Human immunodeficiency virus (HIV) integrase is a Mr 32000 protein encoded by the pol gene of HIV that catalyzes an essential step in the viral replicative cycle to integrate the viral DNA into the host DNA. HIV integrase catalyzes two temporally and spatially separated reactions, including process, where a CA dinucleotide from the 3’-ends of the double stranded viral DNA is cleaved by HIV integrase in cytoplasm generating a double-stranded DNA with a two-base overhang, and strand transfer, where the HIV integrase-and-DNA complex is transferred in to the nucleus. The most well studied HIV integrase is HIV-1 integrase characterized by containing three domains, including the N-terminal domain, the C-terminal domain and the core domain.