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Molecular Docking studies of D2 Dopamine receptor with Risperidone derivatives
English

Kiran Bhargava, Rajendra Nath, Prahlad Kumar Seth, Kamlesh Kumar Pant, Rakesh Kumar Dixit
2014 Bioinformation  
In this work, 3D model of D2 dopamine receptor was determined by comparative homology modeling program MODELLER.  ...  Our results suggests that ligand-receptor binding interactions for D2 employing QSAR modeling seems to be a promising approach for prediction of pKi value of novel antagonists against D2 receptor.  ...  Acknowledgement: The authors are grateful to the Bioinformatics Division of BIOINFORMATION  ... 
doi:10.6026/97320630010008 pmid:24516319 pmcid:PMC3916812 fatcat:iqymqxmeh5ddrgejcjqxdi2n6u

Studies of New Fused Benzazepine as Selective Dopamine D3 Receptor Antagonists Using 3D-QSAR, Molecular Docking and Molecular Dynamics

Jing Liu, Yan Li, Shuwei Zhang, Zhengtao Xiao, Chunzhi Ai
2011 International Journal of Molecular Sciences  
To our best knowledge, this work is the first report on 3D-QSAR modeling of the new fused BAZs as DA D3 antagonists.  ...  In the present work, based on a dataset of 110 collected benzazepine (BAZ) DA D3 antagonists with diverse kinds of structures, a variety of in silico modeling approaches, including comparative molecular  ...  Acknowledgements The authors are grateful to the support of the Doctoral Fund (1000_893361) and Youth Teacher Fund (1000_893231) of Dalian University of Technology.  ... 
doi:10.3390/ijms12021196 pmid:21541053 pmcid:PMC3083700 fatcat:uon6kq32mzgrtd27txsdkk3j24

Predicting targets of compounds against neurological diseases using cheminformatic methodology

Katarina Nikolic, Lazaros Mavridis, Oscar M. Bautista-Aguilera, José Marco-Contelles, Holger Stark, Maria do Carmo Carreiras, Ilaria Rossi, Paola Massarelli, Danica Agbaba, Rona R. Ramsay, John B. O. Mitchell
2014 Journal of Computer-Aided Molecular Design  
OMBA and JMC thenk MINECO (Spain) for a fellowship, and support (SAF2012-33304), respectively.  ...  KN and DA acknowledge project supported by the Ministry of Education and Science of the Republic of Serbia, Contract #172033.  ...  Memantine also acts as a noncompetitive antagonist at the 5-HT 3 receptor and binds to dopamine D 2 receptors and nAChRs [41] .  ... 
doi:10.1007/s10822-014-9816-1 pmid:25425329 fatcat:fc7kyyepdrbqdo7eferw4jrnvy

Recent Developments in New Therapeutic Agents against Alzheimer and Parkinson Diseases: In-Silico Approaches

Pedro Cruz-Vicente, Luís A. Passarinha, Samuel Silvestre, Eugenia Gallardo
2021 Molecules  
These disorders are characterized by a progressive neurodegeneration and are considered one of the main causes of disability and mortality worldwide.  ...  Thus, in this review, an overview of the current therapeutics in use for these two ND, the main targets in drug development, and the primary studies published in the last five years that used in silico  ...  Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/molecules26082193 pmid:33920326 fatcat:bg5bage5f5d2bbufdcxngfchni

Understanding the structural requirements of hybrid (S)-6-((2-(4-phenylpiperazin-1-yl)ethyl)(propyl)amino)-5,6,7,8-tetrahydronaphthalen-1-ol and its analogs as D2/D3 receptor ligands: a 3D QSAR investigation

Gyan Modi, Horrick Sharma, Prashant S. Kharkar, Aloke K. Dutta
2014 MedChemComm  
The present study reports the 3D QSAR of dopamine D2/D3 ligands to gain insights into the structural factors responsible for affinity and D3 selectivity.  ...  Acknowledgments This work is supported by National Institute of Neurological Disorders and Stroke/National Institute of Health (NS047198, AKD). PSK thanks Ms.  ...  Sona Warrier for her help during preparation of this manuscript. Bibliographic References and Notes  ... 
doi:10.1039/c4md00159a pmid:25221669 pmcid:PMC4159175 fatcat:ell2bxevure7rleh2mnmgp2rcy

Three-Dimensional Biologically Relevant Spectrum (BRS-3D): Shape Similarity Profile Based on PDB Ligands as Molecular Descriptors

Ben Hu, Zheng-Kun Kuang, Shi-Yu Feng, Dong Wang, Song-Bing He, De-Xin Kong
2016 Molecules  
on PDB ligands and applied it in ligand-based virtual screening and QSAR study.  ...  In contrast to 2D methods, 3D methods (including 3D-QSAR [8, 9] and pharmacophore modeling [10, 11] ) are based on molecular shape or conformation.  ...  Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/molecules21111554 pmid:27869685 fatcat:4amdmklrxnb2hf5jgas26yv4um

Evaluation of N-phenyl homopiperazine analogs as potential dopamine D3 receptor selective ligands

Aixiao Li, Yogesh Mishra, Maninder Malik, Qi Wang, Shihong Li, Michelle Taylor, David E. Reichert, Robert R. Luedtke, Robert H. Mach
2013 Bioorganic & Medicinal Chemistry  
A series of N-(2-methoxyphenyl)homopiperazine analogs was prepared and their affinities for dopamine D2, D3, and D4 receptors were measured using competitive radioligand binding assays.  ...  When the binding and the intrinsic efficacy of these phenylhomopiperazines was compared to those of previously published phenylpiperazine analogues, it was found that (a) affinity at D2 and D3 dopamine  ...  Acknowledgments This research was funded by DA023957, MH081281 and DA29840 awarded by the National Institutes of Health.  ... 
doi:10.1016/j.bmc.2013.03.074 pmid:23618707 pmcid:PMC3733449 fatcat:pcx4fwarlbgydhajwgwqfvtiwi

Development and application of hybrid structure based method for efficient screening of ligands binding to G-protein coupled receptors

Sandhya Kortagere, William J. Welsh
2006 Journal of Computer-Aided Molecular Design  
The results from this study showed that the 9 top-ranking molecules are indeed analogues of retinal. The method was also tested to identify analogues of dopamine binding to the dopamine D2 receptor.  ...  Six of the ten top-ranking molecules are known analogues of dopamine including a prodrug, while the other thirty-four molecules are currently being tested for their activity against all dopamine receptors  ...  Finally, this study was partially supported by a grant from the National Library of Medicine, National Institutes of Health (G08 LM6230-07).  ... 
doi:10.1007/s10822-006-9077-8 pmid:17054015 pmcid:PMC2756463 fatcat:xnulfzgnlna6vfi4ilmydkday4

Automated discovery of GPCR bioactive ligands

Sebastian Raschka
2019 Current Opinion in Structural Biology  
While G-protein-coupled receptors (GPCRs) constitute the largest class of membrane proteins, structures and endogenous ligands of a large portion of GPCRs remain unknown.  ...  This review describes the most recent and successful applications of machine learning for bioactive ligand discovery, concluding with an outlook on deep learning methods that are capable of automatically  ...  When independent research groups compared different machine learning methods on various bioactivity datasets (including two GPCRs, dopamine D4 receptor and cannabinoid CB1 receptor), the results indicated  ... 
doi:10.1016/j.sbi.2019.02.011 pmid:30909105 fatcat:tm5pfuy4z5dexdsnnlca7rzmgm

Beyond Small-Molecule SAR [chapter]

Thomas M. Keck, Caitlin Burzynski, Lei Shi, Amy Hauck Newman
2014 Advances in Pharmacology  
The dopamine D3 receptor is a target of pharmacotherapeutic interest in a variety of neurological disorders including schizophrenia, restless leg syndrome, and drug addiction.  ...  This review will highlight recent preclinical and clinical studies demonstrating potential utility of D3 receptor-selective ligands in the treatment of addiction.  ...  AHN and LS would like to acknowledge the members of our labs, past and present, and our wonderful collaborators who have helped move our D3 receptor program forward.  ... 
doi:10.1016/b978-0-12-420118-7.00007-x pmid:24484980 pmcid:PMC4924533 fatcat:aq5ksdftsfcpxcqbsasxpb7224

Dopaminergic dysfunction in neuropsychiatric disorders. Pathophysiology, current therapeutics, and future perspectives

Chandrasekhar Chanda, Sobhitha Surepalli
2019 Neuropsychiatria i Neuropsychologia  
A b s t r a c t Dopaminergic signalling is crucial for a variety of brain functions, and abnormal dopamine regulation leads to neuropsychiatric disorders.  ...  The in silico approach can be a tool for studying DA receptors and other protein targets involved in dopaminergic signalling.  ...  Acknowledgements The authors are grateful to the Science Education Research Board (SERB), Department of Science and Technology (DST), Govt. of India for the grant (ECR/2016/001673) and for supporting Ms  ... 
doi:10.5114/nan.2019.87724 fatcat:qqyigwskzbfvhmstca54oijk7u

Introduction to the BioChemical Library (BCL): An Application-Based Open-Source Toolkit for Integrated Cheminformatics and Machine Learning in Computer-Aided Drug Discovery

Benjamin P. Brown, Oanh Vu, Alexander R. Geanes, Sandeepkumar Kothiwale, Mariusz Butkiewicz, Edward W. Lowe, Ralf Mueller, Richard Pape, Jeffrey Mendenhall, Jens Meiler
2022 Frontiers in Pharmacology  
In addition, we have included multiple examples covering areas of advanced use, such as reaction-based library design.  ...  application-based academic open-source software package designed to integrate traditional small molecule cheminformatics tools with machine learning-based quantitative structure-activity/property relationship (QSAR  ...  Multicomponent reaction-based design of dopamine receptor D4 antagonist candidates. (A) The 4-component split-Ugi reaction utilizing a piperazine as the diamine.  ... 
doi:10.3389/fphar.2022.833099 pmid:35264967 pmcid:PMC8899505 fatcat:l5dpfgmkezgybd7qx6xjqxittq

Chemical Structural Novelty: On-Targets and Off-Targets

Emmanuel R. Yera, Ann E. Cleves, Ajay N. Jain
2011 Journal of Medicinal Chemistry  
Given a new molecule along with a set of molecules sharing some biological effect, a single score based on comparison to the known set is produced, reflecting either 2D similarity, 3D similarity, or their  ...  Drug structures may be quantitatively compared based on 2D topological structural considerations and based on 3D characteristics directly related to binding.  ...  Jain has a financial interest in BioPharmics LLC, a biotechnology company whose main focus is in the development of methods for computational modeling in drug discovery.  ... 
doi:10.1021/jm200666a pmid:21916467 pmcid:PMC3188662 fatcat:kdbe7yh4lfhpdcpv6wua3kizqa

A structural chemogenomics analysis of aminergic GPCRs: lessons for histamine receptor ligand design

A J Kooistra, S Kuhne, I J P de Esch, R Leurs, C de Graaf
2013 British Journal of Pharmacology  
G-protein coupled receptors (GPCRs) are a particularly interesting protein family for chemogenomics studies because there is an overwhelming amount of ligand binding affinity data available.  ...  BACKGROUND AND PURPOSE Chemogenomics focuses on the discovery of new connections between chemical and biological space leading to the discovery of new protein targets and biologically active molecules.  ...  Mutation studies in the dopamine D2 and D4 receptors showed that D2/D4 receptor selectivity is not determined by specific single amino acids but rather by a cluster of divergent aromatic residues in TM2  ... 
doi:10.1111/bph.12248 pmid:23713847 pmcid:PMC3764853 fatcat:j4q5s2odz5gjpiw6idj5jwqpvq

Molecular similarity: a key technique in molecular informatics

Andreas Bender, Robert C. Glen
2004 Organic and biomolecular chemistry  
For example, in designing libraries of compounds for lead generation, one approach is to design sets of compounds 'similar' to known active compounds in the hope that alternative molecular structures are  ...  Molecular similarity, as a paradigm, contains many implicit and explicit assumptions in particular with respect to the prediction of the binding and efficacy of molecules at biological receptors.  ...  A number of anonymous referees are thanked for providing valuable input on the manuscript.  ... 
doi:10.1039/b409813g pmid:15534697 fatcat:sci2mbt3p5frhklzytvsiavp5m
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