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He S, Segura Abarrategi J, Bediaga H, Arrasate S, González-Díaz H. On the additive artificial intelligence-based discovery of nanoparticle neurodegenerative disease drug delivery systems. BEILSTEIN JOURNAL OF NANOTECHNOLOGY 2024; 15:535-555. [PMID: 38774585 PMCID: PMC11106676 DOI: 10.3762/bjnano.15.47] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 04/23/2024] [Indexed: 05/24/2024]
Abstract
Neurodegenerative diseases are characterized by slowly progressing neuronal cell death. Conventional drug treatment strategies often fail because of poor solubility, low bioavailability, and the inability of the drugs to effectively cross the blood-brain barrier. Therefore, the development of new neurodegenerative disease drugs (NDDs) requires immediate attention. Nanoparticle (NP) systems are of increasing interest for transporting NDDs to the central nervous system. However, discovering effective nanoparticle neuronal disease drug delivery systems (N2D3Ss) is challenging because of the vast number of combinations of NP and NDD compounds, as well as the various assays involved. Artificial intelligence/machine learning (AI/ML) algorithms have the potential to accelerate this process by predicting the most promising NDD and NP candidates for assaying. Nevertheless, the relatively limited amount of reported data on N2D3S activity compared to assayed NDDs makes AI/ML analysis challenging. In this work, the IFPTML technique, which combines information fusion (IF), perturbation theory (PT), and machine learning (ML), was employed to address this challenge. Initially, we conducted the fusion into a unified dataset comprising 4403 NDD assays from ChEMBL and 260 NP cytotoxicity assays from journal articles. Through a resampling process, three new working datasets were generated, each containing 500,000 cases. We utilized linear discriminant analysis (LDA) along with artificial neural network (ANN) algorithms, such as multilayer perceptron (MLP) and deep learning networks (DLN), to construct linear and non-linear IFPTML models. The IFPTML-LDA models exhibited sensitivity (Sn) and specificity (Sp) values in the range of 70% to 73% (>375,000 training cases) and 70% to 80% (>125,000 validation cases), respectively. In contrast, the IFPTML-MLP and IFPTML-DLN achieved Sn and Sp values in the range of 85% to 86% for both training and validation series. Additionally, IFPTML-ANN models showed an area under the receiver operating curve (AUROC) of approximately 0.93 to 0.95. These results indicate that the IFPTML models could serve as valuable tools in the design of drug delivery systems for neurosciences.
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Affiliation(s)
- Shan He
- Department of Organic and Inorganic Chemistry, University of Basque Country UPV/EHU, 48940 Leioa, Spain
- IKERDATA S.L., ZITEK, UPV/EHU, Rectorate Building, nº6, 48940 Leioa, Greater Bilbao, Basque Country, Spain
| | - Julen Segura Abarrategi
- Department of Organic and Inorganic Chemistry, University of Basque Country UPV/EHU, 48940 Leioa, Spain
| | - Harbil Bediaga
- IKERDATA S.L., ZITEK, UPV/EHU, Rectorate Building, nº6, 48940 Leioa, Greater Bilbao, Basque Country, Spain
- Painting Department, Fine Arts Faculty, University of the Basque Country UPV/EHU, 48940, Leioa, Biscay, Basque Country, Spain
| | - Sonia Arrasate
- Department of Organic and Inorganic Chemistry, University of Basque Country UPV/EHU, 48940 Leioa, Spain
| | - Humberto González-Díaz
- Department of Organic and Inorganic Chemistry, University of Basque Country UPV/EHU, 48940 Leioa, Spain
- Instituto Biofisika (UPV/EHU-CSIC), 48940 Leioa, Spain
- IKERBASQUE, Basque Foundation for Science, 48011 Bilbao, Biscay, Spain
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2
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Naoi M, Maruyama W, Shamoto-Nagai M. Neuroprotective Function of Rasagiline and Selegiline, Inhibitors of Type B Monoamine Oxidase, and Role of Monoamine Oxidases in Synucleinopathies. Int J Mol Sci 2022; 23:ijms231911059. [PMID: 36232361 PMCID: PMC9570229 DOI: 10.3390/ijms231911059] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 09/09/2022] [Accepted: 09/14/2022] [Indexed: 11/27/2022] Open
Abstract
Synucleinopathies are a group of neurodegenerative disorders caused by the accumulation of toxic species of α-synuclein. The common clinical features are chronic progressive decline of motor, cognitive, behavioral, and autonomic functions. They include Parkinson’s disease, dementia with Lewy body, and multiple system atrophy. Their etiology has not been clarified and multiple pathogenic factors include oxidative stress, mitochondrial dysfunction, impaired protein degradation systems, and neuroinflammation. Current available therapy cannot prevent progressive neurodegeneration and “disease-modifying or neuroprotective” therapy has been proposed. This paper presents the molecular mechanisms of neuroprotection by the inhibitors of type B monoamine oxidase, rasagiline and selegiline. They prevent mitochondrial apoptosis, induce anti-apoptotic Bcl-2 protein family, and pro-survival brain- and glial cell line-derived neurotrophic factors. They also prevent toxic oligomerization and aggregation of α-synuclein. Monoamine oxidase is involved in neurodegeneration and neuroprotection, independently of the catalytic activity. Type A monoamine oxidases mediates rasagiline-activated signaling pathways to induce neuroprotective genes in neuronal cells. Multi-targeting propargylamine derivatives have been developed for therapy in various neurodegenerative diseases. Preclinical studies have presented neuroprotection of rasagiline and selegiline, but beneficial effects have been scarcely presented. Strategy to improve clinical trials is discussed to achieve disease-modification in synucleinopathies.
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Affiliation(s)
- Makoto Naoi
- Correspondence: ; Tel.: +81-05-6173-1111 (ext. 3494); Fax: +81-561-731-142
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3
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PTML modeling for peptide discovery: in silico design of non-hemolytic peptides with antihypertensive activity. Mol Divers 2021; 26:2523-2534. [PMID: 34802116 DOI: 10.1007/s11030-021-10350-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 11/05/2021] [Indexed: 01/19/2023]
Abstract
Hypertension is a medical condition that affects millions of people worldwide. Despite the high efficacy of the current antihypertensive drugs, they are associated with serious side effects. Peptides constitute attractive options for chemical therapy against hypertension, and computational models can accelerate the design of antihypertensive peptides. Yet, to the best of our knowledge, all the in silico models predict only the antihypertensive activity of peptides while neglecting their inherent toxic potential to red blood cells. In this work, we report the first sequence-based model that combines perturbation theory and machine learning through multilayer perceptron networks (SB-PTML-MLP) to enable the simultaneous screening of antihypertensive activity and hemotoxicity of peptides. We have interpreted the molecular descriptors present in the model from a physicochemical and structural point of view. By strictly following such interpretations as guidelines, we performed two tasks. First, we selected amino acids with favorable contributions to both the increase of the antihypertensive activity and the diminution of hemotoxicity. Then, we assembled those suitable amino acids, virtually designing peptides that were predicted by the SB-PTML-MLP model as antihypertensive agents exhibiting low hemotoxicity. The potentiality of the SB-PTML-MLP model as a tool for designing potent and safe antihypertensive peptides was confirmed by predictions performed by online computational tools reported in the scientific literature. The methodology presented here can be extended to other pharmacological applications of peptides.
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Diéguez-Santana K, González-Díaz H. Towards machine learning discovery of dual antibacterial drug-nanoparticle systems. NANOSCALE 2021; 13:17854-17870. [PMID: 34671801 DOI: 10.1039/d1nr04178a] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Artificial Intelligence/Machine Learning (AI/ML) algorithms may speed up the design of DADNP systems formed by Antibacterial Drugs (AD) and Nanoparticles (NP). In this work, we used IFPTML = Information Fusion (IF) + Perturbation-Theory (PT) + Machine Learning (ML) algorithm for the first time to study of a large dataset of putative DADNP systems composed by >165 000 ChEMBL AD assays and 300 NP assays vs. multiple bacteria species. We trained alternative models with Linear Discriminant Analysis (LDA), Artificial Neural Networks (ANN), Bayesian Networks (BNN), K-Nearest Neighbour (KNN) and other algorithms. IFPTML-LDA model was simpler with values of Sp ≈ 90% and Sn ≈ 74% in both training (>124 K cases) and validation (>41 K cases) series. IFPTML-ANN and KNN models are notably more complicated even when they are more balanced Sn ≈ Sp ≈ 88.5%-99.0% and AUROC ≈ 0.94-0.99 in both series. We also carried out a simulation (>1900 calculations) of the expected behavior for putative DADNPs in 72 different biological assays. The putative DADNPs studied are formed by 27 different drugs with multiple classes of NP and types of coats. In addition, we tested the validity of our additive model with 80 DADNP complexes experimentally synthetized and biologically tested (reported in >45 papers). All these DADNPs show values of MIC < 50 μg mL-1 (cutoff used) better that MIC of AD and NP alone (synergistic or additive effect). The assays involve DADNP complexes with 10 types of NP, 6 coating materials, NP size range 5-100 nm vs. 15 different antibiotics, and 12 bacteria species. The IFPTML-LDA model classified correctly 100% (80 out of 80) DADNP complexes as biologically active. IFPMTL additive strategy may become a useful tool to assist the design of DADNP systems for antibacterial therapy taking into consideration only information about AD and NP components by separate.
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Affiliation(s)
- Karel Diéguez-Santana
- Department of Organic and Inorganic Chemistry, University of Basque Country UPV/EHU, 48940 Leioa, Spain
| | - Humberto González-Díaz
- Department of Organic and Inorganic Chemistry, University of Basque Country UPV/EHU, 48940 Leioa, Spain
- Basque Center for Biophysics CSIC-UPVEH, University of Basque Country UPV/EHU, 48940 Leioa, Spain.
- IKERBASQUE, Basque Foundation for Science, 48011 Bilbao, Biscay, Spain
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5
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Kleandrova VV, Speck-Planche A. The QSAR Paradigm in Fragment-Based Drug Discovery: From the Virtual Generation of Target Inhibitors to Multi-Scale Modeling. Mini Rev Med Chem 2021; 20:1357-1374. [PMID: 32013845 DOI: 10.2174/1389557520666200204123156] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 10/21/2019] [Accepted: 10/28/2019] [Indexed: 12/24/2022]
Abstract
Fragment-Based Drug Design (FBDD) has established itself as a promising approach in modern drug discovery, accelerating and improving lead optimization, while playing a crucial role in diminishing the high attrition rates at all stages in the drug development process. On the other hand, FBDD has benefited from the application of computational methodologies, where the models derived from the Quantitative Structure-Activity Relationships (QSAR) have become consolidated tools. This mini-review focuses on the evolution and main applications of the QSAR paradigm in the context of FBDD in the last five years. This report places particular emphasis on the QSAR models derived from fragment-based topological approaches to extract physicochemical and/or structural information, allowing to design potentially novel mono- or multi-target inhibitors from relatively large and heterogeneous databases. Here, we also discuss the need to apply multi-scale modeling, to exemplify how different datasets based on target inhibition can be simultaneously integrated and predicted together with other relevant endpoints such as the biological activity against non-biomolecular targets, as well as in vitro and in vivo toxicity and pharmacokinetic properties. In this context, seminal papers are briefly analyzed. As huge amounts of data continue to accumulate in the domains of the chemical, biological and biomedical sciences, it has become clear that drug discovery must be viewed as a multi-scale optimization process. An ideal multi-scale approach should integrate diverse chemical and biological data and also serve as a knowledge generator, enabling the design of potentially optimal chemicals that may become therapeutic agents.
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Affiliation(s)
- Valeria V Kleandrova
- Laboratory of Fundamental and Applied Research of Quality and Technology of Food Production, Moscow State University of Food Production, Volokolamskoe Shosse 11, 125080, Moscow, Russian Federation
| | - Alejandro Speck-Planche
- Department of Chemistry, Institute of Pharmacy, I.M. Sechenov First Moscow State Medical University, Trubetskaya Str., 8, b. 2, 119992, Moscow, Russian Federation
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6
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Kleandrova VV, Scotti L, Bezerra Mendonça Junior FJ, Muratov E, Scotti MT, Speck-Planche A. QSAR Modeling for Multi-Target Drug Discovery: Designing Simultaneous Inhibitors of Proteins in Diverse Pathogenic Parasites. Front Chem 2021; 9:634663. [PMID: 33777898 PMCID: PMC7987820 DOI: 10.3389/fchem.2021.634663] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Accepted: 01/22/2021] [Indexed: 11/21/2022] Open
Abstract
Parasitic diseases remain as unresolved health issues worldwide. While for some parasites the treatments involve drug combinations with serious side effects, for others, chemical therapies are inefficient due to the emergence of drug resistance. This urges the search for novel antiparasitic agents able to act through multiple mechanisms of action. Here, we report the first multi-target model based on quantitative structure-activity relationships and a multilayer perceptron neural network (mt-QSAR-MLP) to virtually design and predict versatile inhibitors of proteins involved in the survival and/or infectivity of different pathogenic parasites. The mt-QSAR-MLP model exhibited high accuracy (>80%) in both training and test sets for the classification/prediction of protein inhibitors. Several fragments were directly extracted from the physicochemical and structural interpretations of the molecular descriptors in the mt-QSAR-MLP model. Such interpretations enabled the generation of four molecules that were predicted as multi-target inhibitors against at least three of the five parasitic proteins reported here with two of the molecules being predicted to inhibit all the proteins. Docking calculations converged with the mt-QSAR-MLP model regarding the multi-target profile of the designed molecules. The designed molecules exhibited drug-like properties, complying with Lipinski’s rule of five, as well as Ghose’s filter and Veber’s guidelines.
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Affiliation(s)
- Valeria V Kleandrova
- Laboratory of Fundamental and Applied Research of Quality and Technology of Food Production, Moscow State University of Food Production, Moscow, Russian Federation
| | - Luciana Scotti
- Postgraduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, João Pessoa, Brazil
| | | | - Eugene Muratov
- Laboratory for Molecular Modeling, The UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Marcus T Scotti
- Postgraduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, João Pessoa, Brazil
| | - Alejandro Speck-Planche
- Postgraduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, João Pessoa, Brazil
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7
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Sampaio-Dias IE, Rodríguez-Borges JE, Yáñez-Pérez V, Arrasate S, Llorente J, Brea JM, Bediaga H, Viña D, Loza MI, Caamaño O, García-Mera X, González-Díaz H. Synthesis, Pharmacological, and Biological Evaluation of 2-Furoyl-Based MIF-1 Peptidomimetics and the Development of a General-Purpose Model for Allosteric Modulators (ALLOPTML). ACS Chem Neurosci 2021; 12:203-215. [PMID: 33347281 DOI: 10.1021/acschemneuro.0c00687] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
This work describes the synthesis and pharmacological evaluation of 2-furoyl-based Melanostatin (MIF-1) peptidomimetics as dopamine D2 modulating agents. Eight novel peptidomimetics were tested for their ability to enhance the maximal effect of tritiated N-propylapomorphine ([3H]-NPA) at D2 receptors (D2R). In this series, 2-furoyl-l-leucylglycinamide (6a) produced a statistically significant increase in the maximal [3H]-NPA response at 10 pM (11 ± 1%), comparable to the effect of MIF-1 (18 ± 9%) at the same concentration. This result supports previous evidence that the replacement of proline residue by heteroaromatic scaffolds are tolerated at the allosteric binding site of MIF-1. Biological assays performed for peptidomimetic 6a using cortex neurons from 19-day-old Wistar-Kyoto rat embryos suggest that 6a displays no neurotoxicity up to 100 μM. Overall, the pharmacological and toxicological profile and the structural simplicity of 6a makes this peptidomimetic a potential lead compound for further development and optimization, paving the way for the development of novel modulating agents of D2R suitable for the treatment of CNS-related diseases. Additionally, the pharmacological and biological data herein reported, along with >20 000 outcomes of preclinical assays, was used to seek a general model to predict the allosteric modulatory potential of molecular candidates for a myriad of target receptors, organisms, cell lines, and biological activity parameters based on perturbation theory (PT) ideas and machine learning (ML) techniques, abbreviated as ALLOPTML. By doing so, ALLOPTML shows high specificity Sp = 89.2/89.4%, sensitivity Sn = 71.3/72.2%, and accuracy Ac = 86.1%/86.4% in training/validation series, respectively. To the best of our knowledge, ALLOPTML is the first general-purpose chemoinformatic tool using a PTML-based model for the multioutput and multicondition prediction of allosteric compounds, which is expected to save both time and resources during the early drug discovery of allosteric modulators.
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Affiliation(s)
- Ivo E. Sampaio-Dias
- LAQV/REQUIMTE, Dept. of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal
| | - José E. Rodríguez-Borges
- LAQV/REQUIMTE, Dept. of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal
| | - Víctor Yáñez-Pérez
- Dept. of Organic Chemistry II, University of Basque Country (UPV-EHU), 48940 Leioa, Spain
| | - Sonia Arrasate
- Dept. of Pharmacology, Faculty of Medicine and Nursing, University of Basque Country (UPV-EHU), 48940 Leioa, Spain
| | - Javier Llorente
- Dept. of Pharmacology, Faculty of Medicine and Nursing, University of Basque Country (UPV-EHU), 48940 Leioa, Spain
- Dept. of Pharmacology, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - José M. Brea
- Innopharma Screening Platform, Biofarma Research group, Centre of Research in Molecular Medicine and Chronic Diseases CIMUS, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Harbil Bediaga
- Dept. of Organic Chemistry II, University of Basque Country (UPV-EHU), 48940 Leioa, Spain
- Dept. of Physical Chemistry, University of Basque Country (UPV-EHU), 48940 Leioa, Spain
| | - Dolores Viña
- Dept. of Pharmacology, Faculty of Pharmacy, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
- Centre of Research in Molecular Medicine and Chronic Diseases CIMUS, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - María Isabel Loza
- Innopharma Screening Platform, Biofarma Research group, Centre of Research in Molecular Medicine and Chronic Diseases CIMUS, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Olga Caamaño
- Dept. of Organic Chemistry, Faculty of Pharmacy, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Xerardo García-Mera
- Dept. of Organic Chemistry, Faculty of Pharmacy, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Humberto González-Díaz
- Dept. of Organic Chemistry II, University of Basque Country (UPV-EHU), 48940 Leioa, Spain
- Basque Center for Biophysics (CSIC UPV/EHU), University of Basque Country (UPV-EHU), 48940 Leioa, Spain
- IKERBASQUE, Basque Foundation for Science, 48011 Bilbao, Spain
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8
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Ortega-Tenezaca B, Quevedo-Tumailli V, Bediaga H, Collados J, Arrasate S, Madariaga G, Munteanu CR, Cordeiro MND, González-Díaz H. PTML Multi-Label Algorithms: Models, Software, and Applications. Curr Top Med Chem 2020; 20:2326-2337. [DOI: 10.2174/1568026620666200916122616] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 07/19/2020] [Accepted: 07/20/2020] [Indexed: 12/17/2022]
Abstract
By combining Machine Learning (ML) methods with Perturbation Theory (PT), it is possible
to develop predictive models for a variety of response targets. Such combination often known as
Perturbation Theory Machine Learning (PTML) modeling comprises a set of techniques that can handle
various physical, and chemical properties of different organisms, complex biological or material
systems under multiple input conditions. In so doing, these techniques effectively integrate a manifold
of diverse chemical and biological data into a single computational framework that can then be applied
for screening lead chemicals as well as to find clues for improving the targeted response(s).
PTML models have thus been extremely helpful in drug or material design efforts and found to be
predictive and applicable across a broad space of systems. After a brief outline of the applied methodology,
this work reviews the different uses of PTML in Medicinal Chemistry, as well as in other
applications. Finally, we cover the development of software available nowadays for setting up PTML
models from large datasets.
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Affiliation(s)
| | | | - Harbil Bediaga
- Department of Organic and Inorganic Chemistry, University of Basque Country UPV/EHU, 48940 Leioa, Spain
| | - Jon Collados
- Department of Organic and Inorganic Chemistry, University of Basque Country UPV/EHU, 48940 Leioa, Spain
| | - Sonia Arrasate
- Department of Organic and Inorganic Chemistry, University of Basque Country UPV/EHU, 48940 Leioa, Spain
| | - Gotzon Madariaga
- Department of Condensed Matter Physics, University of Basque Country UPV/EHU, 48940 Leioa, Spain
| | - Cristian R Munteanu
- RNASA-IMEDIR, Computer Science Faculty, University of A Coruna, 15071 A Coruna, Spain
| | - M. Natália D.S. Cordeiro
- LAQV@REQUIMTE, Department of Chemistry and Biochemistry, University of Porto, 4169-007 Porto, Portugal
| | - Humbert González-Díaz
- Department of Organic and Inorganic Chemistry, University of Basque Country UPV/EHU, 48940 Leioa, Spain
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9
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Kleandrova VV, Scotti MT, Scotti L, Nayarisseri A, Speck-Planche A. Cell-based multi-target QSAR model for design of virtual versatile inhibitors of liver cancer cell lines. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2020; 31:815-836. [PMID: 32967475 DOI: 10.1080/1062936x.2020.1818617] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 08/31/2020] [Indexed: 06/11/2023]
Abstract
Liver cancers are one of the leading fatal diseases among malignant neoplasms. Current chemotherapeutic treatments used to fight these illnesses have become less efficient in terms of both efficacy and safety. Therefore, there is a great need of search for new anti-liver cancer agents and this can be accelerated by using computer-aided drug discovery approaches. In this work, we report the development of the first cell-based multi-target model based on quantitative structure-activity relationships (CBMT-QSAR) for the design and prediction of chemicals as anticancer agents against 17 liver cancer cell lines. While having a good quality and predictive power (accuracy higher than 80%) in the training and test sets, respectively, the CBMT-QSAR model was employed as a tool to directly extract suitable fragments from the physicochemical and structural interpretations of the molecular descriptors. Some of these desirable fragments were assembled, leading to the virtual design of eight molecules with drug-like properties, with six of them being predicted as versatile anticancer agents against the 17 liver cancer cell lines reported here.
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Affiliation(s)
- V V Kleandrova
- Laboratory of Fundamental and Applied Research of Quality and Technology of Food Production, Moscow State University of Food Production , Moscow, Russian Federation
| | - M T Scotti
- Postgraduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba , João Pessoa, Brazil
| | - L Scotti
- Postgraduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba , João Pessoa, Brazil
| | - A Nayarisseri
- In Silico Research Laboratory, Eminent Biosciences , Indore, Madhya Pradesh, India
| | - A Speck-Planche
- Postgraduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba , João Pessoa, Brazil
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10
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Cabrera-Andrade A, López-Cortés A, Munteanu CR, Pazos A, Pérez-Castillo Y, Tejera E, Arrasate S, González-Díaz H. Perturbation-Theory Machine Learning (PTML) Multilabel Model of the ChEMBL Dataset of Preclinical Assays for Antisarcoma Compounds. ACS OMEGA 2020; 5:27211-27220. [PMID: 33134682 PMCID: PMC7594149 DOI: 10.1021/acsomega.0c03356] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 10/06/2020] [Indexed: 06/11/2023]
Abstract
Sarcomas are a group of malignant neoplasms of connective tissue with a different etiology than carcinomas. The efforts to discover new drugs with antisarcoma activity have generated large datasets of multiple preclinical assays with different experimental conditions. For instance, the ChEMBL database contains outcomes of 37,919 different antisarcoma assays with 34,955 different chemical compounds. Furthermore, the experimental conditions reported in this dataset include 157 types of biological activity parameters, 36 drug targets, 43 cell lines, and 17 assay organisms. Considering this information, we propose combining perturbation theory (PT) principles with machine learning (ML) to develop a PTML model to predict antisarcoma compounds. PTML models use one function of reference that measures the probability of a drug being active under certain conditions (protein, cell line, organism, etc.). In this paper, we used a linear discriminant analysis and neural network to train and compare PT and non-PT models. All the explored models have an accuracy of 89.19-95.25% for training and 89.22-95.46% in validation sets. PTML-based strategies have similar accuracy but generate simplest models. Therefore, they may become a versatile tool for predicting antisarcoma compounds.
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Affiliation(s)
- Alejandro Cabrera-Andrade
- Grupo
de Bio-Quimioinformática, Universidad
de Las Américas, de los Granados Avenue, Quito 170125, Ecuador
- Carrera
de Enfermería, Facultad de Ciencias de la Salud, Universidad de Las Américas, de los Granados Avenue, Quito 170125, Ecuador
- RNASA-IMEDIR,
Computer Sciences Faculty, University of
A Coruña, A Coruña 15071, Spain
| | - Andrés López-Cortés
- RNASA-IMEDIR,
Computer Sciences Faculty, University of
A Coruña, A Coruña 15071, Spain
- Centro
de Investigación Genética y Genómica, Facultad
de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Mariscal Sucre Avenue, Quito 170129, Ecuador
| | - Cristian R. Munteanu
- RNASA-IMEDIR,
Computer Sciences Faculty, University of
A Coruña, A Coruña 15071, Spain
- Biomedical
Research Institute of A Coruña (INIBIC), University Hospital Complex of A Coruña (CHUAC), A Coruña 15006, Spain
- Centro de
Investigación en Tecnologías de la Información
y las Comunicaciones (CITIC), Campus de
Elviña s/n, A Coruña 15071, Spain
| | - Alejandro Pazos
- RNASA-IMEDIR,
Computer Sciences Faculty, University of
A Coruña, A Coruña 15071, Spain
- Biomedical
Research Institute of A Coruña (INIBIC), University Hospital Complex of A Coruña (CHUAC), A Coruña 15006, Spain
| | - Yunierkis Pérez-Castillo
- Grupo
de Bio-Quimioinformática, Universidad
de Las Américas, de los Granados Avenue, Quito 170125, Ecuador
- Escuela
de Ciencias Físicas y Matemáticas, Universidad de Las Américas, de los Granados Avenue, Quito 170125, Ecuador
| | - Eduardo Tejera
- Grupo
de Bio-Quimioinformática, Universidad
de Las Américas, de los Granados Avenue, Quito 170125, Ecuador
- Facultad
de Ingeniería y Ciencias Aplicadas, Universidad de Las Américas, de los Granados Avenue, Quito 170125, Ecuador
| | - Sonia Arrasate
- Department
of Organic Chemistry II and Basque Center for Biophysics, University of Basque Country UPV/EHU, Leioa 48940, Biscay, Spain
| | - Humbert González-Díaz
- Department
of Organic Chemistry II and Basque Center for Biophysics, University of Basque Country UPV/EHU, Leioa 48940, Biscay, Spain
- Ikerbasque,
Basque Foundation for Science, Bilbao 48011, Biscay, Spain
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11
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Kleandrova VV, Speck-Planche A. PTML Modeling for Alzheimer’s Disease: Design and Prediction of Virtual Multi-Target Inhibitors of GSK3B, HDAC1, and HDAC6. Curr Top Med Chem 2020; 20:1661-1676. [DOI: 10.2174/1568026620666200607190951] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 12/12/2019] [Accepted: 01/05/2020] [Indexed: 01/23/2023]
Abstract
Background:
Alzheimer’s disease is characterized by a progressive pattern of cognitive and
functional impairment, which ultimately leads to death. Computational approaches have played an important
role in the context of drug discovery for anti-Alzheimer's therapies. However, most of the computational
models reported to date have been focused on only one protein associated with Alzheimer's,
while relying on small datasets of structurally related molecules.
Objective:
We introduce the first model combining perturbation theory and machine learning based on
artificial neural networks (PTML-ANN) for simultaneous prediction and design of inhibitors of three
Alzheimer’s disease-related proteins, namely glycogen synthase kinase 3 beta (GSK3B), histone deacetylase
1 (HDAC1), and histone deacetylase 6 (HDAC6).
Methods:
The PTML-ANN model was obtained from a dataset retrieved from ChEMBL, and it relied on
a classification approach to predict chemicals as active or inactive.
Results:
The PTML-ANN model displayed sensitivity and specificity higher than 85% in both training
and test sets. The physicochemical and structural interpretation of the molecular descriptors in the model
permitted the direct extraction of fragments suggested to favorably contribute to enhancing the multitarget
inhibitory activity. Based on this information, we assembled ten molecules from several fragments
with positive contributions. Seven of these molecules were predicted as triple target inhibitors while the
remaining three were predicted as dual-target inhibitors. The estimated physicochemical properties of
the designed molecules complied with Lipinski’s rule of five and its variants.
Conclusion:
This work opens new horizons toward the design of multi-target inhibitors for anti- Alzheimer's
therapies.
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Affiliation(s)
- Valeria V. Kleandrova
- Laboratory of Fundamental and Applied Research of Quality and Technology of Food Production, Moscow State University of Food Production, Volokolamskoe Shosse 11, 125080, Moscow, Russian Federation
| | - Alejandro Speck-Planche
- Programa Institucional de Fomento a la Investigacion, Desarrollo e Innovacion, Universidad Tecnologica Metropolitana, Ignacio Valdivieso 2409, P.O. Box 8940577, San Joaquin, Santiago, Chile
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12
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Carracedo-Reboredo P, Corona R, Martinez-Nunes M, Fernandez-Lozano C, Tsiliki G, Sarimveis H, Aranzamendi E, Arrasate S, Sotomayor N, Lete E, Munteanu CR, González-Díaz H. MCDCalc: Markov Chain Molecular Descriptors Calculator for Medicinal Chemistry. Curr Top Med Chem 2019; 20:305-317. [PMID: 31878856 DOI: 10.2174/1568026620666191226092431] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 09/17/2019] [Accepted: 09/17/2019] [Indexed: 11/22/2022]
Abstract
AIMS Cheminformatics models are able to predict different outputs (activity, property, chemical reactivity) in single molecules or complex molecular systems (catalyzed organic synthesis, metabolic reactions, nanoparticles, etc.). BACKGROUND Cheminformatics models are able to predict different outputs (activity, property, chemical reactivity) in single molecules or complex molecular systems (catalyzed organic synthesis, metabolic reactions, nanoparticles, etc.). OBJECTIVE Cheminformatics prediction of complex catalytic enantioselective reactions is a major goal in organic synthesis research and chemical industry. Markov Chain Molecular Descriptors (MCDs) have been largely used to solve Cheminformatics problems. There are different types of Markov chain descriptors such as Markov-Shannon entropies (Shk), Markov Means (Mk), Markov Moments (πk), etc. However, there are other possible MCDs that have not been used before. In addition, the calculation of MCDs is done very often using specific software not always available for general users and there is not an R library public available for the calculation of MCDs. This fact, limits the availability of MCMDbased Cheminformatics procedures. METHODS We studied the enantiomeric excess ee(%)[Rcat] for 324 α-amidoalkylation reactions. These reactions have a complex mechanism depending on various factors. The model includes MCDs of the substrate, solvent, chiral catalyst, product along with values of time of reaction, temperature, load of catalyst, etc. We tested several Machine Learning regression algorithms. The Random Forest regression model has R2 > 0.90 in training and test. Secondly, the biological activity of 5644 compounds against colorectal cancer was studied. RESULTS We developed very interesting model able to predict with Specificity and Sensitivity 70-82% the cases of preclinical assays in both training and validation series. CONCLUSION The work shows the potential of the new tool for computational studies in organic and medicinal chemistry.
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Affiliation(s)
- Paula Carracedo-Reboredo
- Department of Computer Science and Information Technologies, Faculty of Computer Science, University of A Coruña, CITIC, Campus Elviña s/n, 15071, A Coruña, Spain.,Group of Artificial Neural Networks and Adaptative Systems, Medical Imaging, and Diagnostic Radiology (RNASA-IMEDIR), Institute of Biomedical Research of Coruna (INIBIC), Hospital Complex of University of A Coruna (CHUAC), Sergas, University of Coruna (UDC), Xubias de arriba 84, 15006, A Coruna, Spain.,Department of Organic Chemistry II, University of the Basque Country UPV/EHU, 48940, Leioa, Bilbao, Spain
| | - Ramiro Corona
- Department of Organic Chemistry II, University of the Basque Country UPV/EHU, 48940, Leioa, Bilbao, Spain
| | - Mikel Martinez-Nunes
- Department of Organic Chemistry II, University of the Basque Country UPV/EHU, 48940, Leioa, Bilbao, Spain
| | - Carlos Fernandez-Lozano
- Department of Computer Science and Information Technologies, Faculty of Computer Science, University of A Coruña, CITIC, Campus Elviña s/n, 15071, A Coruña, Spain.,Group of Artificial Neural Networks and Adaptative Systems, Medical Imaging, and Diagnostic Radiology (RNASA-IMEDIR), Institute of Biomedical Research of Coruna (INIBIC), Hospital Complex of University of A Coruna (CHUAC), Sergas, University of Coruna (UDC), Xubias de arriba 84, 15006, A Coruna, Spain
| | - Georgia Tsiliki
- Institute for the Management of Information Systems, ATHENA Research and Innovation Centre, 15125, Athens, Greece
| | - Haralambos Sarimveis
- School of Chemical Engineering, National Technical University of Athens, Zografou, Campus, 15780, Athens, Greece.,Pharma-Informatics Unit, ATHENA Research and Innovation Centre, 15125, Athens, Greece
| | - Eider Aranzamendi
- Department of Organic Chemistry II, University of the Basque Country UPV/EHU, 48940, Leioa, Bilbao, Spain
| | - Sonia Arrasate
- Department of Organic Chemistry II, University of the Basque Country UPV/EHU, 48940, Leioa, Bilbao, Spain
| | - Nuria Sotomayor
- Group of Artificial Neural Networks and Adaptative Systems, Medical Imaging, and Diagnostic Radiology (RNASA-IMEDIR), Institute of Biomedical Research of Coruna (INIBIC), Hospital Complex of University of A Coruna (CHUAC), Sergas, University of Coruna (UDC), Xubias de arriba 84, 15006, A Coruna, Spain
| | - Esther Lete
- Department of Organic Chemistry II, University of the Basque Country UPV/EHU, 48940, Leioa, Bilbao, Spain
| | - Cristian Robert Munteanu
- Department of Computer Science and Information Technologies, Faculty of Computer Science, University of A Coruña, CITIC, Campus Elviña s/n, 15071, A Coruña, Spain.,Group of Artificial Neural Networks and Adaptative Systems, Medical Imaging, and Diagnostic Radiology (RNASA-IMEDIR), Institute of Biomedical Research of Coruna (INIBIC), Hospital Complex of University of A Coruna (CHUAC), Sergas, University of Coruna (UDC), Xubias de arriba 84, 15006, A Coruna, Spain
| | - Humbert González-Díaz
- Basque Center for Biophysics, University of the Basque Country UPV/EHU, 48940, Leioa, Bilbao, Spain.,IKERBASQUE, Basque Foundation for Science, 48011, Bilbao, Spain
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13
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Diez-Alarcia R, Yáñez-Pérez V, Muneta-Arrate I, Arrasate S, Lete E, Meana JJ, González-Díaz H. Big Data Challenges Targeting Proteins in GPCR Signaling Pathways; Combining PTML-ChEMBL Models and [ 35S]GTPγS Binding Assays. ACS Chem Neurosci 2019; 10:4476-4491. [PMID: 31618004 DOI: 10.1021/acschemneuro.9b00302] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
G-protein-coupled receptors (GPCRs), also known as 7-transmembrane receptors, are the single largest class of drug targets. Consequently, a large amount of preclinical assays having GPCRs as molecular targets has been released to public sources like the Chemical European Molecular Biology Laboratory (ChEMBL) database. These data are also very complex covering changes in drug chemical structure and assay conditions like c0 = activity parameter (Ki, IC50, etc.), c1 = target protein, c2 = cell line, c3 = assay organism, etc., making difficult the analysis of these databases that are placed in the borders of a Big Data challenge. One of the aims of this work is to develop a computational model able to predict new GPCRs targeting drugs taking into consideration multiple conditions of assay. Another objective is to perform new predictive and experimental studies of selective 5-HTA2 receptor agonist, antagonist, or inverse agonist in human comparing the results with those from the literature. In this work, we combined Perturbation Theory (PT) and Machine Learning (ML) to seek a general PTML model for this data set. We analyzed 343 738 unique compounds with 812 072 end points (assay outcomes), with 185 different experimental parameters, 592 protein targets, 51 cell lines, and/or 55 organisms (species). The best PTML linear model found has three input variables only and predicted 56 202/58 653 positive outcomes (sensitivity = 95.8%) and 470 230/550 401 control cases (specificity = 85.4%) in training series. The model also predicted correctly 18 732/19 549 (95.8%) of positive outcomes and 156 739/183 469 (85.4%) of cases in external validation series. To illustrate its practical use, we used the model to predict the outcomes of six different 5-HT2A receptor drugs, namely, TCB-2, DOI, DOB, altanserin, pimavanserin, and nelotanserin, in a very large number of different pharmacological assays. 5-HT2A receptors are altered in schizophrenia and represent drug target for antipsychotic therapeutic activity. The model correctly predicted 93.83% (76 of 86) experimental results for these compounds reported in ChEMBL. Moreover, [35S]GTPγS binding assays were performed experimentally with the same six drugs with the aim of determining their potency and efficacy in the modulation of G-proteins in human brain tissue. The antagonist ketanserin was included as inactive drug with demonstrated affinity for 5-HT2A/C receptors. Our results demonstrate that some of these drugs, previously described as serotonin 5-HT2A receptor agonists, antagonists, or inverse agonists, are not so specific and show different intrinsic activity to that previously reported. Overall, this work opens a new gate for the prediction of GPCRs targeting compounds.
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Affiliation(s)
- Rebeca Diez-Alarcia
- Centro de Investigación Biomédica en Red en Salud Mental, 48940 Leioa, Spain
| | | | | | | | | | - J. Javier Meana
- Centro de Investigación Biomédica en Red en Salud Mental, 48940 Leioa, Spain
| | - Humbert González-Díaz
- Biophysics Institute, CSIC-UPV/EHU, University of the Basque Country UPV/EHU, Leioa, 48940, Spain
- IKERBASQUE, Basque Foundation for Science, 48011 Bilbao, Spain
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14
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Halder AK, Giri AK, Cordeiro MNDS. Multi-Target Chemometric Modelling, Fragment Analysis and Virtual Screening with ERK Inhibitors as Potential Anticancer Agents. Molecules 2019; 24:molecules24213909. [PMID: 31671605 PMCID: PMC6864583 DOI: 10.3390/molecules24213909] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 10/21/2019] [Accepted: 10/25/2019] [Indexed: 02/07/2023] Open
Abstract
Two isoforms of extracellular regulated kinase (ERK), namely ERK-1 and ERK-2, are associated with several cellular processes, the aberration of which leads to cancer. The ERK-1/2 inhibitors are thus considered as potential agents for cancer therapy. Multitarget quantitative structure–activity relationship (mt-QSAR) models based on the Box–Jenkins approach were developed with a dataset containing 6400 ERK inhibitors assayed under different experimental conditions. The first mt-QSAR linear model was built with linear discriminant analysis (LDA) and provided information regarding the structural requirements for better activity. This linear model was also utilised for a fragment analysis to estimate the contributions of ring fragments towards ERK inhibition. Then, the random forest (RF) technique was employed to produce highly predictive non-linear mt-QSAR models, which were used for screening the Asinex kinase library and identify the most potential virtual hits. The fragment analysis results justified the selection of the hits retrieved through such virtual screening. The latter were subsequently subjected to molecular docking and molecular dynamics simulations to understand their possible interactions with ERK enzymes. The present work, which utilises in-silico techniques such as multitarget chemometric modelling, fragment analysis, virtual screening, molecular docking and dynamics, may provide important guidelines to facilitate the discovery of novel ERK inhibitors.
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Affiliation(s)
- Amit Kumar Halder
- Department of Chemistry and Biochemistry, University of Porto, 4169-007 Porto, Portugal.
| | - Amal Kanta Giri
- Department of Chemistry and Biochemistry, University of Porto, 4169-007 Porto, Portugal.
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15
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Pérez-Parras Toledano J, García-Pedrajas N, Cerruela-García G. Multilabel and Missing Label Methods for Binary Quantitative Structure-Activity Relationship Models: An Application for the Prediction of Adverse Drug Reactions. J Chem Inf Model 2019; 59:4120-4130. [PMID: 31514503 DOI: 10.1021/acs.jcim.9b00611] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The prediction of adverse drug reactions in the discovery of new medicines is highly challenging. In the task of predicting the adverse reactions of chemical compounds, information about different targets is often available. Although we can focus on every adverse drug reaction prediction separately, multilabel approaches have been proven useful in many research areas for taking advantage of the relationship among the targets. However, when approaching the prediction problem from a multilabel point of view, we have to deal with the lack of information for some labels. This missing labels problem is a relevant issue in the field of cheminformatics approaches. This paper aims to predict the adverse drug reaction of commercial drugs using a multilabel approach where the possible presence of missing labels is also taken into consideration. We propose the use of multilabel methods to deal with the prediction of a large set of 27 different adverse reaction targets. We also propose the use of multilabel methods specifically designed to deal with the missing labels problem to test their ability to solve this difficult problem. The results show the validity of the proposed approach, demonstrating a superior performance of the multilabel method compared with the single-label approach in addressing the problem of adverse drug reaction prediction.
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Affiliation(s)
- José Pérez-Parras Toledano
- University of Córdoba , Department of Computing and Numerical Analysis, Campus de Rabanales , Albert Einstein Building , E-14071 Córdoba , Spain
| | - Nicolás García-Pedrajas
- University of Córdoba , Department of Computing and Numerical Analysis, Campus de Rabanales , Albert Einstein Building , E-14071 Córdoba , Spain
| | - Gonzalo Cerruela-García
- University of Córdoba , Department of Computing and Numerical Analysis, Campus de Rabanales , Albert Einstein Building , E-14071 Córdoba , Spain
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16
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Vásquez-Domínguez E, Armijos-Jaramillo VD, Tejera E, González-Díaz H. Multioutput Perturbation-Theory Machine Learning (PTML) Model of ChEMBL Data for Antiretroviral Compounds. Mol Pharm 2019; 16:4200-4212. [PMID: 31426639 DOI: 10.1021/acs.molpharmaceut.9b00538] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Retroviral infections, such as HIV, are, until now, diseases with no cure. Medicine and pharmaceutical chemistry need and consider it a huge goal to define target proteins of new antiretroviral compounds. ChEMBL manages Big Data features with a complex data set, which is hard to organize. This makes information difficult to analyze due to a big number of characteristics described in order to predict new drug candidates for retroviral infections. For this reason, we propose to develop a new predictive model combining perturbation theory (PT) bases and machine learning (ML) modeling to create a new tool that can take advantage of all the available information. The PTML model proposed in this work for the ChEMBL data set preclinical experimental assays for antiretroviral compounds consists of a linear equation with four variables. The PT operators used are founded on multicondition moving averages, combining different features and simplifying the difficulty to manage all data. More than 140 000 preclinical assays for 56 105 compounds with different characteristics or experimental conditions have been carried out and can be found in ChEMBL database, covering combinations with 359 biological activity parameters (c0), 55 protein accessions (c1), 83 cell lines (c2), 64 organisms of assay (c3), and 773 subtypes or strains. We have included 150 148 preclinical experimental assays for HIV virus, 1188 for HTLV virus, 84 for simian immunodeficiency virus, 370 for murine leukemia virus, 119 for Rous sarcoma virus, 1581 for MMTV, etc. We also included 5277 assays for hepatitis B virus. The developed PTML model reached considerable values in sensibility (73.05% for training and 73.10% for validation), specificity (86.61% for training and 87.17% for validation), and accuracy (75.84% for training and 75.98% for validation). We also compared alternative PTML models with different PT operators such as covariance, moments, and exponential terms. Finally, we made a comparison between literature ML models with our PTML model and also artificial neural network (ANN) nonlinear models. We conclude that this PTML model is the first one to consider multiple characteristics of preclinical experimental antiretroviral assays combined, generating a simple, useful, and adaptable instrument, which could reduce time and costs in antiretroviral drugs research.
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Affiliation(s)
- Emilia Vásquez-Domínguez
- Department of Organic Chemistry II , University of Basque Country UPV/EHU , 48940 Leioa , Spain.,Faculty of Engineering and Applied Sciences-Biotechnology , Universidad de Las Américas (UDLA) , 170125 Quito , Ecuador
| | - Vinicio Danilo Armijos-Jaramillo
- Faculty of Engineering and Applied Sciences-Biotechnology , Universidad de Las Américas (UDLA) , 170125 Quito , Ecuador.,Bio-chemioinformatics group , Universidad de Las Américas (UDLA) , 170125 Quito , Ecuador
| | - Eduardo Tejera
- Faculty of Engineering and Applied Sciences-Biotechnology , Universidad de Las Américas (UDLA) , 170125 Quito , Ecuador.,Bio-chemioinformatics group , Universidad de Las Américas (UDLA) , 170125 Quito , Ecuador
| | - 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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17
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Halder AK, Cordeiro MNDS. Development of Multi-Target Chemometric Models for the Inhibition of Class I PI3K Enzyme Isoforms: A Case Study Using QSAR-Co Tool. Int J Mol Sci 2019; 20:ijms20174191. [PMID: 31461863 PMCID: PMC6747073 DOI: 10.3390/ijms20174191] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Revised: 08/23/2019] [Accepted: 08/24/2019] [Indexed: 12/12/2022] Open
Abstract
The present work aims at establishing multi-target chemometric models using the recently launched quantitative structure–activity relationship (QSAR)-Co tool for predicting the activity of inhibitor compounds against different isoforms of phosphoinositide 3-kinase (PI3K) under various experimental conditions. The inhibitors of class I phosphoinositide 3-kinase (PI3K) isoforms have emerged as potential therapeutic agents for the treatment of various disorders, especially cancer. The cell-based enzyme inhibition assay results of PI3K inhibitors were curated from the CHEMBL database. Factors such as the nature and mutation of cell lines that may significantly alter the assay outcomes were considered as important experimental elements for mt-QSAR model development. The models, in turn, were developed using two machine learning techniques as implemented in QSAR-Co: linear discriminant analysis (LDA) and random forest (RF). Both techniques led to models with high accuracy (ca. 90%). Several molecular fragments were extracted from the current dataset, and their quantitative contributions to the inhibitory activity against all the proteins and experimental conditions under study were calculated. This case study also demonstrates the utility of QSAR-Co tool in solving multi-factorial and complex chemometric problems. Additionally, the combination of different in silico methods employed in this work can serve as a valuable guideline to speed up early discovery of PI3K inhibitors.
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Affiliation(s)
- Amit Kumar Halder
- Department of Chemistry and Biochemistry, University of Porto, 4169-007 Porto, Portugal
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18
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Sampaio-Dias IE, Silva-Reis SC, García-Mera X, Brea J, Loza MI, Alves CS, Algarra M, Rodríguez-Borges JE. Synthesis, Pharmacological, and Biological Evaluation of MIF-1 Picolinoyl Peptidomimetics as Positive Allosteric Modulators of D 2R. ACS Chem Neurosci 2019; 10:3690-3702. [PMID: 31347842 DOI: 10.1021/acschemneuro.9b00259] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
This work describes the synthesis and pharmacological evaluation of picolinoyl-based peptidomimetics of melanocyte stimulating hormone release inhibiting factor 1 (MIF-1) as dopamine modulating agents. Eight novel peptidomimetics were tested for their ability to enhance the maximal effect of tritiated N-propylapomorphine ([3H]-NPA) at dopamine D2 receptors (D2R). Methyl picolinoyl-l-valyl-l-alaninate (compound 6b) produced a statistically significant increase in the maximal [3H]-NPA response at 0.01 nM (11.9 ± 3.7%), which is close to the effect of MIF-1 in this assay at same concentration (18.3 ± 9.1%). Functional assays measuring cAMP mobilization in the presence of dopamine corroborate the activity of peptidomimetic 6b as a positive allosteric modulator (PAM) of D2R. In this assay, 6b produced a typical bell-shaped dose-response curve similar to that of the parent neuropeptide (18.3 ± 7.1% for 6b vs 15.4 ± 5.5% for MIF-1, both at 0.1 nM). Dose-response curves for dopamine in the presence of 6b show EC50 (0.33 ± 0.21 μM for 6b vs 0.17 ± 0.07 μM for MIF-1) and Emax (86.0 ± 5.4% for 6b vs 93.6 ± 4.4% for MIF-1) comparable to those of MIF-1, both at 0.01 nM. Furthermore, peptidomimetic 6b was tested for agonist activity at the human D2R and the results show that it displays no intrinsic agonism effect, endorsing its activity as a PAM of D2R. Cytotoxic and neurotoxic assays were performed for peptidomimetic 6b using HEK 293T cells and cortex neurons from 19 day old Wistar-Kyoto rat embryos, respectively, suggesting this analogue displays no toxicity effect in these assays up to 100 μM. Conformational energy minimization for 6b shows that this peptidomimetic cannot adopt the postulated type-II β-turn bioactive conformation, endorsing the possibility of an extended bioactive conformation as claimed by other researchers as a second bioactive conformation of MIF-1. Overall, the pharmacological and toxicological profile of peptidomimetic 6b together with its favorable druglike properties and structural simplicity makes it a potential lead compound for further development and optimization.
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Affiliation(s)
- Ivo E. Sampaio-Dias
- LAQV/REQUIMTE, Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal
| | - Sara C. Silva-Reis
- LAQV/REQUIMTE, Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal
| | - Xerardo García-Mera
- Department of Organic Chemistry, Faculty of Pharmacy, University of Santiago de Compostela, E-15782 Santiago de Compostela, Spain
| | - José Brea
- Innopharma Screening Platform, Biofarma Research Group, Centre of Research in Molecular Medicine and Chronic Diseases (CIMUS), University of Santiago de Compostela, E-15782 Santiago de Compostela, Spain
| | - M. Isabel Loza
- Innopharma Screening Platform, Biofarma Research Group, Centre of Research in Molecular Medicine and Chronic Diseases (CIMUS), University of Santiago de Compostela, E-15782 Santiago de Compostela, Spain
| | - Carla S. Alves
- CQM - Centro de Química da Madeira, Universidade da Madeira, Campus Universitário
da Penteada, 9020-105 Funchal, Portugal
| | - Manuel Algarra
- CQM - Centro de Química da Madeira, Universidade da Madeira, Campus Universitário
da Penteada, 9020-105 Funchal, Portugal
| | - José E. Rodríguez-Borges
- LAQV/REQUIMTE, Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal
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19
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Li X, Li X, Li Y, Yu C, Xue W, Hu J, Li B, Wang P, Zhu F. What Makes Species Productive of Anti-Cancer Drugs? Clues from Drugs’ Species Origin, Druglikeness, Target and Pathway. Anticancer Agents Med Chem 2019; 19:194-203. [DOI: 10.2174/1871520618666181029132017] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 08/22/2017] [Accepted: 03/21/2018] [Indexed: 12/18/2022]
Abstract
Background:Despite the substantial contribution of natural products to the FDA drug approval list, the discovery of anti-cancer drugs from the huge amount of species on the planet remains looking for a needle in a haystack. Objective: Drug-productive clusters in the phylogenetic tree are thus proposed to narrow the searching scope by focusing on much smaller amount of species within each cluster, which enable prioritized and rational bioprospecting for novel drug-like scaffolds. However, the way anti-cancer nature-derived drugs distribute in phylogenetic tree has not been reported, and it is oversimplified to just focus anti-cancer drug discovery on the drug-productive clusters, since the number of species in each cluster remains too large to be managed.Objective:Drug-productive clusters in the phylogenetic tree are thus proposed to narrow the searching scope by focusing on much smaller amount of species within each cluster, which enable prioritized and rational bioprospecting for novel drug-like scaffolds. However, the way anti-cancer nature-derived drugs distribute in phylogenetic tree has not been reported, and it is oversimplified to just focus anti-cancer drug discovery on the drug-productive clusters, since the number of species in each cluster remains too large to be managed.Methods:In this study, 260 anti-cancer drugs approved in the past 70 years were comprehensively analyzed by hierarchical clustering of phylogenetic distribution.Results:207 out of these 260 drugs were derived from or inspired by the natural products isolated from 58 species. Phylogenetic distribution of those drugs further revealed that nature-derived anti-cancer drugs originated mostly from drug-productive families that tend to be clustered rather than scattered on the phylogenetic tree. Moreover, based on their productivity, drug-producing species were categorized into productive (CPS), newly emerging (CNS) and lessproductive (CLS). Statistical significances in druglikeness between drugs from CPS and CLS were observed, and drugs from CNS were found to share similar drug-like properties to those from CPS.Conclusion:This finding indicated a great raise in drug approval standard, which suggested us to focus bioprospecting on the species yielding multiple drugs and keeping productive for long period of time.
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Affiliation(s)
- Xiaofeng Li
- Innovative Drug Research and Bioinformatics Group, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Xiaoxu Li
- Innovative Drug Research and Bioinformatics Group, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Yinghong Li
- Innovative Drug Research and Bioinformatics Group, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Chunyan Yu
- Innovative Drug Research and Bioinformatics Group, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Weiwei Xue
- Innovative Drug Research and Bioinformatics Group, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Jie Hu
- School of International Studies, Zhejiang University, Hangzhou 310058, China
| | - Bo Li
- Innovative Drug Research and Bioinformatics Group, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Panpan Wang
- Innovative Drug Research and Bioinformatics Group, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Feng Zhu
- Innovative Drug Research and Bioinformatics Group, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
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Ambure P, Halder AK, González Díaz H, Cordeiro MNDS. QSAR-Co: An Open Source Software for Developing Robust Multitasking or Multitarget Classification-Based QSAR Models. J Chem Inf Model 2019; 59:2538-2544. [PMID: 31083984 DOI: 10.1021/acs.jcim.9b00295] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Quantitative structure-activity relationships (QSAR) modeling is a well-known computational technique with wide applications in fields such as drug design, toxicity predictions, nanomaterials, etc. However, QSAR researchers still face certain problems to develop robust classification-based QSAR models, especially while handling response data pertaining to diverse experimental and/or theoretical conditions. In the present work, we have developed an open source standalone software "QSAR-Co" (available to download at https://sites.google.com/view/qsar-co ) to setup classification-based QSAR models that allow mining the response data coming from multiple conditions. The software comprises two modules: (1) the Model development module and (2) the Screen/Predict module. This user-friendly software provides several functionalities required for developing a robust multitasking or multitarget classification-based QSAR model using linear discriminant analysis or random forest techniques, with appropriate validation, following the principles set by the Organisation for Economic Co-operation and Development (OECD) for applying QSAR models in regulatory assessments.
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Affiliation(s)
- Pravin Ambure
- LAQV@REQUIMTE, Department of Chemistry and Biochemistry , University of Porto , 4169-007 Porto , Portugal
| | - Amit Kumar Halder
- LAQV@REQUIMTE, Department of Chemistry and Biochemistry , University of Porto , 4169-007 Porto , Portugal
| | - Humbert González Díaz
- Department of Organic Chemistry II , University of Basque Country UPV/EHU , 48940 Leioa , Spain
| | - M Natália D S Cordeiro
- LAQV@REQUIMTE, Department of Chemistry and Biochemistry , University of Porto , 4169-007 Porto , Portugal
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21
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Speck-Planche A. Combining Ensemble Learning with a Fragment-Based Topological Approach To Generate New Molecular Diversity in Drug Discovery: In Silico Design of Hsp90 Inhibitors. ACS OMEGA 2018; 3:14704-14716. [PMID: 30555986 PMCID: PMC6289491 DOI: 10.1021/acsomega.8b02419] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 10/23/2018] [Indexed: 05/05/2023]
Abstract
Machine learning methods have revolutionized modern science, providing fast and accurate solutions to multiple problems. However, they are commonly treated as "black boxes". Therefore, in important scientific fields such as medicinal chemistry and drug discovery, machine learning methods are restricted almost exclusively to the task of performing predictions of large and heterogeneous data sets of chemicals. The lack of interpretability prevents the full exploitation of the machine learning models as generators of new chemical knowledge. This work focuses on the development of an ensemble learning model for the prediction and design of potent dual heat shock protein 90 (Hsp90) inhibitors. The model displays accuracy higher than 80% in both training and test sets. To use the ensemble model as a generator of new chemical knowledge, three steps were followed. First, a physicochemical and/or structural interpretation was provided for each molecular descriptor present in the ensemble learning model. Second, the term "pseudolinear equation" was introduced within the context of machine learning to calculate the relative quantitative contributions of different molecular fragments to the inhibitory activity against the two Hsp90 isoforms studied here. Finally, by assembling the fragments with positive contributions, new molecules were designed, being predicted as potent Hsp90 inhibitors. According to Lipinski's rule of five, the designed molecules were found to exhibit potentially good oral bioavailability, a primordial property that chemicals must have to pass early stages in drug discovery. The present approach based on the combination of ensemble learning and fragment-based topological design holds great promise in drug discovery, and it can be adapted and applied to many different scientific disciplines.
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22
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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] [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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23
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Bediaga H, Arrasate S, González-Díaz H. PTML Combinatorial Model of ChEMBL Compounds Assays for Multiple Types of Cancer. ACS COMBINATORIAL SCIENCE 2018; 20:621-632. [PMID: 30240186 DOI: 10.1021/acscombsci.8b00090] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Determining the target proteins of new anticancer compounds is a very important task in Medicinal Chemistry. In this sense, chemists carry out preclinical assays with a high number of combinations of experimental conditions (c j). In fact, ChEMBL database contains outcomes of 65 534 different anticancer activity preclinical assays for 35 565 different chemical compounds (1.84 assays per compound). These assays cover different combinations of c j formed from >70 different biological activity parameters ( c0), >300 different drug targets ( c1), >230 cell lines ( c2), and 5 organisms of assay ( c3) or organisms of the target ( c4). It include a total of 45 833 assays in leukemia, 6227 assays in breast cancer, 2499 assays in ovarian cancer, 3499 in colon cancer, 3159 in lung cancer, 2750 in prostate cancer, 601 in melanoma, etc. This is a very complex data set with multiple Big Data features. This data is hard to be rationalized by researchers to extract useful relationships and predict new compounds. In this context, we propose to combine perturbation theory (PT) ideas and machine learning (ML) modeling to solve this combinatorial-like problem. In this work, we report a PTML (PT + ML) model for ChEMBL data set of preclinical assays of anticancer compounds. This is a simple linear model with only three variables. The model presented values of area under receiver operating curve = AUROC = 0.872, specificity = Sp(%) = 90.2, sensitivity = Sn(%) = 70.6, and overall accuracy = Ac(%) = 87.7 in training series. The model also have Sp(%) = 90.1, Sn(%) = 71.4, and Ac(%) = 87.8 in external validation series. The model use PT operators based on multicondition moving averages to capture all the complexity of the data set. We also compared the model with nonlinear artificial neural network (ANN) models obtaining similar results. This confirms the hypothesis of a linear relationship between the PT operators and the classification as anticancer compounds in different combinations of assay conditions. Last, we compared the model with other PTML models reported in the literature concluding that this is the only one PTML model able to predict activity against multiple types of cancer. This model is a simple but versatile tool for the prediction of the targets of anticancer compounds taking into consideration multiple combinations of experimental conditions in preclinical assays.
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Affiliation(s)
- Harbil Bediaga
- Department of Organic Chemistry II, University of Basque Country UPV/EHU, 48940, Leioa, Spain
| | - Sonia Arrasate
- Department of Organic Chemistry II, University of Basque Country UPV/EHU, 48940, Leioa, 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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24
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Blay V, Yokoi T, González-Díaz H. Perturbation Theory–Machine Learning Study of Zeolite Materials Desilication. J Chem Inf Model 2018; 58:2414-2419. [DOI: 10.1021/acs.jcim.8b00383] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Vincent Blay
- Fisher College of Business, The Ohio State University, Gerlach Hall, 2108 Neil Avenue, Columbus, Ohio 43210, United States
| | - Toshiyuki Yokoi
- Institute of Innovative Research, Chemical Resources Laboratory, Tokyo Institute of Technology, 4259 Nagatsuta,
Midori-ku, Yokohama 226-8503, Japan
| | - 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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25
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Liu J, Ming B, Gong GH, Wang D, Bao GL, Yu LJ. Current research on anti-breast cancer synthetic compounds. RSC Adv 2018. [DOI: 10.1039/c7ra12912b] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Breast cancer (BC) is the most common cancer for females and its incidence tends to increase year by year.
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Affiliation(s)
- Jia Liu
- Medicinal Chemistry and Pharmacology Institute
- Inner Mongolia University for Nationalities
- Tongliao
- People's Republic of China
- Inner Mongolia Key Laboratory of Mongolian Medicine Pharmacology for Cardio-Cerebral Vascular System
| | - Bian Ming
- Medicinal Chemistry and Pharmacology Institute
- Inner Mongolia University for Nationalities
- Tongliao
- People's Republic of China
- Inner Mongolia Key Laboratory of Mongolian Medicine Pharmacology for Cardio-Cerebral Vascular System
| | - Guo-Hua Gong
- First Clinical Medical of Inner Mongolia University for Nationalities
- Tongliao
- People's Republic of China
| | - Di Wang
- Medicinal Chemistry and Pharmacology Institute
- Inner Mongolia University for Nationalities
- Tongliao
- People's Republic of China
- Inner Mongolia Key Laboratory of Mongolian Medicine Pharmacology for Cardio-Cerebral Vascular System
| | - Gui-Lan Bao
- Medicinal Chemistry and Pharmacology Institute
- Inner Mongolia University for Nationalities
- Tongliao
- People's Republic of China
- Inner Mongolia Key Laboratory of Mongolian Medicine Pharmacology for Cardio-Cerebral Vascular System
| | - Li-Jun Yu
- Medicinal Chemistry and Pharmacology Institute
- Inner Mongolia University for Nationalities
- Tongliao
- People's Republic of China
- Inner Mongolia Key Laboratory of Mongolian Medicine Pharmacology for Cardio-Cerebral Vascular System
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26
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Llorach-Pares L, Nonell-Canals A, Sanchez-Martinez M, Avila C. Computer-Aided Drug Design Applied to Marine Drug Discovery: Meridianins as Alzheimer's Disease Therapeutic Agents. Mar Drugs 2017; 15:E366. [PMID: 29186912 PMCID: PMC5742826 DOI: 10.3390/md15120366] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 11/10/2017] [Accepted: 11/14/2017] [Indexed: 01/12/2023] Open
Abstract
Computer-aided drug discovery/design (CADD) techniques allow the identification of natural products that are capable of modulating protein functions in pathogenesis-related pathways, constituting one of the most promising lines followed in drug discovery. In this paper, we computationally evaluated and reported the inhibitory activity found in meridianins A-G, a group of marine indole alkaloids isolated from the marine tunicate Aplidium, against various protein kinases involved in Alzheimer's disease (AD), a neurodegenerative pathology characterized by the presence of neurofibrillary tangles (NFT). Balance splitting between tau kinase and phosphate activities caused tau hyperphosphorylation and, thereby, its aggregation and NTF formation. Inhibition of specific kinases involved in its phosphorylation pathway could be one of the key strategies to reverse tau hyperphosphorylation and would represent an approach to develop drugs to palliate AD symptoms. Meridianins bind to the adenosine triphosphate (ATP) binding site of certain protein kinases, acting as ATP competitive inhibitors. These compounds show very promising scaffolds to design new drugs against AD, which could act over tau protein kinases Glycogen synthetase kinase-3 Beta (GSK3β) and Casein kinase 1 delta (CK1δ, CK1D or KC1D), and dual specificity kinases as dual specificity tyrosine phosphorylation regulated kinase 1 (DYRK1A) and cdc2-like kinases (CLK1). This work is aimed to highlight the role of CADD techniques in marine drug discovery and to provide precise information regarding the binding mode and strength of meridianins against several protein kinases that could help in the future development of anti-AD drugs.
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Affiliation(s)
- Laura Llorach-Pares
- Department of Evolutionary Biology, Ecology and Environmental Sciences, Faculty of Biology and Biodiversity Research Institute (IRBio), Universitat de Barcelona, 08028 Barcelona, Catalonia, Spain.
- Mind the Byte S.L., 08028 Barcelona, Catalonia, Spain.
| | | | | | - Conxita Avila
- Department of Evolutionary Biology, Ecology and Environmental Sciences, Faculty of Biology and Biodiversity Research Institute (IRBio), Universitat de Barcelona, 08028 Barcelona, Catalonia, Spain.
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27
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Liu L, Bai SH, Li Y, Wang LX, Hu Y, Sung HL, Li J. Synthesis of 2,3-Diarylisoindolin-1-one by Copper-Catalyzed Cascade Annulation of 2-Formylbenzonitriles, Arenes, and Diaryliodonium Salts. J Org Chem 2017; 82:11084-11090. [DOI: 10.1021/acs.joc.7b02035] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
| | | | | | | | | | - Hui-Ling Sung
- Division
of Preparatory Programs for Overseas Chinese Students, National Taiwan Normal University, Linkou, 24449, Taiwan
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28
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Wang T, Yuan XS, Wu MB, Lin JP, Yang LR. The advancement of multidimensional QSAR for novel drug discovery - where are we headed? Expert Opin Drug Discov 2017; 12:769-784. [PMID: 28562095 DOI: 10.1080/17460441.2017.1336157] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
INTRODUCTION The Multidimensional quantitative structure-activity relationship (multidimensional-QSAR) method is one of the most popular computational methods employed to predict interesting biochemical properties of existing or hypothetical molecules. With continuous progress, the QSAR method has made remarkable success in various fields, such as medicinal chemistry, material science and predictive toxicology. Areas covered: In this review, the authors cover the basic elements of multidimensional -QSAR including model construction, validation and application. It includes and emphasizes the very recent developments of multidimensional -QSAR such as: HQSAR, G-QSAR, MIA-QSAR, multi-target QSAR. The advantages and disadvantages of each method are also discussed and typical examples of their application are detailed. Expert opinion: Although there are defects in multidimensional-QSAR modeling, it is still of enormous help to chemists, biologists and other researchers in various fields. In the authors' opinion, the latest more precise and feasible QSAR models should be further developed by integrating new descriptors, algorithms and other relevant computational techniques. Apart from being applied in traditional fields (e.g. lead optimization and predictive risk assessment), QSAR should be used more widely as a routine method in other emerging research fields including the modeling of nanoparticles(NPs), mixture toxicity and peptides.
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Affiliation(s)
- Tao Wang
- a School of biological science , Jining Medical University , Jining , China.,b Department of Chemical and Biological Engineering , Zhejiang University , Hangzhou , China
| | - Xin-Song Yuan
- b Department of Chemical and Biological Engineering , Zhejiang University , Hangzhou , China
| | - Mian-Bin Wu
- b Department of Chemical and Biological Engineering , Zhejiang University , Hangzhou , China
| | - Jian-Ping Lin
- b Department of Chemical and Biological Engineering , Zhejiang University , Hangzhou , China
| | - Li-Rong Yang
- b Department of Chemical and Biological Engineering , Zhejiang University , Hangzhou , China
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29
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Speck-Planche A, Cordeiro MNDS. De novo computational design of compounds virtually displaying potent antibacterial activity and desirable in vitro ADMET profiles. Med Chem Res 2017. [DOI: 10.1007/s00044-017-1936-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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30
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Cao Z, Zhu H, Meng X, Guan J, Zhang Q, Tian L, Sun X, Chen G, You J. Metal-Free Reaction ofortho-Carbonylated Alkynyl-Substituted Arylaldehydes with Common Amines: Selective Access to Functionalized Isoindolinone and Indenamine Derivatives. Chemistry 2016; 22:16979-16985. [DOI: 10.1002/chem.201603045] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2016] [Indexed: 12/17/2022]
Affiliation(s)
- Ziping Cao
- School of Chemistry and Chemical Engineering; Qufu Normal University; Shandong Key Laboratory of Life-Organic Analysis; Key Laboratory of Pharmaceutical Intermediates and Analysis of Natural Medicine, Qufu; 273165 Shandong P. R. China
| | - Hongbo Zhu
- School of Chemistry and Chemical Engineering; Qufu Normal University; Shandong Key Laboratory of Life-Organic Analysis; Key Laboratory of Pharmaceutical Intermediates and Analysis of Natural Medicine, Qufu; 273165 Shandong P. R. China
| | - Xin Meng
- School of Chemistry and Chemical Engineering; Qufu Normal University; Shandong Key Laboratory of Life-Organic Analysis; Key Laboratory of Pharmaceutical Intermediates and Analysis of Natural Medicine, Qufu; 273165 Shandong P. R. China
| | - Jun Guan
- School of Chemistry and Chemical Engineering; Qufu Normal University; Shandong Key Laboratory of Life-Organic Analysis; Key Laboratory of Pharmaceutical Intermediates and Analysis of Natural Medicine, Qufu; 273165 Shandong P. R. China
| | - Qiang Zhang
- School of Chemistry and Chemical Engineering; Qufu Normal University; Shandong Key Laboratory of Life-Organic Analysis; Key Laboratory of Pharmaceutical Intermediates and Analysis of Natural Medicine, Qufu; 273165 Shandong P. R. China
| | - Laijin Tian
- School of Chemistry and Chemical Engineering; Qufu Normal University; Shandong Key Laboratory of Life-Organic Analysis; Key Laboratory of Pharmaceutical Intermediates and Analysis of Natural Medicine, Qufu; 273165 Shandong P. R. China
| | - Xuejun Sun
- School of Chemistry and Chemical Engineering; Qufu Normal University; Shandong Key Laboratory of Life-Organic Analysis; Key Laboratory of Pharmaceutical Intermediates and Analysis of Natural Medicine, Qufu; 273165 Shandong P. R. China
| | - Guang Chen
- School of Chemistry and Chemical Engineering; Qufu Normal University; Shandong Key Laboratory of Life-Organic Analysis; Key Laboratory of Pharmaceutical Intermediates and Analysis of Natural Medicine, Qufu; 273165 Shandong P. R. China
| | - Jinmao You
- School of Chemistry and Chemical Engineering; Qufu Normal University; Shandong Key Laboratory of Life-Organic Analysis; Key Laboratory of Pharmaceutical Intermediates and Analysis of Natural Medicine, Qufu; 273165 Shandong P. R. China
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Romero-Durán FJ, Alonso N, Yañez M, Caamaño O, García-Mera X, González-Díaz H. Brain-inspired cheminformatics of drug-target brain interactome, synthesis, and assay of TVP1022 derivatives. Neuropharmacology 2016; 103:270-8. [DOI: 10.1016/j.neuropharm.2015.12.019] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Revised: 11/22/2015] [Accepted: 12/18/2015] [Indexed: 01/22/2023]
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32
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Shar PA, Tao W, Gao S, Huang C, Li B, Zhang W, Shahen M, Zheng C, Bai Y, Wang Y. Pred-binding: large-scale protein-ligand binding affinity prediction. J Enzyme Inhib Med Chem 2016; 31:1443-50. [PMID: 26888050 DOI: 10.3109/14756366.2016.1144594] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Drug target interactions (DTIs) are crucial in pharmacology and drug discovery. Presently, experimental determination of compound-protein interactions remains challenging because of funding investment and difficulties of purifying proteins. In this study, we proposed two in silico models based on support vector machine (SVM) and random forest (RF), using 1589 molecular descriptors and 1080 protein descriptors in 9948 ligand-protein pairs to predict DTIs that were quantified by Ki values. The cross-validation coefficient of determination of 0.6079 for SVM and 0.6267 for RF were obtained, respectively. In addition, the two-dimensional (2D) autocorrelation, topological charge indices and three-dimensional (3D)-MoRSE descriptors of compounds, the autocorrelation descriptors and the amphiphilic pseudo-amino acid composition of protein are found most important for Ki predictions. These models provide a new opportunity for the prediction of ligand-receptor interactions that will facilitate the target discovery and toxicity evaluation in drug development.
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Affiliation(s)
- Piar Ali Shar
- a Bioinformatics Center, College of Life Sciences, Northwest A & F University , Yangling , Shaanxi , China
| | - Weiyang Tao
- a Bioinformatics Center, College of Life Sciences, Northwest A & F University , Yangling , Shaanxi , China
| | - Shuo Gao
- a Bioinformatics Center, College of Life Sciences, Northwest A & F University , Yangling , Shaanxi , China
| | - Chao Huang
- a Bioinformatics Center, College of Life Sciences, Northwest A & F University , Yangling , Shaanxi , China
| | - Bohui Li
- a Bioinformatics Center, College of Life Sciences, Northwest A & F University , Yangling , Shaanxi , China
| | - Wenjuan Zhang
- a Bioinformatics Center, College of Life Sciences, Northwest A & F University , Yangling , Shaanxi , China
| | - Mohamed Shahen
- a Bioinformatics Center, College of Life Sciences, Northwest A & F University , Yangling , Shaanxi , China
| | - Chunli Zheng
- a Bioinformatics Center, College of Life Sciences, Northwest A & F University , Yangling , Shaanxi , China
| | - Yaofei Bai
- a Bioinformatics Center, College of Life Sciences, Northwest A & F University , Yangling , Shaanxi , China
| | - Yonghua Wang
- a Bioinformatics Center, College of Life Sciences, Northwest A & F University , Yangling , Shaanxi , China
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33
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Halder A, Goodarzi M. Recent Advances in Multi-Task QSAR Modeling for Drug Design. PHARMACEUTICAL SCIENCES 2015. [DOI: 10.15171/ps.2015.33] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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34
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Shao Z, Hirayama Y, Yamanishi Y, Saigo H. Mining Discriminative Patterns from Graph Data with Multiple Labels and Its Application to Quantitative Structure-Activity Relationship (QSAR) Models. J Chem Inf Model 2015; 55:2519-27. [PMID: 26549421 DOI: 10.1021/acs.jcim.5b00376] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Graph data are becoming increasingly common in machine learning and data mining, and its application field pervades to bioinformatics and cheminformatics. Accordingly, as a method to extract patterns from graph data, graph mining recently has been studied and developed rapidly. Since the number of patterns in graph data is huge, a central issue is how to efficiently collect informative patterns suitable for subsequent tasks such as classification or regression. In this paper, we consider mining discriminative subgraphs from graph data with multiple labels. The resulting task has important applications in cheminformatics, such as finding common functional groups that trigger multiple drug side effects, or identifying ligand functional groups that hit multiple targets. In computational experiments, we first verify the effectiveness of the proposed approach in synthetic data, then we apply it to drug adverse effect prediction problem. In the latter dataset, we compared the proposed method with L1-norm logistic regression in combination with the PubChem/Open Babel fingerprint, in that the proposed method showed superior performance with a much smaller number of subgraph patterns. Software is available from https://github.com/axot/GLP.
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Affiliation(s)
- Zheng Shao
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology , Iizuka, Fukuoka 820-8502, Japan
| | - Yuya Hirayama
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology , Iizuka, Fukuoka 820-8502, Japan
| | - Yoshihiro Yamanishi
- Division of System Cohort, Multi-Scale Research Center for Medical Science, Medical Institute of Bioregulation, Kyushu University , 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan.,Institute for Advanced Study, Kyushu University , 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan
| | - Hiroto Saigo
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology , Iizuka, Fukuoka 820-8502, Japan
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35
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Casañola-Martin GM, Le-Thi-Thu H, Pérez-Giménez F, Marrero-Ponce Y, Merino-Sanjuán M, Abad C, González-Díaz H. Multi-output model with Box–Jenkins operators of linear indices to predict multi-target inhibitors of ubiquitin–proteasome pathway. Mol Divers 2015; 19:347-56. [DOI: 10.1007/s11030-015-9571-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Accepted: 02/14/2015] [Indexed: 12/29/2022]
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36
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Speck-Planche A, Cordeiro MNDS. Multitasking models for quantitative structure–biological effect relationships: current status and future perspectives to speed up drug discovery. Expert Opin Drug Discov 2015; 10:245-56. [DOI: 10.1517/17460441.2015.1006195] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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Liu Y, Buendía-Rodríguez G, Peñuelas-Rívas CG, Tan Z, Rívas-Guevara M, Tenorio-Borroto E, Munteanu CR, Pazos A, González-Díaz H. Experimental and computational studies of fatty acid distribution networks. MOLECULAR BIOSYSTEMS 2015; 11:2964-77. [DOI: 10.1039/c5mb00325c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
A new PT-LFER model is useful for predicting a distribution network in terms of specific fatty acid distribution.
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Affiliation(s)
- Yong Liu
- Faculty of Veterinary Medicine and Animal Science
- Autonomous University of the State of Mexico
- Toluca
- Mexico
- Key Laboratory of Subtropical Agro-ecological Engineering
| | - Germán Buendía-Rodríguez
- National Center for Disciplinary Research on Animal Physiology and Breeding
- National Institute of Forestry
- Agriculture and Livestock Research
- Queretaro
- Mexico
| | | | - Zhiliang Tan
- Key Laboratory of Subtropical Agro-ecological Engineering
- Institute of Subtropical Agriculture, the Chinese Academy of Sciences
- Changsha
- P. R. China
| | - María Rívas-Guevara
- Ethnobiology and Biodiversity Research Center
- Chapingo Autonomous University
- Texcoco
- Mexico
| | - Esvieta Tenorio-Borroto
- Faculty of Veterinary Medicine and Animal Science
- Autonomous University of the State of Mexico
- Toluca
- Mexico
| | | | | | - Humberto González-Díaz
- Department of Organic Chemistry II
- Faculty of Science and Technology
- University of the Basque Country UPV/EHU
- Leioa
- Spain
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Speck-Planche A, Cordeiro MNDS. A general ANN-based multitasking model for the discovery of potent and safer antibacterial agents. Methods Mol Biol 2015; 1260:45-64. [PMID: 25502375 DOI: 10.1007/978-1-4939-2239-0_4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Bacteria have been one of the world's most dangerous and deadliest pathogens for mankind, nowadays giving rise to significant public health concerns. Given the prevalence of these microbial pathogens and their increasing resistance to existing antibiotics, there is a pressing need for new antibacterial drugs. However, development of a successful drug is a complex, costly, and time-consuming process. Quantitative Structure-Activity Relationships (QSAR)-based approaches are valuable tools for shortening the time of lead compound identification but also for focusing and limiting time-costly synthetic activities and in vitro/vivo evaluations. QSAR-based approaches, supported by powerful statistical techniques such as artificial neural networks (ANNs), have evolved to the point of integrating dissimilar types of chemical and biological data. This chapter reports an overview of the current research and potential applications of QSAR modeling tools toward the rational design of more efficient antibacterial agents. Particular emphasis is given to the setup of multitasking models along with ANNs aimed at jointly predicting different antibacterial activities and safety profiles of drugs/chemicals under diverse experimental conditions.
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Affiliation(s)
- A Speck-Planche
- Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, 4169-007, Porto, Portugal
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Chemoinformatics for medicinal chemistry: in silico model to enable the discovery of potent and safer anti-cocci agents. Future Med Chem 2014; 6:2013-28. [DOI: 10.4155/fmc.14.136] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Background: Gram-positive cocci are increasingly antibiotic-resistant bacteria responsible for causing serious diseases. Chemoinformatics can help to rationalize the discovery of more potent and safer antibacterial drugs. We have developed a chemoinformatic model for simultaneous prediction of anti-cocci activities, and profiles involving absorption, distribution, metabolism, elimination and toxicity (ADMET). Results: A dataset containing 48,874 cases from many different chemicals assayed under dissimilar experimental conditions was created. The best model displayed accuracies around 93% in both training and prediction (test) sets. Quantitative contributions of several fragments to the biological effects were calculated and analyzed. Multiple biological effects of the investigational drug JNJ-Q2 were correctly predicted. Conclusion: Our chemoinformatic model can be used as powerful tool for virtual screening of promising anti-cocci agents.
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Kovačević SZ, Podunavac-Kuzmanović SO, Jevrić LR, Djurendić EA, Ajduković JJ. Non-linear assessment of anticancer activity of 17-picolyl and 17-picolinylidene androstane derivatives – Chemometric guidelines for further syntheses. Eur J Pharm Sci 2014; 62:258-66. [DOI: 10.1016/j.ejps.2014.05.031] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Revised: 05/27/2014] [Accepted: 05/31/2014] [Indexed: 12/17/2022]
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Prediction of multi-target networks of neuroprotective compounds with entropy indices and synthesis, assay, and theoretical study of new asymmetric 1,2-rasagiline carbamates. Int J Mol Sci 2014; 15:17035-64. [PMID: 25255029 PMCID: PMC4200850 DOI: 10.3390/ijms150917035] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Revised: 08/19/2014] [Accepted: 08/21/2014] [Indexed: 11/25/2022] Open
Abstract
In a multi-target complex network, the links (Lij) represent the interactions between the drug (di) and the target (tj), characterized by different experimental measures (Ki, Km, IC50, etc.) obtained in pharmacological assays under diverse boundary conditions (cj). In this work, we handle Shannon entropy measures for developing a model encompassing a multi-target network of neuroprotective/neurotoxic compounds reported in the CHEMBL database. The model predicts correctly >8300 experimental outcomes with Accuracy, Specificity, and Sensitivity above 80%–90% on training and external validation series. Indeed, the model can calculate different outcomes for >30 experimental measures in >400 different experimental protocolsin relation with >150 molecular and cellular targets on 11 different organisms (including human). Hereafter, we reported by the first time the synthesis, characterization, and experimental assays of a new series of chiral 1,2-rasagiline carbamate derivatives not reported in previous works. The experimental tests included: (1) assay in absence of neurotoxic agents; (2) in the presence of glutamate; and (3) in the presence of H2O2. Lastly, we used the new Assessing Links with Moving Averages (ALMA)-entropy model to predict possible outcomes for the new compounds in a high number of pharmacological tests not carried out experimentally.
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Kuyoc-Carrillo VF, Medina-Franco JL. Progress in the Analysis of Multiple Activity Profile of Screening Data Using Computational Approaches. Drug Dev Res 2014; 75:313-23. [DOI: 10.1002/ddr.21209] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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