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Ferreira da Costa J, Silva D, Caamaño O, Brea JM, Loza MI, Munteanu CR, Pazos A, García-Mera X, González-Díaz H. Perturbation Theory/Machine Learning Model of ChEMBL Data for Dopamine Targets: Docking, Synthesis, and Assay of New l-Prolyl-l-leucyl-glycinamide Peptidomimetics. ACS Chem Neurosci 2018; 9:2572-2587. [PMID: 29791132 DOI: 10.1021/acschemneuro.8b00083] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Predicting drug-protein interactions (DPIs) for target proteins involved in dopamine pathways is a very important goal in medicinal chemistry. We can tackle this problem using Molecular Docking or Machine Learning (ML) models for one specific protein. Unfortunately, these models fail to account for large and complex big data sets of preclinical assays reported in public databases. This includes multiple conditions of assays, such as different experimental parameters, biological assays, target proteins, cell lines, organism of the target, or organism of assay. On the other hand, perturbation theory (PT) models allow us to predict the properties of a query compound or molecular system in experimental assays with multiple boundary conditions based on a previously known case of reference. In this work, we report the first PTML (PT + ML) study of a large ChEMBL data set of preclinical assays of compounds targeting dopamine pathway proteins. The best PTML model found predicts 50000 cases with accuracy of 70-91% in training and external validation series. We also compared the linear PTML model with alternative PTML models trained with multiple nonlinear methods (artificial neural network (ANN), Random Forest, Deep Learning, etc.). Some of the nonlinear methods outperform the linear model but at the cost of a notable increment of the complexity of the model. We illustrated the practical use of the new model with a proof-of-concept theoretical-experimental study. We reported for the first time the organic synthesis, chemical characterization, and pharmacological assay of a new series of l-prolyl-l-leucyl-glycinamide (PLG) peptidomimetic compounds. In addition, we performed a molecular docking study for some of these compounds with the software Vina AutoDock. The work ends with a PTML model predictive study of the outcomes of the new compounds in a large number of assays. Therefore, this study offers a new computational methodology for predicting the outcome for any compound in new assays. This PTML method focuses on the prediction with a simple linear model of multiple pharmacological parameters (IC50, EC50, Ki, etc.) for compounds in assays involving different cell lines used, organisms of the protein target, or organism of assay for proteins in the dopamine pathway.
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Affiliation(s)
- Joana Ferreira da Costa
- Department of Organic Chemistry, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - David Silva
- Department of Organic Chemistry, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Olga Caamaño
- Department of Organic Chemistry, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - José M. Brea
- CIMUS, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
- Department of Pharmacology, Pharmacy and Pharmaceutical Technology, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Maria Isabel Loza
- CIMUS, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
- Department of Pharmacology, Pharmacy and Pharmaceutical Technology, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Cristian R. Munteanu
- Instituto de Investigacion Biomedica de A Coruña (INIBIC), Complexo Hospitalario Universitario de A Coruña (CHUAC), A Coruña, 15006, Spain
| | - Alejandro Pazos
- Instituto de Investigacion Biomedica de A Coruña (INIBIC), Complexo Hospitalario Universitario de A Coruña (CHUAC), A Coruña, 15006, Spain
- Computer Science Department, Faculty of Computer Science, University of A Coruna, 15071 A Coruña, Spain
| | - Xerardo García-Mera
- Department of Organic Chemistry, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Humbert González-Díaz
- Department of Organic Chemistry II, University of Basque Country UPV/EHU, 48940 Leioa, Spain
- IKERBASQUE, Basque Foundation for Science, 48011 Bilbao, Spain
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da Costa JF, Garcia-Mera X, Poceiro DS, Caamano O. (±)-3,5-Bis(substitutedmethyl)pyrrolidines: Application to the Synthesis of Analogues of glycine-L-proline-L-glutamic Acid (GPE). Curr Org Synth 2018. [DOI: 10.2174/1570179414666170821115323] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Backiground: Alzheimer's disease is a fatal, complex, neurodegenerative disease over 46 million
people live with dementia in the world characterized by the presence of plaques containing β-amyloid and neuronal
loss. The GPE acts as a survival factor against β-amyloid insult in brain and suggests a possible new
therapeutic strategy for the treatment of Central Nervous System injuries and neurodegenerative disorders. The
structural simplicity of GPE makes it a suitable lead molecule for the development of new drugs that to cross
the blood-brain barrier.
Objective:
With these aims in mind, we embarked on a synthetic program focused on the modification of the Lproline
residue of GPE in order to investigate its importance on the neuroprotective activities.
Method:
The general synthetic strategy involved the preparation of several modified proline residues, which
were subsequently coupled to N-Boc-glycine-OH and glutamic dimethyl ester hydrochloride.
Results:
the mixture of compounds 11 was obtained in good yields (72%) under these conditions, and this was
readily separated by column chromatography and the components were identified by 1H and 13C NMR spectral,
as well as by its EI HRMS.
Conclusion:
Compound (±)-8 was coupled with L-glutamic dimethyl ester hydrochloride gave a mixture of
dipeptides 9a and 9b in a satisfactory yield. The use of T3P as coupling agent of the mixture 10a and 10b with
Boc-glycine provided a new analogue of GPE, tripeptide 11, obtained with an overall yield of 65% from (±)-1.
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Affiliation(s)
- Joana Ferreira da Costa
- Departamento de Quimica Organica, Facultade de Farmacia, Campus Vida s/n, Universidade de Santiago de Compostela, E-15782, Santiago de Compostela, Spain
| | - Xerardo Garcia-Mera
- Departamento de Quimica Organica, Facultade de Farmacia, Campus Vida s/n, Universidade de Santiago de Compostela, E-15782, Santiago de Compostela, Spain
| | - David Silva Poceiro
- Departamento de Quimica Organica, Facultade de Farmacia, Campus Vida s/n, Universidade de Santiago de Compostela, E-15782, Santiago de Compostela, Spain
| | - Olga Caamano
- Departamento de Quimica Organica, Facultade de Farmacia, Campus Vida s/n, Universidade de Santiago de Compostela, E-15782, Santiago de Compostela, Spain
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Sampaio-Dias IE, Sousa CAD, García-Mera X, Ferreira da Costa J, Caamaño O, Rodríguez-Borges JE. Novel l-prolyl-l-leucylglycinamide (PLG) tripeptidomimetics based on a 2-azanorbornane scaffold as positive allosteric modulators of the D2R. Org Biomol Chem 2016; 14:11065-11069. [DOI: 10.1039/c6ob02248k] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Replacement of l-prolyl residue in the PLG sequence by an enantiopure (1R,3S,4S)-2-azanorbornane scaffold afforded active peptidomimetics compatible with suppression of the C-terminal carboxamide pharmacophore.
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Affiliation(s)
- Ivo E. Sampaio-Dias
- UCIBIO/REQUIMTE
- Department of Chemistry and Biochemistry
- Faculty of Sciences
- University of Porto
- 4169-007 Porto
| | - Carlos A. D. Sousa
- LAQV/REQUIMTE
- Department of Chemistry and Biochemistry
- Faculty of Sciences
- University of Porto
- 4169-007 Porto
| | - Xerardo García-Mera
- Department of Organic Chemistry
- Faculty of Pharmacy
- University of Santiago de Compostela
- E-15782 Santiago de Compostela
- Spain
| | | | - Olga Caamaño
- Department of Organic Chemistry
- Faculty of Pharmacy
- University of Santiago de Compostela
- E-15782 Santiago de Compostela
- Spain
| | - José E. Rodríguez-Borges
- UCIBIO/REQUIMTE
- Department of Chemistry and Biochemistry
- Faculty of Sciences
- University of Porto
- 4169-007 Porto
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Ferreira da Costa J, García-Mera X, Caamaño O, Brea JM, Loza MI. Synthesis by microwave-assisted 1,3-dipolar cycloaddition of 1,2,3-triazole 1'-homo-3'-isoazanucleosides and evaluation of their anticancer activity. Eur J Med Chem 2015; 98:212-20. [PMID: 26025141 DOI: 10.1016/j.ejmech.2015.05.029] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 05/18/2015] [Accepted: 05/19/2015] [Indexed: 02/01/2023]
Abstract
Racemic 1'-homo-3'-isoazanucleosides have been obtained by microwave-assisted 1,3-dipolar cycloaddition of 3,5-disubstituted proline derivative (±)-2 with different alkynes. The compounds obtained were evaluated for their cytotoxic activities in vitro against human breast carcinoma cell lines (MCF-7), human ovary carcinoma cell lines (A2780) and human lung carcinoma cell lines (NCI-H460).
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Affiliation(s)
- Joana Ferreira da Costa
- Departamento de Química Orgánica, Facultade de Farmacia, Campus Vida s/n, Universidade de Santiago de Compostela, E-15782, Spain
| | - Xerardo García-Mera
- Departamento de Química Orgánica, Facultade de Farmacia, Campus Vida s/n, Universidade de Santiago de Compostela, E-15782, Spain; Instituto de Farmacia Industrial, Facultade de Farmacia, Campus Vida s/n, Universidade de Santiago de Compostela, E-15782, Spain
| | - Olga Caamaño
- Departamento de Química Orgánica, Facultade de Farmacia, Campus Vida s/n, Universidade de Santiago de Compostela, E-15782, Spain; Instituto de Farmacia Industrial, Facultade de Farmacia, Campus Vida s/n, Universidade de Santiago de Compostela, E-15782, Spain.
| | - José Manuel Brea
- Instituto de Farmacia Industrial, Facultade de Farmacia, Campus Vida s/n, Universidade de Santiago de Compostela, E-15782, Spain; Centro de Investigación CIMUS, Campus Vida s/n, Universidade de Santiago de Compostela, E-15782, Santiago de Compostela, Spain
| | - María Isabel Loza
- Instituto de Farmacia Industrial, Facultade de Farmacia, Campus Vida s/n, Universidade de Santiago de Compostela, E-15782, Spain; Centro de Investigación CIMUS, Campus Vida s/n, Universidade de Santiago de Compostela, E-15782, Santiago de Compostela, Spain
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Ferreira da Costa J, Caamaño O, Fernández F, García-Mera X, Sampaio-Dias IE, Brea JM, Cadavid MI. Synthesis and allosteric modulation of the dopamine receptor by peptide analogs of l-prolyl-l-leucyl-glycinamide (PLG) modified in the l-proline or l-proline and l-leucine scaffolds. Eur J Med Chem 2013; 69:146-58. [DOI: 10.1016/j.ejmech.2013.08.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Revised: 07/30/2013] [Accepted: 08/02/2013] [Indexed: 10/26/2022]
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