Current Pharmaceutical Design - Volume 11, Issue 3, 2005

Advances in protein crystallography and molecular simulations have greatly aided computer aided drug design paradigms and the accuracy of binding affinity predictions. The methods used in the discovery and / or optimization of a lead inhibitor have ranged from graphical visualization of the ligand in the binding site to calculation of relative binding affinities using molecular dynamics simulations in conjunction with the Free Read More

Computational assessment of the binding affinity of enzyme inhibitors prior to synthesis is an important component of computer-aided drug design (CADD) paradigms. The free energy perturbation (FEP) methodology is the most accurate means of estimating relative binding affinities between two inhibitors. However, due to its complexity and computation-intensive nature, practical applications are restricted to analysis of struc Read More

It has been 10 years since a 3-dimensional structure of the catalytic domain of a Matrix Metalloprotease (MMP) was revealed for the first time in 1994. More than 80 structures of different MMPs in apo and inhibited forms, determined by X-ray crystallography and NMR methods, have been published by the end of year 2003. A large number of very potent inhibitors have been disclosed in published and patent literature. Seve Read More

The state of the art of various computational aspects of docking-based virtual screening of database of small molecules is presented. The review encompasses the different search algorithms and the scoring functions used in docking methods and their applications to protein and nucleic acid drug targets. Recent progress made in the development and application of methods to include target flexibility are summarized. The fun Read More

Small research-based pharmaceutical start-ups often lack the budget and do not have the infrastructure available to apply all possible techniques for compound selection. This review details our use of a range of techniques such as high-throughput docking and similarity searching to maximize the success rate when attempting to identify pharmaceutically relevant ligands in a resource-constrained environment.

The hypothesis that the interaction of agouti-related protein (AGRP) and the melanocortin-4 receptor (MC4R) modulates feeding behavior in humans has stimulated the synthesis of conformationally constrained peptides, peptoids and small molecules in efforts to identify novel compounds that can potentially be used in the clinical treatment of obesity and related eating disorders. In addition, the availability of a high-resoluti Read More

Cancer is a general term used to describe many disease states, each of which are characterized by abnormal cell proliferation. The causes which bring about this abnormal cellular behavior are specific to each type of cancer. The success of tumor-targeted therapy is limited by this diversity. One common denominator for all types of cancer is the requirement of a suitable blood supply. Therefore, tumor vasculature has emer Read More

Synthetic gene delivery vectors are gaining increasing importance in gene therapy as an alternative to recombinant viruses. Among the various types of non-viral vectors, cationic lipids are especially attractive as they can be prepared with relative ease and extensively characterised. Further, each of their constituent parts can be modified, thereby facilitating the elucidation of structure-activity relationships. In this forward-look Read More

Thalidomide was developed in the 1950s as a sedative drug and withdrawn in 1961 because of its teratogenic effects, but has been rediscovered as an immuno-modifying drug. It has been administered successfully for the treatment of erythema nodosum leprosum, aphthous ulceration in HIV disease, inflammatory bowel diseases, and multiple myeloma. So far, investigations into the mode of action of thalidomide have focused Read More

The migration of tumor cells is a prerequisite for tumor cell invasion and metastasis development, which accounts for over 90% of cancer mortality. Therefore a major focus of current tumor biological research is the study of those factors that regulate tumor cell migration. Those chemokines and neurotransmitters that bind to G-protein coupled receptors (also known as serpentine receptors) are the most prominent of these f Read More