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Resistance development upon L76V mutation in HIV-1 protease studied - - PowerPoint PPT Presentation
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
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HIV protease
◮ Protein-inhibitor binding strength determined binding free energy ◮ Protein-inhibitors interactions or conformational changes ◮ Structural information is key
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HIV protease
◮ Protein-inhibitor binding strength determined binding free energy ◮ Protein-inhibitors interactions or conformational changes ◮ Structural information is key
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HIV protease
◮ Protein-inhibitor binding strength determined binding free energy ◮ Protein-inhibitors interactions or conformational changes ◮ Structural information is key
PR structures in PDB.
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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.
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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 = MutIC50
WT IC50
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Molecular dynamics
Simulate PR structure on time scale using Newton’s laws
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Molecular dynamics
◮ Gives information on dynamics/relevant conformations ◮ Provides basis for thermodynamic calculations (∆∆G)
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Molecular dynamics
◮ Gives information on dynamics/relevant conformations ◮ Provides basis for thermodynamic calculations (∆∆G)
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Molecular dynamics
◮ Gives information on dynamics/relevant conformations ◮ Provides basis for thermodynamic calculations (∆∆G)
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Molecular dynamics
◮ Gives information on dynamics/relevant conformations ◮ Provides basis for thermodynamic calculations (∆∆G)
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Molecular dynamics
◮ Gives information on dynamics/relevant conformations ◮ Provides basis for thermodynamic calculations (∆∆G)
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Thermodynamic cycle
∆∆G = ∆G4 − ∆G3 = ∆G2 − ∆G1
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Validation ∆∆G calculations
Inhibitor Mutation ∆∆Gexp1 ∆∆Gexp2 ∆∆Gtheor (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
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Validation ∆∆G calculations
Inhibitor Mutation ∆∆Gexp1 ∆∆Gexp2 ∆∆Gtheor (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
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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 ∆∆GL→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
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RU1 with LPV/ATV
ATV interactions. PR structure. R 8 in red. LPV interactions.
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Structural variation of unbound FB15
PCA of FB15 L/V unbound proteins.
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Structural variation of unbound FB15
PCA of FB15 L/V unbound proteins. FB15_L. FB15_V.
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Structural variation of unbound FB15
PCA of FB15 L/V unbound proteins. FB15_L. FB15_V.
Related to selection against 46M + 76V?
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Summary
◮ We can (accurately) estimate free binding energy changes upon mutation ◮ Contributing residues can be identified ◮ Indication of reason for selection against some genotypes
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Summary
◮ We can (accurately) estimate free binding energy changes upon mutation ◮ Contributing residues can be identified ◮ Indication of reason for selection against some genotypes
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Summary
◮ We can (accurately) estimate free binding energy changes upon mutation ◮ Contributing residues can be identified ◮ Indication of reason for selection against some genotypes
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