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Gul S, Rahim F, Isin S, Yilmaz F, Ozturk N, Turkay M, Kavakli IH. Structure-based design and classifications of small molecules regulating the circadian rhythm period. Sci Rep 2021; 11:18510. [PMID: 34531414 PMCID: PMC8445970 DOI: 10.1038/s41598-021-97962-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 08/27/2021] [Indexed: 11/09/2022] Open
Abstract
Circadian rhythm is an important mechanism that controls behavior and biochemical events based on 24 h rhythmicity. Ample evidence indicates disturbance of this mechanism is associated with different diseases such as cancer, mood disorders, and familial delayed phase sleep disorder. Therefore, drug discovery studies have been initiated using high throughput screening. Recently the crystal structures of core clock proteins (CLOCK/BMAL1, Cryptochromes (CRY), Periods), responsible for generating circadian rhythm, have been solved. Availability of structures makes amenable core clock proteins to design molecules regulating their activity by using in silico approaches. In addition to that, the implementation of classification features of molecules based on their toxicity and activity will improve the accuracy of the drug discovery process. Here, we identified 171 molecules that target functional domains of a core clock protein, CRY1, using structure-based drug design methods. We experimentally determined that 115 molecules were nontoxic, and 21 molecules significantly lengthened the period of circadian rhythm in U2OS cells. We then performed a machine learning study to classify these molecules for identifying features that make them toxic and lengthen the circadian period. Decision tree classifiers (DTC) identified 13 molecular descriptors, which predict the toxicity of molecules with a mean accuracy of 79.53% using tenfold cross-validation. Gradient boosting classifiers (XGBC) identified 10 molecular descriptors that predict and increase in the circadian period length with a mean accuracy of 86.56% with tenfold cross-validation. Our results suggested that these features can be used in QSAR studies to design novel nontoxic molecules that exhibit period lengthening activity.
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Affiliation(s)
- Seref Gul
- Department of Chemical and Biological Engineering, Koc University, Rumelifeneri Yolu, Sariyer, Istabul, Turkey
| | - Fatih Rahim
- Department of Industrial Engineering, Koc University, Rumelifeneri Yolu, Sariyer, Istabul, Turkey
| | - Safak Isin
- Department of Molecular Biology and Genetics, Rumelifeneri Yolu, Sariyer, Istabul, Turkey
| | - Fatma Yilmaz
- Department of Molecular Biology and Genetics, Gebze Technical University, Gebze, 41400, Kocaeli, Turkey
| | - Nuri Ozturk
- Department of Molecular Biology and Genetics, Gebze Technical University, Gebze, 41400, Kocaeli, Turkey
| | - Metin Turkay
- Department of Industrial Engineering, Koc University, Rumelifeneri Yolu, Sariyer, Istabul, Turkey.
| | - Ibrahim Halil Kavakli
- Department of Chemical and Biological Engineering, Koc University, Rumelifeneri Yolu, Sariyer, Istabul, Turkey.
- Department of Molecular Biology and Genetics, Rumelifeneri Yolu, Sariyer, Istabul, Turkey.
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2
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Concu R, González-Durruthy M, Cordeiro MNDS. Developing a Multi-target Model to Predict the Activity of Monoamine Oxidase A and B Drugs. Curr Top Med Chem 2021; 20:1593-1600. [PMID: 32493193 DOI: 10.2174/1568026620666200603121224] [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: 11/15/2019] [Revised: 11/19/2019] [Accepted: 11/28/2019] [Indexed: 12/21/2022]
Abstract
INTRODUCTION Monoamine oxidase inhibitors (MAOIs) are compounds largely used in the treatment of Parkinson's disease (PD), Alzheimer's disease and other neuropsychiatric disorders since they are closely related to the MAO enzymes activity. The two isoforms of the MAO enzymes, MAO-A and MAO-B, are responsible for the degradation of monoamine neurotransmitters and due to this, relevant efforts have been devoted to finding new compounds with more selectivity and less side effects. One of the most used approaches is based on the use of computational approaches since they are time and money-saving and may allow us to find a more relevant structure-activity relationship. OBJECTIVE In this manuscript, we will review the most relevant computational approaches aimed at the prediction and development of new MAO inhibitors. Subsequently, we will also introduce a new multitask model aimed at predicting MAO-A and MAO-B inhibitors. METHODS The QSAR multi-task model herein developed was based on the use of the linear discriminant analysis. This model was developed gathering 5,759 compounds from the public dataset Chembl. The molecular descriptors used was calculated using the Dragon software. Classical statistical tests were performed to check the validity and robustness of the model. RESULTS The herein proposed model is able to correctly classify all the 5,759 compounds. All the statistical performed tests indicated that this model is robust and reproducible. CONCLUSION MAOIs are compounds of large interest since they are largely used in the treatment of very serious illness. These inhibitors may lose efficacy and produce severe side effects. Due to this, the development of selective MAO-A or MAO-B inhibitors is crucial for the treatment of these diseases and their effects. The herein proposed multi-target QSAR model may be a relevant tool in the development of new and more selective MAO inhibitors.
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Affiliation(s)
- Riccardo Concu
- LAQV@REQUIMTE/Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal
| | - Michael González-Durruthy
- LAQV@REQUIMTE/Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal
| | - Maria Natália D S Cordeiro
- LAQV@REQUIMTE/Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal
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3
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Kianpour M, Mohammadinasab E, Isfahani TM. Comparison between genetic algorithm‐multiple linear regression and back‐propagation‐artificial neural network methods for predicting the
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50
of organo (phosphate and thiophosphate) compounds. J CHIN CHEM SOC-TAIP 2020. [DOI: 10.1002/jccs.201900514] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Mina Kianpour
- Department of Chemistry, Arak BranchIslamic Azad University Arak Iran
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4
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Ramesh M, Muthuraman A. Quantitative Structure-Activity Relationship (QSAR) Studies for the Inhibition of MAOs. Comb Chem High Throughput Screen 2020; 23:887-897. [PMID: 32208114 DOI: 10.2174/1386207323666200324173231] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 01/20/2020] [Accepted: 02/04/2020] [Indexed: 11/22/2022]
Abstract
Monoamine oxidases are the crucial drug targets for the treatment of neurodegenerative disorders like depression, Parkinson's disease, and Alzheimer's disease. The enzymes catalyze the oxidative deamination of several monoamine containing neurotransmitters, i.e. serotonin (5-HT), melatonin, epinephrine, norepinephrine, phenylethylamine, benzylamine, dopamine, tyramine, etc. The oxidative reaction of monoamine oxidases results in the production of hydrogen peroxide that leads to the neurodegeneration process. Therefore, the inhibition of monoamine oxidases has shown a profound effect against neurodegenerative diseases. At present, the design and development of newer lead molecules for the inhibition of monoamine oxidases are under intensive research in the field of medicinal chemistry. Recently, the advancement in QSAR methodologies has shown considerable interest in the development of monoamine oxidase inhibitors. The present review describes the development of QSAR methodologies, and their role in the design of newer monoamine oxidase inhibitors. It will assist the medicinal chemist in the identification of selective and potent monoamine oxidase inhibitors from various chemical scaffolds.
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Affiliation(s)
- Muthusamy Ramesh
- Department of Pharmaceutical Analysis, Omega College of Pharmacy, Hyderabad-501 301, India
| | - Arunachalam Muthuraman
- Pharmacology Unit, Faculty of Pharmacy, AIMST University, Semeling, 08100 Bedong, Kedah Darul Aman, Malaysia
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Sahin K, Saripinar E. A novel hybrid method named electron conformational genetic algorithm as a 4D QSAR investigation to calculate the biological activity of the tetrahydrodibenzazosines. J Comput Chem 2020; 41:1091-1104. [PMID: 32058616 DOI: 10.1002/jcc.26154] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 12/18/2019] [Accepted: 12/18/2019] [Indexed: 11/11/2022]
Abstract
To understand the structure-activity correlation of a group of tetrahydrodibenzazocines as inhibitors of 17β-hydroxysteroid dehydrogenase type 3, we have performed a combined genetic algorithm (GA) and four-dimensional quantitative structure-activity relationship (4D-QSAR) modeling study. The computed electronic and geometry structure descriptors were regulated as a matrix and named as electron-conformational matrix of contiguity (ECMC). A chemical property-based pharmacophore model was developed for series of tetrahydrodibenzazocines by EMRE software package. GA was employed to choose an optimal combination of parameters. A model has been developed for estimating anticancer activity quantitatively. All QSAR models were established with 40 compounds (training set), then they were considered for selective capability with additional nine compounds (test set). A statistically valid 4D-QSAR ( R training 2 = 0.856 , R test 2 = 0.851 and q2 = 0.650) with good external set prediction was obtained.
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Affiliation(s)
- Kader Sahin
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey
| | - Emin Saripinar
- Science Faculty, Department of Chemistry, Erciyes University, Kayseri, Turkey
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6
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Khan I, Zaib S, Ibrar A. New frontiers in the transition-metal-free synthesis of heterocycles from alkynoates: an overview and current status. Org Chem Front 2020. [DOI: 10.1039/d0qo00698j] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
This review highlights the successful utilization of transition-metal-free approaches for the modular assembly of various heterocycles from alkynoates.
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Affiliation(s)
- Imtiaz Khan
- Department of Chemistry
- School of Natural Sciences
- The University of Manchester
- Manchester M13 9PL
- UK
| | - Sumera Zaib
- Department of Biochemistry
- Faculty of Life Sciences
- University of Central Punjab
- Lahore-54590
- Pakistan
| | - Aliya Ibrar
- Department of Chemistry
- Faculty of Natural Sciences
- The University of Haripur
- Haripur, KPK-22620
- Pakistan
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7
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Olaya MDP, Vergel NE, López JL, Viña D, Guerrero MF. 8-Propyl-6H-[1,3]dioxolo[4,5-g]chromen-6-one: A new coumarin with monoamine oxidase B inhibitory activity and possible anti-parkinsonian effects. BRAZ J PHARM SCI 2020. [DOI: 10.1590/s2175-97902019000317609] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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8
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Lipeeva AV, Zakharov DO, Gatilov YV, Pokrovskii MA, Pokrovskii AG, Shults EE. Design and Synthesis of 3‐(
N
‐Substituted)aminocoumarins as Anticancer Agents from 3‐Bromopeuruthenicin. ChemistrySelect 2019. [DOI: 10.1002/slct.201901377] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Alla V. Lipeeva
- Laboratory of Medicinal ChemistryNovosibirsk institute of Organic Chemistry Lavrentyev Ave 9 630090 Novosibirsk Russian Federation
| | - Danila O. Zakharov
- Laboratory of Medicinal ChemistryNovosibirsk institute of Organic Chemistry Lavrentyev Ave 9 630090 Novosibirsk Russian Federation
- Medicinal departmentNovosibirsk State University Pirogova St. 2 630090 Novosibirsk Russian Federation
| | - Yurii V. Gatilov
- Laboratory of Medicinal ChemistryNovosibirsk institute of Organic Chemistry Lavrentyev Ave 9 630090 Novosibirsk Russian Federation
- Medicinal departmentNovosibirsk State University Pirogova St. 2 630090 Novosibirsk Russian Federation
| | - Mikhail A. Pokrovskii
- Medicinal departmentNovosibirsk State University Pirogova St. 2 630090 Novosibirsk Russian Federation
| | - Andrey G. Pokrovskii
- Medicinal departmentNovosibirsk State University Pirogova St. 2 630090 Novosibirsk Russian Federation
| | - Elvira E. Shults
- Laboratory of Medicinal ChemistryNovosibirsk institute of Organic Chemistry Lavrentyev Ave 9 630090 Novosibirsk Russian Federation
- Medicinal departmentNovosibirsk State University Pirogova St. 2 630090 Novosibirsk Russian Federation
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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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10
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Identification of novel monoamine oxidase selective inhibitors employing a hierarchical ligand-based virtual screening strategy. Future Med Chem 2019; 11:801-816. [PMID: 31140884 DOI: 10.4155/fmc-2018-0596] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Aim: Due to the pivotal role in the oxidative deamination of monoamine neurotransmitters, two distinct monoamine oxidase (MAO) subtypes, MAO-A and MAO-B, present a significant pharmacological interest. Here, we reported a hierarchical and time-efficient ligand-based virtual screening strategy to identify potent selective and reversible MAO inhibitors. Result: A total of 130 compounds were assessed in dose–response biochemical assay against MAOs. Among them, 70 compounds were active with inhibition higher than 70%, involving 25 compounds with IC50 values less than 1 μM. Conclusion: Our research demonstrated the validity of Biologically Relevant Spectrum (BRS-3D) in predicting subtype-selective ligands and afforded a novel highly efficient way to develop selective inhibitors in the early stage of drug discovery.
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11
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Yan LQ, Cai X, He X, Wang H, Xie M, Zuo Y, Shang Y. Synthesis of 4-styrylcoumarins via FeCl3-promoted cascade reactions of propargylamines with β-keto esters. Org Biomol Chem 2019; 17:4005-4013. [DOI: 10.1039/c9ob00323a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
A versatile and highly regioselective FeCl3-promoted tandem cyclization reaction of in situ generated alkynyl o-quinone methides (o-AQMs) with β-keto esters has been developed.
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Affiliation(s)
- Li-Qin Yan
- Key Laboratory of Functional Molecular Solids
- Ministry of Education
- Anhui Laboratory of Molecule-Based Materials (State Key Laboratory Cultivation Base)
- College of Chemistry and Materials Science
- Anhui Normal University
| | - Xiaoting Cai
- Key Laboratory of Functional Molecular Solids
- Ministry of Education
- Anhui Laboratory of Molecule-Based Materials (State Key Laboratory Cultivation Base)
- College of Chemistry and Materials Science
- Anhui Normal University
| | - Xinwei He
- Key Laboratory of Functional Molecular Solids
- Ministry of Education
- Anhui Laboratory of Molecule-Based Materials (State Key Laboratory Cultivation Base)
- College of Chemistry and Materials Science
- Anhui Normal University
| | - Hui Wang
- Key Laboratory of Functional Molecular Solids
- Ministry of Education
- Anhui Laboratory of Molecule-Based Materials (State Key Laboratory Cultivation Base)
- College of Chemistry and Materials Science
- Anhui Normal University
| | - Mengqing Xie
- Key Laboratory of Functional Molecular Solids
- Ministry of Education
- Anhui Laboratory of Molecule-Based Materials (State Key Laboratory Cultivation Base)
- College of Chemistry and Materials Science
- Anhui Normal University
| | - Youpeng Zuo
- Key Laboratory of Functional Molecular Solids
- Ministry of Education
- Anhui Laboratory of Molecule-Based Materials (State Key Laboratory Cultivation Base)
- College of Chemistry and Materials Science
- Anhui Normal University
| | - Yongjia Shang
- Key Laboratory of Functional Molecular Solids
- Ministry of Education
- Anhui Laboratory of Molecule-Based Materials (State Key Laboratory Cultivation Base)
- College of Chemistry and Materials Science
- Anhui Normal University
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12
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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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13
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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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Dhiman P, Malik N, Khatkar A. 3D-QSAR and in-silico Studies of Natural Products and Related Derivatives as Monoamine Oxidase Inhibitors. Curr Neuropharmacol 2018; 16:881-900. [PMID: 29189167 PMCID: PMC6080100 DOI: 10.2174/1570159x15666171128143650] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 11/24/2017] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The computational development of human monoamine oxidase (MAO) inhibitors led to advancement in drug design and the treatment of many neurodegenerative diseases and neuropsychiatric disorders. The computational development of human monoamine oxidase (MAO) inhibitors led to advancement in drug design and the treatment of many neurodegenerative diseases and neuropsychiatric disorders. Different natural heterocyclic structures are reported to display selective MAO inhibitory activity by preclinical and in-silico modeling. OBJECTIVE Currently, the major interest is devoted to the study of natural based therapeutic agents from the different categories. Therefore, we presenting the review to critically discuss and outline the recent advances in our knowledge on the importance of natural and natural based ligand-MAO insilico methods for novel MAO inhibitors. DISCUSSION Several natural and related synthetic heterocyclic compounds such as coumarins, β- carboline, piperine, naphthoquinone, morpholine, caffeine, amphetamine moreover flavonoids, chalcones, xanthones, curcumin are discussed for their MAO inhibitory profile along with molecular docking and quantitative structure-activity relationship studies. CONCLUSION It is clear that, by this computational drug design approach, more particular, reversible and potent compounds can be proposed as MAO inhibitors by exact changes on the fundamental framework.
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Affiliation(s)
- Priyanka Dhiman
- Laboratory for Preservation Technology and Enzyme Inhibition Studies, Faculty of Pharmaceutical Sciences, M.D. University, Rohtak (124001), India
| | - Neelam Malik
- Laboratory for Preservation Technology and Enzyme Inhibition Studies, Faculty of Pharmaceutical Sciences, M.D. University, Rohtak (124001), India
| | - Anurag Khatkar
- Laboratory for Preservation Technology and Enzyme Inhibition Studies, Faculty of Pharmaceutical Sciences, M.D. University, Rohtak (124001), India
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Luechtefeld T, Hartung T. Computational approaches to chemical hazard assessment. ALTEX-ALTERNATIVES TO ANIMAL EXPERIMENTATION 2018; 34:459-478. [PMID: 29101769 PMCID: PMC5848496 DOI: 10.14573/altex.1710141] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2017] [Indexed: 01/10/2023]
Abstract
Computational prediction of toxicity has reached new heights as a result of decades of growth in the magnitude and diversity of biological data. Public packages for statistics and machine learning make model creation faster. New theory in machine learning and cheminformatics enables integration of chemical structure, toxicogenomics, simulated and physical data in the prediction of chemical health hazards, and other toxicological information. Our earlier publications have characterized a toxicological dataset of unprecedented scale resulting from the European REACH legislation (Registration Evaluation Authorisation and Restriction of Chemicals). These publications dove into potential use cases for regulatory data and some models for exploiting this data. This article analyzes the options for the identification and categorization of chemicals, moves on to the derivation of descriptive features for chemicals, discusses different kinds of targets modeled in computational toxicology, and ends with a high-level perspective of the algorithms used to create computational toxicology models.
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Affiliation(s)
- Thomas Luechtefeld
- Johns Hopkins Center for Alternatives to Animal Testing (CAAT), Baltimore, MD, USA
| | - Thomas Hartung
- Johns Hopkins Center for Alternatives to Animal Testing (CAAT), Baltimore, MD, USA.,CAAT-Europe, University of Konstanz, Konstanz, Germany
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16
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Synthesis, biological evaluation and molecular modeling studies of phenyl-/benzhydrylpiperazine derivatives as potential MAO inhibitors. Bioorg Chem 2018; 77:252-262. [DOI: 10.1016/j.bioorg.2018.01.020] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 01/07/2018] [Accepted: 01/12/2018] [Indexed: 11/21/2022]
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17
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Stefanachi A, Leonetti F, Pisani L, Catto M, Carotti A. Coumarin: A Natural, Privileged and Versatile Scaffold for Bioactive Compounds. Molecules 2018; 23:E250. [PMID: 29382051 PMCID: PMC6017103 DOI: 10.3390/molecules23020250] [Citation(s) in RCA: 290] [Impact Index Per Article: 48.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 01/22/2018] [Accepted: 01/25/2018] [Indexed: 12/22/2022] Open
Abstract
Many naturally occurring substances, traditionally used in popular medicines around the world, contain the coumarin moiety. Coumarin represents a privileged scaffold for medicinal chemists, because of its peculiar physicochemical features, and the versatile and easy synthetic transformation into a large variety of functionalized coumarins. As a consequence, a huge number of coumarin derivatives have been designed, synthesized, and tested to address many pharmacological targets in a selective way, e.g., selective enzyme inhibitors, and more recently, a number of selected targets (multitarget ligands) involved in multifactorial diseases, such as Alzheimer's and Parkinson's diseases. In this review an overview of the most recent synthetic pathways leading to mono- and polyfunctionalized coumarins will be presented, along with the main biological pathways of their biosynthesis and metabolic transformations. The many existing and recent reviews in the field prompted us to make some drastic selections, and therefore, the review is focused on monoamine oxidase, cholinesterase, and aromatase inhibitors, and on multitarget coumarins acting on selected targets of neurodegenerative diseases.
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Affiliation(s)
- Angela Stefanachi
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari "Aldo Moro", via E. Orabona 4, I-70125 Bari, Italy.
| | - Francesco Leonetti
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari "Aldo Moro", via E. Orabona 4, I-70125 Bari, Italy.
| | - Leonardo Pisani
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari "Aldo Moro", via E. Orabona 4, I-70125 Bari, Italy.
| | - Marco Catto
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari "Aldo Moro", via E. Orabona 4, I-70125 Bari, Italy.
| | - Angelo Carotti
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari "Aldo Moro", via E. Orabona 4, I-70125 Bari, Italy.
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Li JL, Hu DC, Liang XP, Wang YC, Wang HS, Pan YM. Praseodymium(III)-Catalyzed Regioselective Synthesis of C3-N-Substituted Coumarins with Coumarins and Azides. J Org Chem 2017; 82:9006-9011. [DOI: 10.1021/acs.joc.7b01410] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Jiu-ling Li
- State
Key Laboratory for Chemistry and Molecular Engineering of Medicinal
Resources, School of Chemistry and Pharmaceutical Sciences of Guangxi Normal University, Guilin 541004, People’s Republic of China
| | - Da-chao Hu
- State
Key Laboratory for Chemistry and Molecular Engineering of Medicinal
Resources, School of Chemistry and Pharmaceutical Sciences of Guangxi Normal University, Guilin 541004, People’s Republic of China
| | - Xin-ping Liang
- State
Key Laboratory for Chemistry and Molecular Engineering of Medicinal
Resources, School of Chemistry and Pharmaceutical Sciences of Guangxi Normal University, Guilin 541004, People’s Republic of China
| | - Ying-Chun Wang
- College
of Chemistry and Chemical Engineering, Jishou University, Jishou 416000, People’s Republic of China
| | - Heng-Shan Wang
- State
Key Laboratory for Chemistry and Molecular Engineering of Medicinal
Resources, School of Chemistry and Pharmaceutical Sciences of Guangxi Normal University, Guilin 541004, People’s Republic of China
| | - Ying-ming Pan
- State
Key Laboratory for Chemistry and Molecular Engineering of Medicinal
Resources, School of Chemistry and Pharmaceutical Sciences of Guangxi Normal University, Guilin 541004, People’s Republic of China
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Mangiatordi GF, Alberga D, Pisani L, Gadaleta D, Trisciuzzi D, Farina R, Carotti A, Lattanzi G, Catto M, Nicolotti O. A rational approach to elucidate human monoamine oxidase molecular selectivity. Eur J Pharm Sci 2017; 101:90-99. [DOI: 10.1016/j.ejps.2017.02.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 01/27/2017] [Accepted: 02/05/2017] [Indexed: 02/05/2023]
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20
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Sharifi M, Ghadamyari M, Gholivand K, Valmoozi AAE, Sajedi RH. Characterization of acetylcholinesterase from elm left beetle, Xanthogaleruca luteola and QSAR of temephos derivatives against its activity. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2017; 136:12-22. [PMID: 28187825 DOI: 10.1016/j.pestbp.2016.08.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 08/24/2016] [Accepted: 08/31/2016] [Indexed: 06/06/2023]
Abstract
Insect acetylcholinesterase (AChE) is the principal target for organophosphate (OP) and carbamate (CB) insecticides. In this research, an AChE from third instar larvae of elm left beetle, Xanthogaleruca luteola was purified by affinity chromatography. The enzyme was purified 75.29-fold with a total yield of 8.51%. As shown on denaturing SDS-PAGE, the molecular mass of purified AChE was 70kDa. The enzyme demonstrated maximum activity at pH7 and 35°C. Furthermore, a series of temephos (Tem) derivatives with the general structure of P(O)XP(O) (1-44) were prepared, synthesized and characterized by 31P, 13C, 1H NMR and FT-IR spectral techniques. The toxicity of 36 new Tem derivatives was screened on the third instar larvae and the compound compound 1,2 cyclohexane-N,N'-bis(N,N'-piperidine phosphoramidate) exhibited the highest insecticidal potential. The method of kinetic analysis is applied in order to obtain the maximum velocity (Vmax), the Michaelis constant (Km) and the parameters characterizing the inhibition type for inhibitors with >75% mortality in preliminary bioassay. The inhibition mechanism was mixed and inhibitory constant (Ki) was calculated as 4.70μM-1min-1 for this compound. Quantitative structure-activity relationship (QSAR) equations of these compounds indicated that the electron orbital energy has major effect on insecticidal properties.
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Affiliation(s)
- Mahboobeh Sharifi
- Department of Plant Protection, Faculty of Agricultural Sciences, University of Guilan, Rasht, Iran
| | - Mohammad Ghadamyari
- Department of Plant Protection, Faculty of Agricultural Sciences, University of Guilan, Rasht, Iran.
| | | | | | - Reza H Sajedi
- Department of Biochemistry, Tarbiat Modares University, Tehran, Iran
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Feng S, Li J, Liu Z, Sun H, Shi H, Wang X, Xie X, She X. Visible-light-mediated radical cascade reaction: synthesis of 3-bromocoumarins from alkynoates. Org Biomol Chem 2017; 15:8820-8826. [DOI: 10.1039/c7ob02199b] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The development of a visible-light mediated bromo radical addition/spirocyclization/ester migration cascade reaction to generate 3-bromocoumarins from alkynoates is reported.
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Affiliation(s)
- Shangbiao Feng
- State Key Laboratory of Applied Organic Chemistry
- Department of Chemistry
- Lanzhou University
- Lanzhou
- China
| | - Jinlai Li
- State Key Laboratory of Applied Organic Chemistry
- Department of Chemistry
- Lanzhou University
- Lanzhou
- China
| | - Zaimin Liu
- State Key Laboratory of Applied Organic Chemistry
- Department of Chemistry
- Lanzhou University
- Lanzhou
- China
| | - Haiyu Sun
- State Key Laboratory of Applied Organic Chemistry
- Department of Chemistry
- Lanzhou University
- Lanzhou
- China
| | - Hongliang Shi
- State Key Laboratory of Applied Organic Chemistry
- Department of Chemistry
- Lanzhou University
- Lanzhou
- China
| | - Xiaolei Wang
- State Key Laboratory of Applied Organic Chemistry
- Department of Chemistry
- Lanzhou University
- Lanzhou
- China
| | - Xingang Xie
- State Key Laboratory of Applied Organic Chemistry
- Department of Chemistry
- Lanzhou University
- Lanzhou
- China
| | - Xuegong She
- State Key Laboratory of Applied Organic Chemistry
- Department of Chemistry
- Lanzhou University
- Lanzhou
- China
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Ramsay RR, Majekova M, Medina M, Valoti M. Key Targets for Multi-Target Ligands Designed to Combat Neurodegeneration. Front Neurosci 2016; 10:375. [PMID: 27597816 PMCID: PMC4992697 DOI: 10.3389/fnins.2016.00375] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2016] [Accepted: 08/02/2016] [Indexed: 12/13/2022] Open
Abstract
HIGHLIGHTS Compounds that interact with multiple targets but minimally with the cytochrome P450 system (CYP) address the many factors leading to neurodegeneration.Acetyl- and Butyryl-cholineEsterases (AChE, BChE) and Monoamine Oxidases A/B (MAO A, MAO B) are targets for Multi-Target Designed Ligands (MTDL).ASS234 is an irreversible inhibitor of MAO A >MAO B and has micromolar potency against the cholinesterases.ASS234 is a poor CYP substrate in human liver, yielding the depropargylated metabolite.SMe1EC2, a stobadine derivative, showed high radical scavenging property, in vitro and in vivo giving protection in head trauma and diabetic damage of endothelium.Control of mitochondrial function and morphology by manipulating fission and fusion is emerging as a target area for therapeutic strategies to decrease the pathological outcome of neurodegenerative diseases. Growing evidence supports the view that neurodegenerative diseases have multiple and common mechanisms in their aetiologies. These multifactorial aspects have changed the broadly common assumption that selective drugs are superior to "dirty drugs" for use in therapy. This drives the research in studies of novel compounds that might have multiple action mechanisms. In neurodegeneration, loss of neuronal signaling is a major cause of the symptoms, so preservation of neurotransmitters by inhibiting the breakdown enzymes is a first approach. Acetylcholinesterase (AChE) inhibitors are the drugs preferentially used in AD and that one of these, rivastigmine, is licensed also for PD. Several studies have shown that monoamine oxidase (MAO) B, located mainly in glial cells, increases with age and is elevated in Alzheimer (AD) and Parkinson's Disease's (PD). Deprenyl, a MAO B inhibitor, significantly delays the initiation of levodopa treatment in PD patients. These indications underline that AChE and MAO are considered a necessary part of multi-target designed ligands (MTDL). However, both of these targets are simply symptomatic treatment so if new drugs are to prevent degeneration rather than compensate for loss of neurotransmitters, then oxidative stress and mitochondrial events must also be targeted. MAO inhibitors can protect neurons from apoptosis by mechanisms unrelated to enzyme inhibition. Understanding the involvement of MAO and other proteins in the induction and regulation of the apoptosis in mitochondria will aid progress toward strategies to prevent the loss of neurons. In general, the oxidative stress observed both in PD and AD indicate that antioxidant properties are a desirable part of MTDL molecules. After two or more properties are incorporated into one molecule, the passage from a lead compound to a therapeutic tool is strictly linked to its pharmacokinetic and toxicity. In this context the interaction of any new molecules with cytochrome P450 and other xenobiotic metabolic processes is a crucial point. The present review covers the biochemistry of enzymes targeted in the design of drugs against neurodegeneration and the cytochrome P450-dependent metabolism of MTDLs.
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Affiliation(s)
- Rona R. Ramsay
- Biomedical Sciences Research Complex, University of St. AndrewsSt. Andrews, UK
| | - Magdalena Majekova
- Department of Biochemical Pharmacology, Institute of Experimental Pharmacology and Toxicology, Slovak Academy of SciencesBratislava, Slovakia
| | - Milagros Medina
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias and BIFI, Universidad de ZaragozaZaragoza, Spain
| | - Massimo Valoti
- Dipartimento di Scienze della Vita, Università degli Studi di SienaSiena, Italy
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Yeggoni DPR, Manidhar DM, Suresh Reddy C, Subramanyam R. Investigation of binding mechanism of novel 8-substituted coumarin derivatives with human serum albumin and α-1-glycoprotein. J Biomol Struct Dyn 2016; 34:2023-36. [PMID: 26440860 DOI: 10.1080/07391102.2015.1104264] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Coumarin molecules have biological activities possessing lipid-controlling activity, anti-hepatitis C activity, anti-diabetic, anti-Parkinson activity, and anti-cancer activity. Here, we have presented an inclusive study on the interaction of 8-substituted-7-hydroxy coumarin derivatives (Umb-1/Umb-2) with α-1-glycoprotein (AGP) and human serum albumin (HSA) which are the major carrier proteins in the human blood plasma. Binding constants obtained from fluorescence emission data were found to be KUmb-1=3.1 ± .01 × 10(4) M(-1), KUmb-2 = 7 ± .01 × 10(4) M(-1), which corresponds to -6.1 and -6.5 kcal/mol of free energy for Umb-1 and Umb-2, respectively, suggesting that these derivatives bind strongly to HSA. Also these molecules bind to AGP with binding constants of KUmb-1-AGP=3.1 ± .01 × 10(3) M(-1) and KUmb-2-AGP = 4.6 ± .01 × 10(3) M(-1). Further, the distance, r between the donor (HSA) and acceptor (Umb-1/Umb-2) was calculated based on the Forster's theory of non-radiation energy transfer and the values were observed to be 1.14 and 1.29 nm in Umb-1-HSA and Umb-2-HSA system, respectively. The protein secondary structure of HSA was partially unfolded upon binding of Umb-1 and Umb-2. Furthermore, site displacement experiments with lidocaine, phenylbutazone (IIA), and ibuprofen (IIIA) proves that Umb derivatives significantly bind to subdomain IIIA of HSA which is further supported by docking studies. Furthermore, Umb-1 binds to LYS402 with one hydrogen bond distance of 2.8 Å and Umb-2 binds to GLU354 with one hydrogen bond at a distance of 2.0 Å. Moreover, these molecules are stabilized by hydrophobic interactions and hydrogen bond between the hydroxyl groups of carbon-3 of coumarin derivatives.
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Affiliation(s)
- Daniel Pushpa Raju Yeggoni
- a Department of Plant Sciences , School of Life Sciences, University of Hyderabad , Hyderabad 500046 , India
| | - Darla Mark Manidhar
- b Department of Chemistry , Sri Venkateswara University , Tirupati , Andhra Pradesh 517502 , India
| | - Cirandur Suresh Reddy
- b Department of Chemistry , Sri Venkateswara University , Tirupati , Andhra Pradesh 517502 , India
| | - Rajagopal Subramanyam
- a Department of Plant Sciences , School of Life Sciences, University of Hyderabad , Hyderabad 500046 , India
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Amr AEGE, Omar MAA, Abdalla MM. Monoamino Oxidase Inhibitors Activities of Some Synthesized 2,6-bis (Tetracarboxamide)-pyridine and Macrocyclic Octacarboxamide Derivatives. INT J PHARMACOL 2016. [DOI: 10.3923/ijp.2016.66.73] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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25
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26
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Speck-Planche A, Kleandrova VV, Luan F, Cordeiro MNDS. Computational modeling in nanomedicine: prediction of multiple antibacterial profiles of nanoparticles using a quantitative structure-activity relationship perturbation model. Nanomedicine (Lond) 2015; 10:193-204. [PMID: 25600965 DOI: 10.2217/nnm.14.96] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
AIMS We introduce the first quantitative structure-activity relationship (QSAR) perturbation model for probing multiple antibacterial profiles of nanoparticles (NPs) under diverse experimental conditions. MATERIALS & METHODS The dataset is based on 300 nanoparticles containing dissimilar chemical compositions, sizes, shapes and surface coatings. In general terms, the NPs were tested against different bacteria, by considering several measures of antibacterial activity and diverse assay times. The QSAR perturbation model was created from 69,231 nanoparticle-nanoparticle (NP-NP) pairs, which were randomly generated using a recently reported perturbation theory approach. RESULTS The model displayed an accuracy rate of approximately 98% for classifying NPs as active or inactive, and a new copper-silver nanoalloy was correctly predicted by this model with consensus accuracy of 77.73%. CONCLUSION Our QSAR perturbation model can be used as an efficacious tool for the virtual screening of antibacterial nanomaterials.
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Affiliation(s)
- Alejandro Speck-Planche
- REQUIMTE/Department of Chemistry & Biochemistry, University of Porto, 4169-007 Porto, Portugal
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27
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Medimagh-Saidana S, Romdhane A, Daami-Remadi M, Jabnoun-Khiareddine H, Touboul D, Jannet HB, Hamza MA. Synthesis and antimicrobial activity of novel coumarin derivatives from 4-methylumbelliferone. Med Chem Res 2015. [DOI: 10.1007/s00044-015-1368-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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28
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Structure- and ligand-based virtual screening identifies new scaffolds for inhibitors of the oncoprotein MDM2. PLoS One 2015; 10:e0121424. [PMID: 25884407 PMCID: PMC4401541 DOI: 10.1371/journal.pone.0121424] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 02/13/2015] [Indexed: 11/19/2022] Open
Abstract
A major challenge in the field of ligand discovery is to identify chemically useful fragments that can be developed into inhibitors of specific protein-protein interactions. Low molecular weight fragments (with molecular weight less than 250 Da) are likely to bind weakly to a protein’s surface. Here we use a new virtual screening procedure which uses a combination of similarity searching and docking to identify chemically tractable scaffolds that bind to the p53-interaction site of MDM2. The binding has been verified using capillary electrophoresis which has proven to be an excellent screening method for such small, weakly binding ligands.
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He X, Shang Y, Zhou Y, Yu Z, Han G, Jin W, Chen J. Synthesis of coumarin-3-carboxylic esters via FeCl3-catalyzed multicomponent reaction of salicylaldehydes, Meldrum's acid and alcohols. Tetrahedron 2015. [DOI: 10.1016/j.tet.2014.12.042] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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30
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Lan JS, Pan LF, Xie SS, Wang XB, Kong LY. Synthesis and evaluation of 6-methylcoumarin derivatives as potent and selective monoamine oxidase B inhibitors. MEDCHEMCOMM 2015. [DOI: 10.1039/c4md00437j] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Compound 5n was a potent and selective inhibitor of hMAO-B.
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Affiliation(s)
- Jin-Shuai Lan
- State Key Laboratory of Natural Medicines
- Department of Natural Medicinal Chemistry
- China Pharmaceutical University
- Nanjing 210009
- People's Republic of China
| | - Long-Fei Pan
- State Key Laboratory of Natural Medicines
- Department of Natural Medicinal Chemistry
- China Pharmaceutical University
- Nanjing 210009
- People's Republic of China
| | - Sai-Sai Xie
- State Key Laboratory of Natural Medicines
- Department of Natural Medicinal Chemistry
- China Pharmaceutical University
- Nanjing 210009
- People's Republic of China
| | - Xiao-Bing Wang
- State Key Laboratory of Natural Medicines
- Department of Natural Medicinal Chemistry
- China Pharmaceutical University
- Nanjing 210009
- People's Republic of China
| | - Ling-Yi Kong
- State Key Laboratory of Natural Medicines
- Department of Natural Medicinal Chemistry
- China Pharmaceutical University
- Nanjing 210009
- People's Republic of China
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31
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Naganaboina RT, Nayak A, Peddinti RK. Trifluoroacetic acid-promoted Michael addition-cyclization reactions of vinylogous carbamates. Org Biomol Chem 2014; 12:3366-70. [PMID: 24756460 DOI: 10.1039/c4ob00437j] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A simple and efficient methodology has been developed for the synthesis of pyrrolobenzoxazine and 3-arylamino coumarin derivatives promoted by trifluoroacetic acid. The initial step in the current protocol involves a Michael addition of the 1,4-benzoxazinone derivatives, a novel class of vinylogous carbamates to the Michael acceptors and subsequent cyclization.
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Affiliation(s)
- Ram Tilak Naganaboina
- The Department of Chemistry, Indian Institute of Technology, Roorkee-247667, Uttarakhand, India.
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Munteanu CR, Pedreira N, Dorado J, Pazos A, Pérez-Montoto LG, Ubeira FM, González-Díaz H. LECTINPred: web Server that Uses Complex Networks of Protein Structure for Prediction of Lectins with Potential Use as Cancer Biomarkers or in Parasite Vaccine Design. Mol Inform 2014; 33:276-85. [DOI: 10.1002/minf.201300027] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Accepted: 12/11/2014] [Indexed: 01/05/2023]
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Exploring the adenylation domain repertoire of nonribosomal peptide synthetases using an ensemble of sequence-search methods. PLoS One 2013; 8:e65926. [PMID: 23874386 PMCID: PMC3712989 DOI: 10.1371/journal.pone.0065926] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Accepted: 05/01/2013] [Indexed: 11/24/2022] Open
Abstract
The introduction of two-dimension (2D) graphs and their numerical characterization for comparative analyses of DNA/RNA and protein sequences without the need of sequence alignments is an active yet recent research topic in bioinformatics. Here, we used a 2D artificial representation (four-color maps) with a simple numerical characterization through topological indices (TIs) to aid the discovering of remote homologous of Adenylation domains (A-domains) from the Nonribosomal Peptide Synthetases (NRPS) class in the proteome of the cyanobacteria Microcystis aeruginosa. Cyanobacteria are a rich source of structurally diverse oligopeptides that are predominantly synthesized by NPRS. Several A-domains share amino acid identities lower than 20 % being a possible source of remote homologous. Therefore, A-domains cannot be easily retrieved by BLASTp searches using a single template. To cope with the sequence diversity of the A-domains we have combined homology-search methods with an alignment-free tool that uses protein four-color-maps. TI2BioP (Topological Indices toBioPolymers) version 2.0, available at http://ti2biop.sourceforge.net/ allowed the calculation of simple TIs from the protein sequences (four-color maps). Such TIs were used as input predictors for the statistical estimations required to build the alignment-free models. We concluded that the use of graphical/numerical approaches in cooperation with other sequence search methods, like multi-templates BLASTp and profile HMM, can give the most complete exploration of the repertoire of highly diverse protein families.
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Eichmann K. New section: memories and retrospectives. Cell Mol Life Sci 2013; 70:2223-4. [PMID: 23685904 PMCID: PMC11113540 DOI: 10.1007/s00018-013-1368-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Klaus Eichmann
- Max-Planck-Institute of Immunobiology and Epigenetics, Stübeweg 51, 9108 Freiburg, Germany
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35
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Maiti G, Karmakar R, Kayal U, Bhattacharya RN. An efficient route to coumarin derivatives under dual catalysis, an organo- and a Lewis acid catalyst. Tetrahedron 2012. [DOI: 10.1016/j.tet.2012.07.092] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Hossein nia R, Mamaghani M, Tabatabaeian K, Shirini F, Rassa M. An expeditious regioselective synthesis of novel bioactive indole-substituted chromene derivatives via one-pot three-component reaction. Bioorg Med Chem Lett 2012; 22:5956-60. [DOI: 10.1016/j.bmcl.2012.07.059] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2012] [Revised: 06/29/2012] [Accepted: 07/13/2012] [Indexed: 11/30/2022]
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Carradori S, Secci D, Bolasco A, Chimenti P, D'Ascenzio M. Patent-related survey on new monoamine oxidase inhibitors and their therapeutic potential. Expert Opin Ther Pat 2012; 22:759-801. [DOI: 10.1517/13543776.2012.698613] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Michael Initiated Ring Closure (MIRC) reaction on in situ generated benzylidenecyclohexane-1,3-diones for the construction of chromeno[3,4-b]quinoline derivatives. Tetrahedron Lett 2012. [DOI: 10.1016/j.tetlet.2012.02.114] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Viña D, Matos MJ, Ferino G, Cadoni E, Laguna R, Borges F, Uriarte E, Santana L. 8-Substituted 3-Arylcoumarins as Potent and Selective MAO-B Inhibitors: Synthesis, Pharmacological Evaluation, and Docking Studies. ChemMedChem 2012; 7:464-70. [PMID: 22287164 DOI: 10.1002/cmdc.201100538] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2011] [Revised: 01/13/2012] [Indexed: 01/05/2023]
Affiliation(s)
- Dolores Viña
- Departamento de Farmacología, Facultad de Farmacia, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain
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González-Díaz H, Munteanu CR, Postelnicu L, Prado-Prado F, Gestal M, Pazos A. LIBP-Pred: web server for lipid binding proteins using structural network parameters; PDB mining of human cancer biomarkers and drug targets in parasites and bacteria. MOLECULAR BIOSYSTEMS 2012; 8:851-62. [DOI: 10.1039/c2mb05432a] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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2D MI-DRAGON: A new predictor for protein–ligands interactions and theoretic-experimental studies of US FDA drug-target network, oxoisoaporphine inhibitors for MAO-A and human parasite proteins. Eur J Med Chem 2011; 46:5838-51. [DOI: 10.1016/j.ejmech.2011.09.045] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2011] [Revised: 09/22/2011] [Accepted: 09/26/2011] [Indexed: 11/20/2022]
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López-Vallejo F, Peppard TL, Medina-Franco JL, Martínez-Mayorga K. Computational methods for the discovery of mood disorder therapies. Expert Opin Drug Discov 2011; 6:1227-45. [PMID: 22647063 DOI: 10.1517/17460441.2011.637106] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
INTRODUCTION Despite the significant progress, research is still needed to reveal details of the complex and dynamic chemical processes operating in the central nervous system (CNS) and their relationship to psychological effects such as mood disorders. The incidence of behavioral depression is widely spread worldwide, with an estimated 14.8 million adults diagnosed yearly in the United States alone. The efficacy of current antidepressants on 50 - 60% of patients, their slow onset of action and the prevalence of adverse side effects highlight the need for developing a new generation of improved antidepressants. Computational methods have the potential to aid in the discovery of mood modulators. AREAS COVERED This review contains three main sections: historical evolution of marketed antidepressants, physicochemical and structural properties of antidepressant compounds reported in the ChEMBL database and recent efforts in the design and discovery of antidepressants using computational methods. The authors provide details of the computational methods employed, from chemoinformatic analyses to molecular modeling. EXPERT OPINION While there have been numerous and important findings in depression research, the high cost and time spent on research into new therapies for brain disorders is a risky undertaking. Computational methodologies can be employed to speed up the discovery of new antidepressants and to detect new sources of chemical compounds with potential antidepressant activity. Compound collections containing compounds already approved in the pharmaceutical and food industries that cover the property space and complement the structural space of CNS drugs represent a promising starting point for the discovery of new antidepressant agents.
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Lipeeva AV, Shul’ts EE, Shakirov MM, Tolstikov GA. Plant coumarins: VII. Amination of oreoselone trifluoromethanesulfonate. RUSSIAN JOURNAL OF ORGANIC CHEMISTRY 2011. [DOI: 10.1134/s1070428011090235] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Synthesis and selective human monoamine oxidase inhibition of 3-carbonyl, 3-acyl, and 3-carboxyhydrazido coumarin derivatives. Eur J Med Chem 2011; 46:4846-52. [DOI: 10.1016/j.ejmech.2011.07.017] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2011] [Revised: 06/15/2011] [Accepted: 07/09/2011] [Indexed: 01/23/2023]
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Matos MJ, Terán C, Pérez-Castillo Y, Uriarte E, Santana L, Viña D. Synthesis and study of a series of 3-arylcoumarins as potent and selective monoamine oxidase B inhibitors. J Med Chem 2011; 54:7127-37. [PMID: 21923181 DOI: 10.1021/jm200716y] [Citation(s) in RCA: 129] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
New series of 6-substituted-3-arylcoumarins displaying several alkyl, hydroxyl, halogen, and alkoxy groups in the two benzene rings have been designed, synthesized, and evaluated in vitro as human monoamine oxidase A and B (hMAO-A and hMAO-B) inhibitors. Most of the studied compounds showed a high affinity and selectivity to the hMAO-B isoenzyme, with IC(50) values on nanomolar and picomolar range. Ten of the 22 described compounds displayed higher MAO-B inhibitory activity and selectivity than selegiline. Coumarin 7 is the most active compound of this series, being 64 times more active than selegiline and also showing the highest hMAO-B specificity. In addition, docking experiments were carried out on hMAO-A and h-MAO-B structures. This study provided new information about the enzyme-inhibitor interaction and the potential therapeutic application of this 3-arylcoumarin scaffold.
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Affiliation(s)
- Maria J Matos
- Department of Organic Chemistry, Faculty of Pharmacy, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain.
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Soussi MA, Audisio D, Messaoudi S, Provot O, Brion JD, Alami M. Palladium-Catalyzed Coupling of 3-Halo-Substituted Coumarins, Chromenes, and Quinolones with Various Nitrogen-Containing Nucleophiles. European J Org Chem 2011. [DOI: 10.1002/ejoc.201100480] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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47
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MAO inhibitory activity modulation: 3-Phenylcoumarins versus 3-benzoylcoumarins. Bioorg Med Chem Lett 2011; 21:4224-7. [PMID: 21684743 DOI: 10.1016/j.bmcl.2011.05.074] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2011] [Revised: 05/18/2011] [Accepted: 05/20/2011] [Indexed: 01/08/2023]
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González-Díaz H, Prado-Prado F, Sobarzo-Sánchez E, Haddad M, Maurel Chevalley S, Valentin A, Quetin-Leclercq J, Dea-Ayuela MA, Teresa Gomez-Muños M, Munteanu CR, José Torres-Labandeira J, García-Mera X, Tapia RA, Ubeira FM. NL MIND-BEST: A web server for ligands and proteins discovery—Theoretic-experimental study of proteins of Giardia lamblia and new compounds active against Plasmodium falciparum. J Theor Biol 2011; 276:229-49. [DOI: 10.1016/j.jtbi.2011.01.010] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2010] [Revised: 12/02/2010] [Accepted: 01/10/2011] [Indexed: 10/18/2022]
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González-Díaz H, Muíño L, Anadón AM, Romaris F, Prado-Prado FJ, Munteanu CR, Dorado J, Sierra AP, Mezo M, González-Warleta M, Gárate T, Ubeira FM. MISS-Prot: web server for self/non-self discrimination of protein residue networks in parasites; theory and experiments in Fasciola peptides and Anisakis allergens. MOLECULAR BIOSYSTEMS 2011; 7:1938-55. [PMID: 21468430 DOI: 10.1039/c1mb05069a] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Infections caused by human parasites (HPs) affect the poorest 500 million people worldwide but chemotherapy has become expensive, toxic, and/or less effective due to drug resistance. On the other hand, many 3D structures in Protein Data Bank (PDB) remain without function annotation. We need theoretical models to quickly predict biologically relevant Parasite Self Proteins (PSP), which are expressed differentially in a given parasite and are dissimilar to proteins expressed in other parasites and have a high probability to become new vaccines (unique sequence) or drug targets (unique 3D structure). We present herein a model for PSPs in eight different HPs (Ascaris, Entamoeba, Fasciola, Giardia, Leishmania, Plasmodium, Trypanosoma, and Toxoplasma) with 90% accuracy for 15 341 training and validation cases. The model combines protein residue networks, Markov Chain Models (MCM) and Artificial Neural Networks (ANN). The input parameters are the spectral moments of the Markov transition matrix for electrostatic interactions associated with the protein residue complex network calculated with the MARCH-INSIDE software. We implemented this model in a new web-server called MISS-Prot (MARCH-INSIDE Scores for Self-Proteins). MISS-Prot was programmed using PHP/HTML/Python and MARCH-INSIDE routines and is freely available at: . This server is easy to use by non-experts in Bioinformatics who can carry out automatic online upload and prediction with 3D structures deposited at PDB (mode 1). We can also study outcomes of Peptide Mass Fingerprinting (PMFs) and MS/MS for query proteins with unknown 3D structures (mode 2). We illustrated the use of MISS-Prot in experimental and/or theoretical studies of peptides from Fasciola hepatica cathepsin proteases or present on 10 Anisakis simplex allergens (Ani s 1 to Ani s 10). In doing so, we combined electrophoresis (1DE), MALDI-TOF Mass Spectroscopy, and MASCOT to seek sequences, Molecular Mechanics + Molecular Dynamics (MM/MD) to generate 3D structures and MISS-Prot to predict PSP scores. MISS-Prot also allows the prediction of PSP proteins in 16 additional species including parasite hosts, fungi pathogens, disease transmission vectors, and biotechnologically relevant organisms.
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Affiliation(s)
- Humberto González-Díaz
- Department of Microbiology & Parasitology, Faculty of Pharmacy, University of Santiago de Compostela, 15782, Santiago de Compostela, Spain.
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Discovery and synthesis of novel 3-phenylcoumarin derivatives as antidepressant agents. Bioorg Med Chem Lett 2011; 21:1937-41. [DOI: 10.1016/j.bmcl.2011.02.040] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2010] [Revised: 02/09/2011] [Accepted: 02/11/2011] [Indexed: 01/11/2023]
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