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Special Issue "QSAR and QSPR: Recent Developments and Applications"

A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Theoretical Chemistry".

Deadline for manuscript submissions: 31 January 2019

Special Issue Editor

Guest Editor
Prof. Kok Hwa Lim

Singapore Institute of Technology, Singapore City, Singapore
Website | E-Mail
Interests: computational chemistry and material sciences; heterogeneous catalytic reactions and surface sciences; green chemistry and processes; process safety; QSAR analysis of biological activity

Special Issue Information

Dear Colleagues,

QSAR modeling is an integral part of rational drug design (RDD). Despite the prediction of biological activities, QSAR models help to identify the parameters responsible for biological response that is essential for lead compound optimization. In addition, recent developments in molecular docking have been successful to provide information such relative orientation of drug molecules binding to their targeted receptor leading to optimization of lead compound to achieve more potent and selective analogs. Despite the successful application of QSAR to predict biological activities, few QSAR studies have been reported on biological activities of metal-complexes, probably due to the lack of specific metal ligand parameters. Recently, the successful use of density functional theory (DFT) to calculate chemical descriptors of metal complexes also open-up new era for QSAR studies on metal complexes. This Special Issue of Molecules will consider submissions related to QSAR of biological activities. For examples, prediction of biological activities of metal-complexes or molecular entities using physicochemical, steric, topological, as well as ab-initio quantum chemical, pharmacophore mapping and molecular docking descriptors.

Prof. Kok Hwa Lim
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 papers will be 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. Molecules is an international peer-reviewed open access monthly 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

  • Ab-initio
  • semi-empirical quantum chemical methods
  • topological
  • physicochemical
  • electronic descriptors
  • metal complexes
  • pharmacophore mapping
  • molecular docking
  • lead compound optimization

Related Special Issue

Published Papers (3 papers)

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Research

Open AccessArticle QSAR Study of N-Myristoyltransferase Inhibitors of Antimalarial Agents
Molecules 2018, 23(9), 2348; https://doi.org/10.3390/molecules23092348
Received: 12 August 2018 / Revised: 6 September 2018 / Accepted: 12 September 2018 / Published: 13 September 2018
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Abstract
Malaria is a disease caused by protozoan parasites of the genus Plasmodium that affects millions of people worldwide. In recent years there have been parasite resistances to several drugs, including the first-line antimalarial treatment. With the aim of proposing new drugs candidates for
[...] Read more.
Malaria is a disease caused by protozoan parasites of the genus Plasmodium that affects millions of people worldwide. In recent years there have been parasite resistances to several drugs, including the first-line antimalarial treatment. With the aim of proposing new drugs candidates for the treatment of disease, Quantitative Structure–Activity Relationship (QSAR) methodology was applied to 83 N-myristoyltransferase inhibitors, synthesized by Leatherbarrow et al. The QSAR models were developed using 63 compounds, the training set, and externally validated using 20 compounds, the test set. Ten different alignments for the two test sets were tested and the models were generated by the technique that combines genetic algorithms and partial least squares. The best model shows r2 = 0.757, q2adjusted = 0.634, R2pred = 0.746, R2m = 0.716, ∆R2m = 0.133, R2p = 0.609, and R2r = 0.110. This work suggested a good correlation with the experimental results and allows the design of new potent N-myristoyltransferase inhibitors. Full article
(This article belongs to the Special Issue QSAR and QSPR: Recent Developments and Applications)
Figures

Graphical abstract

Open AccessArticle Novel Group of AChE Reactivators—Synthesis, In Vitro Reactivation and Molecular Docking Study
Molecules 2018, 23(9), 2291; https://doi.org/10.3390/molecules23092291
Received: 15 August 2018 / Revised: 3 September 2018 / Accepted: 5 September 2018 / Published: 7 September 2018
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Abstract
The acetylcholinesterase (AChE) reactivators (e.g., obidoxime, asoxime) became an essential part of organophosphorus (OP) poisoning treatment, together with atropine and diazepam. They are referred to as a causal treatment of OP poisoning, because they are able to split the OP moiety from AChE
[...] Read more.
The acetylcholinesterase (AChE) reactivators (e.g., obidoxime, asoxime) became an essential part of organophosphorus (OP) poisoning treatment, together with atropine and diazepam. They are referred to as a causal treatment of OP poisoning, because they are able to split the OP moiety from AChE active site and thus renew its function. In this approach, fifteen novel AChE reactivators were determined. Their molecular design originated from former K-oxime compounds K048 and K074 with remaining oxime part of the molecule and modified part with heteroarenium moiety. The novel compounds were prepared, evaluated in vitro on human AChE (HssAChE) inhibited by tabun, paraoxon, methylparaoxon or DFP and compared to commercial HssAChE reactivators (pralidoxime, methoxime, trimedoxime, obidoxime, asoxime) or previously prepared compounds (K048, K074, K075, K203). Some of presented oxime reactivators showed promising ability to reactivate HssAChE comparable or higher than the used standards. The molecular modelling study was performed with one compound that presented the ability to reactivate GA-inhibited HssAChE. The SAR features concerning the heteroarenium part of the reactivator’s molecule are described. Full article
(This article belongs to the Special Issue QSAR and QSPR: Recent Developments and Applications)
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Figure 1

Open AccessArticle Discovery of High-Affinity Cannabinoid Receptors Ligands through a 3D-QSAR Ushered by Scaffold-Hopping Analysis
Molecules 2018, 23(9), 2183; https://doi.org/10.3390/molecules23092183
Received: 23 August 2018 / Revised: 26 August 2018 / Accepted: 28 August 2018 / Published: 30 August 2018
PDF Full-text (7117 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Two 3D quantitative structure–activity relationships (3D-QSAR) models for predicting Cannabinoid receptor 1 and 2 (CB1 and CB2) ligands have been produced by way of creating a practical tool for the drug-design and optimization of CB1 and CB2 ligands.
[...] Read more.
Two 3D quantitative structure–activity relationships (3D-QSAR) models for predicting Cannabinoid receptor 1 and 2 (CB1 and CB2) ligands have been produced by way of creating a practical tool for the drug-design and optimization of CB1 and CB2 ligands. A set of 312 molecules have been used to build the model for the CB1 receptor, and a set of 187 molecules for the CB2 receptor. All of the molecules were recovered from the literature among those possessing measured Ki values, and Forge was used as software. The present model shows high and robust predictive potential, confirmed by the quality of the statistical analysis, and an adequate descriptive capability. A visual understanding of the hydrophobic, electrostatic, and shaping features highlighting the principal interactions for the CB1 and CB2 ligands was achieved with the construction of 3D maps. The predictive capabilities of the model were then used for a scaffold-hopping study of two selected compounds, with the generation of a library of new compounds with high affinity for the two receptors. Herein, we report two new 3D-QSAR models that comprehend a large number of chemically different CB1 and CB2 ligands and well account for the individual ligand affinities. These features will facilitate the recognition of new potent and selective molecules for CB1 and CB2 receptors. Full article
(This article belongs to the Special Issue QSAR and QSPR: Recent Developments and Applications)
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Figure 1

Planned Papers

The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.

Author: Sakander Hayat
Affiliation:
University of Science and Technology of China, China
 
Author: Yu Li
Affiliation: College of Environmental Science and Engineering, North China Electric Power University, China
 
Author: Yongqiang Zhu
Affiliation: College of Life Science, Nanjing Normal University, China
 
Authors: Marjana Novic and  Marjan Vračko
Affiliation: National Institute of Chemistry Ljubljana, Slovenia
 
Authors: Lucia Pintilie and Amalia Stefaniu
Affiliation: National Institute for Chemical-Pharmaceutical Research and Development, Bucharest, Romania
Tentative title: MOLECULAR DOCKING STUDIES OF SOME NOVEL FLUOROQUINOLONE DERIVATIVES
Abstract: An important parameter in the development of a new drug is the drug's affinity to the identified target (protein/enzyme). Predicting the ligand binding to the target (protein/enzyme) by molecular simulation would allow the synthesis to be restricted to the most promising compounds.A restricted hybrid HF-DFT calculation was performed in order to obtain the most stable conformer of each ligand and a series of DFT calculations using the B3LYP levels with 6-31G* basis set   has been conducted. The docking studies of the quinolone compounds will be performed with the CLC Drug Discovery Workbench to identify and visualize the ligand-receptor interaction mode.
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