HIV protease protein sequence alignment

For fun and curiosity, I pulled the peptide sequences of all the HIV protease entries on Uniprot, and aligned them using Vector NTI.

The HIV protease is essential for HIV particle maturation, and hence the virus life cycle. If one could design or isolate a small molecule that could specifically inhibit the protease, it should greatly decrease the spread of HIV.

It is important to note that a specific protease inhibitor would drive selection for a variant protease sequence that is not inhibited by the small molecule.

Hence, by aligning the known protease sequences, we can begin to identify the sequence in the protease that is most flexible/amenable to variation, as well as identify the conserved residues that are likely important for the protein's overall structure and function.

Perhaps a cocktail of small molecules that inhibit all possible isoforms in the HIV protease sequence space would be effective at putting the breaks on HIV spread.

Screen/dream away.