Related Experiment Video

Updated: Feb 14, 2026

Use of Viral Entry Assays and Molecular Docking Analysis for the Identification of Antiviral Candidates against Coxsackievirus A16

Use of Viral Entry Assays and Molecular Docking Analysis for the Identification of Antiviral Candidates against Coxsackievirus A16

Published on: July 15, 2019

A novel identification approach for discovery of 5-HydroxyTriptamine 2A antagonists: combination of 2D/3D similarity

Rakesh Kumar¹, Dhananjay Jade¹, Dinesh Gupta¹

¹a Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology (ICGEB) , Aruna Asaf Ali Marg, New Delhi 110067 , India.

Journal of Biomolecular Structure & Dynamics

|February 23, 2018

Abstract:

5-HydroxyTriptamine 2A antagonists are potential targets for treatment of various cerebrovascular and cardiovascular disorders. In this study, we have developed and performed a unique screening pipeline for filtering ZINC database compounds on the basis of similarities to known antagonists to determine novel small molecule antagonists of 5-HydroxyTriptamine 2A. The screening pipeline is based on 2D similarity, 3D dissimilarity and a combination of 2D/3D similarity. The shortlisted compounds were docked to a 5-HydroxyTriptamine 2A homology-based model, and complexes with low binding energies (287 complexes) were selected for molecular dynamics (MD) simulations in a lipid bilayer. The MD simulations of the shortlisted compounds in complex with 5-HydroxyTriptamine 2A confirmed the stability of the complexes and revealed novel interaction insights. The receptor residues S239, N343, S242, S159, Y370 and D155 predominantly participate in hydrogen bonding. π-π stacking is observed in F339, F340, F234, W151 and W336, whereas hydrophobic interactions are observed amongst V156, F339, F234, V362, V366, F340, V235, I152 and W151. The known and potential antagonists shortlisted by us have similar overlapping molecular interaction patterns. The 287 potential 5-HydroxyTriptamine 2A antagonists may be experimentally verified.

Keywords:

, tanimoto coefficient 2D similarity 2D, two-dimensional space 2D/3D screening 3D similarity 3D, three-dimensional space 5HT 5HT, 5-HydroxyTryptamine ADHD, attention deficit hyperactivity disorders BLAST, basic local alignment search tool CNS, central nervous system Cl ions, chloride ions DOPE, discrete optimized protein energy G-protein coupled receptor GPCRs, G protein-coupled receptors HB, hydrogen bond HBA, hydrogen bond acceptors HBD, hydrogen bond donors JC virus, John Cunningham virus Ki, equilibrium dissociation constant for the ligand LBVS, ligand-based virtual screening MD, molecular dynamic MSD, mean square displacement MW, molecular weight NHB, number of hydrogen bonds OCD, obsessive compulsive disorder P5/P95, percentile calculation PAINS, Pan assay interference compounds PDB, protein data bank PLIP, protein–ligand interaction profiler PME, Particle Mesh Ewald PNS, peripheral nervous system POPC, 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine RMSD, root mean square deviation RMSF, root mean square fluctuations Rg, radius of gyration SASA, solvent accessible surface area SCA, stochastic clustering algorithm SD, steepest descent SDF, structure data file SPC, single point charge SPD, simple point charge SSE, secondary structure elements Sn-1/sn-2, Stereospecific number TM, Transmembrane TPSA, topological polar surface area drug discovery fs, femtosecond kJ/mol, kilo Joule per mol kcal/mol, kilocalorie per mole sn-1 ligand-based virtual screening nm, nanomolar ns, nanosecond Å Ångström β2-AR, β2 adrenergic receptor μM, micromolar

More Related Videos

Author Spotlight: Integrating 2D-HPLC-MS and Molecular Networking in Natural Medicine Analysis

Author Spotlight: Integrating 2D-HPLC-MS and Molecular Networking in Natural Medicine Analysis

Published on: December 8, 2023

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis

Published on: June 20, 2025

Related Concept Videos

Molecular Shapes

Molecular Shapes

Molecules have characteristic shapes that are crucial for their function. The arrangement of various electron groups around the central atom dictates their molecular geometry. Electron pairs in the valence shell of a central atom will adopt an arrangement that minimizes repulsions between the electron pairs by maximizing the distance between them. The valence electrons form either bonding pairs, located primarily between bonded atoms, or lone pairs.
Two regions of electron density in a diatomic...

Molecular Orbital Theory I

Molecular Orbital Theory I

Overview of Molecular Orbital Theory

Molecular Models

Molecular Models

Physical models representing molecular architectures of chemical compounds play essential roles in understanding chemistry. The use of molecular models makes it easier to visualize the structures and shapes of atoms and molecules.

Kinetic Molecular Theory: Molecular Velocities, Temperature, and Kinetic Energy

Kinetic Molecular Theory: Molecular Velocities, Temperature, and Kinetic Energy

The kinetic molecular theory qualitatively explains the behaviors described by the various gas laws. The postulates of this theory may be applied in a more quantitative fashion to derive these individual laws.

Molecular Orbital Theory II

Molecular Orbital Theory II

Molecular Orbital Energy Diagrams

Predicting Molecular Geometry

Predicting Molecular Geometry

VSEPR Theory for Determination of Electron Pair Geometries

Articles linked to this work by shared authors, journal, and citation graph.

LncRNACNVIntegrateR: a novel framework for correlating long non-coding RNAs with copy number variation abnormalities and disease progression.

PeerJ·2025

Role of novel mutations in food vacuole transporters beyond K13-mediated artemisinin resistance in Plasmodium falciparum.

Antimicrobial agents and chemotherapy·2025

Whole Exome Sequencing Based Diagnostics in Complex Childhood Epilepsy Syndromes-A Cohort Study on Clinical Utility.

Clinical genetics·2025

Modified Lipid Particle Recognition: A Link Between Atherosclerosis and Cancer?

Biology·2025

A Novel Three-Stage AI-Assisted Approach for Accurate Differential Diagnosis and Classification of NIFTP and Thyroid Neoplasms.

Endocrine pathology·2025

Structure and function of MDM2 and MDM4 in health and disease.

The Biochemical journal·2025

See all related articles