Cysteine proteases, earlier referred to as thiol proteases are more or less universal being present in viruses, bacteria, protozoa, plants, animals and even fungi. Cysteine proteases for the hydrolysis requires essential cysteine residue in the active site. The close proximity of histidine in active site acts as a proton donor thereby enhancing the nucleophilicity of the thiol group. Thus, a thiolate-imidazolium charge relay dyad arises due to the sulfhydryl or ‘-SH’ group of cysteine side chains and the imidazole of histidine (Fig2). This dyad is sometimes, but not always, stabilised by a highly conserved asparagine. The oxyanion hole is formed by a highly conserved glutamine which is highly important in forming an electrophilic centre stabilising the tetrahedral intermediate formed during the hydrolysis. Fig 2: Schematic of the close spacial proximity in the active site showing: (1) the sulfhydryl of cysteine to the imidazole group of histidine, and the equilibrium with (2) the thiolate–imidazolium charge relay diad. The shaded area represents a delocalised electron dense cloud. The thiolate-imidazolium diad have two ionisable groups allowing the cysteine proteases with a broad pH range of enzymatic activity based on the pKa of cysteine of around 4.0 and that of histidine around 8.5. the chemical environment of the active site further stabilises the charge relay system. Papain-like cysteine proteases are thought to interact with their substrate at S2, S1 and S71(Turk et al., 1998). Hydrolysis mechanism of cysteine proteases has been well elucidated and documented. The cysteine protease enzyme transiently bounds to the substrate forming unstable tetrahedral intermediates and thereby taking an active enzymatic conformation. Many cysteine proteases are synthesized in the form of zymogen containing a pro-domain and a mature (catalytic) domain. The pro-domain region has evolved and performs functions in protein folding by acting as an intramolecular chaperone, in regulating protease activity by behaving as an endogenous inhibitor, and signalling the protease to its intracellular location. Cysteine proteases carry a signal sequence or a leader sequence of 15-22 amino acids consisting of a hydrophobic stretch in case to be secreted or to be targeted to intracellular compartments (Sajid and McKerrow, 2002).