Patent ID: 8095350

Claim:
A method for identifying a compound that selectively binds to a target site of an Apolipoprotein B mRNA-editing enzyme catalytic polypeptide-2 (APOBEC-2) protein or a structural homologue of the Apolipoprotein B mRNA-editing enzyme catalytic polypeptide-2 (APOBEC-2) protein, the method comprising: (a) generating on a computer the three dimensional structural features of the Apolipoprotein B mRNA-editing enzyme catalytic polypeptide-2 (APOBEC-2) protein according to FIG. 6 , wherein the three dimensional structural features comprise a tetramer of the Apolipoprotein B mRNA-editing enzyme catalytic polypeptide-2 (APOBEC-2) protein, wherein the tetramer is formed by combination of two dimers of the Apolipoprotein B mRNA-editing enzyme catalytic polypeptide-2 (APOBEC-2) protein joined through head-to-head interactions, and each dimer is formed by combination of two monomers; (b) designing a compound capable of selectively binding to the target site in the Apolipoprotein B mRNA-editing enzyme catalytic polypeptide-2 (APOBEC-2) protein or the structural homologue of the Apolipoprotein B mRNA-editing enzyme catalytic polypeptide-2 (APOBEC-2) protein; wherein the target site comprises an interface between the monomer, the dimer and the tetramer of the Apolipoprotein B mRNA-editing enzyme catalytic polypeptide-2 (APOBEC-2), the structural homologue of the Apolipoprotein B mRNA-editing enzyme catalytic polypeptide-2 (APOBEC-2) protein, an active site of the Apolipoprotein B mRNA-editing enzyme catalytic polypeptide-2 (APOBEC-2), or the structural homologue of the Apolipoprotein B mRNA-editing enzyme catalytic polypeptide-2 (APOBEC-2) protein, wherein zinc is coordinated within the active site of the Apolipoprotein B mRNA-editing enzyme catalytic polypeptide-2 (APOBEC-2), and wherein the three dimensional structural features of the dimers and the tetramer are necessary for deamination of deoxyribonucleic acid (DNA) or ribonucleic acid (RNA) substrates: (c) synthesizing the compound; (d) contacting the monomer, the dimer or the tetramer of the Apolipoprotein B mRNA-editing enzyme catalytic polypeptide-2 (APOBEC-2) protein or the structural homologue of the Apolipoprotein B mRNA-editing enzyme catalytic polypeptide-2 (APOBEC-2) protein with the compound; and (e) identifying a candidate compound that selectively binds to the target site, wherein selective binding of the candidate compound to the target site interferes with at least one biological activity of the Apolipoprotein B mRNA-editing enzyme catalytic polypeptide-2 (APOBEC-2) or the structural homologue of the Apolipoprotein B mRNA-editing enzyme catalytic polypeptide-2 (APOBEC-2).