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Discovery Novel Allosteric Fragment
Inhibitors of HIV-1 Reverse
Transcriptase for HIV Prevention
A/Prof Gilda Tachedjian
Retroviral Biology and Antivirals Laboratory
Centre for Biomedical Research
Burnet Institute
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Discover Novel Allosteric Inhibitors of HIV-1 RT
HIV RT inhibitors approved or being developed for oral and topical
PrEP same drug classes used for therapy
Potential for drug resistance in the context
of PrEP use in a real life setting
13 RT inhibitors used in the clinic they only
belong to two classes: NRTIs and NNRTIs
Conformational flexibility of RT – function
Polymerase active site
Additional druggable allosteric sites in RT
NNRTI binding pocket
RNase H active site
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Fragment Based Drug Discovery (FBDD)
• “Fragments” are chemicals MW < 250 Da
• More efficient at probing the chemical space – sample greater
chemical diversity by screening a smaller library
• Bind with weak affinity
• Strategically elaborated into larger high affinity inhibitors
• Validated approach – US FDA approved drug Vemurafinib
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Three Novel Fragments Inhibit NNRTI
Resistant HIV-1 RT
Inhibition of HIV-1 RT DDDP
Screen
13%
4A2 inhibits RNase H
1.1%
IC50 178 µM
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V89 and 4A2 Competes with Template/Primer
and Cell culture data
V89 Competes with dNTP
Ki 220 ± 74 µM
4A2 Competes with T/P
IC50 93 ± 1 µM
4A2 inhibits HIV-1
EC50 18 ± 4 µM
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Summary
Identified fragments with novel scaffolds and modes of action
compared to HIV RT inhibitors used clinically
Structure activity relationship (SAR) and X-ray crystallography
studies are in progress to:
- identify optimised fragments (more potent than original hits)
- identify binding sites on HIV-1 RT
- elaborate fragments into potent inhibitors by
structure-based drug design
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Acknowledgments
Tachedjian Lab
Monash Institute of Pharmaceutical Sciences (MIPS)
David Chalmers
Martin Scanlon
Steve Headey
Univ of Pittsburgh
Nicolas Sluis-Cremer
Jennifer La
Cath Latham
David Tyssen
Adam Johnson
Rutgers University
Eddy Arnold
Joe Bauman
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Saturation Transfer Difference Nuclear Magnetic
Resonance (STD NMR)
•Detects weak binders
•Can screen mixtures of compounds (x 5)
•Pulse saturates entire protein (receptor) with magnetization transferring to
protein bound ligand
•Once ligand dissociates, saturated ligands can be detected
•Resonances of small fragments not directly affected by pulse
Magnetisation
transfer to fragment
Magnetic Field
fragment
Dissociate
Detect bound
fragments
RT
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Fragment Library
•
Library of 630 fragments (ave MW 208)
- Astex “Rule of Three” to make sure fragment like i.e.
mass≤300 Da, ≤3 H-bond acceptors, ≤3H-bond donors, a clogP of
≤3, rotatable bonds ≤3 and a polar surface <60A2
Maybridge Ro3 library
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Fragments are generally less potent against
MoMLV and do not inhibit Klenow DNA pol
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