Footprint-based identification of viral entry inhibitors targeting

HIVgp41

Mr. Holden9/18/2012

Paper

• Holden, P. M.; Kaur, H.; Gochin, M.; Rizzo, R. C. Footprint-based identification of HIVgp41 inhibitors, Bioorg. Med. Chem. Lett., 2012, 22, 3011–3016 dx.doi.org/10.1016/j.bmcl.2012.02.017

Outline

• The AIDS/HIV epidemic• Current treatments• HIVgp41• DOCKing– What is it, how it functions, scoring functions

• Footprints – a new scoring function• Methods• Results• Conclusion and Future Work

AIDS/HIV Statistics

• CDC – as of 2009, estimated 1,148,200 people living with HIV in the US

http://www.cdc.gov/hiv/topics/surveillance/basic.htm#hivesthttp://www.who.int/hiv/data/2011_epi_core_en.png

Current Treatments• Non-nucleoside reverse transcriptase inhibitors (NNRTIs). NNRTIs disable a protein

needed by HIV to make copies of itself. Examples include efavirenz (Sustiva), etravirine (Intelence) and nevirapine (Viramune).

• Nucleoside reverse transcriptase inhibitors (NRTIs). NRTIs are faulty versions of building blocks that HIV needs to make copies of itself. Examples include Abacavir (Ziagen), and the combination drugs emtricitabine and tenofovir (Truvada), and lamivudine and zidovudine (Combivir).

• Protease inhibitors (PIs). PIs disable protease, another protein that HIV needs to make copies of itself. Examples include atazanavir (Reyataz), darunavir (Prezista), fosamprenavir (Lexiva) and ritonavir (Norvir).

• Entry or fusion inhibitors. These drugs block HIV's entry into CD4 cells. Examples include enfuvirtide (Fuzeon) and maraviroc (Selzentry).

• Integrase inhibitors. Raltegravir (Isentress) works by disabling integrase, a protein that HIV uses to insert its genetic material into CD4 cells.

Text from: http://www.mayoclinic.com/health/hiv-aids/DS00005/DSECTION=treatments-and-drugs (Bold added for emphasis)

HIVgp41

PNAS September 25, 2001 vol. 98 no. 20 11187-11192

HIVgp41 as a protein

• 6 Helix Bundle• Inner coiled-coil is target• Highly-conserved binding pocket

http://www.entropyforce.org/?q=node/2

Docking – How it works

• Each molecule is broken by rotatable bonds

• The scaffold is positioned in the pocket

• The fragments are then added in layers to the scaffold

• At each stage, scaffold and fragments are minimized

http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm

Docking - Scoring

• To score molecules, scoring function uses two parameters– Electrostatic Interactions– Van der Waals Interactions

• Also use footprint descriptor score– To be discussed later

Interlude – Van Der Waals and Electrostatics

• Electrostatics – interaction between charges– Each atom is assigned a partial charge– These are summed over all atoms

interacting

• Van Der Waals – attraction or repulsion between electron clouds

New Scoring Function - Footprints

Why use footprints?

• Can tailor the docking results to a user input– Find molecules that mimic:• A native substrate• An existing drug• A composite of drug properties

– Can focus just on van der waals or electrostatics or the sum of both

Flowchart of Experiment

Docking Results - Example

• Examples of different docked molecules and footprints • Reference side chains in green

Docking Results – Top Scoring Molecules

Docking Results – Top Scoring Molecules

Fluorescence Binding Assay

• Molecule to be tested is dissolved and mixed with a modified gp41 protein

• If it inhibits the protein, the fluorescently tagged protein fragment is released and then the fluorescence is measured (think p-glow lab)

Biol Chem. 2006 Apr;387(4):477-83.

Resulting Leads

All values in micromolar (uM)

Conclusions and Future Work

• Seven currently-identified leads• Multiple Projects– Lead Refinement through computational work– Co-crystallize with HIVgp41 for accurate picture– Denovo design using footprints

• Must obtain nanomolar activity before moving forward with drug trials