Structural Studies of Cysteine and Serine Protease Inhibitors Towards Therapeutic Applications

Abstract

Proteases play a very important role in a multitude of physiological reactions such as cell signaling, migration, immunological defense, wound healing and apoptosis and are crucial for disease propagation. In this study we have selected the cysteine and serine protease inhibitor complexes to understand their inhibition mechanisms. Both proteases share similar catalytic triad. Many of these proteases are secreted as inactive forms called zymogens and subsequently activated by proteolysis. Cathepsin L, a cysteine protease, plays a vital role in many pathophysiological conditions including rheumatoid arthritis, tumour invasion and metastasis, bone resorption and remodeling. We have designed and studied a series of noncovalent, reversible propeptide mimic inhibitors of cathepsin L. A few representatives of these new inhibitors have been crystallized with human cathepsin L, and the structures have been determined. These inhibitors extend farther into the S? subsites of cathepsins than any inhibitors reported in the literature thus far (Shenoy RT et al., (2009) Journal of Medicinal Chemistry). Subsequently for comparison, we have determined the structure of two covalent dipeptidyl inhibitors in complex with cathepsin-L. These two inhibitors have different groups in S1 subsite, and one of them has a Ki of 0.6nM, a most potent, synthetic peptidyl reversible inhibitor of cathepsin L reported to date. These inhibitors have a substrate-like interaction with the active site cysteine (Shenoy RT et al., (2010) Journal of Structural Biology). Our studies on the cathepsin inhibitor complexes have the potential leading to further optimization of these inhibitors towards therapeutic intervention. The second part of my project deals with serine protease and its inhibitor complex. Serine proteases play a crucial role in host-pathogen interactions. In the innate immune system of invertebrates, multidomain protease inhibitors are important in regulating host-pathogen interactions and antimicrobial activities. Serine protease inhibitors of 9.3 kDa were identified from Carcinoscorpius rotundicauda (CrSPI, isoforms 1 and 2). CrSPI-1 potently inhibits subtilisin (Ki=1.43nM). These inhibitors are grouped with non-classical Kazal-type inhibitors. The crystal structure of CrSPI-1 in complex with subtilisin (protein:protein complex) and its biophysical interaction studies revealed that two domains of the inhibitor molecule act as two heads to independently interact with two separate subtilisin molecules resulting in the inhibition of subtilisin activity at a ratio of 1:2 (inhibitor: protease). We propose that domain-2 is more potent and specific towards the bacterial protease subtilisin, and domain-1 is likely to interact with the host protease, Furin, acting like an ?on-off? switch in the regulation of host?s and pathogen?s proteases. Our studies will help to understand the innate immune system at a molecular level.