HIV-1 Protease Mutations and Inhibitor Modifications. Results from a Series of X-ray Structures

T. Skálová, J. Dohnálek, J. Dušková, H. Petroková, J. Hašek

Institute of Macromolecular Chemistry, Czech Academy of Sciences, Heyrovskeho nam. 2, 162 06 Praha 6, Czech Republic.

skalova@imc.cas.cz

Two new X-ray structures of (A71V, V82T, I84V) HIV-1 protease – inhibitor complexes were determined. This contribution presents their comparison with previously determined structures. Altogether, there are four pairs of similar peptidomimetic inhibitors [1] – with ethyleneamine [2-3], hydroxyethylene [4] and two with S-hydroxyethylamine isostere [5-6] – each in complex with wild-type and (A71V, V82T, I84V) HIV-1 protease (range of inhibition constants 0.1 – 1000 nM). This series makes it possible to see structural changes caused by protease mutations and inhibitor modifications.

It was found that all inhibitors form a saturated network of hydrogen bonds to both wild-type and mutant protease. Extreme cases of inhibition constants in the series can be explained by structural changes in inhibitor binding caused by inhibitor modifications (mainly the length of the isostere and fit of P₁ and P₁’ side chains in the protease binding pockets).

Moreover, some systematic structural changes may be explained as consequences of protease mutations (including effects of mutation of residue 71 which lies ca. 16 Å from active site): 1. Mutant protease-inhibitor complexes show higher conformational strain in inhibitors than in wild-type complexes in all four cases. 2. Three of the four pairs of complexes show a shorter hydrogen bond between the catalytic residues Asp 25 and Asp 125 in the mutant complexes than in the wild-type complexes.

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2. H. Petrokova et al, Eur. J. Biochem., 271, (2004), 4451.

3. T. Skalova et al, J. Med. Chem., 46, (2003), 1636.

4. J. Weber et al, J. Mol. Biol., 324, (2002), 739.

5. J. Dušková et al, Acta Crystallogr., D62, (2006) , 489.

6. J. Dohnalek et al , J. Med. Chem., 45, (2002), 1432.

Acknowledgements.

This work was funded by the Grant Agency of the Academy of Sciences of the Czech Republic (projects KJB4050312 and A4050811) and by the Ministry of Education, Youth and Sports of the Czech Republic under support of R&D (project 1K05008).

The authors wish to thank the staff of ESRF in Grenoble, beamline ID14-1.