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de Albuquerque KCO, da Veiga ADSS, Silveira FT, Campos MB, da Costa APL, Brito AKM, Melo PRDS, Percario S, de Molfetta FA, Dolabela MF. Anti-leishmanial activity of Eleutherine plicata Herb. and predictions of isoeleutherin and its analogues. Front Chem 2024; 12:1341172. [PMID: 38510811 PMCID: PMC10950963 DOI: 10.3389/fchem.2024.1341172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Accepted: 02/16/2024] [Indexed: 03/22/2024] Open
Abstract
Introduction: Leishmaniasis is caused by protozoa of the genus Leishmania, classified as tegumentary and visceral. The disease treatment is still a serious problem, due to the toxic effects of available drugs, the costly treatment and reports of parasitic resistance, making the search for therapeutic alternatives urgent. This study assessed the in vitro anti-leishmanial potential of the extract, fractions, and isoeleutherin from Eleutherine plicata, as well as the in silico interactions of isoeleutherin and its analogs with Trypanothione Reductase (TR), in addition to predicting pharmacokinetic parameters. Methods: From the ethanolic extract of E. plicata (EEEp) the dichloromethane fraction (FDEp) was obtained, and isoeleutherin isolated. All samples were tested against promastigotes, and parasite viability was evaluated. Isoeleutherin analogues were selected based on similarity in databases (ZINK and eMolecules) to verify the impact on structural change. Results and Discussion: The extract and its fractions were not active against the promastigote form (IC50 > 200 μg/mL), while isoeleutherin was active (IC50 = 25 μg/mL). All analogues have high intestinal absorption (HIA), cell permeability was moderate in Caco2 and low to moderate in MDCK. Structural changes interfered with plasma protein binding and blood-brain barrier permeability. Regarding metabolism, all molecules appear to be CYP3A4 metabolized and inhibited 2-3 CYPs. Molecular docking and molecular dynamics assessed the interactions between the most stable configurations of isoeleutherin, analogue compound 17, and quinacrine (control drug). Molecular dynamics simulations demonstrated stability and favorable interactions with TR. In summary, fractionation contributed to antileishmanial activity and isoleutherin seems to be promising. Structural alterations did not contribute to improve pharmacokinetic aspects and analogue 17 proved to be more promising than isoeleutherin, presenting better stabilization in TR.
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Affiliation(s)
| | | | | | | | - Ana Paula Lima da Costa
- Laboratory of Molecular Modeling, Institute of Exact and Natural Sciences, Federal University of Pará, Belém, PA, Brazil
| | | | | | - Sandro Percario
- Biotechnology and Biodiversity Postgraduate Program (BIONORTE), Federal University of Pará, Belém, PA, Brazil
| | - Fábio Alberto de Molfetta
- Laboratory of Molecular Modeling, Institute of Exact and Natural Sciences, Federal University of Pará, Belém, PA, Brazil
| | - Maria Fâni Dolabela
- Biotechnology and Biodiversity Postgraduate Program (BIONORTE), Federal University of Pará, Belém, PA, Brazil
- Pharmaceutical Innovation Postgraduate Program, Federal University of Pará, Belém, PA, Brazil
- Faculty of Pharmacy, Federal University of Pará, Belém, PA, Brazil
- Pharmaceutical Sciences Postgraduate Program, Federal University of Pará, Belém, PA, Brazil
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2
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Paes SS, Silva-Silva JV, Portal Gomes PW, da Silva LO, da Costa APL, Lopes Júnior ML, Hardoim DDJ, Moragas-Tellis CJ, Taniwaki NN, Bertho AL, de Molfetta FA, Almeida-Souza F, Santos LS, Calabrese KDS. (-)-5-Demethoxygrandisin B a New Lignan from Virola surinamensis (Rol.) Warb. Leaves: Evaluation of the Leishmanicidal Activity by In Vitro and In Silico Approaches. Pharmaceutics 2023; 15:2292. [PMID: 37765261 PMCID: PMC10535778 DOI: 10.3390/pharmaceutics15092292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 08/17/2023] [Accepted: 08/21/2023] [Indexed: 09/29/2023] Open
Abstract
Leishmaniasis is a complex disease caused by infection with different Leishmania parasites. The number of medications used for its treatment is still limited and the discovery of new drugs is a valuable approach. In this context, here we describe the in vitro leishmanicidal activity and the in silico interaction between trypanothione reductase (TryR) and (-)-5-demethoxygrandisin B from the leaves of Virola surinamensis (Rol.) Warb. The compound (-)-5-demethoxygrandisin B was isolated from V. surinamensis leaves, a plant found in the Brazilian Amazon, and it was characterized as (7R,8S,7'R,8'S)-3,4,5,3',4'-pentamethoxy-7,7'-epoxylignan. In vitro antileishmanial activity was examined against Leishmania amazonensis, covering both promastigote and intracellular amastigote phases. Cytotoxicity and nitrite production were gauged using BALB/c peritoneal macrophages. Moreover, transmission electron microscopy was applied to probe ultrastructural alterations, and flow cytometry assessed the shifts in the mitochondrial membrane potential. In silico methods such as molecular docking and molecular dynamics assessed the interaction between the most stable configuration of (-)-5-demethoxygrandisin B and TryR from L. infantum (PDB ID 2JK6). As a result, the (-)-5-demethoxygrandisin B was active against promastigote (IC50 7.0 µM) and intracellular amastigote (IC50 26.04 µM) forms of L. amazonensis, with acceptable selectivity indexes. (-)-5-demethoxygrandisin B caused ultrastructural changes in promastigotes, including mitochondrial swelling, altered kDNA patterns, vacuoles, vesicular structures, autophagosomes, and enlarged flagellar pockets. It reduced the mitochondria membrane potential and formed bonds with important residues in the TryR enzyme. The molecular dynamics simulations showed stability and favorable interaction with TryR. The compound targets L. amazonensis mitochondria via TryR enzyme inhibition.
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Affiliation(s)
- Steven Souza Paes
- Institute of Exact and Natural Sciences, Federal University of Pará, Belém 66075-110, PA, Brazil
| | - João Victor Silva-Silva
- Laboratory of Protozoology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro 21041-250, RJ, Brazil (K.d.S.C.)
- Laboratory of Medicinal and Computational Chemistry, Institute of Physics of São Carlos, University of São Paulo, São Carlos 13418-900, SP, Brazil
| | - Paulo Wender Portal Gomes
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, CA 92123, USA
| | | | - Ana Paula Lima da Costa
- Institute of Exact and Natural Sciences, Federal University of Pará, Belém 66075-110, PA, Brazil
| | - Manoel Leão Lopes Júnior
- Institute of Exact and Natural Sciences, Federal University of Pará, Belém 66075-110, PA, Brazil
| | - Daiana de Jesus Hardoim
- Laboratory of Protozoology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro 21041-250, RJ, Brazil (K.d.S.C.)
| | - Carla J. Moragas-Tellis
- Laboratory of Natural Products for Public Health, Pharmaceutical Technology Institute, Farmanguinhos, Oswaldo Cruz Foundation, Rio de Janeiro 21040-900, RJ, Brazil
| | | | - Alvaro Luiz Bertho
- Laboratory of Immunoparasitology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro 21040-900, RJ, Brazil;
- Flow Cytometry Core Facility, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro 21040-900, RJ, Brazil
| | - Fábio Alberto de Molfetta
- Laboratory of Molecular Modeling, Institute of Exact and Natural Sciences, Federal University of Pará, Belém 66075-110, PA, Brazil;
| | - Fernando Almeida-Souza
- Laboratory of Protozoology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro 21041-250, RJ, Brazil (K.d.S.C.)
- Postgraduate Program in Animal Science, State University of Maranhão, Sao Luis 65055-310, MA, Brazil
| | - Lourivaldo Silva Santos
- Institute of Exact and Natural Sciences, Federal University of Pará, Belém 66075-110, PA, Brazil
| | - Kátia da Silva Calabrese
- Laboratory of Protozoology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro 21041-250, RJ, Brazil (K.d.S.C.)
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3
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da Costa APL, Cardoso FJB, Molfetta FAD. An in silico molecular modeling approach of halolactone derivatives as potential inhibitors for human immunodeficiency virus type-1 reverse transcriptase enzyme. J Biomol Struct Dyn 2023; 41:1715-1729. [PMID: 34996334 DOI: 10.1080/07391102.2021.2024256] [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: 02/03/2023]
Abstract
Acquired Immune Deficiency Syndrome (AIDS) is an infectious disease caused by Human Immunodeficiency Virus (HIV) infection and its replication requires the Reverse Transcriptase (RT) enzyme. RT plays a key role in the HIV life cycle, making it one of the most important targets for designing new drugs. Thus, in order to increase therapeutic options against AIDS, halolactone derivatives (D-halolactone) that have been showed as potential non-nucleoside inhibitors of the RT enzyme were studied. In the present work, a series of D-halolactone were investigated by molecular modeling studies, combining Three-dimensional Quantitative Structure-Activity Relationship (3 D-QSAR), molecular docking and Molecular Dynamics (MD) techniques, to understand the molecular characteristics that promote biological activity. The internal and external validation parameters indicated that the 3 D-QSAR model has good predictive capacity and statistical significance. Contour maps provided useful information on the structural characteristics of compounds for anti-HIV-1 activity. The docking results showed that D-halolactone present good complementarity by the RT allosteric site. In MD simulations it was observed that the formation of enzyme-ligand complexes were favorable, and from the free energy decomposition it was found that Leu100, Val106, Tyr181, Try188, and Trp229 are key residues for stabilization in the enzymatic site. Thus, the results showed that the proposed models can be used to design promising HIV-1 RT inhibitors. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ana Paula Lima da Costa
- Laboratório de Modelagem Molecular, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Fábio José Bonfim Cardoso
- Laboratório de Modelagem Molecular, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Fábio Alberto de Molfetta
- Laboratório de Modelagem Molecular, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, Pará, Brazil
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4
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Cofas-Vargas LF, Mendoza-Espinosa P, Avila-Barrientos LP, Prada-Gracia D, Riveros-Rosas H, García-Hernández E. Exploring the druggability of the binding site of aurovertin, an exogenous allosteric inhibitor of FOF1-ATP synthase. Front Pharmacol 2022; 13:1012008. [PMID: 36313289 PMCID: PMC9615146 DOI: 10.3389/fphar.2022.1012008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 10/03/2022] [Indexed: 11/13/2022] Open
Abstract
In addition to playing a central role in the mitochondria as the main producer of ATP, FOF1-ATP synthase performs diverse key regulatory functions in the cell membrane. Its malfunction has been linked to a growing number of human diseases, including hypertension, atherosclerosis, cancer, and some neurodegenerative, autoimmune, and aging diseases. Furthermore, inhibition of this enzyme jeopardizes the survival of several bacterial pathogens of public health concern. Therefore, FOF1-ATP synthase has emerged as a novel drug target both to treat human diseases and to combat antibiotic resistance. In this work, we carried out a computational characterization of the binding sites of the fungal antibiotic aurovertin in the bovine F1 subcomplex, which shares a large identity with the human enzyme. Molecular dynamics simulations showed that although the binding sites can be described as preformed, the inhibitor hinders inter-subunit communications and exerts long-range effects on the dynamics of the catalytic site residues. End-point binding free energy calculations revealed hot spot residues for aurovertin recognition. These residues were also relevant to stabilize solvent sites determined from mixed-solvent molecular dynamics, which mimic the interaction between aurovertin and the enzyme, and could be used as pharmacophore constraints in virtual screening campaigns. To explore the possibility of finding species-specific inhibitors targeting the aurovertin binding site, we performed free energy calculations for two bacterial enzymes with experimentally solved 3D structures. Finally, an analysis of bacterial sequences was carried out to determine conservation of the aurovertin binding site. Taken together, our results constitute a first step in paving the way for structure-based development of new allosteric drugs targeting FOF1-ATP synthase sites of exogenous inhibitors.
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Affiliation(s)
- Luis Fernando Cofas-Vargas
- Universidad Nacional Autónoma de México, Instituto de Química, Ciudad Universitaria, Mexico City, Mexico
| | - Paola Mendoza-Espinosa
- Universidad Nacional Autónoma de México, Instituto de Química, Ciudad Universitaria, Mexico City, Mexico
- Tecnologico de Monterrey, The Institute for Obesity Research, Monterrey, Mexico
| | | | - Diego Prada-Gracia
- Unidad de Investigación en Biología Computacional y Diseño de Fármacos, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | - Héctor Riveros-Rosas
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Avenida Universidad 3000, Cd. Universitaria, Mexico City, Mexico
| | - Enrique García-Hernández
- Universidad Nacional Autónoma de México, Instituto de Química, Ciudad Universitaria, Mexico City, Mexico
- *Correspondence: Enrique García-Hernández,
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Correia LC, Ferreira JV, de Lima HB, Silva GM, da Silva CHTP, de Molfetta FA, Hage-Melim LIS. Pharmacophore-based virtual screening from phytocannabinoids as antagonist r-CB1. J Mol Model 2022; 28:258. [PMID: 35978141 DOI: 10.1007/s00894-022-05219-3] [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: 06/17/2021] [Accepted: 06/26/2022] [Indexed: 11/29/2022]
Abstract
Search for new pharmacological alternatives for obesity is based on the design and development of compounds that can aid in weight loss so that they can be used safely and effectively over a long period while maintaining their function. The endocannabinoid system is related to obesity by increasing orexigenic signals and reducing satiety signals. Cannabis sativa is a medicinal plant of polypharmaceutical potential that has been widely studied for various medicinal purposes. The in silico evaluation of their natural cannabinoids (also called phytocannabinoids) for anti-obesity purpose stems from the existence of synthetic cannabinoid compounds that have already presented this result, but which did not guarantee patient safety. In order to find new molecules from C. sativa phytocannabinoids, with the potential to interact peripherally with the pharmacological target cannabinoid receptor 1, a pharmacophore-based virtual screening was performed, including the evaluation of physicochemical, pharmacokinetic, toxicological predictions and molecular docking. The results obtained from the ZINC12 database pointed to Zinc 69 (ZINC33053402) and Zinc 70 (ZINC19084698) molecules as promising anti-obesity agents. Molecular dynamics (MD) studies disclose that both complexes were stable by analyzing the RMSD (root mean square deviation) values, and the binding free energy values demonstrate that the selected structures can interact and inhibit their catalytic activity.
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Affiliation(s)
- Lenir C Correia
- Laboratory of Pharmaceutical and Medicinal Chemistry (PharMedChem), Federal University of Amapá, Rod. JK, Km 02, Macapá, Brazil
| | - Jaderson V Ferreira
- Laboratory of Pharmaceutical and Medicinal Chemistry (PharMedChem), Federal University of Amapá, Rod. JK, Km 02, Macapá, Brazil
| | - Henrique B de Lima
- Laboratory of Pharmaceutical and Medicinal Chemistry (PharMedChem), Federal University of Amapá, Rod. JK, Km 02, Macapá, Brazil
| | - Guilherme M Silva
- Computational Laboratory of Pharmaceutical Chemistry, Department of Pharmaceutical Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil.,Department of Chemistry. School of Philosophy, Sciences and Letters of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Carlos H T P da Silva
- Computational Laboratory of Pharmaceutical Chemistry, Department of Pharmaceutical Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil.,Department of Chemistry. School of Philosophy, Sciences and Letters of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Fábio A de Molfetta
- Laboratório de Modelagem Molecular, Federal University of Pará, Belém-PA, Brazil
| | - Lorane I S Hage-Melim
- Laboratory of Pharmaceutical and Medicinal Chemistry (PharMedChem), Federal University of Amapá, Rod. JK, Km 02, Macapá, Brazil.
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Novel Azine Linked Hybrids of 2-indolinone and Thiazolodinone Scaffolds as CDK2 inhibitors with potential anticancer activity: In Silico Design, Synthesis, Biological, Molecular Dynamics and Binding Free Energy Studies. Bioorg Chem 2022; 126:105884. [PMID: 35623140 DOI: 10.1016/j.bioorg.2022.105884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 04/28/2022] [Accepted: 05/17/2022] [Indexed: 11/23/2022]
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7
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Pestana-Nobles R, Aranguren-Díaz Y, Machado-Sierra E, Yosa J, Galan-Freyle NJ, Sepulveda-Montaño LX, Kuroda DG, Pacheco-Londoño LC. Docking and Molecular Dynamic of Microalgae Compounds as Potential Inhibitors of Beta-Lactamase. Int J Mol Sci 2022; 23:1630. [PMID: 35163569 PMCID: PMC8836116 DOI: 10.3390/ijms23031630] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/21/2022] [Accepted: 01/22/2022] [Indexed: 01/07/2023] Open
Abstract
Bacterial resistance is responsible for a wide variety of health problems, both in children and adults. The persistence of symptoms and infections are mainly treated with β-lactam antibiotics. The increasing resistance to those antibiotics by bacterial pathogens generated the emergence of extended-spectrum β-lactamases (ESBLs), an actual public health problem. This is due to rapid mutations of bacteria when exposed to antibiotics. In this case, β-lactamases are enzymes used by bacteria to hydrolyze the beta-lactam rings present in the antibiotics. Therefore, it was necessary to explore novel molecules as potential β-lactamases inhibitors to find antibacterial compounds against infection caused by ESBLs. A computational methodology based on molecular docking and molecular dynamic simulations was used to find new microalgae metabolites inhibitors of β-lactamase. Six 3D β-lactamase proteins were selected, and the molecular docking revealed that the metabolites belonging to the same structural families, such as phenylacridine (4-Ph), quercetin (Qn), and cryptophycin (Cryp), exhibit a better binding score and binding energy than commercial clinical medicine β-lactamase inhibitors, such as clavulanic acid, sulbactam, and tazobactam. These results indicate that 4-Ph, Qn, and Cryp molecules, homologous from microalgae metabolites, could be used, likely as novel β-lactamase inhibitors or as structural templates for new in-silico pharmaceutical designs, with the possibility of combatting β-lactam resistance.
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Affiliation(s)
- Roberto Pestana-Nobles
- Life Science Research Center, Universidad Simón Bolívar, Barranquilla 080002, Colombia; (R.P.-N.); (Y.A.-D.); (E.M.-S.); (J.Y.); (N.J.G.-F.)
| | - Yani Aranguren-Díaz
- Life Science Research Center, Universidad Simón Bolívar, Barranquilla 080002, Colombia; (R.P.-N.); (Y.A.-D.); (E.M.-S.); (J.Y.); (N.J.G.-F.)
| | - Elwi Machado-Sierra
- Life Science Research Center, Universidad Simón Bolívar, Barranquilla 080002, Colombia; (R.P.-N.); (Y.A.-D.); (E.M.-S.); (J.Y.); (N.J.G.-F.)
| | - Juvenal Yosa
- Life Science Research Center, Universidad Simón Bolívar, Barranquilla 080002, Colombia; (R.P.-N.); (Y.A.-D.); (E.M.-S.); (J.Y.); (N.J.G.-F.)
| | - Nataly J. Galan-Freyle
- Life Science Research Center, Universidad Simón Bolívar, Barranquilla 080002, Colombia; (R.P.-N.); (Y.A.-D.); (E.M.-S.); (J.Y.); (N.J.G.-F.)
| | | | - Daniel G. Kuroda
- Department of Chemistry, Louisiana State University, Baton Rouge, LA 70803, USA; (L.X.S.-M.); (D.G.K.)
| | - Leonardo C. Pacheco-Londoño
- Life Science Research Center, Universidad Simón Bolívar, Barranquilla 080002, Colombia; (R.P.-N.); (Y.A.-D.); (E.M.-S.); (J.Y.); (N.J.G.-F.)
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Ortiz-Zamora L, Ferreira JV, de Oliveira NKS, de Molfetta FA, Hage-Melim LIS, Fernandes CP, Oliveira AEMFM. Potential implications of vouacapan compounds for insecticidal activity: an in silico study. Recent Pat Biotechnol 2022; 16:155-173. [PMID: 34994338 DOI: 10.2174/1872208316666220106110902] [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: 08/04/2021] [Revised: 08/11/2021] [Accepted: 11/30/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND From the fruits and seeds of the species of Pterodon, it is possible to obtain two main products: the essential oil and oleoresin. In oleoresin, numerous vouacapan compounds have been demonstrated to have biological potential, including insecticidal activity. OBJECTIVE In silico studies were performed to identify potential candidates for natural insecticides among the vouacapans present in the genus Pterodon. MATERIALS AND METHODS Molecular docking and molecular dynamics studies were performed to analyze the interaction of vouacapan compounds with acetylcholinesterase of Drosophila melanogaster. Pharmacokinetic parameters regarding physicochemical properties, plasma protein binding, and activity in the central nervous system were evaluated. The toxicological properties of the selected molecules were predicted using Malathion as the reference compound. RESULTS 6α,7β-dimethoxivouacapan-17-ene (15) showed a high number of interactions and scores in molecular docking studies. This result suggests that this compound exhibits an inhibitory activity of the enzyme acetylcholinesterase. Regarding physicochemical properties, this compound showed the best results, besides presenting low cutaneous permeability values, suggesting null absorption. Molecular dynamics studies demonstrated few conformational changes in the structure of the complex formed by compound 4 and acetylcholinesterase enzyme throughout the simulation time. CONCLUSION It was determined that compound 4 (vouacapan 6α,7β,17β,19-tetraol) is an excellent candidate for usage as a natural insecticide.
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Affiliation(s)
- Lisset Ortiz-Zamora
- Post-Graduate Program in Tropical Biodiversity, Amapá Federal University, Macapá, Amapá, Brazil
- Laboratory of Phytopharmaceutical Nanobiotechnology, Amapá Federal University, Macapá, Amapá, Brazil
| | - Jaderson V Ferreira
- Laboratory of Pharmaceutical and Medicinal Chemistry (PharMedChem), Federal University of Amapá, Macapá, Amapá, Brazil
| | - Nayana K S de Oliveira
- Laboratory of Pharmaceutical and Medicinal Chemistry (PharMedChem), Federal University of Amapá, Macapá, Amapá, Brazil
| | - Fábio A de Molfetta
- Institute of Exact and Natural Sciences, Federal University of Pará, Belém, Pará, Brazil
| | - Lorane I S Hage-Melim
- Laboratory of Pharmaceutical and Medicinal Chemistry (PharMedChem), Federal University of Amapá, Macapá, Amapá, Brazil
- Post-Graduate Program in Pharmaceutical Sciences, Amapá Federal University, Macapá, Amapá, Brazil
| | - Caio P Fernandes
- Post-Graduate Program in Pharmaceutical Sciences, Amapá Federal University, Macapá, Amapá, Brazil
| | - Anna E M F M Oliveira
- Post-Graduate Program in Pharmaceutical Sciences, Amapá Federal University, Macapá, Amapá, Brazil
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9
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Ashraf S, Ranaghan KE, Woods CJ, Mulholland AJ, Ul-Haq Z. Exploration of the structural requirements of Aurora Kinase B inhibitors by a combined QSAR, modelling and molecular simulation approach. Sci Rep 2021; 11:18707. [PMID: 34548506 PMCID: PMC8455585 DOI: 10.1038/s41598-021-97368-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 07/21/2021] [Indexed: 02/04/2023] Open
Abstract
Aurora kinase B plays an important role in the cell cycle to orchestrate the mitotic process. The amplification and overexpression of this kinase have been implicated in several human malignancies. Therefore, Aurora kinase B is a potential drug target for anticancer therapies. Here, we combine atom-based 3D-QSAR analysis and pharmacophore model generation to identify the principal structural features of acylureidoindolin derivatives that could potentially be responsible for the inhibition of Aurora kinase B. The selected CoMFA and CoMSIA model showed significant results with cross-validation values (q2) of 0.68, 0.641 and linear regression values (r2) of 0.971, 0.933 respectively. These values support the statistical reliability of our model. A pharmacophore model was also generated, incorporating features of reported crystal complex structures of Aurora kinase B. The pharmacophore model was used to screen commercial databases to retrieve potential lead candidates. The resulting hits were analyzed at each stage for diversity based on the pharmacophore model, followed by molecular docking and filtering based on their interaction with active site residues and 3D-QSAR predictions. Subsequently, MD simulations and binding free energy calculations were performed to test the predictions and to characterize interactions at the molecular level. The results suggested that the identified compounds retained the interactions with binding residues. Binding energy decomposition identified residues Glu155, Trp156 and Ala157 of site B and Leu83 and Leu207 of site C as major contributors to binding affinity, complementary to 3D-QSAR results. To best of our knowledge, this is the first comparison of WaterSwap field and 3D-QSAR maps. Overall, this integrated strategy provides a basis for the development of new and potential AK-B inhibitors and is applicable to other protein targets.
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Affiliation(s)
- Sajda Ashraf
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK
| | - Kara E Ranaghan
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK
| | - Christopher J Woods
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK
| | - Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK.
| | - Zaheer Ul-Haq
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan.
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10
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Silva JRA, Kruger HG, Molfetta FA. Drug repurposing and computational modeling for discovery of inhibitors of the main protease (M pro) of SARS-CoV-2. RSC Adv 2021; 11:23450-23458. [PMID: 35479789 PMCID: PMC9036595 DOI: 10.1039/d1ra03956c] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 06/25/2021] [Indexed: 01/08/2023] Open
Abstract
The main protease (Mpro or 3CLpro) is a conserved cysteine protease from the coronaviruses and started to be considered an important drug target for developing antivirals, as it produced a deadly outbreak of COVID-19. Herein, we used a combination of drug reposition and computational modeling approaches including molecular docking, molecular dynamics (MD) simulations, and the calculated binding free energy to evaluate a set of drugs in complex with the Mpro enzyme. Particularly, our results show that darunavir and triptorelin drugs have favorable binding free energy (−63.70 and −77.28 kcal mol−1, respectively) in complex with the Mpro enzyme. Based on the results, the structural and energetic features that explain why some drugs can be repositioned to inhibit Mpro from SARS-CoV-2 were exposed. These features should be considered for the design of novel Mpro inhibitors. Structural and energetic features explain why some drugs can be repositioned to inhibit Mpro from SARS-CoV-2.![]()
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Affiliation(s)
- José Rogério A Silva
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará Belém Pará 66075-110 Brazil
| | - Hendrik G Kruger
- Catalysis and Peptide Research Unit, University of KwaZulu-Natal Durban 4000 South Africa
| | - Fábio A Molfetta
- Laboratório de Modelagem Molecular, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará CP 11101 60075-110 Belém PA Brazil
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11
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Oliveira ASF, Ibarra AA, Bermudez I, Casalino L, Gaieb Z, Shoemark DK, Gallagher T, Sessions RB, Amaro RE, Mulholland AJ. A potential interaction between the SARS-CoV-2 spike protein and nicotinic acetylcholine receptors. Biophys J 2021; 120:983-993. [PMID: 33609494 PMCID: PMC7889469 DOI: 10.1016/j.bpj.2021.01.037] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 01/11/2021] [Accepted: 01/13/2021] [Indexed: 01/08/2023] Open
Abstract
Changeux et al. (Changeux et al. C. R. Biol. 343:33-39.) recently suggested that the SARS-CoV-2 spike protein may interact with nicotinic acetylcholine receptors (nAChRs) and that such interactions may be involved in pathology and infectivity. This hypothesis is based on the fact that the SARS-CoV-2 spike protein contains a sequence motif similar to known nAChR antagonists. Here, we use molecular simulations of validated atomically detailed structures of nAChRs and of the spike to investigate the possible binding of the Y674-R685 region of the spike to nAChRs. We examine the binding of the Y674-R685 loop to three nAChRs, namely the human α4β2 and α7 subtypes and the muscle-like αβγδ receptor from Tetronarce californica. Our results predict that Y674-R685 has affinity for nAChRs. The region of the spike responsible for binding contains a PRRA motif, a four-residue insertion not found in other SARS-like coronaviruses. The conformational behavior of the bound Y674-R685 is highly dependent on the receptor subtype; it adopts extended conformations in the α4β2 and α7 complexes but is more compact when bound to the muscle-like receptor. In the α4β2 and αβγδ complexes, the interaction of Y674-R685 with the receptors forces the loop C region to adopt an open conformation, similar to other known nAChR antagonists. In contrast, in the α7 complex, Y674-R685 penetrates deeply into the binding pocket in which it forms interactions with the residues lining the aromatic box, namely with TrpB, TyrC1, and TyrC2. Estimates of binding energy suggest that Y674-R685 forms stable complexes with all three nAChR subtypes. Analyses of simulations of the glycosylated spike show that the Y674-R685 region is accessible for binding. We suggest a potential binding orientation of the spike protein with nAChRs, in which they are in a nonparallel arrangement to one another.
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Affiliation(s)
- A Sofia F Oliveira
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, United Kingdom; Bristol Synthetic Biology Centre, BrisSynBio, Bristol, United Kingdom
| | - Amaurys Avila Ibarra
- Research Software Engineering, Advanced Computing Research Centre, University of Bristol, Bristol, United Kingdom
| | - Isabel Bermudez
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, United Kingdom
| | - Lorenzo Casalino
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California
| | - Zied Gaieb
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California
| | - Deborah K Shoemark
- School of Biochemistry, University of Bristol, Bristol, United Kingdom; Bristol Synthetic Biology Centre, BrisSynBio, Bristol, United Kingdom
| | - Timothy Gallagher
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, United Kingdom
| | | | - Rommie E Amaro
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California
| | - Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, United Kingdom.
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12
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Oliveira ASF, Ibarra AA, Bermudez I, Casalino L, Gaieb Z, Shoemark DK, Gallagher T, Sessions RB, Amaro RE, Mulholland AJ. Simulations support the interaction of the SARS-CoV-2 spike protein with nicotinic acetylcholine receptors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.07.16.206680. [PMID: 32743575 PMCID: PMC7386492 DOI: 10.1101/2020.07.16.206680] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Changeux et al. recently suggested that the SARS-CoV-2 spike (S) protein may interact with nicotinic acetylcholine receptors (nAChRs). Such interactions may be involved in pathology and infectivity. Here, we use molecular simulations of validated atomically detailed structures of nAChRs, and of the S protein, to investigate this 'nicotinic hypothesis'. We examine the binding of the Y674-R685 loop of the S protein to three nAChRs, namely the human α4β2 and α7 subtypes and the muscle-like αβγδ receptor from Tetronarce californica. Our results indicate that Y674-R685 has affinity for nAChRs and the region responsible for binding contains the PRRA motif, a four-residue insertion not found in other SARS-like coronaviruses. In particular, R682 has a key role in the stabilisation of the complexes as it forms interactions with loops A, B and C in the receptor's binding pocket. The conformational behaviour of the bound Y674-R685 region is highly dependent on the receptor subtype, adopting extended conformations in the α4β2 and α7 complexes and more compact ones when bound to the muscle-like receptor. In the α4β2 and αβγδ complexes, the interaction of Y674-R685 with the receptors forces the loop C region to adopt an open conformation similar to other known nAChR antagonists. In contrast, in the α7 complex, Y674-R685 penetrates deeply into the binding pocket where it forms interactions with the residues lining the aromatic box, namely with TrpB, TyrC1 and TyrC2. Estimates of binding energy suggest that Y674-R685 forms stable complexes with all three nAChR subtypes. Analyses of the simulations of the full-length S protein show that the Y674-R685 region is accessible for binding, and suggest a potential binding orientation of the S protein with nAChRs.
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Affiliation(s)
- A. Sofia F. Oliveira
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, UK
| | - Amaurys Avila Ibarra
- Research Software Engineering, Advanced Computing Research Centre, University of Bristol, Bristol BS1 5QD, UK
| | - Isabel Bermudez
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford OX30BP, UK
| | - Lorenzo Casalino
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093 USA
| | - Zied Gaieb
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093 USA
| | | | - Timothy Gallagher
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, UK
| | | | - Rommie E. Amaro
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093 USA
| | - Adrian J. Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, UK
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13
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Javier GM. Computational insight into the selective allosteric inhibition for PTP1B versus TCPTP: a molecular modelling study. J Biomol Struct Dyn 2020; 39:5399-5410. [PMID: 32643532 DOI: 10.1080/07391102.2020.1790421] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
All over the world, diabetes mellitus type 2 has spread as a problematic pandemic. Despite currently available treatments, approved drugs still show undesirable side effects and loss of efficacy or target symptoms instead of causes. Protein tyrosine phosphatase 1B (PTP1B), since its discovery, has emerged as a very promising target against this disease. Although the information regarding the enzyme is immense, little is known about the selectivity between this enzyme and its closest homologue, lymphocyte T tyrosine phosphatase (TCPTP), which is responsible for complicated side effects. In this study, on the basis of different computational approaches, we are able to highlight the importance of a phenylalanine residue located in PTP1B, but not in TCPTP, as a crucial hotspot that causes selectivity and stability for the whole ligand bound system. These results not only allow to explain the selectivity determinants of PTP1B but also provide a useful guide for the design of new allosteric inhibitors. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Garcia-Marin Javier
- Facultad de Farmacia, Departamento de Química Orgánica y Química Inorgánica, Universidad de Alcalá, Alcalá de Henares, Spain.,Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain.,Facultad de Farmacia, Instituto de Investigación Química Andrés M. del Río, Universidad de Alcalá, Alcalá de Henares, Spain
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14
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Kumar SP, Patel CN, Rawal RM, Pandya HA. Energetic contributions of amino acid residues and its cross‐talk to delineate ligand‐binding mechanism. Proteins 2020; 88:1207-1225. [DOI: 10.1002/prot.25894] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 02/20/2020] [Accepted: 04/03/2020] [Indexed: 02/02/2023]
Affiliation(s)
| | - Chirag N. Patel
- Department of Botany, Bioinformatics, and Climate Change Impacts ManagementUniversity School of Sciences, Gujarat University Ahmedabad India
| | - Rakesh M. Rawal
- Department of Life SciencesUniversity School of Sciences, Gujarat University Ahmedabad India
| | - Himanshu A. Pandya
- Department of Life SciencesUniversity School of Sciences, Gujarat University Ahmedabad India
- Department of Botany, Bioinformatics, and Climate Change Impacts ManagementUniversity School of Sciences, Gujarat University Ahmedabad India
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15
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Kiani YS, Ranaghan KE, Jabeen I, Mulholland AJ. Molecular Dynamics Simulation Framework to Probe the Binding Hypothesis of CYP3A4 Inhibitors. Int J Mol Sci 2019; 20:ijms20184468. [PMID: 31510073 PMCID: PMC6769491 DOI: 10.3390/ijms20184468] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 08/22/2019] [Accepted: 09/01/2019] [Indexed: 12/20/2022] Open
Abstract
The Cytochrome P450 family of heme-containing proteins plays a major role in catalyzing phase I metabolic reactions, and the CYP3A4 subtype is responsible for the metabolism of many currently marketed drugs. Additionally, CYP3A4 has an inherent affinity for a broad spectrum of structurally diverse chemical entities, often leading to drug-drug interactions mediated by the inhibition or induction of the metabolic enzyme. The current study explores the binding of selected highly efficient CYP3A4 inhibitors by docking and molecular dynamics (MD) simulation protocols and their binding free energy calculated using the WaterSwap method. The results indicate the importance of binding pocket residues including Phe57, Arg105, Arg106, Ser119, Arg212, Phe213, Thr309, Ser312, Ala370, Arg372, Glu374, Gly481 and Leu483 for interaction with CYP3A4 inhibitors. The residue-wise decomposition of the binding free energy from the WaterSwap method revealed the importance of binding site residues Arg106 and Arg372 in the stabilization of all the selected CYP3A4-inhibitor complexes. The WaterSwap binding energies were further complemented with the MM(GB/PB)SA results and it was observed that the binding energies calculated by both methods do not differ significantly. Overall, our results could guide towards the use of multiple computational approaches to achieve a better understanding of CYP3A4 inhibition, subsequently leading to the design of highly specific and efficient new chemical entities with suitable ADMETox properties and reduced side effects.
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Affiliation(s)
- Yusra Sajid Kiani
- Research Center for Modeling and Simulation (RCMS), National University of Sciences and Technology (NUST), Islamabad 44000, Pakistan.
| | - Kara E Ranaghan
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, UK.
| | - Ishrat Jabeen
- Research Center for Modeling and Simulation (RCMS), National University of Sciences and Technology (NUST), Islamabad 44000, Pakistan.
| | - Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, UK.
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16
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Chen L, Baker B, Santos E, Sheep M, Daftarian D. A Visualization Tool for Cryo-EM Protein Validation with an Unsupervised Machine Learning Model in Chimera Platform. MEDICINES (BASEL, SWITZERLAND) 2019; 6:E86. [PMID: 31390767 PMCID: PMC6789601 DOI: 10.3390/medicines6030086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 07/31/2019] [Accepted: 08/02/2019] [Indexed: 11/22/2022]
Abstract
Background: Cryo-electron microscopy (cryo-EM) has become a major technique for protein structure determination. However, due to the low quality of cryo-EM density maps, many protein structures derived from cryo-EM contain outliers introduced during the modeling process. The current protein model validation system lacks identification features for cryo-EM proteins making it not enough to identify outliers in cryo-EM proteins. Methods: This study introduces an efficient unsupervised outlier detection model for validating protein models built from cryo-EM technique. The current model uses a high-resolution X-ray dataset (<1.5 Å) as the reference dataset. The distal block distance, side-chain length, phi, psi, and first chi angle of the residues in the reference dataset are collected and saved as a database of the histogram-based outlier score (HBOS). The HBOS value of the residues in target cryo-EM proteins can be read from this HBOS database. Results: Protein residues with a HBOS value greater than ten are labeled as outliers by default. Four datasets containing proteins derived from cryo-EM density maps were tested with this probabilistic anomaly detection model. Conclusions: According to the proposed model, a visualization assistant tool was designed for Chimera, a protein visualization platform.
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Affiliation(s)
- Lin Chen
- Department of Computer Science, Valdosta State University, Valdosta, GA 31693, USA.
| | - Brandon Baker
- Department of Natural Science, Elizabeth City State University, Elizabeth City, NC 27909, USA
| | - Eduardo Santos
- Department of Natural Science, Elizabeth City State University, Elizabeth City, NC 27909, USA
| | - Michell Sheep
- Department of Mathematics & Computer Science, Elizabeth City State University, Elizabeth City, NC 27909, USA
| | - Darius Daftarian
- Department of Mathematics & Computer Science, Elizabeth City State University, Elizabeth City, NC 27909, USA
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