Special Issue "Molecular Docking in Marine Drug Discovery & Design"

A special issue of Marine Drugs (ISSN 1660-3397).

Deadline for manuscript submissions: closed (31 March 2020) | Viewed by 5305

Special Issue Editor

Dr. Rosa Maria Vitale
E-Mail Website
Guest Editor
Institute of Biomolecular Chemistry (ICB), National Research Council of Italy, Via Campi Flegrei 34, 80078 Pozzuoli, NA, Italy
Interests: molecular docking; molecular dynamics; virtual screening; natural products; drug design; structure-activity relationships
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Special Issue Information

Dear Colleagues,

Natural products from marine sources represent an invaluable inspiration for medicinal chemistry due to their high scaffold diversity and the occurrence of heteroatoms able to engage in specific interactions with a variety of molecular targets. However, the major issue of marine compounds that usually prevents the full exploitation of their pharmacological potential is their limited availability. Computational approaches can overcome this bottleneck by driving and orienting pharmacological evaluation in a more focused way. In fact, they can help the search for new drugs by easing both the discovery of potential lead compounds through the identification of possible pharmacological targets, and their subsequent optimization by rational design.

The purpose of this Special Issue is to collect papers where computational approaches, alone or in combination with organic synthesis, strongly contribute to any or all of the following: i) the identification of novel molecular targets for marine compounds; ii) the determination of structure–activity relationships; iii) drug design inspired by marine compounds; and iv) the optimization of lead compounds from marine sources. Thus, I strongly encourage the submission of original papers focused on the role of molecular docking in particular, and computational methods in general, in the discovery and/or optimization of bioactive marine compounds. Theoretical studies should be supported and validated by experimental data.

Dr. Rosa Maria Vitale
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. Marine Drugs 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 2400 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

  • molecular docking 
  • virtual screening 
  • drug design 
  • drug discovery 
  • structure–activity relationships 
  • marine compounds 
  • structural characterization 
  • pharmacological assays

Published Papers (2 papers)

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Research

Article
Fourfold Filtered Statistical/Computational Approach for the Identification of Imidazole Compounds as HO-1 Inhibitors from Natural Products
Mar. Drugs 2019, 17(2), 113; https://doi.org/10.3390/md17020113 - 12 Feb 2019
Cited by 15 | Viewed by 2388
Abstract
Over-regulation of Heme oxygenase 1 (HO-1) has been recently identified in many types of human cancer, and in these cases, poor clinical outcomes are normally reported. Indeed, the inhibition of HO-1 is being considered as an anticancer approach. Imidazole scaffold is normally present [...] Read more.
Over-regulation of Heme oxygenase 1 (HO-1) has been recently identified in many types of human cancer, and in these cases, poor clinical outcomes are normally reported. Indeed, the inhibition of HO-1 is being considered as an anticancer approach. Imidazole scaffold is normally present in most of the classical HO-1 inhibitors and seems indispensable to the inhibitory activity due to its strong interaction with the Fe(II) of the heme group. In this paper, we searched for new potentially HO-1 inhibitors among three different databases: Marine Natural Products (MNP), ZINC Natural Products (ZNP) and Super Natural II (SN2). 484,527 compounds were retrieved from the databases and filtered through four statistical/computational filters (2D descriptors, 2D-QSAR pharmacophoric model, 3D-QSAR pharmacophoric model, and docking). Different imidazole-based compounds were suggested by our methodology to be potentially active in inhibiting the HO-1, and the results have been rationalized by the bioactivity of the filtered molecules reported in the literature. Full article
(This article belongs to the Special Issue Molecular Docking in Marine Drug Discovery & Design)
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Article
In Silico Identification and Experimental Validation of (−)-Muqubilin A, a Marine Norterpene Peroxide, as PPARα/γ-RXRα Agonist and RARα Positive Allosteric Modulator
Mar. Drugs 2019, 17(2), 110; https://doi.org/10.3390/md17020110 - 12 Feb 2019
Cited by 6 | Viewed by 2619
Abstract
The nuclear receptors (NRs) RARα, RXRα, PPARα, and PPARγ represent promising pharmacological targets for the treatment of neurodegenerative diseases. In the search for molecules able to simultaneously target all the above-mentioned NRs, we screened an in-house developed molecular database using a ligand-based approach, [...] Read more.
The nuclear receptors (NRs) RARα, RXRα, PPARα, and PPARγ represent promising pharmacological targets for the treatment of neurodegenerative diseases. In the search for molecules able to simultaneously target all the above-mentioned NRs, we screened an in-house developed molecular database using a ligand-based approach, identifying (−)-Muqubilin (Muq), a cyclic peroxide norterpene from a marine sponge, as a potential hit. The ability of this compound to stably and effectively bind these NRs was assessed by molecular docking and molecular dynamics simulations. Muq recapitulated all the main interactions of a canonical full agonist for RXRα and both PPARα and PPARγ, whereas the binding mode toward RARα showed peculiar features potentially impairing its activity as full agonist. Luciferase assays confirmed that Muq acts as a full agonist for RXRα, PPARα, and PPARγ with an activity in the low- to sub-micromolar range. On the other hand, in the case of RAR, a very weak agonist activity was observed in the micromolar range. Quite surprisingly, we found that Muq is a positive allosteric modulator for RARα, as both luciferase assays and in vivo analysis using a zebrafish transgenic retinoic acid (RA) reporter line showed that co-administration of Muq with RA produced a potent synergistic enhancement of RARα activation and RA signaling. Full article
(This article belongs to the Special Issue Molecular Docking in Marine Drug Discovery & Design)
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