The HIV protease and therapies for AIDS

Barriers to Alzheimer disease drug discovery and development in academia

The drug discovery and the drug development processes represent a continuum of recursive activities that range from initial drug target identification to final Food and Drug Administration approval and marketing of a new therapeutic. Drug discovery, as its name implies, is more exploratory and less focused in many cases, whereas drug development has a clinically defined endpoint and a specific disease goal. Academia has historically made major contributions to this process at the early discovery phases. However, current trends in the organization of the pharmaceutical industry suggest an expanded role for academia in the near future. Megamergers among major pharmaceutical corporations indicate their movement toward a focus on end-stage clinical trials, manufacturing, and marketing. There has been a parallel increase in outsourcing of intermediate steps to specialty small pharmaceutical, biotechnology, and contract service companies. The new paradigm suggests that academia will play an increasingly important role at the proof-of-principle stage of basic and clinical drug discovery research, in training the future skilled work force, and in close partnerships with small pharmaceutical and biotechnology companies. However, academic drug discovery research faces a set of barriers to progress, the relative importance of which varies with the home institution and the details of the research area. These barriers fall into four general categories: (1) the historical administrative structure and environment of academia; (2) the structure and emphasis of peer review panels that control research funding by government and private agencies; (3) the organization and operation of the academic infrastructure; and (4) the structure and availability of specialized resources and information management. Selected examples of barriers to drug discovery and drug development research and training in academia are presented, as are some specific recommendations designed to minimize or circumvent these barriers. In some cases, precedents established by other disease-focused areas may be relevant to Alzheimer disease and related disorders, but the overall impact of any changes requires adaptation at the top of the administrative structures in academia and funding agencies to support and encourage cooperative efforts among faculty investigators.

Bacterial proteinases as targets for the development of second-generation antibiotics

The emergence of bacterial pathogen resistance to common antibiotics strongly supports the necessity to develop alternative mechanisms for combating drug-resistant forms of these infective organisms. Currently, few pharmaceutical companies have attempted to investigate the possibility of interrupting metabolic pathways other than those that are known to be involved in cell wall biosynthesis. In this review, we describe multiple, novel roles for bacterial proteinases during infection using, as a specific example, the enzymes from the organism Porphyromonas gingivalis, a periodontopathogen, which is known to be involved in the development and progression of periodontal disease. In this manner, we are able to justify the concept of developing synthetic inhibitors against members of this class of enzymes as potential second-generation antibiotics. Such compounds could not only prove valuable in retarding the growth and proliferation of bacterial pathogens but also lead to the use of this class of inhibitors against invasion by other infective organisms.

HIV protease: enzyme function and drug resistance

HIV protease is responsible for processing of the gag and gag-pol polyproteins during virion maturation. The activity of this enzyme is essential for virus infectivity, rendering the protein a major therapeutic target for AIDS treatment. This articles reviews the biochemical and biophysical properties of the enzyme. The clinical and in vitro observations of resistance to protease inhibitors are discussed from the perspective of drug resistance mechanisms of HIV protease mutants.

Natural protease inhibitors to hemorrhagins in snake venoms and their potential use in medicine

Snake venoms are complex mixtures of many toxins and enzymes which effectively immobilize prey without a struggle and assist in digestion. Certain animals have a remarkable resistance to envenomation of snakes. Naturally occurring factors that neutralize snake venoms have been found in the sera of most snakes and a few warm-blooded animals. These antihemorrhagic and antineurotoxic factors have been purified from snake and mammalian sera. The antihemorrhagins are not immunoglobulins since they have different physical and chemical characteristics. The natural immunity to hemorrhagins is the result of tissue inhibitors of metalloproteinases (TIMP) found in animal sera of resistant animals. Most animals have matrix metalloproteinases (MMP) and TIMP that are implicated in a wide variety of normal physiological processes and pathological conditions. MMP in animals have many biological functions in embryogenesis, morphogenesis and tissue remodeling. MMP activities are precisely regulated by endogenous TIMP. Disruption of the balance between MMP and TIMP causes various diseases such as arthritis, periodontal diseases, diabetes, ophthalmologic conditions, neoplasia, metabolic bone disease, atherosclerosis and orthopedic conditions. Resistant animals that have a high titer of TIMP would have a survival advantage when bitten by poisonous snakes. Snake venoms are abundant and stable sources of MMP which are medically important. The venom MMP which cause unregulated destruction of tissue have sequences which have some degree of homology with mammalian MMP which control normal biological processes. Resistant animals are important sources of TIMP which can be used to study metalloproteinase related diseases. For these reasons the MMP in snakes and TIMP in resistant animal are excellent candidates for developing new drug therapies.

Structural role of the 30's loop in determining the ligand specificity of the human immunodeficiency virus protease

The structural basis of ligand specificity in human immunodeficiency virus (HIV) protease has been investigated by determining the crystal structures of three chimeric HIV proteases complexed with SB203386, a tripeptide analogue inhibitor. The chimeras are constructed by substituting amino acid residues in the HIV type 1 (HIV-1) protease sequence with the corresponding residues from HIV type 2 (HIV-2) in the region spanning residues 31-37 and in the active site cavity. SB203386 is a potent inhibitor of HIV-1 protease (Ki = 18 nM) but has a decreased affinity for HIV-2 protease (Ki = 1280 nM). Crystallographic analysis reveals that substitution of residues 31-37 (30's loop) with those of HIV-2 protease renders the chimera similar to HIV-2 protease in both the inhibitor binding affinity and mode of binding (two inhibitor molecules per protease dimer). However, further substitution of active site residues 47 and 82 has a compensatory effect which restores the HIV-1-like inhibitor binding mode (one inhibitor molecule in the center of the protease active site) and partially restores the affinity. Comparison of the three chimeric protease structures with those of HIV-1 and SIV proteases complexed with the same inhibitor reveals structural changes in the flap regions and the 80's loops, as well as changes in the dimensions of the active site cavity. The study provides structural evidence of the role of the 30's loop in conferring inhibitor specificity in HIV proteases.