Current Pharmaceutical Design - Volume 8, Issue 28, 2002

Alzheimer's disease is an age-related neurodegenerative disease which causes global loss of cognitive function. Drug treatment for Alzheimer's disease has been limited to agents that ameliorate behavioral symptoms but these agents are without effect on disease progression. Rational drug design for the treatment of Alzheimer's disease now seems possible. As a result of major advances in medical research in this area, knowledge of the etiology of Alzheimer's disease is rapidly being understood. This information has uncovered relevant and novel targets for treatment. At the center of the etiological progression of this disease is β-amyloid. A substantial body of evidence strongly suggests that this small protein is critical to the development of Alzheimer's disease. The β-amyloid protein is generated by two different proteolytic cleavages. Recently, the proteases responsible for producing the β-amyloid protein have been identified. The proteases represent viable targets for therapeutic intervention against Alzheimer's disease. In this review, we describe the biological characteristics of the β-amyloid-forming proteases in the context of pharmaceutical development.

New treatments for HCV (Hepatitis C virus) infections are likely to arise from inhibition of the essential, virally-encoded enzymes. These targets include the serine protease required for processing of the HCV polyprotein. The protease constitutes one functional domain of the bifunctional HCV NS3 (non-structural protein 3). Here, insights regarding the NS3 structure and recently synthesized NS3 inhibitors are reviewed. Interestingly, many NS3 protease inhibitors have taken advantage of an unusual product inhibition by Nterminal products of cleavage at the polyprotein processing sites.

Human urokinase-type plasminogen activator (uPA or uPA) has been implicated in the regulation and control of basement membrane and interstitial protein degradation. Since Urokinase plays a role in tissue remodeling, it may be responsible, in part, for the disease progression of cancer. Inhibitors of urokinase may then be useful in the treatment of cancer by retarding tumor growth and metastasis. Urokinase is a multidomain protein, two regions of the protein are most responsible for the observed proteolytic activity in cancer disease and progression. The N-terminal domain or ATF binds to a Urokinase receptor (uPAR) on the cell surface and the C-terminal serine protease domain, then, activates plasminogen to plasmin, beginning a cascade of events leading to the progression of cancer. Investigations of urokinase inhibition has been an area of ongoing research for the past 3 decades. It began with the discovery of small natural and unnatural amino acid derivatives or peptide analogs which exhibited weak inhibition of uPA. The last decade has seen the generation of several classes of potent and selective Urokinase inhibitor directed to the serine protease domain of the protein which have shown potential anti-cancer effects. The availability of structural information of enzyme-inhibitor complexes either by nuclear magnetic spectroscopy (NMR) or crystallography has allowed a detailed analysis of inhibitor protein interactions that contribute to observed inhibitor potency. Structural studies of specific inhibitor-uPA complexes will be discussed as well as the contributions of specific inhibitor protein interactions that are important for overall inhibitor potency. These data were used to discover a class of urokinase inhibitor based on the 2-Naphthamidine template that exhibits potent urokinase inhibition and excellent selectivity for urokinase over similar trypsin family serine proteases.

There is an increasing need to rapidly determine the specificity of proteases that potentially play a role in human and animal disease. Substrates for novel proteases can be discovered by testing standard protease substrates such as oxidized insulin B-chain, by screening commercially available substrates for other proteases, or by preparing derivatives of known biological targets. The relative importance of each substrate residue can be determined through alanine-scanning, or by preparing incremental changes at one or more positions within the known substrate. More efficient methods such as coupled liquid chromatography - mass spectrometry (LC-MS) or C-terminal / N-terminal sequencing of reaction products allow the selection of improved substrates from mixtures of peptides. In other cases mixtures of substrates can be spatially segregated prior to protease treatment during chemical synthesis on beads or membranes. Positional scanning libraries can be used to find substrates for proteases with interdependent subsites, while minimizing required synthetic and screening effort. As proteases catalyze both hydrolysis and amide bond formation, acyl transfer from protease-substrate intermediates to mixtures of peptide nucleophiles provide substrate sequence information. Genetic methods including substrate phage display, retroviral display, bacterial display, and yeast a-halo assays combine selection with the ability to propagate selected sequences and directly deconvolute the cleaved peptide via sequencing of substrate-coding DNA. This review describes various methods for optimizing protease substrates for biological activity and the use of optimized substrates in pharmaceutical discovery.