1,6 glycosidic bond, as evidenced by the obtained scores. In addition, molecular dynamics simulations were performed to demonstrate the structural behavior of nPELa in aqueous solution. In solution, nPELa was highly stable, and structural modifications in its carbohydrate recognition site allowed interaction between the lectin and the different ligands. Different modifications were observed during simulations for each one of the glycans, which included different hydrogen bonds and hydrophobic interactions through changes in the relevant residues. In addition, nPELa was evaluated for its nociceptive activity in mice and was reported to be the first lectin of the Dalbergieae tribe to show CRD-dependent hypernociceptive activity.
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