Current Topics in Medicinal Chemistry - Volume 10, Issue 7, 2010

The catalytic site of cathepsin cysteine proteases is located within the binding region which has subsites for substrate amino acids in both the N- and C-terminal direction from the scissile bond. The catalytic site is highly conserved and formed by three residues: Cys, His and Asn. The crucial step of the catalytic process involves formation of a reactive thiolate/imidazolium ion pair, which results from proton transfer between Cys and His, resulting in forming an active Cys residue. In most cases, the development of selective cathepsin inhibitors is moving forward on the basis of: information on the subsites for substrate amino acids, and the warhead which binds to a thiol group of the active center of cathepsins. The various reversible or irreversible cathepsin inhibitors, which were designed over the past 15 years, underscore the importance of inactivation of the cathepsins which are involved in particular diseases. In this special issue of Current Topics in Medicinal Chemistry with the title “The Medicinal Chemistry of the Cathepsin Cysteine Proteases”, the authors provide refined reviews that give a critical update on the current understanding and advance of the medicinal chemistry on the selective cathepsins C, S and K inhibitors developed by many institutes. The human cysteine cathepsin family comprises 11 genes (cathepsins B, C, H, F, K, L, O, S, V, W, and X/Z). Since some of cathepsins are implicated in many physiological processes such as protein degradation, antigen presentation, bone resorption, we now understand how important a role of cathepsins play. Additionally, it has been found that some cathepsins are involved in a number of degradative and invasive processes such as arthritis, tumor invasion and metastasis and muscular dystrophy as well. There exists a discrepancy in the physiological processes that arise from the primary, secondary and tertiary structures of each cathepsin. The understanding of tertiary structure of target enzymes has especially provided a wealth of information to help speed up drug discovery research and bring newer and better therapies to the market place. Tomoo elaborates recent advances in structure of cathepsins B, K, L and S, and also provides a thorough overview of structural features of cathepsins and his approach in structure-based design of cathepsin B specific inhibitors. Like other cysteine proteases cathepsin C is involved in intracellular protein degradation even though the enzyme is the noted exception, existing as an oligomeric enzyme with a molecular weight of 200kDa. Cathepsin C is the physiological activator of groups of serine proteases within immune and inflammatory cells that are vital for the defense of an organism. Percival et al. discuss the therapeutic utility and recent progress in medicinal chemistry of cathepsin C inhibitors. Current marketed therapies for neuropathic pain are based largely on two well established classes: the analgesics opiates and the nonsteroidal anti-inflammatory drugs. Both classes of drugs have limited efficacy and evoke undesirable side effects. The lack of suitable therapies has stimulated research regarding target identification for neuropathic pain. It has been reported that the mRNA encoding cathepsin S was up-regulated in rat dorsal root ganglia following peripheral nerve injury. Cathepsin S is expressed in professional antigen presentation cells such as dendritic cells, B lymphocytes, and macrophages. Hence, the major role of cathepsin S in these cells is in the important proteolytic events that lead to antigen presentation. Cathepsin S inhibitors are thus being developed as immunological therapeutic agents. Wiener et al. review the recent advance in the various peptidic and non-peptidic cathepsin S inhibitors using the structure activity relationship both with and without warhead. Since the discovery of the cysteine protease cathepsin K, many studies have shown that this enzyme is of importance in bone resorption. Kometani et al. provide insights into the hurdles in the drug discovery of cathepsin K inhibitors for the treatment of bone resorption. Odanacatib is the most advanced cathepsin K inhibitor for which the phase III study is currently proceeding to treat post-menopausal osteoporosis. Black discusses the design of Odanacatib and peptidic and non-peptidic analogs derived from Odanacatib. Teno et al. review small molecule non-peptidic inhibitors possessing pyrrolopyrimidine as a new scaffold for cathepsin K.

The cathepsins are a family of lysosomal cysteine proteases that are abundant in living cells and play important roles in intracellular proteolysis. Cathepsins are necessary for cell survival, and disruption of regulation of the activity of these enzymes causes serious diseases including allergy, atherosclerosis, muscular dystrophy, Alzheimer's disease and cancer. Therefore, the design of inhibitors for cathepsins is important in development of therapeutic agents. This review will focus on the features of the tertiary structure and substrate-binding specificity of cathepsins B, L, S and K, based on X-ray crystal structures of their complexes with inhibitors. To illustrate an approach to drug design, an example of structure-based design of a cathepsin B-specific inhibitor is described.

The lysosomal cysteine protease cathepsin C (Cat C), also known as dipeptidyl peptidase I, activates a number of granule-associated serine proteases with pro-inflammatory and immune functions by removal of their inhibitory N-terminal dipeptides. Thus, Cat C is a therapeutic target for the treatment of a number of inflammatory and autoimmune diseases. Cathepsin C null mice and humans with Cat C loss of function mutations (Papillon-Lefevre syndrome) show deficiencies in disease-relevant proteases including neutrophil elastase, cathepsin G, chymases and granzymes and the Cat C mice are protected in a number of disease models. Several methodologies have been recently reported for assessing the effects of Cat C inhibitors on serine protease activities in cellular assays and prolonged treatment of rats with a reversible, selective Cat C inhibitor reduced the activity of three leukocyte serine proteases. Nearly all potent and selective Cat C inhibitors described are based on the preferred dipeptide substrates bearing either irreversible (e.g. diazomethylketone, acyloxymethyl ketone, o-acyl hydroxamic acid and vinyl sulfone) or reversible (e.g. semicarbazide, nitrile and cyanamide) electrophilic warheads. While potent and highly selective, the best inhibitors described to date still have poor stability and/or rodent pharmacokinetics, likely resulting from their peptidic nature. The lack of selective compounds with appropriate rodent pharmacokinetic properties has hampered the assessment of the effects of Cat C inhibitors on the activation of disease-relevant proteases in vivo and the full evaluation of the therapeutic utility of Cat C inhibitors.

Cathepsin S has been of increasing interest as a target of medicinal chemistry efforts given its role in modulating antigen-presentation by major histocompatibility class II (MHC II) molecules as well as its involvement in extracellular proteolytic activities. Inhibition of the cathepsin S enzyme reduces degradation of the invariant chain, a crucial chaperon which also blocks peptide-binding by MHC II molecules, thereby decreasing antigen presentation to CD4+ T-cells. Extracellular cathepsin S may also be involved in angiogenesis and initiation and/or maintenance of neuropathic pain by cleavage of the membrane-bound chemokine fractalkine (CX3CL1). Cathepsin S inhibitors have thus been suggested to hold potential as therapeutics for a variety of diseases. The initial development of cathepsin S inhibitors targeted irreversible, covalent inhibitors, but more recently the focus has been on reversible inhibitors, representing both covalent modifiers of the enzyme and, of late, noncovalent inhibitors. This review details advances in cathepsin S inhibitor design as reported in the primary literature since 2006, focusing especially on structure-activity relationships of the various covalent and noncovalent inhibitor series.

There were many hurdles in the drug discovery of cathepsin K inhibitors such as species differences not only in bone metabolism but also in amino acid sequences in the critical site of the target enzyme, discrepancies between PK/PD due to unique tissue distribution of the inhibitor affecting both efficacy and side effects originated from a characteristic intracellular or tissue distribution of some classes of compounds. The value of this new therapeutic approach over the launched indirect competitors should be further clarified from the efficacy and side effect point of view. The cathepsin K inhibitor drug discovery was initiated based on a strong and osteoclast-specific expression of this enzyme. However, the tissues and cells expressing cathepsin K have been expanding as the investigation on pathological conditions progressed with respect to side effects as well as new possible indications.

Cathepsin K (Cat K) is the primary enzyme involved in Type I collagen degradation in bone resorption. The development of a Cat K inhibitor should provide an effective treatment for osteoporosis. Key components of a clinically viable inhibitor are oral bioavailability, high selectivity over related cathepsins, and a covalent, reversible warhead to bind to the active site cysteine of the enzyme. This article reviews recent advances in the design of inhibitors derived from peptidic leads that contain either a ketone or nitrile electrophile. Three of these compounds have progressed into clinical trials and one, odanacatib (5), is currently in Phase III studies for the treatment of post-menopausal osteoporosis.

The recent emergence of osteoporosis as a major health threat in people of advanced age has intensified the search for novel and effective pharmacologic treatments. Given that bone resorption is exceeding bone formation, a reduction in bone mass leads to disease conditions including post-menopausal osteoporosis and tumor-induced osteolysis. Our efforts in this area have focused on the optimization of non-peptidic cathepsin K inhibitors for affinity and selectivity, from an heteroaromatic nitrile as a novel scaffold. This approach has resulted in the discovery of the potent and selective cathepsin K inhibitor, 44. The concentration of cathepsin K inhibitors, including compound 44, in the target tissues such as bone marrow cavity, were predictive parameters for antibone resorptive efficacy in vivo in the rat. The high level of distribution to the bone marrow was also observed for compounds containing pyrrolopyrimidines with novel spirostructures as the P3 moiety. In a monkey study with the representative inhibitor 44, the antibone resorptive efficacy was detected 8 h after the compound administration. The efficacy persisted throughout the repeated treatment period of 14 days without any evidence for the development of tolerance. This article constitutes a near comprehensive review of the published scientific literature on small molecule non-peptidic inhibitors for cathepsin K developed by Novartis.