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Discovery Novel Allosteric Fragment Inhibitors of HIV-1 Reverse Transcriptase for HIV Prevention

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. Discover Novel Allosteric Inhibitors of HIV-1 RT. Polymerase active site

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Discovery Novel Allosteric Fragment Inhibitors of HIV-1 Reverse Transcriptase for HIV Prevention

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  1. 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

  2. Discover Novel Allosteric Inhibitors of HIV-1 RT Polymerase active site NNRTI binding pocket RNase H active site HIV RT inhibitors approved or being developed for oral and topical PrEPsame 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 Additional druggable allosteric sites in RT

  3. 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

  4. Three Novel Fragments Inhibit NNRTI Resistant HIV-1 RT Screen Inhibition of HIV-1 RT DDDP 13% 4A2 inhibits RNase H 1.1% IC50 178 µM

  5. V89 and 4A2 Competes with Template/Primer and Cell culture data V89 Competes with dNTP 4A2 Competes with T/P IC50 93 ± 1 µM Ki 220 ± 74 µM 4A2 inhibits HIV-1 EC50 18 ± 4 µM

  6. 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

  7. 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

  8. Saturation Transfer Difference Nuclear Magnetic Resonance (STD NMR) Magnetisation transfer to fragment Magnetic Field fragment Dissociate Detect bound fragments RT • 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

  9. 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

  10. Fragments are generally less potent against MoMLV and do not inhibit Klenow DNA pol

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