Structure-based combinatorial library design: discovery of non-peptidic inhibitors of caspases 3 and 8

Docking methods for structure-based library design

The drug discovery process mainly relies on the experimental high-throughput screening of huge compound libraries in their pursuit of new active compounds. However, spiraling research and development costs and unimpressive success rates have driven the development of more rational, efficient, and cost-effective methods. With the increasing availability of protein structural information, advancement in computational algorithms, and faster computing resources, in silico docking-based methods are increasingly used to design smaller and focused compound libraries in order to reduce screening efforts and costs and at the same time identify active compounds with a better chance of progressing through the optimization stages. This chapter is a primer on the various docking-based methods developed for the purpose of structure-based library design. Our aim is to elucidate some basic terms related to the docking technique and explain the methodology behind several docking-based library design methods. This chapter also aims to guide the novice computational practitioner by laying out the general steps involved for such an exercise. Selected successful case studies conclude this chapter.

Neuroprotection and acute spinal cord injury: a reappraisal

It has long been recognized that much of the post-traumatic degeneration of the spinal cord following injury is caused by a multi-factorial secondary injury process that occurs during the first minutes, hours, and days after spinal cord injury (SCI). A key biochemical event in that process is reactive oxygen-induced lipid peroxidation (LP). In 1990 the results of the Second National Acute Spinal Cord Injury Study (NASCIS II) were published, which showed that the administration of a high-dose regimen of the glucocorticoid steroid methylprednisolone (MP), which had been previously shown to inhibit post-traumatic LP in animal models of SCI, could improve neurological recovery in spinal-cord-injured humans. This resulted in the registration of high-dose MP for acute SCI in several countries, although not in the U.S. Nevertheless, this treatment quickly became the standard of care for acute SCI since the drug was already on the U.S. market for many other indications. Subsequently, it was demonstrated that the non-glucocorticoid 21-aminosteroid tirilazad could duplicate the antioxidant neuroprotective efficacy of MP in SCI models, and evidence of human efficacy was obtained in a third NASCIS trial (NASCIS III). In recent years, the use of high-dose MP in acute SCI has become controversial largely on the basis of the risk of serious adverse effects versus what is perceived to be on average a modest neurological benefit. The opiate receptor antagonist naloxone was also tested in NASCIS II based upon the demonstration of its beneficial effects in SCI models. Although it did not a significant overall effect, some evidence of efficacy was seen in incomplete (i.e., paretic) patients. The monosialoganglioside GM1 has also been examined in a recently completed clinical trial in which the patients first received high-dose MP treatment. However, GM1 failed to show any evidence of a significant enhancement in the extent of neurological recovery over the level afforded by MP therapy alone. The present paper reviews the past development of MP, naloxone, tirilazad, and GM1 for acute SCI, the ongoing MP-SCI controversy, identifies the regulatory complications involved in future SCI drug development, and suggests some promising neuroprotective approaches that could either replace or be used in combination with high-dose MP.