Special Issue "Simulation Studies for Marine Drug Discovery"

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

Deadline for manuscript submissions: 31 January 2021.

Special Issue Editors

Prof. Dr. Juan Frau
Website
Guest Editor
Department of Chemistry, Universitat de les Illes Balears, Palma, Spain
Interests: theoretical chemistry; ab initio calculations; density functional theory; chemical biology; pharmaceutical development; hydrogen bonding; molecular modeling
Prof. Dr. Rodrigo Casasnovas
Website
Guest Editor
Department of Chemistry, Universitat de les Illes Balears, Palma, Spain
Interests: theoretical chemistry; ab initio calculations; density functional theory; chemical biology; pharmaceutical development; hydrogen bonding; molecular modeling

Special Issue Information

Dear Colleagues,

Simulations are extraordinary techniques for studying molecular biology since they provide an understanding of the molecular processes of life and knowledge to ideate strategies to intervene against diseases. Methods such as molecular dynamics and Monte Carlo simulations currently allow the rational design of new drugs, the structural and dynamical characterization of biological targets and the description of drug–target interaction at the molecular level. The plethora of free energy methods/enhanced sampling techniques have pushed the horizons further, allowing for the quantitative calculation of thermodynamic and kinetic parameters such as binding affinities, on and off rates, transport properties and catalytic constants, among others. On the other hand, the marine world is an abundant source of chemical and biological diversity to be explored. As a result, the possibilities of obtaining new therapeutic agents are countless.

This Special Issue aims to motivate original research and review articles on the application of simulation techniques for marine drug discovery, marine-inspired drug design, molecular descriptions of their action mechanisms or advances in marine-related therapeutic strategies.

Prof. Dr. Juan Frau
Prof. Dr. Rodrigo Casasnovas
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. 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 2000 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

  • computer simulation
  • simulation methods
  • molecular dynamics
  • Monte Carlo
  • free energy methods
  • enhanced sampling
  • forcefields
  • molecular mechanics
  • ab initio and QM/MM methods

Published Papers (1 paper)

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Research

Open AccessArticle
Identification of Conomarphin Variants in the Conus eburneus Venom and the Effect of Sequence and PTM Variations on Conomarphin Conformations
Mar. Drugs 2020, 18(10), 503; https://doi.org/10.3390/md18100503 - 01 Oct 2020
Abstract
Marine cone snails belonging to the Conidae family make use of neuroactive peptides in their venom to capture prey. Here we report the proteome profile of the venom duct of Conus eburneus, a cone snail belonging to the Tesseliconus clade. Through tandem [...] Read more.
Marine cone snails belonging to the Conidae family make use of neuroactive peptides in their venom to capture prey. Here we report the proteome profile of the venom duct of Conus eburneus, a cone snail belonging to the Tesseliconus clade. Through tandem mass spectrometry and database searching against the C. eburneus transcriptome and the ConoServer database, we identified 24 unique conopeptide sequences in the venom duct. The majority of these peptides belong to the T and M gene superfamilies and are disulfide-bonded, with cysteine frameworks V, XIV, VI/VII, and III being the most abundant. All seven of the Cys-free peptides are conomarphin variants belonging to the M superfamily that eluted out as dominant peaks in the chromatogram. These conomarphins vary not only in amino acid residues in select positions along the backbone but also have one or more post-translational modifications (PTMs) such as proline hydroxylation, C-term amidation, and γ-carboxylation of glutamic acid. Using molecular dynamics simulations, the conomarphin variants were predicted to predominantly have hairpin-like or elongated structures in acidic pH. These two structures were found to have significant differences in electrostatic properties and the inclusion of PTMs seems to complement this disparity. The presence of polar PTMs (hydroxyproline and γ-carboxyglutamic acid) also appear to stabilize hydrogen bond networks in these conformations. Furthermore, these predicted structures are pH sensitive, becoming more spherical and compact at higher pH. The subtle conformational variations observed here might play an important role in the selection and binding of the peptides to their molecular targets. Full article
(This article belongs to the Special Issue Simulation Studies for Marine Drug Discovery)
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