Current Topics in Medicinal Chemistry - Volume 5, Issue 8, 2005

Ligand flexibility is an important problem in molecular docking and virtual screening. To address this challenge, we investigate a hierarchical pre-organization of multiple conformations of small molecules. Such organization of pre-calculated conformations removes the exploration of ligand conformational space from the docking calculation and allows for concise representation of what can be thousands of conformations. T Read More

According to Hann's model of molecular complexity an increased probability of detection binding to a target protein can be expected when small, low complex molecular fragments are screened with high sensitivity instead of fullsized ligands with lower sensitivity. Analysis of the HTS summary data of Novartis and comparison with NMR screening results obtained on generic fragment libraries indicate this expectation to be true Read More

Nuclear receptors form a family of ligand-activated transcription factors that regulate a wide variety of biological processes and are thus generally considered relevant targets in drug discovery. We have constructed an annotated compound library directed to nuclear receptors (NRacl) as a means for integrating the chemical and biological data being generated within this family. Special care has been put in the appropriate s Read More

Motivated by the need to augment Merck's in-house small molecule collection, web-based tools for designing, enumerating, optimizing and tracking compound libraries have been developed. The path leading to the current version of this Virtual Library Tool Kit (VLTK) is discussed in context of the (then) available commercial offerings and the constraints and requirements imposed by the end users. Though the effort was initiated to Read More

Information extraction approaches have been successfully applied to mine the scientific literature in biology and medicine. So far, the main focus of research and development in this domain was on the recognition and extraction of gene and protein names in the context of molecular biology and genome research and on disease names and other medical terms in the context of clinical research. Similar to biology and medical scie Read More

Partitioning algorithms are described that operate in chemical reference spaces formed by combinations of binary-transformed molecular descriptors and aim at the identification of potent hits in ligand-based virtual screening. One of these approaches depends on mapping of consensus positions of compound activity sets in descriptor spaces followed by step-wise extension of the dimensionality of these spaces Read More

The original publication of Mortlock, A.; Keen, N. J.; Jung, F. H.; Heron, N. M.; Foote, K. M.; Wilkinson, R.; Green, R. Progress in the Development of Selective Inhibitors of Aurora Kinases, 2005, 5, 199-214 contained numerous errors, and the properly corrected version is reprinted here in it's entirety.

Errors in the mitotic process are thought to be one of the principal sources of the genetic instability that hallmarks cancer. Unsurprisingly, many of the proteins that regulate mitosis are aberrantly expressed in tumour cells when compared to their normal counterparts. These may represent a good source of targets for the development of novel anticancer agents. The Aurora kinases represent one such family of mitotic regulat Read More