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Chemistry
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Molecular Docking in Drug Discovery
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Molecular Docking in Drug Discovery

A special issue of Chemistry (ISSN 2624-8549). This special issue belongs to the section "Medicinal Chemistry".

Deadline for manuscript submissions: closed (15 April 2021) | Viewed by 6123

Special Issue Editor

Dr. Micholas Dean Smith

E-Mail Website
Guest Editor
Department of Biochemistry, Cellular & Molecular Biology, The University of Tennessee, Knoxville, TN 37996, USA
Interests: molecular docking; drug discovery; protein folding; biopolymers; aggregation; solvent–protein interactions; salt–protein interactions
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The accurate in silico prediction of small molecule-receptor complex geometries, i.e., molecular docking, offers great promise in driving the rational development of novel small-molecule therapeutics. Despite successes over the past 20 years in aiding drug development, persistent open questions as to how to improve both the accuracy of ligand-binding pose and affinity predictions, while also increasing computational efficiency, remain. It is important to note, that although these open questions remain, recent methodological developments are now providing pathways towards overcoming previously “undruggable” targets. In this Special Issue, we seek to highlight methodological reviews, novel molecular docking approaches, and new performance benchmarks, to guide future methodological development. Innovative applications of current docking methods are also of interest, particularly docking campaigns against traditionally “undruggable” targets.

You may choose our Joint Special Issue in Molecules.

Dr. Micholas Dean Smith
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

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. Chemistry is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1800 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • computational drug discovery
  • docking
  • induced fit
  • ligand ranking
  • pose prediction
  • binding affinity
  • rescoring

Published Papers (2 papers)

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Research

16 pages, 9109 KiB  
Article
Insight into Tyrosine-Containing Pharmaceuticals as Potential Inhibitors of SARS-CoV-2 3CLpro and NSP16: Structural Analysis, Docking Studies, Molecular Dynamics Simulations, and Density Functional Theory Investigations
by Mohamed R. Elamin, Tarek A. Yousef and Amin O. Elzupir
Chemistry 2023, 5(2), 762-777; https://0-doi-org.brum.beds.ac.uk/10.3390/chemistry5020054 - 03 Apr 2023
Viewed by 1244
Abstract
Tyrosine-containing pharmaceuticals’ (TPh) potential to inhibit SARS CoV-2 3-chymotrypsin-like proteases (3CLpro) and nonstructural protein 16 (NSP16) has been explored using docking studies, molecular dynamics simulations, and density functional theory. The TPh with FDA approval showed excellent contact with the active site [...] Read more.
Tyrosine-containing pharmaceuticals’ (TPh) potential to inhibit SARS CoV-2 3-chymotrypsin-like proteases (3CLpro) and nonstructural protein 16 (NSP16) has been explored using docking studies, molecular dynamics simulations, and density functional theory. The TPh with FDA approval showed excellent contact with the active site pockets of 3CLpro and NSP16. Their binding affinity scores ranged from −5.8 to −4.9 kcal/mol and −6.3 to −4.8 for 3CLpro and NSP16, respectively. A 100-ns molecular dynamics simulation confirmed the stability of the carbidopa/NSP16 complex and N-acetyl tyrosine with both target enzymes. Further, the HOMO-LUMO transitions, molecular orbitals, and dipole moments of carbidopa, droxidopa, and N-acetyl tyrosine were computed using density functional theory (DFT). Considering N-acetyl tyrosine and carbidopa’s substantial inhibitory activity, it is recommended to investigate them further in order to explore their application for the treatment of COVID-19 or any other coronaviruses in the future. Full article
(This article belongs to the Special Issue Molecular Docking in Drug Discovery)
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14 pages, 6743 KiB  
Article
Molecular Docking and Molecular Dynamics Simulation Studies of Quinoline-3-Carboxamide Derivatives with DDR Kinases–Selectivity Studies towards ATM Kinase
by Srimadhavi Ravi, Bhanu Priya, Pankaj Dubey, Vijay Thiruvenkatam and Sivapriya Kirubakaran
Chemistry 2021, 3(2), 511-524; https://0-doi-org.brum.beds.ac.uk/10.3390/chemistry3020036 - 11 Apr 2021
Cited by 6 | Viewed by 4272
Abstract
Quinoline-3-carboxamides are an essential class of drug-like small molecules that are known to inhibit the phosphatidylinositol 3-kinase-related kinases (PIKK) family kinases. The quinoline nitrogen is shown to bind to the hinge region of the kinases, making them competitive inhibitors of adenosine triphosphate (ATP). [...] Read more.
Quinoline-3-carboxamides are an essential class of drug-like small molecules that are known to inhibit the phosphatidylinositol 3-kinase-related kinases (PIKK) family kinases. The quinoline nitrogen is shown to bind to the hinge region of the kinases, making them competitive inhibitors of adenosine triphosphate (ATP). We have previously designed and synthesized quinoline-3-carboxamides as potential ataxia telangiectasia mutated (ATM) kinase inhibitors to function as an adjuvant treatment with DNA damaging agents. This article discusses the molecular docking studies performed with these derivatives with the DNA damage and response (DDR) kinases-ATM, ataxia telangiectasia and rad3 related (ATR), and DNA dependent protein kinase catalytic subunit (DNA-PKcs) and highlights their selectivity towards ATM kinase. Docking studies were also performed with mTOR and PI3Kγ, which are close homologs of the DDR kinases. Molecular dynamics simulations were performed for one of the inhibitors against all the enzymes to establish the stability of the interactions involved. Finally, the absorption, distribution, metabolism, and excretion (ADME) properties of the inhibitors were predicted using the QikProp manual in Maestro. In conclusion, the molecules synthesized showed high selectivity towards the ATM kinase in comparison with the other kinases, though the sequence similarity between them was relatively high. Full article
(This article belongs to the Special Issue Molecular Docking in Drug Discovery)
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