HIV-1 Protease Inhibitors from Inverse Design in the Substrate Envelope Exhibits Subnanomolar Bindin...
This presentation is the property of its rightful owner.
Sponsored Links
1 / 34

Altman et al. JACS 2008, 130 6099-6113 Presented By Swati Jain PowerPoint PPT Presentation


  • 72 Views
  • Uploaded on
  • Presentation posted in: General

HIV-1 Protease Inhibitors from Inverse Design in the Substrate Envelope Exhibits Subnanomolar Binding to Drug Resistant Variants. Altman et al. JACS 2008, 130 6099-6113 Presented By Swati Jain. Drug Resistance.

Download Presentation

Altman et al. JACS 2008, 130 6099-6113 Presented By Swati Jain

An Image/Link below is provided (as is) to download presentation

Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author.While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server.


- - - - - - - - - - - - - - - - - - - - - - - - - - E N D - - - - - - - - - - - - - - - - - - - - - - - - - -

Presentation Transcript


Altman et al jacs 2008 130 6099 6113 presented by swati jain

HIV-1 Protease Inhibitors from Inverse Design in the Substrate Envelope Exhibits Subnanomolar Binding to Drug Resistant Variants

Altman et al. JACS 2008, 130 6099-6113

Presented By Swati Jain


Drug resistance

Drug Resistance

  • Mutations in drug target – selective lower inhibitor affinity – maintenance of normal function.

  • Approach – drugs for known resistant mutants.

  • Problems – potential to introduce new drug resistant mutations.

  • New techniques – not induce viable mutations, work with unknown modes of resistance.


Substrate envelope hypothesis

Substrate envelope Hypothesis

Figure taken from : Altman et al. JACS 2008 130 (19) 6099-6113


Inverse inhibitor design algorithm

Inverse Inhibitor Design Algorithm

  • Generate substrate envelope.

  • Select scaffolds. Choose functional groups.

  • Generate conformational ensembles.

  • Place scaffold in the substrate envelope – single and pair-wise energies - DEE/A* - energy ranked compounds.

  • Refine the list - more accurate energy functions.


Hiv 1 protease as target model

HIV-1 Protease as target model

  • Homodimer – each subunit made up of 99 amino acids.

  • Well studied protein

  • Aspartic protease:

    Asp-Thr-Gly active site.

Figure taken from Wikipedia.


Known hiv 1 substrates and inhibitor

Known HIV-1 Substrates and Inhibitor

Figure taken from King et al. Chem bio 11 1333-1338.


Substrate and maximal envelope

Substrate and Maximal Envelope


Substrate and maximal envelope1

Substrate and Maximal Envelope


Scaffold and functional groups

Scaffold and functional groups

Functional Groups

Amprenavir scaffold

  • Carboxylic acids – R1. Primary amines - R2.

    Sulfonyl chlorides – R3

  • Criterion: < four rotatable bonds. (ignoring the bond to the active group).

Figure taken from : Altman et al. JACS 2008 130 (19) 6099-6113


Conformational ensembles

Conformational Ensembles

  • Hydrogen atoms placed at attachment sites for both scaffold and functional groups.

  • Geometry Optimization.

  • Scaffold and Functional Groups: Sampling dihedral angles about each rotatable bond. (every 30 degrees for sp3-sp3, sp2-sp3 and every 45 degrees for sp2-sp2 bond).


Energy calculations

Energy calculations

  • Substrate bound protease structure

  • Inactivating mutation reversed.

  • Assigned force field parameters.

  • Substrate envelope placed inside the active site.

  • Three components: Van der Waal’s packing term, screened electrostatic interaction term, Desolvation penalties for both ligand and receptor.


Grid based energy calculations

Grid based energy calculations

  • Receptor shape and charges fixed.

  • Basis points within the ligand – points of cubic grid inside substrate envelope.

  • Van der Waal’s energies – each atom type at each grid point.

  • Electrostatic – 1 electron charge at each grid point.

  • Desolvation – change in solvation potential for all grid points when one grid point is charged.


Energy calculations contd

Energy calculations contd …

  • Van der Waal’s energy – interpolating energies from grid points.

  • Electrostatic and desolvation – projecting partial charges to grid points.

Figure taken from Wikipedia.


Scoring function

Scoring function

  • Constant term – Binding energy of blunt scaffold + receptor desolvation term.

  • Self energy of functional group – Binding energy with receptor + desolvation between functional group and scaffold.

  • Pair wise energies – desolvation penalties between two functional groups.

  • Clashes – energy infinite.


Scaffold into the envelope

Scaffold into the Envelope

  • Placed the scaffold in the envelope.

  • Scaffold position accepted – all atoms within the envelope + required hydrogen bonding + no clashes.

  • For each scaffold placement – discrete ensembles of every functional group attached – self energies.

  • Pairs of functional groups attached – pair wise energies.


Dee a

DEE/A*

  • Self and pair wise energies sum to the total energy calculated.

  • For each scaffold (backbone) conformation – ensemble (rotamers) of functional groups (side-chains) and the self and pair wise energy contribution to the total energy.

  • Used DEE/A* to generate the list of energy ranked conformations.

  • A common list for all scaffold positions.


Hierarchical energy functions

Hierarchical energy functions

  • Assumption – energies calculated using substrate envelope.

  • Generated list re-evaluated.

  • More sophisticated energy function – true molecular surface.

  • Higher Grid resolution.


First round design

First Round Design

  • Design repeated eight times

    • Tight and loose substrate envelope

    • Doubly deprotonated and deprotonated protease structure.

    • Rigid and flexible scaffold placement.

  • 20 compounds selected based on robustness to parameters.

  • 15 synthesized and tested.


First round inhibitor affinities

First round Inhibitor Affinities

Figure taken from : Altman et al. JACS 2008 130 (19) 6099-6113


Second round design

Second round design

  • Selection of functional groups – based on successful compounds from the first round.

  • Inhibitor bound protease structure used for the design.

  • Only doubly-deprotonated protease structure.

  • Tighter definition of substrate envelope.

  • 36 compounds synthesized and tested.


Second round design results

Second round design results

Figure taken from : Altman et al. JACS 2008 130 (19) 6099-6113


Binding affinities drug resistant protease

Binding Affinities – Drug resistant protease


Binding affinities drug resistant protease1

Binding Affinities – Drug resistant protease


Correlation between calculated and observed binding free energies

Correlation between calculated and observed binding free energies

Figure taken from : Altman et al. JACS 2008 130 (19) 6099-6113


Crystal structures of the inhibitors

Crystal structures of the inhibitors

  • Structures done – four first round, five second round.

  • Scaffold preserved hydrogen bonding network.

  • First round inhibitors – mostly inside substrate envelope except one functional group.

  • Second round inhibitors – Mostly inside substrate envelope with one exception.


Predicted and determined structures

Predicted and Determined structures

Figure taken from : Altman et al. JACS 2008 130 (19) 6099-6113


Substrate envelope

Substrate envelope

Figure taken from : Altman et al. JACS 2008 130 (19) 6099-6113


Crystal structures relation to resistance profile

Crystal structures – Relation to Resistance profile.

Figure taken from : Altman et al. JACS 2008 130 (19) 6099-6113


Testing the algorithm for separating binders and non binders

Testing the algorithm for separating binders and non-binders

Figure taken from: Huggins et al. Proteins 75: 168-186.


Differences from earlier algorithm

Differences from earlier algorithm

  • Geometry Optimization of the Protein structure.

  • Scaffold and side groups - the set of known binders and non binders.

  • Maximal envelope

  • Torsion angle of the bond attaching functional group to scaffold – 10 degrees.

  • Minimization.


Enrichment for binders

Enrichment for binders

Figure taken from: Huggins et al. Proteins 75: 168-186.


Contribution of electrostatic energy

Contribution of electrostatic energy

Figure taken from: Huggins et al. Proteins 75: 168-186.


Explicit water model

Explicit water model

Figure taken from: Huggins et al. Proteins 75: 168-186.


Issues and improvement

Issues and Improvement

  • Inhibitors have lower binding energies outside the substrate envelope – factors beyond substrate envelope important.

  • Finer Sampling - better results – generates too many placements.

  • Scoring functions – minimization gives better results – MinDEE??.

  • Flexible receptor.

  • Certain functional groups and solubility prediction.


  • Login