Discovery of a similar region on two protein surfaces can lead to important inference about the functional role or molecular interaction of this region for one of the proteins if such information is available for the other. We propose a new characterization of protein surfaces based on a spin-image representation of the surfaces that facilitates the simultaneous search of the entire surface of ...

Pathogenic Gram-negative bacteria have developed resistance to antibiotics due to their ability in creating an envelope on the outer layer of lipooligosaccharides (LOS). The cationic phosphoethanolamine (PEA) decoration of LOS lipid A is regulated by lipid A–PEA transferase (EptA) which may serve as a prominent target for developing new antibiotics. The structural characterization of Neisserial...

We describe the methodology, parametrization, and application of a conformational search method, called ConfGen, designed to efficiently generate bioactive conformers. We define efficiency as the ability to generate a bioactive conformation within a small total number of conformations using a reasonable amount of computer time. The method combines physics-based force field calculations with emp...

Charcot-Marie-Tooth (CMT) disease is an inherited peripheral neuromuscular disorder characterized by length-dependent and progressive degeneration of peripheral nerves, leading to muscular weakness. Research has shown that mutated HSPB8 may be responsible for depression, neurodegenerative disorders, and improper functioning of peripheral nerves, resulting in neuromuscular disorders like CMT. In...

Dihydroorotate Dehydrogenase (DHODH) is a mitochondrial protein involved in de novo pyrimidine biosynthesis, catalyzing the ubiquinone-mediated oxidation of dihydroorotate (DHO) to orotate. DHODH is considered to be a validated target for the development of immune-modulating agents. In this work two different approaches were used to create a pharmacophore model, which was subsequently used in a...

Small molecule modulators of mitochondrial function have been attracted much attention in recent years due to their potential therapeutic applications for neurodegenerative diseases. The translocator protein (TSPO) is a promising target such compounds, given its involvement the formation permeability transition pore response stress. In this study, we performed ligand-based pharmacophore design ...

Through a ligand-based pharmacophore model (S)-proline based compounds were identified as potent cannabinoid receptor 2 (CB2) agonists with high selectivity over the cannabinoid receptor 1 (CB1). Structure-activity relationship investigations for this compound class lead to oxo-proline compounds 21 and 22 which combine an impressive CB1 selectivity profile with good pharmacokinetic properties. ...

The structure of epothilone A, bound to , -tubulin in zinc-stabilized sheets, was determined by a combination of electron crystallography at 2.89 angstrom resolution and nuclear magnetic resonance–based conformational analysis. The complex explains both the broad-based epothilone structureactivity relationship and the known mutational resistance profile. Comparison with Taxol shows that the lon...

3-hydroxy-3-methylglutaryl coenzyme A reductase (HMGR) catalyzes the conversion of HMG-CoA to mevalonate using NADPH and the enzyme is involved in rate-controlling step of mevalonate. Inhibition of HMGR is considered as effective way to lower cholesterol levels so it is drug target to treat hypercholesterolemia, major risk factor of cardiovascular disease. To discover novel HMGR inhibitor, we p...

Ligandcentric virtual screening techniques employ in most cases three-dimensional Gaussians in order to define a molecule’s entire pharmacophoric properties (ideally of a co-crystallised ligand) [1] and have been applied successfully in many prospective and retrospective drug discovery campaign [2]. Here, the development of a new pharmacophoric binding site descriptor in the spirit of Cavbase [...