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Optimizing Binding Kinetics in Medicinal Chemistry: Facts Or Fantasy?

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Optimizing Binding Kinetics in Medicinal Chemistry: Facts Or Fantasy? Optimizing Binding Kinetics in Medicinal Chemistry: facts or fantasy? ‡ -Gon /RT kon e -G‡ /RT ‡ off ΔG on koff e -ΔGd/RT Kd e koff /kon P + L ‡ ΔG off ΔGd PL Gerhard Müller Ex-Head of Med Chem Mercachem, Nijmegen, NL Binding coordinate 11 The topic is hot, complex, and I am just an end-user & controversial “You can’t optimize koff, and you don’t need to optimize koff, you simply need to optimize Kd ! ” Head Med Chem, (top-5 Pharma), West Coast, US, Jan 2016 Optimizing Binding Kinetics in Medicinal Chemistry: facts or fantasy? ‡ -Gon /RT kon e -G‡ /RT ‡ off ΔG on koff e -ΔGd/RT Kd e koff /kon P + L ‡ ΔG off ΔGd PL Gerhard Müller Chief Scientific Officer Gotham Therapeutics, New YorkBinding coordinate 2 confidential Streetlight effect in medicinal chemistry Top-heavy distributions, rich-get-richer mechanisms 5% / 75% J. Med. Chem., 54 ,6405–6416 (2011) Vertex Pharmaceuticals, US J. Org. Chem. 73, 4443-4451 (2008) MW clogP shape clogP flatness Fsp3 flatland J. Med. Chem., 58, 2390−2405 (2015) para meta ortho J. Med. Chem., 59, 4443–4458 (2016) 3 Cheminformatics Analysis – Kinase Family Ligand and target promiscuity (ChEMBL21) Hu, Kunimoto, Bajorath Chemical Biology & Drug Design, 89, 834-845 (2017) quantitative kinome coverage 270 kinases with high-confidence data Top-10 kinases (45% of human kinome still unexplored) VEGFR2 TK 2239 erbB1 TK 1814 22.537 distinct IC50 values p38a CMGC 1509 9191 distinct scaffolds HGFR TK 1411 31.873 kinase-inhibitor combinations PI3a lipid 844 erbB-2 TK 768 GSK3b CMGC 743 SRC TK 709 Chk1 CAMK 693 AKT AGC 621 S 11351 PI3g lipid 567 Aurora-A OTHER 558 LCK TK 489 c-Jun CMGC 478 Aurora-B OTHER 445 FLT3 TK 444 4 35 Approved Kinase Inhibitors - I Wave of low-molecular weight compounds F O O Cl O O S N N O O HN Cl HN O N NH H N O O N N N N N N O N H H F3C N N N N O H H N O N O N FASUDIL (Eril) GLEEVEC (Imatinib) IRESSA (Gefitinib) TARCEVA (Erlotinib) NEXAVAR (Sorafenib) Ischemia CML, GIST NSCLC NSCLC Renal tumors RHO-kinase (AGC) Bcr-Abl, c-Kit, PDGFR EGFR EGFR RAF, KDR, PDGF, Flt3, c-Kit Asahi Kasei (JP) 1995 Novartis (CH) 2001 F AstraZeneca (US) 2003 OSI/Genentech/Roche (US) 2004 Onyx/Bayer (US) 2005 HO Cl N N H O O H N N N S S F N N N H O H N N N N NH N H N N N HN O HN O NH O O O Cl N TASIGNA (Nilotinib) CF SPRYCEL (Dasatinib) 3 SUTENT (Sunitinib) TYKERB (Lapatinib) resistant CML resistant CML RCC, GIST breast cancer N Bcr-Abl, c-Kit, PDGFR Bcr-Abl, Src, Lck, c-Kit, PDGFR Flt3, c-Kit, KDR, PDGFR … EGFR Novartis (CH) 2007 BMS (US) 2006 Sugen/Pfizer (US) 2006 GSK (UK) 2007 F Br O N HN S O N *ALS N F H N O H N N N N N N N 2 N N H H S N N N H N O H O O N O N H N Masitinib VOTRIENT (Pazopanib) Toceranib (SU-11654) Vandetinib (ZD-6474) Mast cell tumors - DOGS Renal tumors Mast cell tumors - DOGS Medullary thyroid cancer FGFRs, PDGFRs,cKit VEGF’s, PDGF’s, c-Kit, … FGFRs, PDGFRs,cKit VEGFRs, EGFRs, others AB Science (F) 2008 GSK (UK) 2009 Pfizer (US) 2009 AstraZeneca (US) 2011 5 35 Approved Kinase Inhibitors - II Wave of low-molecular weight compounds F Cl Cl chiral N NH 2 Cl N N Cl O O N F N N O HN OMe N O S N N chiral N MeO CN O chiral F H N N H N Cl N N N N H N O N N H Crizotinib (PF-02341066) Ruxolitinib (INCB-018424) Vemurafenib (PLX-4032) N Bosulif (Bosutinib) NSCLC Myelofibrosis, bone marrow cancer Metastatic melanoma Xeljanz (Tofacitinib) N CML H Alk, cMet, RON Jak1, Jak2 B-Raf, SRMS, ACK1, FGR, … RA, proriasis, iBD Src, Bcr-Abl Pfizer (US) 2011 Incyte /Novartis (US) 2011 Plexxikon/Daiichi/Roche (US) 2011 JAK3 Wyeth/Pfizer (US) 2012 Pfizer (US) 2012 N HH O NN Cl O O N ONO H H H O Cl N N N N F C N N MeO N 3 H H S H F O O O F Axitinib (AG013736) MeO NTivopath (Tivozanib) HN O MeO Renal cell carcinoma Cometriq (Cabozantinib) renal cancer VEGFR1,2,3, PDGFR,cKit Stivarga (Regorafenib) metastatic medullary thyroid cancer VEGFRs Pfizer (US) 2012 anti-angiogenic MeO N Ret, Met, Flt1, KDR, Kit, Axl, Tie2,... AVEO Pharm (US) 2012 VEGFR2, Tie2 Exelixis (US) 2012 Bayer (D) 2012 N F F F N covalent O N H S N N O N O O N S F N HN Cl N N CF O O H H 3 F N N N N HN H N O NH2 O N N I O N O Iclusig (Ponatinib, AP24534) Tafinlar (Dabrafenib) Mekinist (Trametinib) Gilotrif (Afatinib) CML, ALL metastatic melanoma metastatic melanoma NSCLC, breast cancer multi-target TK inhibitor b-RAF (V600E) mutant MEK EGFRs ARIAD Pharma. (US) 2012 GSK (UK) 2013 GSK (UK) 2013 Boehringer Ingelheim (D) 2013 6 35 Approved Kinase Inhibitors - III Wave of low-molecular weight compounds Cl N N F O N H covalent O N 2 HN N NH O O N N N O S N N O HN N Nintedanib Zydelig (Idelalisib) Imbruvica (Ibrutinib) Pulmonary fibrosis Zykadia (Ceritinib) CLL mantle cell lymphoma HN N PDGFR, VEGFR ALK-positive NSCLC PI3Kd BTK N Boehringer Ingelheim 2014 ALK, IGF-1R, InsR, ROS1 Gilead (US), 2014 Celera, Pharmacyclis, J&J (US) 2013 NH Novartis (CH), 2014 covalent O Cl HN O HN F 2 H I N O N N H O N O H N N N N N O O N H F N N Lenvima (Lenvatinib) H O Ibrance (Palbociclib) H Tagrisso (osimertinib) Thyroid cancer F Breast cancer Astra Zeneca Multi kinase inhibitor, VEGF‘s Cotellic (Cobimetinib) CDK4,6 inhibitor Eisai (JP) 2015 TK (EGFR) Pfizer (US) 2015 Breast cancer Lung cancer MEK FDA-approved in November 2015 Exelixix, Roche (US) 2015 HN N O N NNNNN H Kisqali (ribociclib) Alecensa (alecitinib) Aliqopa (copanlisib) Verzenio (abemaciclib, LY2835219) Hoffmann-La Roche Novartis Bayer CDK4/6 inhibitor Eli Lilly Multi-kinase inhibitor (ALK, RET) Follicular Lymphoma adv metastatic breast cancer ALK-positive non-small lung cancer combi with letrozole – breast PI3K-inhibitor approved March 2017 CDK4/6-inhibitor FDA-approved in December 2015 Approved Sep 2017 Approved Sep 2017 7 Dominating Inhibitor Design Paradigm type I inhibitors Long tradition: Traxler scheme Bioorg. Med. Chem. Lett. 23, 1238–1244 (2013) N-terminal domain E470 O H H HN N Cl L471 N O hinge N N H N L472 N O IC50: 0.6 µM OH ATP-binding cleft H H N N N N O H IC : 40 nM modified from: MeO 50 P. Furet et al. J. Comp.-Aid. Mol Des. 1995, 9, 465-472 P. Traxler, Exp.Opin. Ther. Patents 1998, 8, 1599-1625 C-terminal domain NF-kB-inducing kinase (NIK) inhibitors – Amgen, US 8 DFG-in, -out, -undefined: spine functional connection between C- and N-lobe: dynamics Cl PD173955 : c-Abl N O Gleevec : c-Abl N N N N N N Cl H H S N N N O H N competitive inhibition of active state stabilizing inactive kinase conformation type I type II DFG-in DFG-out 1m52.pdb 1iep.pdb DFGin DFGout A.P. Kornev, N. M. Haste, S. S. Taylor, L. F. Ten Eyck, Proc. Natl. Acad. Sci., 103, 17783 (2006) • mutations/inhibitors change dynamic infrastructure of kinases A.P. Kornev, S. S. Taylor, L. F. Ten Eyck, Proc. Natl. Acad. Sci., 105, 14377 (2008) • structure and function are mediated by dynamics, even when A.P. Kornev, S. S. Taylor, Biochim. Biophys. Acta, 1804, 440-444 (2010) major structural changes are not apparent H.S. Meharena, et al, PLOS Biology, 11 (10), 1-11 (2013) 9 Sorafenib:CDK8 vs. Lapatinib:EGFR Various mechanisms to disturb intact spine arrangement type II (DMG-out) C-helix shift – type ? Cl O O S F O C F 3 H N O O N H O HN Lapatinib: off-rate: 0.0023 min-1 N O N N Cl N -1 H H (koff) = RT = 435 min N Sorafenib IC50 (CDK8): 74 nM (k )-1 = RT = 576 min off J.Mol.Biol. 412, 251-266 (2011) Cancer Research, 64, 6652-59 (2004) 10 CDK8 – Transcription Regulation CDK8 deregulated in solid tumors: Colon // Gastric // Melanoma // Breast // AML PharmacologyHN & Therapeutics, 2017 inO press N N N N N N O CMGC: H CDK, MAPK, Palbociclib GSK, CLK families) approved 2015 (Pfizer) HN N O N NNNNN H CDK8:Cyclin C transiently associated with the Ribociclib 1.2 MDa Mediator complex (regulates transcription through RNA polymerase approved 2017 (Novartis) II interaction) combi with letrozole (aromatase inh) Two major groups of CDKs: • Cell cycle regulating CDKs 1-6, 11, 14-18 Abemaciclib • transcription regulators Approved Sept 2017 (Eli Lilly) 7-13, 19, 20 11 Sorafenib inhibits CDK8 (in 2011) Retro-Design: targeting conformational states by deep pocket-directed scaffolds traditional type I CDK inhibitors novel type II CDK inhibitors Retro-Design Approach: new artifacts that refer to ➢ ATP competitive inhibitors ➢ acting through induced fit mechanism Sets out with type III inhibitors particular modes, motifs, models, ➢ accomodated in ATP binding site ➢ accomodated in deep pocket ▪ Disrupt hydrophobic spine techniques, and materials of the ➢ no binding kinetic signature ➢ hydrophobic R spine disrupted ▪ Long residence time on target; slow k past.
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