ELIXIR-A: An Interactive Visualization Tool for Multi-Target Pharmacophore Refinement

Wang, Haoqi; Mulgaonkar, Nirmitee; Pérez, Lisa M.; Fernando, Sandun

doi:10.1021/acsomega.1c07144

Cited by 7 publications

(3 citation statements)

References 79 publications

(117 reference statements)

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“…[35][36][37][38] One of the approaches to the drug design of multitarget compounds and the prediction of the biotarget spectrum of molecules can be the identification of basic pharmacophore models. [39,40] Previously, we published a review that describes a large set of different cardioprotective agents with different mechanisms of action, corresponding to a single pharmacophore model. [41] This model contains two aromatic cycles (marked violet) connected by a linker (indicated by green) with the length of about 5-15 bonds and with at least one heteroatom in it (Figure 1).…”

Section: Cvd and Multitargetingmentioning

confidence: 99%

Multitargeting in cardioprotection: An example of biaromatic compounds

Mokrov

2023

Archiv der Pharmazie

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A multitarget drug design approach is actively developing in modern medicinal chemistry and pharmacology, especially with regard to multifactorial diseases such as cardiovascular diseases, cancer, and neurodegenerative diseases. A detailed study of many well‐known drugs developed within the single‐target approach also often reveals additional mechanisms of their real pharmacological action. One of the multitarget drug design approaches can be the identification of the basic pharmacophore models corresponding to a wide range of the required target ligands. Among such models in the group of cardioprotectors is the linked biaromatic system. This review develops the concept of a “basic pharmacophore” using the biaromatic pharmacophore of cardioprotectors as an example. It presents an analysis of possible biological targets for compounds corresponding to the biaromatic pharmacophore and an analysis of the spectrum of biological targets for the five most known and most studied cardioprotective drugs corresponding to this model, and their involvement in the biological effects of these drugs.

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Section: Cvd and Multitargetingmentioning

confidence: 99%

Multitargeting in cardioprotection: An example of biaromatic compounds

Mokrov

2023

Archiv der Pharmazie

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“…7 Prediction accuracy of active compounds (sensitivity) on the combined set, %. 8 Prediction accuracy of inactive compounds (specificity) on the combined set, %. 9 Accuracy according to ROCanalysis on the combined set, %.…”

Section: Neural Network Modelingmentioning

confidence: 99%

“…An increase in the accuracy of building visualized multitarget 3D pharmacophores is provided by the ELIXIR-A plugin for VMD, which is used to refine pharmacophore interaction points between several ligands and several receptors [ 8 ].…”

Section: Introductionmentioning

confidence: 99%

Consensus Ensemble Multitarget Neural Network Model of Anxiolytic Activity of Chemical Compounds and Its Use for Multitarget Pharmacophore Design

et al. 2023

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A classification consensus ensemble multitarget neural network model of the dependence of the anxiolytic activity of chemical compounds on the energy of their docking in 17 biotargets was developed. The training set included compounds thathadalready been tested for anxiolytic activity and were structurally similar to the 15 studied nitrogen-containing heterocyclic chemotypes. Seventeen biotargets relevant to anxiolytic activity were selected, taking into account the possible effect on them of the derivatives of these chemotypes. The generated model consistedof three ensembles of artificial neural networks for predicting three levels of anxiolytic activity, with sevenneural networks in each ensemble. A sensitive analysis of neurons in an ensemble of neural networks for a high level of activity made it possible to identify four biotargets ADRA1B, ADRA2A, AGTR1, and NMDA-Glut, which were the most significant for the manifestation of the anxiolytic effect. For these four key biotargets for 2,3,4,5-tetrahydro-11H-[1,3]diazepino[1,2-a]benzimidazole and [1,2,4]triazolo[3,4-a][2,3]benzodiazepine derivatives, eight monotarget pharmacophores of high anxiolytic activity were built. Superposition of monotarget pharmacophores built two multitarget pharmacophores of high anxiolytic activity, reflecting the universal features of interaction 2,3,4,5-tetrahydro-11H-[1,3]diazepino[1,2-a]benzimidazole and [1,2,4]triazolo[3,4-a][2,3]benzodiazepine derivatives with the most significant biotargets ADRA1B, ADRA2A, AGTR1, and NMDA-Glut.

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Computational Approaches for Structure-Assisted Drug Discovery and Repurposing

Pandey,

Verma

2024

Unraveling New Frontiers and Advances in Bioinformatics

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ELIXIR-A: An Interactive Visualization Tool for Multi-Target Pharmacophore Refinement

Cited by 7 publications

References 79 publications

Multitargeting in cardioprotection: An example of biaromatic compounds

Multitargeting in cardioprotection: An example of biaromatic compounds

Consensus Ensemble Multitarget Neural Network Model of Anxiolytic Activity of Chemical Compounds and Its Use for Multitarget Pharmacophore Design

Computational Approaches for Structure-Assisted Drug Discovery and Repurposing

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