Alexander L. Perryman, Jung-Hsin Lin and J. Andrew McCammon. Protein Science 2004 13: 1108-1123

1. HIV-1 protease molecular dynamics of a wild-type and of the V82F/I84V mutant: Possible contributions to drug resistance and a potential new target site for drugs Alexander L. Perryman, Jung-Hsin Lin and J. Andrew McCammon. Protein Science 2004 13: 1108-1123 Presented by Ankit Garg

2. Problem: HIV-1 protease • Virus is mutating • Mutants are more drug-resistant than wild-type • for one strain, resistance to a drug increased from 3.4% (1995-1998) to 12.4% (1999-2000) • Resistance to multiple different drugs increased from 1.1% to 6.2% in the same time period • Comparing simulations of both the wild-type and a mutant could lend insight into the cause for drug resistance and ways to overcome it

3. Method: 22 ns simulations • Simulation appropriate because indirect effects are involved in drug resistance • “If residue B has a hydrogen bond with a drug, that is an example of a direct effect on the drug; however, if residue X has interactions that affect the position of that residue B, then residue X has an indirect effect on the drug” • Entire range of flap motion is visible in the n-sec timeframe – this will be clear in next slide

4. The importance of flaps • Flap dynamics emerged as a determining factor: • Flap opening/closing affects association/disassociation rates of drug – further evidence of this via NMR • Flap motion also affects free energy barrier of enzymatic reaction by controlling distance between the substrate and the catalytic aspartate

5. Mutant vs Wild-type flaps • Mutant flaps “curl” faster and more frequently • Flap curling is a precursor to flap opening and closing

6. Mutant vs Wild-type flaps • Mutant flaps opened more than the wild-type flaps • Authors used various measures to determine flap openness

7. Flap opening and drug resistance • It is thought that the larger and more frequent opening of flaps in the mutant encourages dissociation of the substrate, hence causing drug resistance

8. An interesting finding: • Flap-to-asp distance values are anticorrelated to Ear-to-Cheek values • The Ear-Cheek interface region could potentially be targeted by new allosteric inhibitor drugs!

9. Proposal: “double protease cocktails” • Treat patients with original drug + a drug acting on the Ear-Cheek interface • Allosteric-Flap-Openers (AFOs) • Pinch Ear-Cheek interface, forcing active site flaps to open so they are not catalytically competent. • Allosteric-Flap-Closers (AFCs) • Expand Ear-Cheek interface, encouraging active site flaps to stay closed, increasing their binding affinities for the original drug

10. Discussion • Have these recommendations been followed up on experimentally? • How do we know drug dissociation is being caused by flap opening and closing, rather than a conformational change to the binding site itself? • The authors chose to look at the Ear-Cheek interface primarily because it was physically close to the active site. Could they be missing some other, more important correlation? Should we be worried about their approach in actively seeking a correlation with that region’s morphology?