Resistance development upon L76V mutation in HIV-1 protease studied - PowerPoint PPT Presentation

Resistance development upon L76V mutation in HIV-1 protease studied using molecular dynamics Tomas Bastys

HIV protease ◮ Protein-inhibitor binding strength determined binding free energy ◮ Protein-inhibitors interactions or conformational changes ◮ Structural information is key

HIV protease ◮ Protein-inhibitor binding strength determined binding free energy ◮ Protein-inhibitors interactions or conformational changes ◮ Structural information is key

HIV protease ◮ Protein-inhibitor binding strength determined binding free energy ◮ Protein-inhibitors interactions or conformational changes ◮ Structural information is key

HIV protease ◮ Protein-inhibitor binding strength determined binding free energy ◮ Protein-inhibitors interactions or conformational changes ◮ Structural information is key PR structures in PDB.

PR Drug Resistance-associated Mutations (RAMs) Most of RAMs are found at the active site RAMs in magenta (L76V) and cyan (other) [1] . [1] Stanford University HIV drug resistance database.

HIV resistance mutations HIV protease L76V mutation has sensitizing and resistance effect Genotype LPV SQV ATV FB15 14.1 74 63 FB15 (L → V) 9.9 4.6 2.3 GH9 146 18.6 90 GH9 (L → V) > 116 1.2 2.4 RU1 (V → L) 46 0.7 9 RU1 157 1.1 2.7 PR median resistance factor ( RF ) values for genotypes with 76L/V. Values by H. Walter RF = Mut IC 50 WT IC 50

Molecular dynamics Simulate PR structure on time scale using Newton’s laws

Molecular dynamics ◮ Gives information on dynamics/relevant conformations ◮ Provides basis for thermodynamic calculations ( ∆∆ G )

Molecular dynamics ◮ Gives information on dynamics/relevant conformations ◮ Provides basis for thermodynamic calculations ( ∆∆ G )

Molecular dynamics ◮ Gives information on dynamics/relevant conformations ◮ Provides basis for thermodynamic calculations ( ∆∆ G )

Molecular dynamics ◮ Gives information on dynamics/relevant conformations ◮ Provides basis for thermodynamic calculations ( ∆∆ G )

Molecular dynamics ◮ Gives information on dynamics/relevant conformations ◮ Provides basis for thermodynamic calculations ( ∆∆ G )

Thermodynamic cycle ∆∆ G = ∆ G 4 − ∆ G 3 = ∆ G 2 − ∆ G 1

Validation ∆∆ G calculations Inhibitor Mutation ∆∆ G exp1 ∆∆ G exp2 ∆∆ G theor (kcal/mol) (kcal/mol) (kcal/mol) ATV I50V 2 . 7 – 0 . 43 ± 0 . 2 LPV I50V 2 . 6 – 1 . 54 ± 0 . 18 TPV I50V 2 . 1 – 0 . 75 ± 0 . 15 SQV G48V 3 . 02 1 . 60 3 . 6 ± 0 . 65 SQV L90M 1 . 79 0 . 67 1 . 3 ± 0 . 29 SQV G48V/ 4 . 09 3 . 72 4 . 45 ± 1 . 03 L90M Experimental [1-3] and theoretical ∆∆ G upon mutation ◮ Experimental results are (largely) reproducible [1] Wang et al. 2007 [2] Maschera et al. 1996 [3] Ermolieff et al. 1997

Validation ∆∆ G calculations Inhibitor Mutation ∆∆ G exp1 ∆∆ G exp2 ∆∆ G theor (kcal/mol) (kcal/mol) (kcal/mol) ATV I50V 2 . 7 – 0 . 43 ± 0 . 2 LPV I50V 2 . 6 – 1 . 54 ± 0 . 18 TPV I50V 2 . 1 – 0 . 75 ± 0 . 15 SQV G48V 3 . 02 1 . 60 3 . 6 ± 0 . 65 SQV L90M 1 . 79 0 . 67 1 . 3 ± 0 . 29 SQV G48V/ 4 . 09 3 . 72 4 . 45 ± 1 . 03 L90M Experimental [1-3] and theoretical ∆∆ G upon mutation ◮ Experimental results are (largely) reproducible [1] Wang et al. 2007 [2] Maschera et al. 1996 [3] Ermolieff et al. 1997

L76V ∆∆ G calculations Genotype LPV SQV ATV FB15 14.1 74 63 FB15 (L → V) 9.9 4.6 2.3 GH9 146 18.6 90 GH9 (L → V) > 116 1.2 2.4 RU1 (V → L) 46 0.7 9 RU1 157 1.1 2.7 Theoretical ∆∆ G L → V (kcal/mol): Ligand LPV SQV ATV FB15 – 2 . 29 ± 0 . 36 1 . 55 ± 0 . 48 GH9 – 0 . 52 ± 0 . 38 − 0 . 69 ± 0 . 41 RU1 0 . 78 ± 0 . 4 – − 0 . 68 ± 0 . 41

RU1 with LPV/ATV ATV interactions. LPV interactions. PR structure. R 8 in red.

Structural variation of unbound FB15 PCA of FB15 L/V unbound proteins.

Structural variation of unbound FB15 PCA of FB15 L/V unbound proteins. FB15_L. FB15_V.

Structural variation of unbound FB15 PCA of FB15 L/V unbound proteins. FB15_L. FB15_V. Related to selection against 46M + 76V?

Summary ◮ We can (accurately) estimate free binding energy changes upon mutation ◮ Contributing residues can be identified ◮ Indication of reason for selection against some genotypes

Summary ◮ We can (accurately) estimate free binding energy changes upon mutation ◮ Contributing residues can be identified ◮ Indication of reason for selection against some genotypes

Summary ◮ We can (accurately) estimate free binding energy changes upon mutation ◮ Contributing residues can be identified ◮ Indication of reason for selection against some genotypes

Thank you! Olga Kalinina Nadezhda Doncheva Mario Albrecht Vytautas Gapsys Bert de Groot Hauke Walter Rolf Kaiser