Proteolytic cleavages of viral proteins by cellular or viral proteases are necessary for host cell attachment, invasion, and reproduction of viral progeny. Host serine proteases are essential for the influenza virus life cycle because the viral hemagglutinin is synthesized as a precursor which requires proteolytic maturation (Garten and Klenk, 2008) . Recently, the non-structural 3 protease (NS3 -is a chymotrypsin-like serine protease which requires a polypeptide cofactor NS2B for activation) has been shown to be responsible for cleavage of the viral polyprotein precursor and to play a pivotal role in the replication of flaviviruses (Falgout et al., 1991; Mukhopadhyay et al., 2005; Chappell et al., 2006) including Hepatitis C (HCV), West Nile virus, and Dengue virus. NS3 also facilitates viral pathogenicity by cleaving host proteins and down-regulating the innate immune response of the cell (Failla et al., 1994; Meylan et al., 2005) . In fact, site-directed mutagenesis www.frontiersin.org that focused on the NS3 cleavage sites in the polyprotein precursor abolishes viral infectivity (Chappell et al., 2006) . Cell culture models provided important clues about potential inhibition of several protease inhibitors against NS3 for Dengue virus and West Nile virus (Cregar-Hernandez et al., 2011; Steuer et al., 2011) . Clinical trials of NS3 serine protease inhibitors showed good success rates (Lee et al., 2012) as anti-HCV. Therefore, NS3 is one of the most promising targets for drug development against Flaviviridae infections (Kolykhalov et al., 2000; Chappell et al., 2008) . Other serine proteases involved in the pathogenesis and virus life cycles are being considered as targets for chemotherapy. The catalytic activity of the herpes simplex virus type 1 serine protease is essential for viral nucleocapsid formation and for viral replication (Gao et al., 1994) . A trypsin-like serine protease is involved in pseudorabies viral penetration of the basement membrane during mucosal invasion (Glorieux et al., 2011) . Serine protease inhibitors inhibit pseudorabies virus invasion in basal membranes. A vaccinia virus serine protease inhibitor prevents virus induced cell fusion (Law and Smith, 1992) . Serine protease inhibitor AEBSF and pAB significantly reduce influenza A virus replication in mouse models (Bahgat et al., 2011) . However, identification of active SHS and their functional characterization are necessary for better understanding the molecular pathogenesis and development of antiviral strategies.