Fragment shuffling: an automated workflow for three-dimensional fragment-based ligand design.

Fragment-based approaches display a promising alternative in lead discovery. Herein, we present the automated fragment shuffling workflow for the identification of novel lead compounds combining central elements from fragment-based lead identification and structure-based de novo design. Our method is based on sets of aligned 3D ligand structures binding to the same target or target family.

From virtuality to reality - Virtual screening in lead discovery and lead optimization: a medicinal chemistry perspective.

Drug discovery and development is an interdisciplinary, expensive and time-consuming process. Scientific advancements during the past two decades have altered the way pharmaceutical research produces novel bio-active molecules. Advances in computational techniques and hardware solutions have enabled in silico methods, and in particular virtual screening, to speed up modern lead identification and lead optimization.

Prediction of CNS activity of compound libraries using substructure analysis.

An in silico ADME/Tox prediction tool based on substructural analysis has been developed. The tool called SUBSTRUCT has been used to predict CNS activity. Data sets with CNS active and nonactive drugs were extracted from the World Drug Index (WDI).

Cloning, purification, crystallization and preliminary X-ray diffraction analysis of the antistasin-type inhibitor ghilanten (domain I) from Haementeria ghilianii in complex with porcine beta-trypsin.

Ghilanten, isolated from the leech Haementeria ghilianii, is a potent two-domain anticoagulant protein homologous to the factor Xa inhibitor antistasin. A synthetic gene encoding the amino-terminal domain of ghilanten (ghilanten-D1) was constructed, expressed in the methylotrophic yeast Pichia pastoris and purified by heparin-Sepharose chromatography. Recombinant ghilanten-D1 inhibits bovine trypsin and human factor Xa with equilibrium inhibition constants (K(i)) of 126 and 1.

L-Isoaspartate 115 of porcine beta-trypsin promotes crystallization of its complex with bdellastasin.

Bdellastasin is a 59-amino-acid, cysteine-rich, antistasin-type inhibitor of sperm acrosin, plasmin and trypsin, isolated from the medicinal leech Hirudo medicinalis. The complex formed between bdellastasin and porcine beta-trypsin has previously been crystallized in the presence of PEG in a tetragonal crystal form of space group P4(3)2(1)2 and has now been found to crystallize under high-salt conditions in the enantiomorphic space group P4(1)2(1)2. These structures have been solved and refined to 2.