Effects of pH and aggregation in the human prion conversion into scrapie form: a study using molecular dynamics with excited normal modes.

There are two different prion conformations: (1) the cellular natural (PrP) and (2) the scrapie (PrP), an infectious form that tends to aggregate under specific conditions. PrP and PrP are widely different regarding secondary and tertiary structures. PrP contains more and longer β-strands compared to PrP.

Molecular cloning and in silico characterization of knottin peptide, U2-SCRTX-Lit2, from brown spider (Loxosceles intermedia) venom glands.

Inhibitor cystine knots (ICKs) are a family of structural peptides with a large number of cysteine residues that form intramolecular disulfide bonds, resulting in a knot. These peptides are involved in a variety of biological functions including predation and defense, and are found in various species, such as spiders, scorpions, sea anemones, and plants. The Loxosceles intermedia venom gland transcriptome identified five groups of ICK peptides that represent more than 50 % of toxin-coding transcripts.

Binding of phenothiazines into allosteric hydrophobic pocket of human thioredoxin 1.

Thioredoxins are multifunctional oxidoreductase proteins implicated in the antioxidant cellular apparatus and oxidative stress. They are involved in several pathologies and are promising anticancer targets. Identification of noncatalytic binding sites is of great interest for designing new allosteric inhibitors of thioredoxin.

Use of machine learning approaches for novel drug discovery.

Introduction: The use of computational tools in the early stages of drug development has increased in recent decades. Machine learning (ML) approaches have been of special interest, since they can be applied in several steps of the drug discovery methodology, such as prediction of target structure, prediction of biological activity of new ligands through model construction, discovery or optimization of hits, and construction of models that predict the pharmacokinetic and toxicological (ADMET) profile of compounds.

Areas Covered: This article presents an overview on some applications of ML techniques in drug design.

Binding sites and hydrophobic pockets in Human Thioredoxin 1 determined by normal mode analysis.

The Thioredoxin (Trx) system plays important roles in several diseases (e.g. cancer, viral infections, cardiovascular and neurodegenerative diseases).