E-Mail Alert

Add your e-mail address to receive forthcoming issues of this journal:

Journal Browser

Journal Browser

Special Issue "Receptor-Dependent QSAR Methods"

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

Deadline for manuscript submissions: 31 July 2019

Special Issue Editors

Guest Editor
Prof. Mircea V. Diudea

Department of Chemistry, Faculty of Chemistry and Chemical Engineering, Babes-Bolyai University, Arany J. street 11, Cluj 400028, Romania
Website | E-Mail
Interests: QSAR; molecular graphs; molecular design; ligand–receptor interaction
Guest Editor
Dr. Claudiu N. Lungu

Universitatea Babes-Bolyai din Cluj-Napoca, Department of Chemistry, Cluj Napoca, Romania
E-Mail
Interests: QSAR; protein–protein interaction; drug design; bioactivity

Special Issue Information

Dear Colleagues,

The trend in actual QSAR methods evolved, in the last years, from pure statistical methods (using topological, quantum or functional molecular descriptors in providing a mathematical equation, linear or linearizable one, to account for a Quantitative Structure–Activity Relationship—methods independent of the receptor structure and/or independent of the ligands alignment vs. the receptor) to methods more sensitive to the chemical nature and 3D-structure of the receptor, methods called here “receptor-dependent QSAR methods”, where from the title of the proposed issue comes from. In this new view, interactions of ligands with the active site of a protein (i.e., receptor) are of particular interest. Considering QSAR to be only a step in the more complex activity of drug design, also protein primary structure, protein folding/spatial properties which ensure their specificity, the general molecular design and pharmacological properties of ligands will be considered in finding of bioactivity, the main goal in drug discovery. The keywords of interest are listed below.

Prof. Mircea V. Diudea
Dr. Claudiu N. Lungu
Guest Editors

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 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

  • QSAR
  • QSAR space
  • Drug design
  • Bioactivity
  • Ligand-receptor interaction
  • Protein folding
  • Protein-protein interaction
  • Molecular design (Quantum calculations)

Published Papers (3 papers)

View options order results:
result details:
Displaying articles 1-3
Export citation of selected articles as:

Research

Open AccessArticle Aflatoxin B1–Formamidopyrimidine DNA Adducts: Relationships between Structures, Free Energies, and Melting Temperatures
Molecules 2019, 24(1), 150; https://doi.org/10.3390/molecules24010150
Received: 5 December 2018 / Revised: 21 December 2018 / Accepted: 26 December 2018 / Published: 2 January 2019
PDF Full-text (1459 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Thermal stabilities of DNA duplexes containing Gua (g), α- (a) or β-anomer of formamidopyrimidine-N7-9-hydroxy-aflatoxin B1 (b) differ markedly (Tm: a<g<b), but the underlying molecular origin of this experimentally observed [...] Read more.
Thermal stabilities of DNA duplexes containing Gua (g), α- (a) or β-anomer of formamidopyrimidine-N7-9-hydroxy-aflatoxin B1 (b) differ markedly (Tm: a < g < b ), but the underlying molecular origin of this experimentally observed phenomenon is yet to be identified and determined. Here, by employing explicit-solvent molecular dynamics simulations coupled with free-energy calculations using a combined linear-interaction-energy/linear-response-approximation approach, we explain the quantitative differences in T m in terms of three structural features (bulkiness, order, and compactness) and three energetical contributions (non-polar, electrostatic, and preorganized-electrostatic), and thus advance the current understanding of the relationships between structures, free energies, and thermal stabilities of DNA double helices. Full article
(This article belongs to the Special Issue Receptor-Dependent QSAR Methods)
Figures

Graphical abstract

Open AccessArticle Inverse Molecular Docking as a Novel Approach to Study Anticarcinogenic and Anti-Neuroinflammatory Effects of Curcumin
Molecules 2018, 23(12), 3351; https://doi.org/10.3390/molecules23123351
Received: 29 October 2018 / Revised: 7 December 2018 / Accepted: 17 December 2018 / Published: 18 December 2018
Cited by 2 | PDF Full-text (1897 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Research efforts are placing an ever increasing emphasis on identifying signal transduction pathways related to the chemopreventive activity of curcumin. Its anticarcinogenic effects are presumably mediated by the regulation of signaling cascades, including nuclear factor κB (NF-κB), activator protein 1 (AP-1), and mitogen-activated [...] Read more.
Research efforts are placing an ever increasing emphasis on identifying signal transduction pathways related to the chemopreventive activity of curcumin. Its anticarcinogenic effects are presumably mediated by the regulation of signaling cascades, including nuclear factor κB (NF-κB), activator protein 1 (AP-1), and mitogen-activated protein kinases (MAPK). By modulating signal transduction pathways, curcumin induces apoptosis in malignant cells, thus inhibiting cancer development and progression. Due to the lack of mechanistic insight in the scientific literature, we developed a novel inverse molecular docking protocol based on the CANDOCK algorithm. For the first time, we performed inverse molecular docking of curcumin into a collection of 13,553 available human protein structures from the Protein Data Bank resulting in prioritized target proteins of curcumin. Our predictions were in agreement with the scientific literature and confirmed that curcumin binds to folate receptor β, DNA (cytosine-5)-methyltransferase 3A, metalloproteinase-2, mitogen-activated protein kinase 9, epidermal growth factor receptor and apoptosis-inducing factor 1. We also identified new potential protein targets of curcumin, namely deoxycytidine kinase, NAD-dependent protein deacetylase sirtuin-1 and -2, ecto-5′-nucleotidase, core histone macro-H2A.1, tyrosine-protein phosphatase non-receptor type 11, macrophage colony-stimulating factor 1 receptor, GTPase HRas, aflatoxin B1 aldehyde reductase member 3, aldo-keto reductase family 1 member C3, amiloride-sensitive amine oxidase, death-associated protein kinase 2 and tryptophan-tRNA ligase, that may all play a crucial role in its observed anticancer effects. Moreover, our inverse docking results showed that curcumin potentially binds also to the proteins cAMP-specific 3′,5′-cyclic phosphodiesterase 4D and 17-β-hydroxysteroid dehydrogenase type 10, which provides a new explanation for its efficiency in the treatment of Alzheimer’s disease. We firmly believe that our computational results will complement and direct future experimental studies on curcumin’s anticancer activity as well as on its therapeutic effects against Alzheimer’s disease. Full article
(This article belongs to the Special Issue Receptor-Dependent QSAR Methods)
Figures

Graphical abstract

Open AccessArticle Cube-Rhombellane Related Structures: A Drug Perspective
Molecules 2018, 23(10), 2533; https://doi.org/10.3390/molecules23102533
Received: 12 September 2018 / Revised: 1 October 2018 / Accepted: 2 October 2018 / Published: 4 October 2018
Cited by 1 | PDF Full-text (11751 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Rhombellanes represent a new class of structures, of which homeomorphs may be synthesized as real molecules. Cube-rhombellane is a double-shell structure, with vertices of degree 3 and 6, respectively. Several hypothetical structures/molecules were proposed and computed using molecular graph theory and coordination chemistry [...] Read more.
Rhombellanes represent a new class of structures, of which homeomorphs may be synthesized as real molecules. Cube-rhombellane is a double-shell structure, with vertices of degree 3 and 6, respectively. Several hypothetical structures/molecules were proposed and computed using molecular graph theory and coordination chemistry principles. Some geometries were optimized at the B3LYP/6-31G (d, p) level of theory, followed by harmonic vibrational frequency analysis at the same level of theory, single point data were collected in view of molecular stability evaluation. Some of the bioactive functionalized structures were also proposed and explored by molecular mechanics (MM)-based conformational analysis, to check their internal mobility. Drug-like properties of the proposed molecular structures were compared with some existing nano-molecules (fullerenes, nanotubes). ADME and other physico-chemical characteristics were computed using commercial software. Substructures of the proposed molecules, useful in a future synthesis, were provided by retro combinatorial synthesis (RECAP). Computational results obtained are promising regarding ADME properties, drug-likeness and nano-properties. Full article
(This article belongs to the Special Issue Receptor-Dependent QSAR Methods)
Figures

Figure 1

Molecules EISSN 1420-3049 Published by MDPI AG, Basel, Switzerland RSS E-Mail Table of Contents Alert
Back to Top