Biomedical subjects

Peter Kolb

Publications and source records attributed to Peter Kolb.

6 recordsLinked to original sources

PubMed2006

Automatic and efficient decomposition of two-dimensional structures of small molecules for fragment-based high-throughput docking.

The computer program DAIM (Decomposition and Identification of Molecules) has been developed to automatically break up compounds in small-molecule libraries for fragment-based docking as well as database analysis. Here, DAIM is evaluated on 130 ligands derived from known crystal structures of ligand-protein complexes. The decomposition and a new fingerprint-based identification technique are used to select anchor fragments for docking. The docking results show that the DAIM selection is superior to size-based or random selection of fragments. To evaluate the usefulness for analyzing the fragment composition of a large library, DAIM is applied to a collection of about 1.85 million commercially available compounds. Interestingly, it is found that the set of most frequent cyclic and acyclic fragments originating from the decomposition of the 1.85 million molecules shows a large overlap with the most frequent fragments in a library of 5120 known drugs. DAIM has been successfully used in the in silico screening for inhibitors of beta-secretase and EphB4 kinase by fragment-based high-throughput docking. Possible future applications for de novo ligand design are briefly discussed.

Amyloid Precursor Protein Secretases↗

PubMed2006

In silico discovery of beta-secretase inhibitors.

Alzheimer's disease, the most common amyloid-associated disorder, accounts for the majority of the dementia diagnosed after the age of 60. The cleavage of the beta-amyloid precursor protein is initiated by beta-secretase (BACE-1), a membrane-bound aspartic protease, which has emerged as an important but difficult protein target. Here, an in silico screening approach consisting of fragment-based docking, ligand conformational search by a genetic algorithm, and evaluation of free energy of binding was used to identify low-molecular-weight inhibitors of BACE-1. More than 300,000 small molecules were docked and about 15,000 prioritized according to a linear interaction energy model with evaluation of solvation by continuum electrostatics. Eighty-eight compounds were tested in vitro, and 10 of them showed an IC(50) value lower than 100 microM in a BACE-1 enzymatic assay. Interestingly, the 10 active compounds shared a triazine scaffold. Moreover, four of them were active in an assay with mammalian cells (EC(50) < 20 microM), indicating that they are cell-permeable. Therefore, these triazine derivatives are very promising lead candidates for BACE-1 inhibition. The discoveries of this series and two other series of nonpeptidic BACE-1 inhibitors demonstrate the usefulness of our in silico high-throughput screening approach.

Amyloid Precursor Protein Secretases↗

PubMed2006

Obsessive-compulsive disorder and rectal prolapse.

A 47-year-old woman with a long-standing history of obsessive-compulsive disorder relating to dirt and germs is presented. Her fear of developing bowel cancer led her to manually evacuate faeces from her rectum five times a day and to a resultant rectal prolapse. Treatment involved prolonged graduated exposure to the patient's feared contaminants and ritual avoidance. After 5 months of inpatient therapy, the patient reported a subjective 70% improvement in her symptoms. As her obsessive-compulsive disorder symptoms improved, the patient's rectal prolapse disappeared.

Behavior Therapy↗

PubMed2005

Discovery of cell-permeable non-peptide inhibitors of beta-secretase by high-throughput docking and continuum electrostatics calculations.

A fragment-based docking procedure followed by substructure search were used to identify active-site beta-secretase inhibitors from a composite set of about 300 000 and a library of nearly 180 000 small molecules, respectively. EC(50) values less than 10 microM were measured in at least one of two different mammalian cell-based assays for 12 of the 72 purchased compounds. In particular, the phenylureathiadiazole 2 and the diphenylurea derivative 3 are promising lead compounds for beta-secretase inhibition.

Amyloid Precursor Protein Secretases↗

PubMed2004

Automated docking of highly flexible ligands by genetic algorithms: a critical assessment.

An improved version of the fragment-based flexible ligand docking approach SEED-FFLD is tested on inhibitors of human immunodeficiency virus type 1 protease, human alpha-thrombin and the estrogen receptor beta. The docking results indicate that it is possible to correctly reproduce the binding mode of inhibitors with more than ten rotatable bonds if the strain in their covalent geometry upon binding is not large. A high degree of convergence towards a unique binding mode in multiple runs of the genetic algorithm is proposed as a necessary condition for successful docking.

Algorithms↗

PubMed1996

Tetrachloro- and Tetrabromostibonium(V) Cations: Raman and (19)F, (121)Sb, and (123)Sb NMR Spectroscopic Characterization and X-ray Crystal Structures of SbCl(4)(+)Sb(OTeF(5))(6)(-) and SbBr(4)(+)Sb(OTeF(5))(6)(-).

The stable salts, SbCl(4)(+)Sb(OTeF(5))(6)(-) and SbBr(4)(+)Sb(OTeF(5))(6)(-), have been prepared by oxidation of Sb(OTeF(5))(3) with Cl(2) and Br(2), respectively. The SbBr(4)(+) cation is reported for the first time and is only the second example of a tetrahalostibonium(V) cation. The SbCl(4)(+) cation had been previously characterized as the Sb(2)F(11)(-), Sb(2)Cl(2)F(9)(-), and Sb(2)Cl(0.5)F(10.5)(-) salts. Both Sb(OTeF(5))(6)(-) salts have been characterized in the solid state by low-temperature Raman spectroscopy and X-ray crystallography. Owing to the weakly coordinating nature of the Sb(OTeF(5))(6)(-) anion, both salts are readily soluble in SO(2)ClF and have been characterized in solution by (121)Sb, (123)Sb, and (19)F NMR spectroscopy. The tetrahedral environments around the Sb atoms of the cations result in low electric field gradients at the quadrupolar (121)Sb and (123)Sb nuclei and correspondingly long relaxation times, allowing the first solution NMR characterization of a tetrahalocation of the heavy pnicogens. The following crystal structures are reported: SbCl(4)(+)Sb(OTeF(5))(6)(-), trigonal system, space group P&thremacr;, a = 10.022(1) Å, c = 18.995(4) Å, V = 1652.3(6) Å(3), D(calc) = 3.652 g cm(-)(3), Z = 2, R(1) = 0.0461; SbBr(4)(+)Sb(OTeF(5))(6)(-), trigonal system, space group P&thremacr;, a = 10.206(1) Å, c = 19.297(3) Å, V = 1740.9(5) Å(3), D(calc) = 3.806 g cm(-)(3), Z = 2, R(1) = 0.0425. The crystal structures of both Sb(OTeF(5))(6)(-) salts are similar and reveal considerably weaker interactions between anion and cation than in previously known SbCl(4)(+) salts. Both cations are undistorted tetrahedra with bond lengths of 2.221(3) Å for SbCl(4)(+) and 2.385(2) Å for SbBr(4)(+). The Raman spectra are consistent with undistorted SbX(4)(+) tetrahedra and have been assigned under T(d)() point symmetry. Trends within groups 15 and 17 are noted among the general valence force constants of the PI(4)(+), AsF(4)(+), AsBr(4)(+), AsI(4)(+), SbCl(4)(+) and SbBr(4)(+) cations, which have been calculated for the first time, and the previously determined force constants for NF(4)(+), NCl(4)(+), PF(4)(+), PCl(4)(+), PBr(4)(+), and AsCl(4)(+), which have been recalculated for the P and As cations in the present study. The SbCl(4)(+) salt is stable in SO(2)ClF solution, whereas the SbBr(4)(+) salt decomposes slowly in SO(2)ClF at room temperature and rapidly in the presence of Br(-) ion and in CH(3)CN solution at low temperatures. The major products of the decompositions are SbBr(2)(+)Sb(OTeF(5))(6)(-), as an adduct with CH(3)CN in CH(3)CN solvent, and Br(2).

Journal Article↗