Computational methodologies in the exploration of marine natural product leads

Research output: Contribution to journalReview article

13 Citations (Scopus)

Abstract

Computational methodologies are assisting the exploration of marine natural products (MNPs) to make the discovery of new leads more efficient, to repurpose known MNPs, to target new metabolites on the basis of genome analysis, to reveal mechanisms of action, and to optimize leads. In silico efforts in drug discovery of NPs have mainly focused on two tasks: dereplication and prediction of bioactivities. The exploration of new chemical spaces and the application of predicted spectral data must be included in new approaches to select species, extracts, and growth conditions with maximum probabilities of medicinal chemistry novelty. In this review, the most relevant current computational dereplication methodologies are highlighted. Structure-based (SB) and ligand-based (LB) chemoinformatics approaches have become essential tools for the virtual screening of NPs either in small datasets of isolated compounds or in large-scale databases. The most common LB techniques include Quantitative Structure–Activity Relationships (QSAR), estimation of drug likeness, prediction of adsorption, distribution, metabolism, excretion, and toxicity (ADMET) properties, similarity searching, and pharmacophore identification. Analogously, molecular dynamics, docking and binding cavity analysis have been used in SB approaches. Their significance and achievements are the main focus of this review.

Original languageEnglish
Article number236
JournalMarine Drugs
Volume16
Issue number7
DOIs
Publication statusPublished - 1 Jul 2018

Fingerprint

Biological Products
Ligands
Pharmaceutical Chemistry
Drug Discovery
Molecular Dynamics Simulation
Computer Simulation
Adsorption
Genome
Databases
Growth
Pharmaceutical Preparations
Datasets
Identification (Psychology)

Keywords

  • Bioinformatics
  • Chemoinformatics
  • Computer-aided drug design (CADD)
  • Drug discovery
  • Machine learning (ML)
  • Marine natural products (MNPs)

Cite this

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title = "Computational methodologies in the exploration of marine natural product leads",
abstract = "Computational methodologies are assisting the exploration of marine natural products (MNPs) to make the discovery of new leads more efficient, to repurpose known MNPs, to target new metabolites on the basis of genome analysis, to reveal mechanisms of action, and to optimize leads. In silico efforts in drug discovery of NPs have mainly focused on two tasks: dereplication and prediction of bioactivities. The exploration of new chemical spaces and the application of predicted spectral data must be included in new approaches to select species, extracts, and growth conditions with maximum probabilities of medicinal chemistry novelty. In this review, the most relevant current computational dereplication methodologies are highlighted. Structure-based (SB) and ligand-based (LB) chemoinformatics approaches have become essential tools for the virtual screening of NPs either in small datasets of isolated compounds or in large-scale databases. The most common LB techniques include Quantitative Structure–Activity Relationships (QSAR), estimation of drug likeness, prediction of adsorption, distribution, metabolism, excretion, and toxicity (ADMET) properties, similarity searching, and pharmacophore identification. Analogously, molecular dynamics, docking and binding cavity analysis have been used in SB approaches. Their significance and achievements are the main focus of this review.",
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Computational methodologies in the exploration of marine natural product leads. / Pereira, Florbela ; Aires-de-Sousa, Joao.

In: Marine Drugs, Vol. 16, No. 7, 236, 01.07.2018.

Research output: Contribution to journalReview article

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