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.

The Role of QSAR and Virtual Screening Studies in Type 2 Diabetes Drug Discovery.

Background: Due to the increasing number of diabetes cases worldwide, there is an international concern to provide even more effective treatments to control this condition.

Methods: This review brings together a selection of studies that helped to broaden the comprehension of various biological targets and associated mechanisms involved in type 2 diabetes mellitus.

Results: Such studies demonstrated that QSAR techniques and virtual screenings have been successfully employed in drug design projects.

Structure and functional dynamics characterization of the ion channel of the human respiratory syncytial virus (hRSV) small hydrophobic protein (SH) transmembrane domain by combining molecular dynamics with excited normal modes.

The human respiratory syncytial virus (hRSV) is the major cause of lower respiratory tract infection in children and elderly people worldwide. Its genome encodes 11 proteins including SH protein, whose functions are not well known. Studies show that SH protein increases RSV virulence degree and permeability to small compounds, suggesting it is involved in the formation of ion channels.

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.

Recovery of the wild type atomic flexibility in the HIV-1 protease double mutants.

The emergence of drug resistant mutations due to the selective pressure exerted by antiretrovirals, including protease inhibitors (PIs), remains a major problem in the treatment of AIDS. During PIs therapy, the occurrence of primary mutations in the wild type HIV-1 protease reduces both the affinity for the inhibitors and the viral replicative capacity compared to the wild type (WT) protein, but additional mutations compensate for this reduced viral fitness. To investigate this phenomenon from the structural point of view, we combined Molecular Dynamics and Normal Mode Analysis to analyze and compare the variations of the flexibility of C-alpha atoms and the differences in hydrogen bond (h-bond) network between the WT and double mutants.

A cell-based reporter assay for screening for EcR agonist/antagonist activity of natural ecdysteroids in Lepidoptera (Bm5) and Diptera (S2) cell cultures, followed by modeling of ecdysteroid-EcR interactions and normal mode analysis.

Ecdysteroid signal transduction is a key process in insect development and therefore an important target for insecticide development. We employed an in vitro cell-based reporter bioassay for the screening of potential ecdysone receptor (EcR) agonistic and antagonistic compounds. Natural ecdysteroids were assayed with ecdysteroid-responsive cell line cultures that were transiently transfected with the reporter plasmid ERE-b.

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).

Self-assembly of Arg-Phe nanostructures via the solid-vapor phase method.

We report for the first time on the self-assembly of nanostructures composed exclusively of alternating positively charged and hydrophobic amino acids. A novel arginine/phenylalanine octapeptide, RF8, was synthesized. Because the low hydrophobicity of this sequence makes its spontaneous ordering through solution-based methods difficult, a recently proposed solid-vapor approach was used to obtain nanometric architectures on ITO/PET substrates.

Relation between flexibility and positively selected HIV-1 protease mutants against inhibitors.

The antiretroviral chemotherapy helps to reduce the mortality of HIVs infected patients. However, RNA dependant virus replication has a high mutation rate. Human immunodeficiency virus Type 1 protease plays an essential role in viral replication cycle.