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Oliveira LPS, Lima LR, Silva LB, Cruz JN, Ramos RS, Lima LS, Cardoso FMN, Silva AV, Rodrigues DP, Rodrigues GS, Proietti-Junior AA, dos Santos GB, Campos JM, Santos CBR. Hierarchical Virtual Screening of Potential New Antibiotics from Polyoxygenated Dibenzofurans against Staphylococcus aureus Strains. Pharmaceuticals (Basel) 2023; 16:1430. [PMID: 37895901 PMCID: PMC10610096 DOI: 10.3390/ph16101430] [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: 08/16/2023] [Revised: 09/25/2023] [Accepted: 10/01/2023] [Indexed: 10/29/2023] Open
Abstract
Staphylococcus aureus is a microorganism with high morbidity and mortality due to antibiotic-resistant strains, making the search for new therapeutic options urgent. In this context, computational drug design can facilitate the drug discovery process, optimizing time and resources. In this work, computational methods involving ligand- and structure-based virtual screening were employed to identify potential antibacterial agents against the S. aureus MRSA and VRSA strains. To achieve this goal, tetrahydroxybenzofuran, a promising antibacterial agent according to in vitro tests described in the literature, was adopted as the pivotal molecule and derivative molecules were considered to generate a pharmacophore model, which was used to perform virtual screening on the Pharmit platform. Through this result, twenty-four molecules were selected from the MolPort® database. Using the Tanimoto Index on the BindingDB web server, it was possible to select eighteen molecules with greater structural similarity in relation to commercial antibiotics (methicillin and oxacillin). Predictions of toxicological and pharmacokinetic properties (ADME/Tox) using the eighteen most similar molecules, showed that only three exhibited desired properties (LB255, LB320 and LB415). In the molecular docking study, the promising molecules LB255, LB320 and LB415 showed significant values in both molecular targets. LB320 presented better binding affinity to MRSA (-8.18 kcal/mol) and VRSA (-8.01 kcal/mol) targets. Through PASS web server, the three molecules, specially LB320, showed potential for antibacterial activity. Synthetic accessibility (SA) analysis performed on AMBIT and SwissADME web servers showed that LB255 and LB415 can be considered difficult to synthesize and LB320 is considered easy. In conclusion, the results suggest that these ligands, particularly LB320, may bind strongly to the studied targets and may have appropriate ADME/Tox properties in experimental studies.
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Affiliation(s)
- Lana P. S. Oliveira
- Graduate Program in Biotechnology and Biodiversity-Network BIONORTE, Federal University of Amapá, Macapá 68903-419, Brazil; (L.P.S.O.); (R.S.R.); (F.M.N.C.); (A.V.S.); (A.A.P.-J.)
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapá 68902-280, Brazil; (L.R.L.); (L.B.S.); (J.N.C.)
| | - Lúcio R. Lima
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapá 68902-280, Brazil; (L.R.L.); (L.B.S.); (J.N.C.)
- Graduate Program in Network in Pharmaceutical Innovation, Federal University of Amapá, Macapá 68902-280, Brazil
- Graduate Program in Medicinal Chemistry and Molecular Modeling, Health Science Institute, Federal Univesity of Pará, Belém 66075-110, Brazil
| | - Luciane B. Silva
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapá 68902-280, Brazil; (L.R.L.); (L.B.S.); (J.N.C.)
- Graduate Program in Medicinal Chemistry and Molecular Modeling, Health Science Institute, Federal Univesity of Pará, Belém 66075-110, Brazil
| | - Jorddy N. Cruz
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapá 68902-280, Brazil; (L.R.L.); (L.B.S.); (J.N.C.)
| | - Ryan S. Ramos
- Graduate Program in Biotechnology and Biodiversity-Network BIONORTE, Federal University of Amapá, Macapá 68903-419, Brazil; (L.P.S.O.); (R.S.R.); (F.M.N.C.); (A.V.S.); (A.A.P.-J.)
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapá 68902-280, Brazil; (L.R.L.); (L.B.S.); (J.N.C.)
| | - Luciana S. Lima
- Special Laboratory of Applied Microbiology, Department of Biological and Health Sciences, Federal University of Amapá, Macapá 68902-280, Brazil;
| | - Francy M. N. Cardoso
- Graduate Program in Biotechnology and Biodiversity-Network BIONORTE, Federal University of Amapá, Macapá 68903-419, Brazil; (L.P.S.O.); (R.S.R.); (F.M.N.C.); (A.V.S.); (A.A.P.-J.)
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapá 68902-280, Brazil; (L.R.L.); (L.B.S.); (J.N.C.)
- Special Laboratory of Applied Microbiology, Department of Biological and Health Sciences, Federal University of Amapá, Macapá 68902-280, Brazil;
| | - Aderaldo V. Silva
- Graduate Program in Biotechnology and Biodiversity-Network BIONORTE, Federal University of Amapá, Macapá 68903-419, Brazil; (L.P.S.O.); (R.S.R.); (F.M.N.C.); (A.V.S.); (A.A.P.-J.)
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapá 68902-280, Brazil; (L.R.L.); (L.B.S.); (J.N.C.)
| | - Dália P. Rodrigues
- Laboratory of Bacterial Enteric Pathogens, Oswaldo Cruz Foundation, FIOCRUZ, Rio de Janeiro 21045-900, Brazil;
| | - Gabriela S. Rodrigues
- Graduate Program in Health Sciences, Institute of Collective Health, Federal University of Western Pará, Santarém 68270-000, Brazil; (G.S.R.); (G.B.d.S.)
| | - Aldo A. Proietti-Junior
- Graduate Program in Biotechnology and Biodiversity-Network BIONORTE, Federal University of Amapá, Macapá 68903-419, Brazil; (L.P.S.O.); (R.S.R.); (F.M.N.C.); (A.V.S.); (A.A.P.-J.)
- Special Laboratory of Applied Microbiology, Department of Biological and Health Sciences, Federal University of Amapá, Macapá 68902-280, Brazil;
| | - Gabriela B. dos Santos
- Graduate Program in Health Sciences, Institute of Collective Health, Federal University of Western Pará, Santarém 68270-000, Brazil; (G.S.R.); (G.B.d.S.)
| | - Joaquín M. Campos
- Department of Pharmaceutical and Organic Chemistry, Faculty of Pharmacy, Institute of Biosanitary Research ibs. GRANADA, University of Granada, 18071 Granada, Spain;
| | - Cleydson B. R. Santos
- Graduate Program in Biotechnology and Biodiversity-Network BIONORTE, Federal University of Amapá, Macapá 68903-419, Brazil; (L.P.S.O.); (R.S.R.); (F.M.N.C.); (A.V.S.); (A.A.P.-J.)
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapá 68902-280, Brazil; (L.R.L.); (L.B.S.); (J.N.C.)
- Graduate Program in Network in Pharmaceutical Innovation, Federal University of Amapá, Macapá 68902-280, Brazil
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Coumarin-Based Sulfonamide Derivatives as Potential DPP-IV Inhibitors: Pre-ADME Analysis, Toxicity Profile, Computational Analysis, and In Vitro Enzyme Assay. Molecules 2023; 28:molecules28031004. [PMID: 36770672 PMCID: PMC9921777 DOI: 10.3390/molecules28031004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 12/31/2022] [Accepted: 01/04/2023] [Indexed: 01/20/2023] Open
Abstract
Recent research on dipeptidyl peptidase-IV (DPP-IV) inhibitors has made it feasible to treat type 2 diabetes mellitus (T2DM) with minimal side effects. Therefore, in the present investigation, we aimed to discover and develop some coumarin-based sulphonamides as potential DPP-IV inhibitors in light of the fact that molecular hybridization of many bioactive pharmacophores frequently results in synergistic activity. Each of the proposed derivatives was subjected to an in silico virtual screening, and those that met all of the criteria and had a higher binding affinity with the DPP-IV enzyme were then subjected to wet lab synthesis, followed by an in vitro biological evaluation. The results of the pre-ADME and pre-tox predictions indicated that compounds 6e, 6f, 6h, and 6m to 6q were inferior and violated the most drug-like criteria. It was observed that 6a, 6b, 6c, 6d, 6i, 6j, 6r, 6s, and 6t displayed less binding free energy (PDB ID: 5Y7H) than the reference inhibitor and demonstrated drug-likeness properties, hence being selected for wet lab synthesis and the structures being confirmed by spectral analysis. In the in vitro enzyme assay, the standard drug Sitagliptin had an IC50 of 0.018 µM in the experiment which is the most potent. All the tested compounds also displayed significant inhibition of the DPP-IV enzyme, but 6i and 6j demonstrated 10.98 and 10.14 µM IC50 values, respectively, i.e., the most potent among the synthesized compounds. Based on our findings, we concluded that coumarin-based sulphonamide derivatives have significant DPP-IV binding ability and exhibit optimal enzyme inhibition in an in vitro enzyme assay.
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Chavan PA, Jadhav SB. Synthesis, Characterization and Screening of Some Novel 2-Methyl-N'-
[(Z)-Substituted-Phenyl ethylidene] Imidazo [1, 2-a] Pyridine-3-Carbohy
drazide Derivatives as DPP-IV Inhibitors for the Treatment of Type 2 Diabetes
Mellitus. LETT DRUG DES DISCOV 2022. [DOI: 10.2174/1570180818666210901125958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
One of the leading global metabolic diseases marked by insulin resistance and
chronic hyperglycemia is type 2 diabetes mellitus (T2DM). Since the last decade, DPP-4 enzyme inhibition
has proven to be a successful, safe, and well-established therapy for the treatment of T2DM.
Objective:
The present work reports the synthesis, characterization, and screening of some novel 2-
methyl-N'-[(Z)-substituted-phenyl ethylidene] imidazo [1, 2-a] pyridine-3-carbohydrazide derivatives as
DPP-IV inhibitors for the treatment of T2DM.
Methods:
The molecular docking was performed to study these derivatives' binding mode in the enzyme's
allosteric site. All the synthesized compounds were subjected for DPP-IV enzyme assay and in vivo antihyperglycemic
activity in STZ-induced diabetic rats.
Results:
The synthesized derivatives exhibited potent antidiabetic activity as compared to the standard
drug Sitagliptin. Out of sixteen compounds, A1, A4, B4, C2, C3, and D4 have shown promising antidiabetic
activity against the DPP-IV enzyme. The most promising compound, C2, showed a percentage inhibition
of 72.02±0.27 at 50 μM concentration. On the 21st-day, compound C2 showed a significant reduction
in serum blood glucose level, i.e., 156.16±4.87 mg/dL, then diabetic control, which was
280.00±13.29 mg/dL whereas, standard Sitagliptin showed 133.50±11.80 mg/dL. In the in vivo antihyperglycemic
activity, the compounds have exhibited good hypoglycemic potential in fasting blood glucose
in the T2DM animal model. All the docked molecules have exhibited perfect binding affinity towards
the active pocket of the enzyme. The synthesized derivatives were screened through Lipinski's rule
of five for better optimization, and fortunately, none of them violated the rule.
Conclusion:
The above results indicate that compound C2 is a relatively active and selective hit molecule
that can be structurally modified to enhance the DPP-IV inhibitor's potency and overall pharmacological
profile. From the present work, it has been concluded that substituted pyridine-3-carbohydrazide derivatives
possess excellent DPP-IV inhibitory potential and can be better optimized further by generating
more in vivo, in vitro models.
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Affiliation(s)
- Prerana A. Chavan
- Department of Pharmaceutical Chemistry, PES\'s Modern College of Pharmacy, Nigdi, Pune, Maharashtra 411044,
India
| | - Shailaja B. Jadhav
- Department of Pharmaceutical Chemistry, PES\'s Modern College of Pharmacy, Nigdi, Pune, Maharashtra 411044,
India
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4
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Neto RDAM, Santos CBR, Henriques SVC, Machado LDO, Cruz JN, da Silva CHTDP, Federico LB, Oliveira EHCD, de Souza MPC, da Silva PNB, Taft CA, Ferreira IM, Gomes MRF. Novel chalcones derivatives with potential antineoplastic activity investigated by docking and molecular dynamics simulations. J Biomol Struct Dyn 2020; 40:2204-2216. [DOI: 10.1080/07391102.2020.1839562] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Raimundo de A. M. Neto
- Departamento de Ciências Biológicas e da Saúde, Universidade Federal do Amapá, Macapá, Brasil
| | - Cleydson B. R. Santos
- Departamento de Ciências Biológicas e da Saúde, Universidade Federal do Amapá, Macapá, Brasil
| | | | - Letícia de O. Machado
- Departamento de Ciências Biológicas e da Saúde, Universidade Federal do Amapá, Macapá, Brasil
| | - Jorddy N. Cruz
- Departamento de Ciências Biológicas e da Saúde, Universidade Federal do Amapá, Macapá, Brasil
| | | | - Leonardo B. Federico
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brasil
| | | | | | | | - Carlton A. Taft
- Centro Brasileiro de Pesquisas Físicas, Urca, Rio de Janeiro, Brasil
| | | | - Madson R. F. Gomes
- Departamento de Ciências Biológicas e da Saúde, Universidade Federal do Amapá, Macapá, Brasil
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5
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Santos CBR, Santos KLB, Cruz JN, Leite FHA, Borges RS, Taft CA, Campos JM, Silva CHTP. Molecular modeling approaches of selective adenosine receptor type 2A agonists as potential anti-inflammatory drugs. J Biomol Struct Dyn 2020; 39:3115-3127. [PMID: 32338151 DOI: 10.1080/07391102.2020.1761878] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Adenosine A2A receptor (A2AR) is the predominant receptor in immune cells, where its activation triggers cAMP-mediated immunosuppressive signaling and the underlying inhibition of T cells activation and T cells-induced effects mediated by cAMP-dependent kinase proteins mechanisms. In this study, were used ADME/Tox, molecular docking and molecular dynamics simulations to investigate selective adenosine A2AR agonists as potential anti-inflammatory drugs. As a result, we obtained two promising compounds (A and B) that have satisfactory pharmacokinetic and toxicological properties and were able to interact with important residues of the A2AR binding cavity and during the molecular dynamics simulations were able to keep the enzyme complexed.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Cleydson B R Santos
- Graduate Program in Biotechnology and Biodiversity-Network BIONORTE, Federal University of Amapá, Macapá, Brazil.,Laboratory of Modeling and Computational Chemistry, Department of Biological Sciences and Health, Federal University of Amapá, Macapá, Brazil.,Graduate Program in Medicinal Chemistry and Molecular Modeling, Institute of Health Sciences, Federal University of Pará, Belém, Brazil.,Computational Laboratory of Pharmaceutical Chemistry, Faculty of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Kelton L B Santos
- Graduate Program in Biotechnology and Biodiversity-Network BIONORTE, Federal University of Amapá, Macapá, Brazil.,Laboratory of Modeling and Computational Chemistry, Department of Biological Sciences and Health, Federal University of Amapá, Macapá, Brazil.,Graduate Program in Medicinal Chemistry and Molecular Modeling, Institute of Health Sciences, Federal University of Pará, Belém, Brazil
| | - Jorddy N Cruz
- Laboratory of Modeling and Computational Chemistry, Department of Biological Sciences and Health, Federal University of Amapá, Macapá, Brazil
| | - Franco H A Leite
- Laboratory of Molecular Modeling, State University of Feira de Santana, Feira de Santana-Bahia, Brazil
| | - Rosivaldo S Borges
- Graduate Program in Medicinal Chemistry and Molecular Modeling, Institute of Health Sciences, Federal University of Pará, Belém, Brazil
| | - Carlton A Taft
- Brazilian Center for Physical Research, Rio de Janeiro, Brazil
| | - Joaquín M Campos
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Biosanitary Institute of Granada (Ibs.GRANADA), Campus of Cartuja, University of Granada, Granada, Spain
| | - Carlos H T P Silva
- Computational Laboratory of Pharmaceutical Chemistry, Faculty of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil.,Department of Chemistry, Faculty of Philosophy, Sciences and Letters of Ribeirão Preto, University of São Paulo, Ribeirão Preto-SP, Brazil
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6
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Identification of Novel Chemical Entities for Adenosine Receptor Type 2A Using Molecular Modeling Approaches. Molecules 2020; 25:molecules25051245. [PMID: 32164183 PMCID: PMC7179438 DOI: 10.3390/molecules25051245] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 03/01/2020] [Accepted: 03/06/2020] [Indexed: 12/20/2022] Open
Abstract
Adenosine Receptor Type 2A (A2AAR) plays a role in important processes, such as anti-inflammatory ones. In this way, the present work aimed to search for compounds by pharmacophore-based virtual screening. The pharmacokinetic/toxicological profiles of the compounds, as well as a robust QSAR, predicted the binding modes via molecular docking. Finally, we used molecular dynamics to investigate the stability of interactions from ligand-A2AAR. For the search for A2AAR agonists, the UK-432097 and a set of 20 compounds available in the BindingDB database were studied. These compounds were used to generate pharmacophore models. Molecular properties were used for construction of the QSAR model by multiple linear regression for the prediction of biological activity. The best pharmacophore model was used by searching for commercial compounds in databases and the resulting compounds from the pharmacophore-based virtual screening were applied to the QSAR. Two compounds had promising activity due to their satisfactory pharmacokinetic/toxicological profiles and predictions via QSAR (Diverset 10002403 pEC50 = 7.54407; ZINC04257548 pEC50 = 7.38310). Moreover, they had satisfactory docking and molecular dynamics results compared to those obtained for Regadenoson (Lexiscan®), used as the positive control. These compounds can be used in biological assays (in vitro and in vivo) in order to confirm the potential activity agonist to A2AAR.
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7
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Keita H, dos Santos CBR, Ramos MM, Padilha EC, Serafim RB, Castro AN, Amado JRR, da Silva GM, Ferreira IM, Giuliatti S, Carvalho JCT. Assessment of the hypoglycemic effect of Bixin in alloxan-induced diabetic rats: in vivo and in silico studies. J Biomol Struct Dyn 2020; 39:1017-1028. [DOI: 10.1080/07391102.2020.1724567] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Hady Keita
- Laboratory of Drugs Discovery, Department of Biological Sciences and Health, Federal University of Amapá, Macapá, Brazil
- Division of Post-Grade, University of the Sierra, Ixtlán de Juárez, México
| | - Cleydson Breno Rodrigues dos Santos
- Laboratory of Drugs Discovery, Department of Biological Sciences and Health, Federal University of Amapá, Macapá, Brazil
- Laboratory of Modeling and Computational Chemistry, Department of Biological Sciences and Health, Federal University of Amapa, Macapá, Brazil
| | - Matheus Mercês Ramos
- Research Group Biocatalysis and Apllied Organic Synthesis, Federal University of Amapa, Macapá, Brazil
| | - Elias Carvalho Padilha
- Department of Natural Active Principles and Toxicology, Faculty of Pharmaceutical Sciences, São Paulo State University, Araraquara, Brazil
| | - Rodolfo Bortolozo Serafim
- Department of Cellular and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo (USP), Ribeirão Preto, Brazil
| | - Andres Navarrete Castro
- Laboratory of Pharmacology of Natural Products, Faculty of Chemistry, Department of Pharmacy, Universidad Autonoma Nacional de Mexico, Ciudad de Mexico, Mexico
| | - Jesus Rafael Rodriguez Amado
- Laboratory of Drugs Discovery, Department of Biological Sciences and Health, Federal University of Amapá, Macapá, Brazil
| | - Gabriel Monteiro da Silva
- Bioinformatics Group, Department of Genetics, Ribeirão Preto Medical School, University of São Paulo (USP), Ribeirão Preto, Brazil
| | - Irlon Maciel Ferreira
- Research Group Biocatalysis and Apllied Organic Synthesis, Federal University of Amapa, Macapá, Brazil
| | - Silvana Giuliatti
- Bioinformatics Group, Department of Genetics, Ribeirão Preto Medical School, University of São Paulo (USP), Ribeirão Preto, Brazil
| | - José Carlos Tavares Carvalho
- Laboratory of Drugs Discovery, Department of Biological Sciences and Health, Federal University of Amapá, Macapá, Brazil
- Laboratory of Modeling and Computational Chemistry, Department of Biological Sciences and Health, Federal University of Amapa, Macapá, Brazil
- Research Group Biocatalysis and Apllied Organic Synthesis, Federal University of Amapa, Macapá, Brazil
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8
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Identification of New Inhibitors with Potential Antitumor Activity from Polypeptide Structures via Hierarchical Virtual Screening. Molecules 2019; 24:molecules24162943. [PMID: 31416180 PMCID: PMC6720962 DOI: 10.3390/molecules24162943] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 08/08/2019] [Accepted: 08/10/2019] [Indexed: 12/12/2022] Open
Abstract
Leukemias are neoplasms that affect hematopoietic cells, which are developed by genetic alterations (mutations) that lead to the loss of proliferation control mechanisms (maturation and/or cell death). The α4β1 integrin receptor is a therapeutic target for inflammation, autoimmune diseases and lymphoid tumors. This study was carried out to search through the antagonists-based virtual screening for α4β1 receptor. Initially, seventeen (17) structures were selected (based on the inhibitory activity values, IC50) and the structure with the best value was chosen as the pivot. The pharmacophoric pattern was determined from the online PharmaGist server and resulted in a model of score value equal to 97.940 with 15 pharmacophoric characteristics that were statistically evaluated via Pearson correlations, principal component analysis (PCA) and hierarchical clustering analysis (HCA). A refined model generated four pharmacophoric hypotheses totaling 1.478 structures set of Zinc_database. After, the pharmacokinetic, toxicological and biological activity predictions were realized comparing with pivot structure that resulted in five (ZINC72088291, ZINC68842860, ZINC14365931, ZINC09588345 and ZINC91247798) structures with optimal in silico predictions. Therefore, future studies are needed to confirm antitumor potential activity of molecules selected this work with in vitro and in vivo assays.
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9
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“Ideal correlations” for biological activity of peptides. Biosystems 2019; 181:51-57. [DOI: 10.1016/j.biosystems.2019.04.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 02/18/2019] [Accepted: 04/12/2019] [Indexed: 02/08/2023]
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10
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Bittencourt JAHM, Neto MFA, Lacerda PS, Bittencourt RCVS, Silva RC, Lobato CC, Silva LB, Leite FHA, Zuliani JP, Rosa JMC, Borges RS, Santos CBR. In Silico Evaluation of Ibuprofen and Two Benzoylpropionic Acid Derivatives with Potential Anti-Inflammatory Activity. Molecules 2019; 24:E1476. [PMID: 30991684 PMCID: PMC6515000 DOI: 10.3390/molecules24081476] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2019] [Revised: 04/07/2019] [Accepted: 04/11/2019] [Indexed: 12/19/2022] Open
Abstract
Inflammation is a complex reaction involving cellular and molecular components and an unspecific response to a specific aggression. The use of scientific and technological innovations as a research tool combining multidisciplinary knowledge in informatics, biotechnology, chemistry and biology are essential for optimizing time and reducing costs in the drug design. Thus, the integration of these in silico techniques makes it possible to search for new anti-inflammatory drugs with better pharmacokinetic and toxicological profiles compared to commercially used drugs. This in silico study evaluated the anti-inflammatory potential of two benzoylpropionic acid derivatives (MBPA and DHBPA) using molecular docking and their thermodynamic profiles by molecular dynamics, in addition to predicting oral bioavailability, bioactivity and toxicity. In accordance to our predictions the derivatives proposed here had the potential capacity for COX-2 inhibition in the human and mice enzyme, due to containing similar interactions with the control compound (ibuprofen). Ibuprofen showed toxic predictions of hepatotoxicity (in human, mouse and rat; toxicophoric group 2-arylacetic or 3-arylpropionic acid) and irritation of the gastrointestinal tract (in human, mouse and rat; toxicophoric group alpha-substituted propionic acid or ester) confirming the literature data, as well as the efficiency of the DEREK 10.0.2 program. Moreover, the proposed compounds are predicted to have a good oral bioavailability profile and low toxicity (LD50 < 700 mg/kg) and safety when compared to the commercial compound. Therefore, future studies are necessary to confirm the anti-inflammatory potential of these compounds.
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Affiliation(s)
- José A H M Bittencourt
- Graduate Program of Pharmaceutical Innovation, Federal University of Amapá, Macapá-AP 68902-280, Brazil.
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapá-AP 68902-280, Brazil.
| | - Moysés F A Neto
- Laboratory of Molecular Modeling, State University of Feira de Santana, Feira de Santana-BA 44036-900, Brazil.
| | - Pedro S Lacerda
- Laboratory of Bioinformatics and Molecular Modeling, School of Pharmacy, Federal University of Bahia, Barão de Jeremoabo Street, Salvador 40170-115, BA, Brazil.
| | - Renata C V S Bittencourt
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapá-AP 68902-280, Brazil.
| | - Rai C Silva
- Computational Laboratory of Pharmaceutical Chemistry, University of Sao Paulo, Av. Prof. do Café, s/n - Monte Alegre, Ribeirão Preto, São Paulo 14040-903, Brazil.
| | - Cleison C Lobato
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapá-AP 68902-280, Brazil.
- Nucleus of Studies and Selection of Bioactive Molecules, Institute of Health Sciences, Federal University of Pará, Belém-PA 66075-110, Brazil.
| | - Luciane B Silva
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapá-AP 68902-280, Brazil.
| | - Franco H A Leite
- Laboratory of Molecular Modeling, State University of Feira de Santana, Feira de Santana-BA 44036-900, Brazil.
| | - Juliana P Zuliani
- Laboratory Cellular Immunology Applied to Health, Oswaldo Cruz Foundation, FIOCRUZ Rondônia, Rua da Beira, 7671 BR-364, Porto Velho-RO 78912-000, Brazil.
| | - Joaquín M C Rosa
- Department of Pharmaceutical and Organic Chemistry, Faculty of Pharmacy, Institute of Biosanitary Research ibs.GRANADA. University of Granada, 18071 Granada, Spain.
| | - Rosivaldo S Borges
- Graduate Program of Pharmaceutical Innovation, Federal University of Amapá, Macapá-AP 68902-280, Brazil.
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapá-AP 68902-280, Brazil.
- Nucleus of Studies and Selection of Bioactive Molecules, Institute of Health Sciences, Federal University of Pará, Belém-PA 66075-110, Brazil.
| | - Cleydson B R Santos
- Graduate Program of Pharmaceutical Innovation, Federal University of Amapá, Macapá-AP 68902-280, Brazil.
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapá-AP 68902-280, Brazil.
- Nucleus of Studies and Selection of Bioactive Molecules, Institute of Health Sciences, Federal University of Pará, Belém-PA 66075-110, Brazil.
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Ramos RDS, Costa JDS, Silva RC, da Costa GV, Rodrigues ABL, Rabelo ÉDM, Souto RNP, Taft CA, Silva CHTDPD, Rosa JMC, Santos CBRD, Macêdo WJDC. Identification of Potential Inhibitors from Pyriproxyfen with Insecticidal Activity by Virtual Screening. Pharmaceuticals (Basel) 2019; 12:E20. [PMID: 30691028 PMCID: PMC6469432 DOI: 10.3390/ph12010020] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 01/17/2019] [Accepted: 01/19/2019] [Indexed: 01/15/2023] Open
Abstract
Aedes aegypti is the main vector of dengue fever transmission, yellow fever, Zika, and chikungunya in tropical and subtropical regions and it is considered to cause health risks to millions of people in the world. In this study, we search to obtain new molecules with insecticidal potential against Ae. aegypti via virtual screening. Pyriproxyfen was chosen as a template compound to search molecules in the database Zinc_Natural_Stock (ZNSt) with structural similarity using ROCS (rapid overlay of chemical structures) and EON (electrostatic similarity) software, and in the final search, the top 100 were selected. Subsequently, in silico pharmacokinetic and toxicological properties were determined resulting in a total of 14 molecules, and these were submitted to the PASS online server for the prediction of biological insecticide and acetylcholinesterase activities, and only two selected molecules followed for the molecular docking study to evaluate the binding free energy and interaction mode. After these procedures were performed, toxicity risk assessment such as LD50 values in mg/kg and toxicity class using the PROTOX online server, were undertaken. Molecule ZINC00001624 presented potential for inhibition for the acetylcholinesterase enzyme (insect and human) with a binding affinity value of -10.5 and -10.3 kcal/mol, respectively. The interaction with the juvenile hormone was -11.4 kcal/mol for the molecule ZINC00001021. Molecules ZINC00001021 and ZINC00001624 had excellent predictions in all the steps of the study and may be indicated as the most promising molecules resulting from the virtual screening of new insecticidal agents.
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Affiliation(s)
- Ryan da Silva Ramos
- Postgraduate Program in Biotechnology and Biodiversity-Network BIONORTE, Federal University of Amapá, Macapá, Amapá 68903-419, Brazil.
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapá 68902-280, AP, Brazil.
- Laboratory of Molecular Modeling and Simulation System, Federal Rural University of Amazônia, Capanema, Pará 68700-030, Brazil.
| | - Josivan da Silva Costa
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapá 68902-280, AP, Brazil.
- Laboratory of Molecular Modeling and Simulation System, Federal Rural University of Amazônia, Capanema, Pará 68700-030, Brazil.
| | - Rai Campos Silva
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapá 68902-280, AP, Brazil.
- Computational Laboratory of Pharmaceutical Chemistry, Faculty of Pharmaceutical Sciences of Ribeirão Preto, São Paulo 14040-903, Brazil;.
| | - Glauber Vilhena da Costa
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapá 68902-280, AP, Brazil.
| | - Alex Bruno Lobato Rodrigues
- Postgraduate Program in Biotechnology and Biodiversity-Network BIONORTE, Federal University of Amapá, Macapá, Amapá 68903-419, Brazil.
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapá 68902-280, AP, Brazil.
| | - Érica de Menezes Rabelo
- Postgraduate Program in Biotechnology and Biodiversity-Network BIONORTE, Federal University of Amapá, Macapá, Amapá 68903-419, Brazil.
| | | | | | - Carlos Henrique Tomich de Paula da Silva
- Laboratory of Molecular Modeling and Simulation System, Federal Rural University of Amazônia, Capanema, Pará 68700-030, Brazil.
- Computational Laboratory of Pharmaceutical Chemistry, Faculty of Pharmaceutical Sciences of Ribeirão Preto, São Paulo 14040-903, Brazil;.
| | | | - Cleydson Breno Rodrigues Dos Santos
- Postgraduate Program in Biotechnology and Biodiversity-Network BIONORTE, Federal University of Amapá, Macapá, Amapá 68903-419, Brazil.
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapá 68902-280, AP, Brazil.
- Computational Laboratory of Pharmaceutical Chemistry, Faculty of Pharmaceutical Sciences of Ribeirão Preto, São Paulo 14040-903, Brazil;.
| | - Williams Jorge da Cruz Macêdo
- Postgraduate Program in Biotechnology and Biodiversity-Network BIONORTE, Federal University of Amapá, Macapá, Amapá 68903-419, Brazil.
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapá 68902-280, AP, Brazil.
- Laboratory of Molecular Modeling and Simulation System, Federal Rural University of Amazônia, Capanema, Pará 68700-030, Brazil.
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12
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Borges RS, Palheta IC, Ota SSB, Morais RB, Barros VA, Ramos RS, Silva RC, Costa JDS, Silva CHTP, Campos JM, Santos CBR. Toward of Safer Phenylbutazone Derivatives by Exploration of Toxicity Mechanism. Molecules 2019; 24:molecules24010143. [PMID: 30609687 PMCID: PMC6337259 DOI: 10.3390/molecules24010143] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Revised: 12/12/2018] [Accepted: 12/15/2018] [Indexed: 12/18/2022] Open
Abstract
A drug design for safer phenylbutazone was been explored by reactivity and docking studies involving single electron transfer mechanism, as well as toxicological predictions. Several approaches about its structural properties were performed through quantum chemistry calculations at the B3LYP level of theory, together with the 6-31+G(d,p) basis sets. Molecular orbital and ionization potential were associated to electron donation capacity. The spin densities contribution showed a preferential hydroxylation at the para-positions of phenyl ring when compared to other positions. In addition, on electron abstractions the aromatic hydroxylation has more impact than alkyl hydroxylation. Docking studies indicate that six structures 1, 7, 8 and 13–15 have potential for inhibiting human as well as murine COX-2, due to regions showing similar intermolecular interactions to the observed for the control compounds (indomethacin and refecoxib). Toxicity can be related to aromatic hydroxylation. In accordance to our calculations, the derivatives here proposed are potentially more active as well safer than phenylbutazone and only structures 8 and 13–15 were the most promising. Such results can explain the biological properties of phenylbutazone and support the design of potentially safer candidates.
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Affiliation(s)
- Rosivaldo S Borges
- Núcleo de Estudos e Seleção de Moléculas Bioativas-NESBio, College of Pharmacy, Health Sciences Institute, Federal University of Pará, Belém 66075-110, PA, Brazil.
- Programa de Pós-Graduação em Química Medicinal e Modelagem Molecular, Health Science Institute, Federal University of Pará, Belém 66075-110, PA, Brazil.
| | - Ivanete C Palheta
- Núcleo de Estudos e Seleção de Moléculas Bioativas-NESBio, College of Pharmacy, Health Sciences Institute, Federal University of Pará, Belém 66075-110, PA, Brazil.
| | - Sirlene S B Ota
- Núcleo de Estudos e Seleção de Moléculas Bioativas-NESBio, College of Pharmacy, Health Sciences Institute, Federal University of Pará, Belém 66075-110, PA, Brazil.
- Programa de Pós-Graduação em Química Medicinal e Modelagem Molecular, Health Science Institute, Federal University of Pará, Belém 66075-110, PA, Brazil.
| | - Roberto B Morais
- Núcleo de Estudos e Seleção de Moléculas Bioativas-NESBio, College of Pharmacy, Health Sciences Institute, Federal University of Pará, Belém 66075-110, PA, Brazil.
- Programa de Pós-Graduação em Química Medicinal e Modelagem Molecular, Health Science Institute, Federal University of Pará, Belém 66075-110, PA, Brazil.
| | - Valéria A Barros
- Núcleo de Estudos e Seleção de Moléculas Bioativas-NESBio, College of Pharmacy, Health Sciences Institute, Federal University of Pará, Belém 66075-110, PA, Brazil.
- Programa de Pós-Graduação em Química Medicinal e Modelagem Molecular, Health Science Institute, Federal University of Pará, Belém 66075-110, PA, Brazil.
| | - Ryan S Ramos
- Programa de Pós-Graduação em Biodiversidade e Biotecnologia-Rede BIONORTE, Federal University of Amapá, Macapá 68902-280, AP, Brazil.
| | - Rai C Silva
- Programa de Pós-Graduação em Química Medicinal e Modelagem Molecular, Health Science Institute, Federal University of Pará, Belém 66075-110, PA, Brazil.
- Laboratorio de Modelagem e Química Computacional-LMQC, Federal University of Amapá, Department of Biological Sciences. Rod. Juscelino Kubitschek, Km 02, Macapá 68902-280, AP, Brazil.
| | - Josivan da S Costa
- Laboratorio de Modelagem e Química Computacional-LMQC, Federal University of Amapá, Department of Biological Sciences. Rod. Juscelino Kubitschek, Km 02, Macapá 68902-280, AP, Brazil.
| | - Carlos H T P Silva
- Laboratório Computacional de Química Farmacêutica, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, University of Sao Paulo, São Paulo 14040-903, SP, Brazil.
| | - Joaquín M Campos
- Department of Pharmaceutical Organic Chemistry, University of Granada, 18071 Granada, Spain.
| | - Cleydson B R Santos
- Programa de Pós-Graduação em Química Medicinal e Modelagem Molecular, Health Science Institute, Federal University of Pará, Belém 66075-110, PA, Brazil.
- Programa de Pós-Graduação em Biodiversidade e Biotecnologia-Rede BIONORTE, Federal University of Amapá, Macapá 68902-280, AP, Brazil.
- Laboratorio de Modelagem e Química Computacional-LMQC, Federal University of Amapá, Department of Biological Sciences. Rod. Juscelino Kubitschek, Km 02, Macapá 68902-280, AP, Brazil.
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13
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Costa JDS, Ramos RDS, Costa KDSL, Brasil DDSB, Silva CHTDPD, Ferreira EFB, Borges RDS, Campos JM, Macêdo WJDC, Santos CBRD. An In Silico Study of the Antioxidant Ability for Two Caffeine Analogs Using Molecular Docking and Quantum Chemical Methods. Molecules 2018; 23:molecules23112801. [PMID: 30380600 PMCID: PMC6278550 DOI: 10.3390/molecules23112801] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Revised: 10/01/2018] [Accepted: 10/11/2018] [Indexed: 12/13/2022] Open
Abstract
The antioxidant activity of molecules constitutes an important factor for the regulation of redox homeostasis and reduction of the oxidative stress. Cells affected by oxidative stress can undergo genetic alteration, causing structural changes and promoting the onset of chronic diseases, such as cancer. We have performed an in silico study to evaluate the antioxidant potential of two molecules of the zinc database: ZINC08706191 (Z91) and ZINC08992920 (Z20). Molecular docking, quantum chemical calculations (HF/6-31G**) and Pearson’s correlation have been performed. Molecular docking results of Z91 and Z20 showed both the lower binding affinity (BA) and inhibition constant (Ki) values for the receptor-ligand interactions in the three tested enzymes (cytochrome P450—CP450, myeloperoxidase—MP and NADPH oxidase—NO) than the control molecules (5-fluorouracil—FLU, melatonin—MEL and dextromethorphan—DEX, for each receptor respectively). Molecular descriptors were correlated with Ki and strong correlations were observed for the CP450, MP and NO receptors. These and other results attest the significant antioxidant ability of Z91 and Z20, that may be indicated for further analyses in relation to the control of oxidative stress and as possible antioxidant agents to be used in the pharmaceutical industry.
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Affiliation(s)
- Josivan da Silva Costa
- Postgraduate Program in Biotechnology and Biodiversity-Network BIONORTE, Federal University of Pará, Rua Augusto Corrêa, 01, Belém, Pará 66075110, Brazil.
- Laboratory of Modeling and Computational Chemistry, Department of Biological Sciences, Federal University of Amapá, Rod. Juscelino Kubitschek, Km 02, s/n, Macapá, Amapá 68902-280, Brazil.
- Laboratory of Molecular Modeling and Simulation System, Federal Rural University of Amazônia, Rua João Pessoa, 121, Capanema, Pará 68700-030, Brazil.
| | - Ryan da Silva Ramos
- Laboratory of Modeling and Computational Chemistry, Department of Biological Sciences, Federal University of Amapá, Rod. Juscelino Kubitschek, Km 02, s/n, Macapá, Amapá 68902-280, Brazil.
- Laboratory of Molecular Modeling and Simulation System, Federal Rural University of Amazônia, Rua João Pessoa, 121, Capanema, Pará 68700-030, Brazil.
| | - Karina da Silva Lopes Costa
- Laboratory of Modeling and Computational Chemistry, Department of Biological Sciences, Federal University of Amapá, Rod. Juscelino Kubitschek, Km 02, s/n, Macapá, Amapá 68902-280, Brazil.
| | | | | | - Elenilze Figueiredo Batista Ferreira
- Laboratory of Modeling and Computational Chemistry, Department of Biological Sciences, Federal University of Amapá, Rod. Juscelino Kubitschek, Km 02, s/n, Macapá, Amapá 68902-280, Brazil.
| | - Rosivaldo Dos Santos Borges
- Postgraduate Program in Biotechnology and Biodiversity-Network BIONORTE, Federal University of Pará, Rua Augusto Corrêa, 01, Belém, Pará 66075110, Brazil.
| | - Joaquín María Campos
- Department of Pharmaceutical and Organic Chemistry, University of Granada, Campus of Cartuja, 18071 Granada, Spain.
| | - Williams Jorge da Cruz Macêdo
- Postgraduate Program in Biotechnology and Biodiversity-Network BIONORTE, Federal University of Pará, Rua Augusto Corrêa, 01, Belém, Pará 66075110, Brazil.
- Laboratory of Molecular Modeling and Simulation System, Federal Rural University of Amazônia, Rua João Pessoa, 121, Capanema, Pará 68700-030, Brazil.
| | - Cleydson Breno Rodrigues Dos Santos
- Laboratory of Modeling and Computational Chemistry, Department of Biological Sciences, Federal University of Amapá, Rod. Juscelino Kubitschek, Km 02, s/n, Macapá, Amapá 68902-280, Brazil.
- Laboratory of Molecular Modeling and Simulation System, Federal Rural University of Amazônia, Rua João Pessoa, 121, Capanema, Pará 68700-030, Brazil.
- Department of Pharmaceutical and Organic Chemistry, University of Granada, Campus of Cartuja, 18071 Granada, Spain.
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Computational design of new protein kinase 2 inhibitors for the treatment of inflammatory diseases using QSAR, pharmacophore-structure-based virtual screening, and molecular dynamics. J Mol Model 2018; 24:225. [PMID: 30088101 DOI: 10.1007/s00894-018-3756-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2018] [Accepted: 07/20/2018] [Indexed: 12/14/2022]
Abstract
Receptor-interacting protein kinase 2 (RIPK2) plays an essential role in autoimmune response and is suggested as a target for inflammatory diseases. A pharmacophore model was built from a dataset with ponatinib (template) and 18 RIPK2 inhibitors selected from BindingDB database. The pharmacophore model validation was performed by multiple linear regression (MLR). The statistical quality of the model was evaluated by the correlation coefficient (R), squared correlation coefficient (R2), explanatory variance (adjusted R2), standard error of estimate (SEE), and variance ratio (F). The best pharmacophore model has one aromatic group (LEU24 residue interaction) and two hydrogen bonding acceptor groups (MET98 and TYR97 residues interaction), having a score of 24.739 with 14 aligned inhibitors, which were used in virtual screening via ZincPharmer server and the ZINC database (selected in function of the RMSD value). We determined theoretical values of biological activity (logRA) by MLR, pharmacokinetic and toxicology properties, and made molecular docking studies comparing binding affinity (kcal/mol) results with the most active compound of the study (ponatinib) and WEHI-345. Nine compounds from the ZINC database show satisfactory results, yielding among those selected, the compound ZINC01540228, as the most promising RIPK2 inhibitor. After binding free energy calculations, the following molecular dynamics simulations showed that the receptor protein's backbone remained stable after the introduction of ligands.
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15
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An Antioxidant Potential, Quantum-Chemical and Molecular Docking Study of the Major Chemical Constituents Present in the Leaves of Curatella americana Linn. Pharmaceuticals (Basel) 2018; 11:ph11030072. [PMID: 30036950 PMCID: PMC6161303 DOI: 10.3390/ph11030072] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Revised: 07/09/2018] [Accepted: 07/12/2018] [Indexed: 12/13/2022] Open
Abstract
Reactive oxygen species (ROS) are continuously generated in the normal biological systems, primarily by enzymes as xanthine oxidase (XO). The inappropriate scavenging or inhibition of ROS has been considered to be linked with aging, inflammatory disorders, and chronic diseases. Therefore, many plants and their products have been investigated as natural antioxidants for their potential use in preventive medicine. The leaves and bark extracts of Curatella americana Linn. were described in scientific research as anti-inflammatory, vasodilator, anti-ulcerogenic, and hypolipidemic effects. So, the aim of this study was to evaluate the antioxidant potentials of leaf hydroalcoholic extract from C. americana (HECA) through the scavenging DPPH assay and their main chemical constituents, evaluated by the following quantum chemical approaches (DFT B3LYP/6-31G**): Maps of Molecular Electrostatic Potential (MEP), Frontier Orbital’s (HOMO and LUMO) followed by multivariate analysis and molecular docking simulations with the xanthine oxidase enzyme. The hydroalcoholic extract showed significant antioxidant activity by free radical scavenging probably due to the great presence of flavonoids, which were grouped in the PCA and HCA analysis with the standard gallic acid. In the molecular docking study, the compounds studied presented the binding free energy (ΔG) values close each other, due to the similar interactions with amino acids residues at the activity site. The descriptors Gap and softness were important to characterize the molecules with antioxidant potential by capturing oxygen radicals.
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16
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Kwofie SK, Dankwa B, Odame EA, Agamah FE, Doe LPA, Teye J, Agyapong O, Miller WA, Mosi L, Wilson MD. In Silico Screening of Isocitrate Lyase for Novel Anti-Buruli Ulcer Natural Products Originating from Africa. Molecules 2018; 23:E1550. [PMID: 29954088 PMCID: PMC6100440 DOI: 10.3390/molecules23071550] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 06/16/2018] [Accepted: 06/25/2018] [Indexed: 12/15/2022] Open
Abstract
Buruli ulcer (BU) is caused by Mycobacterium ulcerans and is predominant in both tropical and subtropical regions. The neglected debilitating disease is characterized by chronic necrotizing skin lesions attributed to a mycolactone, which is a macrolide toxin secreted by M. ulcerans. The preferred treatment is surgical excision of the lesions followed by a prolonged combination antibiotic therapy using existing drugs such as rifampicin and streptomycin or clarithromycin. These antibiotics appear not to be adequately potent and efficacious against persistent and late stage ulcers. In addition, emerging drug resistance to treatment poses great challenges. There is a need to identify novel natural product-derived lead compounds, which are potent and efficacious for the treatment of Buruli ulcer. Natural products present a rich diversity of chemical compounds with proven activity against various infectious diseases, and therefore, are considered in this study. This study sought to computationally predict natural product-derived lead compounds with the potential to be developed further into potent drugs with better therapeutic efficacy than the existing anti-buruli ulcer compounds. The three-dimensional (3D) structure of Isocitrate lyase (ICL) of Mycobacterium ulcerans was generated using homology modeling and was further scrutinized with molecular dynamics simulations. A library consisting of 885 compounds retrieved from the AfroDb database was virtually screened against the validated ICL model using AutoDock Vina. AfroDb is a compendium of “drug-like” and structurally diverse 3D structures of natural products originating from different geographical regions in Africa. The molecular docking with the ICL model was validated by computing a Receiver Operating Characteristic (ROC) curve with a reasonably good Area Under the Curve (AUC) value of 0.89375. Twenty hit compounds, which docked firmly within the active site pocket of the ICL receptor, were assessed via in silico bioactivity and pharmacological profiling. The three compounds, which emerged as potential novel leads, comprise ZINC38143792 (Euscaphic acid), ZINC95485880, and ZINC95486305 with reasonable binding energies (high affinity) of −8.6, −8.6, and −8.8 kcal/mol, respectively. Euscaphic acid has been reported to show minimal inhibition against a drug-sensitive strain of M. tuberculosis. The other two leads were both predicted to possess dermatological activity while one was antibacterial. The leads have shown promising results pertaining to efficacy, toxicity, pharmacokinetic, and safety. These leads can be experimentally characterized to assess their anti-mycobacterial activity and their scaffolds may serve as rich skeletons for developing anti-buruli ulcer drugs.
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Affiliation(s)
- Samuel K Kwofie
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic and Applied Sciences, University of Ghana, P. O. Box LG 77, Legon, Accra, Ghana.
- Department of Biochemistry, Cell and Molecular Biology, West African Center for Cell Biology and Infectious Pathogens, University of Ghana, P. O. Box LG 77, Legon, Accra, Ghana.
| | - Bismark Dankwa
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic and Applied Sciences, University of Ghana, P. O. Box LG 77, Legon, Accra, Ghana.
| | - Emmanuel A Odame
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic and Applied Sciences, University of Ghana, P. O. Box LG 77, Legon, Accra, Ghana.
| | - Francis E Agamah
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic and Applied Sciences, University of Ghana, P. O. Box LG 77, Legon, Accra, Ghana.
| | - Lady P A Doe
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic and Applied Sciences, University of Ghana, P. O. Box LG 77, Legon, Accra, Ghana.
| | - Joshua Teye
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic and Applied Sciences, University of Ghana, P. O. Box LG 77, Legon, Accra, Ghana.
| | - Odame Agyapong
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic and Applied Sciences, University of Ghana, P. O. Box LG 77, Legon, Accra, Ghana.
- Department of Parasitology, Noguchi Memorial Institute for Medical Research (NMIMR), College of Health Sciences (CHS), University of Ghana, P. O. Box LG 77, Legon, Accra, Ghana.
| | - Whelton A Miller
- Department of Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA 19104, USA.
- Department of Chemistry & Physics, College of Science and Technology, Lincoln University, Philadelphia, PA 19104, USA.
| | - Lydia Mosi
- Department of Biochemistry, Cell and Molecular Biology, West African Center for Cell Biology and Infectious Pathogens, University of Ghana, P. O. Box LG 77, Legon, Accra, Ghana.
| | - Michael D Wilson
- Department of Parasitology, Noguchi Memorial Institute for Medical Research (NMIMR), College of Health Sciences (CHS), University of Ghana, P. O. Box LG 77, Legon, Accra, Ghana.
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Identification of Novel Protein Kinase Receptor Type 2 Inhibitors Using Pharmacophore and Structure-Based Virtual Screening. Molecules 2018; 23:molecules23020453. [PMID: 29463017 PMCID: PMC6017386 DOI: 10.3390/molecules23020453] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Revised: 01/26/2018] [Accepted: 02/01/2018] [Indexed: 12/31/2022] Open
Abstract
The Protein Kinase Receptor type 2 (RIPK2) plays an important role in the pathogenesis of inflammatory diseases; it signals downstream of the NOD1 and NOD2 intracellular sensors and promotes a productive inflammatory response. However, excessive NOD2 signaling has been associated with various diseases, including sarcoidosis and inflammatory arthritis; the pharmacological inhibition of RIPK2 is an affinity strategy that demonstrates an increased expression of pro-inflammatory secretion activity. In this study, a pharmacophoric model based on the crystallographic pose of ponatinib, a potent RIPK2 inhibitor, and 30 other ones selected from the BindingDB repository database, was built. Compounds were selected based on the available ZINC compounds database and in silico predictions of their pharmacokinetic, toxicity and potential biological activity. Molecular docking was performed to identify the probable interactions of the compounds as well as their binding affinity with RIPK2. The compounds were analyzed to ponatinib and WEHI-345, which also used as a control. At least one of the compounds exhibited suitable pharmacokinetic properties, low toxicity and an interesting binding affinity and high fitness compared with the crystallographic pose of WEHI-345 in complex with RIPK2. This compound also possessed suitable synthetic accessibility, rendering it a potential and very promising RIPK2 inhibitor to be further investigated in regards to different diseases, particularly inflammatory ones.
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