Protein-Ligand Structure Discovery

A special issue of Biomolecules (ISSN 2218-273X). This special issue belongs to the section "Molecular Structure and Dynamics".

Deadline for manuscript submissions: closed (15 November 2019)

Special Issue Editor


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Guest Editor
Southern Illinois University at Edwardsville, Edwardsville, IL, USA
Interests: protein-ligand structure discovery

Special Issue Information

Dear Colleagues,

The “one drug, one target” paradigm has been the focus of drug discovery for decades now. Knowledge of the structure of the macromolecular targets has enhanced our understanding of ligand–receptor complexes, pertaining, in particular, to G protein coupled receptors, ion channels, and nuclear receptors. However, small molecules can act at multiple biomolecular targets, which have been positively directed toward drug repurposing enterprises. Because the distribution of families targeted by drugs is rather limited, expanding the target space to protein–protein interactions has seen a renaissance in recent years. The latter offer an enriched perspective to disease pathways, disease genes, and improved biomarkers. None of these approaches would have been as fruitful, had it not been for fast computing and macromolecular structure availability.  

In this Special Issue, we will consider computational advances made toward ligand–protein and protein–protein recognition. Publications on the following topics are welcome:

Molecular recognition

Structure-guided drug discovery

Protein–protein complex prediction

Protein–protein druggability

Macromolecular structure-driven hit/lead identification

Algorithms expediting drug discovery

Prof. Maria Kontoyianni
Guest Editor

Manuscript Submission Information

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Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Biomolecules is an international peer-reviewed open access monthly journal published by MDPI.

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Published Papers (1 paper)

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Research

18 pages, 4627 KiB  
Article
Pharmacophore Directed Screening of Agonistic Natural Molecules Showing Affinity to 5HT2C Receptor
by Ganesh Kumar Veeramachaneni, V B S C Thunuguntla, Maharshi Bhaswant, Michael L. Mathai and Jayakumar Singh Bondili
Biomolecules 2019, 9(10), 556; https://doi.org/10.3390/biom9100556 - 1 Oct 2019
Cited by 13 | Viewed by 3896
Abstract
Obesity prevalence continues to be a foremost health concern across the globe leading to the development of major health risk conditions like type II diabetes, hyperlipidemia, hypertension and even cancers. Because of the deprived drug-based management system, there is an urgent need for [...] Read more.
Obesity prevalence continues to be a foremost health concern across the globe leading to the development of major health risk conditions like type II diabetes, hyperlipidemia, hypertension and even cancers. Because of the deprived drug-based management system, there is an urgent need for the development of new drugs aiming at satiety and appetite control targets. Among the reported satiety signaling targets, 5HT2C receptor plays a crucial role in decreasing appetite and has become a promising target for the development of anti-obesity drugs. Lorcaserin, a 5HT2C receptor agonist and the only drug available in the market, was designed based on the receptor mechanism of action. Due to limited drug options available and considering the adverse drug effects of Lorcaserin, the development of new drugs which are highly specific toward the 5HT2C target and with lesser side effects is essential. The present study is majorly focused on developing new 5HT2C agonists through computational approaches like screening, docking, and simulation using Phase, QikProp, Glide and Desmond applications of the Schrodinger suite. Screening protocols resulted in eight best hit molecules with affinity for the receptor and among them, five hits displayed binding affinity toward the conserved residue Asp 134 of the receptor. The stability of the five molecules in complex with the 5HT2C receptor was studied through molecular dynamic simulations. Three molecules, ZINC32123870, ZINC40312983 and ZINC32124535, maintained stable interactions with the Asp 134 residue throughout the 50 ns simulation run time. Further, due to the high sequence similarity seen among the receptors of 5HT2 family, the three potential hits were cross validated against other subtypes 5HT2A and 5HT2B of the 5HT2 family to determine the specificity of the molecules against the target. Among the three hits, ZINC32124535 was identified as the best potential hit based on the hydrogen bond interaction percentage with Asp residue [5HT2A (Asp 155:60%); 5HT2B (Asp155: No interaction); 5HT2C (Asp 134:86%)]. The ZINC32124535 molecule produced one salt bridge and hydrogen bond interactions with Asp 134, alike the known drug Lorcaserin. Based on the results, ZINC32124535 was identified as the best potential hit against the 5HT2C receptor. Full article
(This article belongs to the Special Issue Protein-Ligand Structure Discovery)
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