Discovery and development of odanacatib: A selective cathepsin K inhibitor for the treatment of osteoporosis Shawn J. Stachel On behalf of the odanacatib discovery and product development teams Merck Research Laboratories 8th RSC-SCI Symposium on Proteinase Inhibitor Design April 16, 2013 1 Acknowledgements Biology Christine Brideau Wanda Cromlish Sylvie Desmarais Jean-Pierre Falgueyret Louis-Jacques Fortin Sonia Lamontagne France Landry Frederic Masse Dave Percival Denis Riendeau Paul Tawa Jennifer Wang Comp. Med. Stephanie Alleyn Liette Belair Joel Bosquet Carl Brière Nancy Kelly Gayle Lapointe Mira Lavoie Sonia Lesvesque Denis Normandin Karen Ortega Roberta Rasori Josianne Rozon Wayne Sturkenboom Simon Wong Chemistry Kevin Bateman Christopher Bayly Cameron Black Michael Boyd Nathalie Chauret Sheldon Crane Stephen Day Jacques Yves Gauthier Robert Houle Elise Isabel C.K. Lau Serge Leger Tammy LeRiche Jean-Francois Levesque Chun-Sing Li Christophe Mellon Renata Oballa Joel Robichaud Bruno Roy John Scheigetz Carmai Seto Michel Therien Laird Trimble Jean-Francois Truchon Vouy-Linh Truong Qingping Wang Bone Biology (WP) Process Chemistry Don Kimmel Paul O’Shea Sevgi Rodan Dean Bender Gideon Rodan Mirlinda Biba Le Duong Jennifer Chilenski Pat Masarachia Jimmy DaSilva Brenda Pennypacker Rich Desmond Maureen Pickarski Paul Devine Gregg Wesolowski Pete Dormer Ya Zhuo Bruce Foster Pharmaceutical R&D Don Guathier Cynthia Bazin Danny Gauvreau Sophie-Dorothee Clas Francis Gosselin Elizabeth Kwong Derek Henderson Pauline Luk Greg Hughes Rafik Naccache John Leazer Wayne Parent Bill Leonard Suzanne Spagnoli John Limanto Dendi Susanto Christian Nadeau Hongshi Yu Thorsten Rosner Safety Assessment Kara Rubin Laura Gumprecht Ali Shafiee Cindy Fishman Veena Upadhyay Pharmacology Chris Welch Sylvie Toulmond Clinical Development Aubrey Stoch Tony Lombardi Deborah Miller Albert Leung Celera 2 Osteoporosis: A Continuing Disease Burden Osteoporosis: “porous bones” A progressive bone disease characterized by decreased bone density and mass. Leads to an increased risk of fracture Trabecular bone deteriorated Normal Osteoporosis From the International Osteoporosis Foundation Estimated 200 million women worldwide with osteoporosis.1 Only ~20% of osteoporosis patients are currently treated Hip fractures cause high morbidity and mortality2 − ~20% die in the 1st year − ~33% are totally dependent or in a nursing home after one year 1 Kanis JA (2007) WHO Technical Report, University of Sheffield, UK: 66 Osteoporosis Foundation statistics. 2 International 3 Bone Remodeling Healthy: Bone resorption = formation Osteoporosis: Bone resorption > formation 4 Osteoclast – The Target Cell for Cathepsin K Inhibition Trans- endocytosis Electron micrograph of an osteoclast on bone N N Lysosomes Sealing Zone Cathepsin K pH=5 Collagen Bone resorption by osteoclasts is the initial step in remodeling Rodan & Duong Bone Key 2008, 5, 6 5 Cathepsin K Deficiency Discovered in 19951 – Highly expressed in osteoclast – Cleaves at multiple sites in triple helical region of collagen type I and II Pycnodysostosis is a genetic disease associated with cathepsin K deficiency2,3 – Rare autosomal recessive skeletal dysplasia – ~150 cases reported worldwide – Short stature with high bone mass and increased fragility associated with high risk of fracture – Normal intelligence, sexual development and lifespan Cat K null Henri de Toulouse-Lautrec mice4 1 Inaoka, et al, BBRC 1995, 206, 89 Schilling, et al, Osteoporosis Int 2007, 18, 659 3 Saftig PNAS 1998, 95, 13453. 4 Gelb, et al, Science 1996, 273, 1236 – Osteopetrotic phenotype – Increased bone density – Otherwise healthy and fertile 2 6 Cathepsin K as a Therapeutic Target Data suggestive that cathepsin K represents a promising target for treatment of osteoporosis – Human and mouse genetic data – Cathepsin K collagenase activity – Restricted cellular distribution Goal: To develop an orally active, selective and reversible cathepsin K inhibitor for treatment of osteoporosis 7 Substrate to Inhibitor: Warhead Use knowledge of mechanism to convert substrate into inhibitor: HS-Enz O R HO S-Enz N H R' R N H R' Tetrahedral intermediate O O H2O - H2N-R' R S-Enz + Enz-SH R OH Acyl enzyme intermediate Replace scissile bond with an electrophile (warhead) that reacts with active site cysteine: Palmer, J. T.; Rasnick, D.; Klaus, J. L.; Brömme, D. J. Med. 8 Chem. 1995, 38, 3193 Substrate to Inhibitor: Recognition Sequence Cathepsin K cleaves Type I collagen at multiple positions Recognition sequence1: Gly-Leu-Lys—Gly-His P3 P2 P1 P1’ P2’ P2 P2 P1' H N O N H H N O O N H P3 O H N N HN O N P1 NH2 N P2' N H H N O O S O P3 P1 APC3328 Recognition sequence combined with electrophilic warhead gives a mechanism based-inhibitor of cathepsin K2,3 1Atley, M.; Mort, J. S.; Lalumiere, M.; Eyre, D. R. Bone 2000, 26, 241 M. E.; Klaus, J. L; Barnes, M. G.; Brömme, D. Nat. Struct. Biol. 1997, 4, 105 3Brömme, D.; Klaus, J. L.; Okamoto, K.; Rasnick, D.; Palmer, J. T Biochem. J. 1996, 315, 85 9 2McGrath, Opportunities for Inhibitor Design • Co-crystal reveals key interactions with cathepsin K and opportunities for obtaining selectivity – S1 pocket is a narrow groove on enzyme – S2 pocket suggests accommodation of alternative hydrophobic groups – S3 sub-site contains aspartic acid (Asp61) that may be exploitable for selectivity – P2-P1 amide forms key interaction with enzyme backbone (Gly66, Asn158) – P2-P3 amide: NH hydrogen-bond to Gly66, oxygen points towards solvent S2 O S3 N HN N H H N O O S O S1 McGrath, M. E.; Klaus, J. L; Barnes, M. G.; Brömme, D Nat. Struct. Biol. 1997, 4, 105 10 Reversible Inhibitors Irreversible inhibitors have potential liabilities Vinyl sulfone can be replaced by nitrile (electrophilic) – Adds cysteine reversibly to form thioimidate O N HN N H H N O O Enz-SH S O Nitrile-based inhibitor Optimization to dipeptide nitrile L-006235 Cat K IC50 = 0.2 nM J. Palmer. et. al. J. Med. Chem. 2005, 48, 7520 11 Selective Inhibition of Cathepsin K is Important to Avoid Potential Off -target Activity Off-target Cathepsins Cysteine Cathepsins B, C, F, H, K, L, O, S, V, W, Z Aspartyl Cathepsins D, E Serine Cathepsins A, G Fifteen human cathepsins are present inside cells within acidic compartments called lysosomes Potential consequences of off-target inhibition − Cat L: cardiomyopathy, impaired neovascularization − Cat F: neuronal ceroid lipofuscinosis − Cat S: impaired immune response High selectivity for cathepsin K desired to avoid potential off-target effects F. Lecaille Chem. Rev. 2002, 102, 4459. 12 L-006235 : A Potent, Selective, Reversible Dipeptidic Nitrile Inhibitor of Cathepsin K Cat K 0.2 IC50 (nM) Cat B Cat L Cat S Cat F 1100 47000 3000 6300 – >5000-fold selective in purified enzyme assays – Active in rabbit and monkey models of osteoporosis J. Palmer. et. al. J. Med. Chem. 2005, 48, 7520 13 LL-006235 -006235 in Cathepsin K Asp61 2.9 2.9 Asn166 Cys25 3.0 Gly66 14 Loss of Specificity of Cathepsin K Inhibition: Whole Cell Assay Inhibition of Cathepsins, IC50 (nM) Cathepsin K Enzyme Cell L-006235 0.2 5 Cathepsin B Cathepsin L Enzyme Cell Enzyme Cell 1100 17 6300 340 Cathepsin S Enzyme 47000 L-006235 – High selectivity profile of L-006235 is lost in whole cell assays J. Palmer. et. al. J. Med. Chem. 2005, 48, 7520 15 Cell 790 Hypothesis: Basic Inhibitors Accumulate in Acidic Lysosomes and Inhibit Off-Target Cathepsins Lysosomotropism: accumulation of lipophilic weak bases in acidic sub-cellular compartments Lysosome Plasma Membrane pH ~7 pH ~5 BH+ L-006235 Merged B B pH ~7 DNDDND-99 (lyso) L-006,235 Co-localization in live HUVECs weak basic amine J. Falgueyret et. al. J. Med. Chem 2005, 48, 7535 16 Cat K Inhibitors in Whole Cell Assays Inhibition of Cathepsins, IC50 (nM) Cathepsin K Enzyme Enzyme Cell 0.2 2.3 1100 4200 17 2900 L-006235 Cmpd 2 O Basic N N N S Cathepsin L Cathepsin B N H H N Enzyme 6300 24000 O O L-006235 Cell Enzyme N N S N H H N O Cmpd 2 – Non-basic analogs show reduced activity in cell-based assays – Non-basic P3 groups are generally less active J. Falgueyret et. al. J. Med. Chem 2005, 48, 7535 17 Cell 340 47000 >10000 27000 O Neutral N Cathepsin S N 790 >10000 Why have a Basic Substituent? 10- to 100-fold increase in intrinsic potency Improved enzyme selectivity Enhanced pharmacokinetics (bioavailability, half-life) Liability of basic group: – Lysosomotropism leading to loss of functional selectivity 18 SAR Optimization Efforts N N N N O O O N N N N H N H N CN O O S Ar N R S R O O S R R H N O – Extensive SAR studies on dipeptide framework resulted in loss of selectivity and/or potency – Abandoned dipeptide series of inhibitors 19 Amide Replacement P2-P1 amide forms key interaction with enzyme backbone (Gly66, Asn158) but, P2-P3 amide NH hydrogen-bond to Gly66, oxygen points towards solvent O Loss of N H selectivity Cat K = Cat L = Cat S = Cat B = 73 nM 3666 nM (50x) 3401 nM (46x) >10000 nM (137x) CN O Cat K = 51 nM Cat L = 42 nM (0.8x) Cat S = 41 nM (0.8x) Cat B = 1903 nM (37x) Cat K = 56 nM Cat L = 498 nM (9x) Cat S = 1578 nM (28x) Cat B = >10000 nM (>180) Increase in selectivity Amide bond can be replaced but loss in Cat K potency Selectivity can still be achieved without P2-P3 amide J. Robichaud et. al. BMCL 2004, 14, 4291 H N 20 Further Optimization of Amide Replacement High selectivity can still be achieved without P2-P3 amide with addition of basic P3 group HN N H N Potency O selectivity (R)-2 Cat K = 56 nM Cat L = 498 nM (9x) Cat S = 1578 nM (28x) Cat B = >10000 nM (>180) J. Robichaud et. al. BMCL 2004, 14, 4291 J. Robichaud et. al. J. Med. Chem. 2003, 46, 3709 Cat K = 11 nM Cat L = 3950 nM (359x) Cat S = 2010 nM (183x) Cat B = 3725 nM (339x) 21 CN Re-Addition of a Hydrogen-Bond Donor Additional of hydrogen bond donor is favorable for cat K potency. X = Cat K (IC50) NH 54 nM O 1147 nM CH2 2353 nM J. Robichaud et. al. BMCL 2004, 14, 4291 X = Cat K (IC50) NH 72 nM O 1475 nM CH2 3394 nM 22 X = Cat K (IC50) NH 208 nM O 2999 nM CH2 2349 nM Potency and Selectivity Optimization selectivity Cat K = Cat L = Cat S = Cat B = 2 nM 108 nM (54x) 24 nM (12x) 26 nM (13x) Cat K = Cat L = Cat S = Cat B = 3 nM 2101 nM (700x) 158 nM (53x) 1812 nM (604x) Selectivity and potency can still be achieved without P2-P3 amide with addition of basic P3 group HN N Cat K = 11 nM H Cat L = 3950 nM (359x) N CN Cat S = 2010 nM (183x) O Cat B = 3725 nM (339x) (R)-2 J. Robichaud et. al. BMCL 2004, 14, 4291 23 Another Peptidomimetic O N N N N H H N CN O S How can P2-amide be replaced while maintaining H-bond capability? H-bond donor requires non-basic nitrogen – Non-basic amine (pKa = 1.5) is not protonated at physiological pH Retains the H-bond donating properties of an amide bond O O N H CF3 O O N H M. Zanda et. al ChemMedChem 2007, 2,1693 O 24 N H N H CF3 Amide Replacement: P2 Leucine vs Cyclohexyl 50 50 O O N H H N CN N H O H N CN O Trifluoroethylamine is an effective amide isostere Cyclohexyl ring in P2 is much less potent than the isobutyl side-chain Modeling suggests loss of potency in cyclohexyl analog is a result of steric interactions between P2 and the CF3 group W. C. Black et. al. BMCL 2005, 15, 4741 Black, W. C.; Percival, M. D. ChemBioChem 2006, 7, 1525 25 CF3 Amide Replacement IC50 (nM) O L-006235 N N N S 3 N N N N H H N Cat B Cat L Cat S 0.2 1100 6300 47000 0.03 3315 26 848 0.005 1110 47 451 CN O CF3 N H Cat K H N CN O S CF3 N H 4 H N O CN N HN Phenyl piperazine has greater potency and selectivity than thiazole piperazine Can this exquiste potency/selectivity advantage be extended to non-basic inhibitors? W. C. Black et. al. BMCL 2005, 15, 4741 26 “Non-basic” P3 Substituents L-873724 Non-basic derivatives in this series are potent and selective L-873724 stands out as best compound in this series C. S. Li et al. BMCL 1985,16, 1985 27 X-ray structure of Why are Trifluoroethylamines so Potent? Cat K -Complex CF3 H2NO2S 28 N H H N O CN L-873724 has Similar Potency in Whole Cells and Purified Cathepsins Trifluoroethylamine isostere gave enough potency to remove the basic P3 Selectivity profile of L-873724 is maintained in whole cell assays O N N N H N S H N CF3 H N CN N H O MeO2S L-006235 CN O L-873724 Inhibition of Cathepsins, IC50 (nM) Cathepsin B Cathepsin L Cathepsin S Enzyme Cell Enzyme Cell Enzyme Cell L-006235 1100 17 6300 340 47000 790 L-873724 5240 4800 264 1220 178 94 C. S. Li et al. BMCL 1985,16, 1985 29 L-873724 Metabolism L-872724 is extensively metabolized in human hepatocytes (56% metabolism) CF3 H N N H NC 70141-2225 hum heps L-873,724 t=2 25Oct02-014 100 18.92 Human hepatocytes 2: Diode Array 263.801_271.9 5.22e4 N O MeSO2 L-873,724 ~50% metabolism OH M7 M12 16.12 CF3 17.63 N H % R M13 H N CF3 N N H O R M7: leucine hydroxylation 17.85 ? M8 14.45 14.72 OH 15.03 15.77 CF3 10 N H Time 12.00 13.00 14.00 15.00 16.00 O M13: acid ? 19.58 OH 17.00 18.00 19.00 R N H O M12: lactone formation 30 CF3 O R OH O M8: hydroxyacid Modifications to Reduce Metabolism Modify P2 to block metabolism CF3 N H H N N O Add substituent to block amide cleavage and lactonization MeO2S 31 L-873,724 has Similar Potency in Whole Cells and Purified Cathepsins Modifications result in odanacatib which maintains excellent selectivity and activity in both enzymatic and cell-based assays L-873724 Odanacatib Inhibition of Cathepsins, IC50 (nM) Cathepsin K Enzyme Cell L-873724 Odanacatib 0.2 0.2 3 5 Cathepsin B Cathepsin L Cathepsin S Enzyme Cell Enzyme Cell Enzyme Cell 5240 1034 4800 1050 264 2995 1220 4843 178 60 94 45 J. Gauthier et. al. BMCL 2008, 18, 923 32 Odanacatib has Improved Pharmacokinetics in Preclinical Species Modification of L-873724 to block sites of oxidative metabolism provides a superior pharmacokinetic profile. High recovery (>99%) after incubation with dog and human hepatocytes Odanacatib L-873724 Pharmacokinetics Dog Rat Cl(ml/min/kg) L-873724 Odanacatib 6.3 2 J. Gauthier et. al. BMCL 2008, 18, 923 t1/2 (h) 2.7 6 Cl(ml/min/kg) 1.12 0.13 33 Rhesus Monkey t1/2 (h) 6 57 Cl(ml/min/kg) t1/2 (h) 7.5 6.1 1.7 18 Mean Concentration Profile of Odanacatib in Women Administered Once-Weekly Doses for 3 Weeks 0 0 6 W O g m 5 2 Cat B,L,S,F IC90 W O g m 0 5 0 0 5 W O g m 0 0 1 0 0 4 0 0 3 0 0 2 M n , n o i t a r t n e c n o C 0 0 1 Cat K IC90 (bone res) 0 4 1 3 1 2 1 1 1 03 1k 9e e 8W 7 s 6y a 5D 4 3 2 1 0 7 6 1 5k e 4e W 3 2s y 1a D 0 ︵ ︶ ︵ ︶ – Human half-life similar to dog; human t1/2 = 60-70 h – At therapeutic exposures, odanacatib maintains selectivity over other cathepsins Stoch, A. et. al. Clin. Pharm. & Ther. 2009, 86, 175 34 Effect of Odanacatib on Bone Resorption After 3 Weeks of Once -Weekly Dosing Once-Weekly S-CTx Mean Percent Change (95%CI) from Baseline S-CTX-I % Change from Baseline 75 Placebo 50 mg 5 mg 100 mg 25 mg 50 25 0 -25 -50 -75 -100 0 1 3 5 7 9 11 14 16 18 21 24 Day Dose Dose Stoch, A. et. al. Clin. Pharm. & Ther. 2009, 86, 175 Dose N = 9-12/group 35 28 Selectivity of Other Cathepsin K Inhibitors Relacatib has low selectivity towards related cathepsins (L, V, B, S) in enzymatic assays − Relacatib clinical development was halted after Phase I studies Balicatib is very selective towards related cathepsins in enzymatic assays − Development of balicatib was discontinued during Phase IIb due to morphea-like skin changes − Cathepsin B, K, L, S and V are all expressed in human skin and have collagenase activity − Postulate that morphea is due to lysosomotropic-based loss of selectivity Basic O O N H H N O N H O O N N O S N N O Relacatib (GSK) Brömme, D. Expert Opin. Investig. Drugs. 2009, 18, 585 Desmarais, S. et al Molecular Pharmacology 2008, 73, 147 Balicatib (Novartis) 36 H N O CN Odanacatib has Similar Potency in Whole Cells and Purified Cathepsins Inhibition of Cathepsins, IC50 (nM) Cathepsin K Enzyme Cell Odanacatib Balicatib 0.2 0.6 5 22 Cathepsin B Cathepsin L Enzyme Cell Enzyme Cell 1034 4800 1050 61 2995 503 4843 48 Cathepsin S Enzyme 45 60 65000 2900 Basic Odanacatib (MK-0822) Balicatib The low level of off-target activity of odanacatib in enzyme assays is maintained in whole cell assays 37 Cell Effect of Cat K Inhibitors on Collagen Accumulation in Dermal Fibroblasts (Fluorescence intensity, fold Increased over vehicle) Intracellular Collagen Accumulation Develop model of intracellular collagen accumulation in primary human dermal fibroblasts 7 6 5 Balicatib Relacatib Odanacatib 4 3 2 1 0 0.01 0.1 1 10 Inhibitor Concentration (µM) Odanacatib has a minimal effect on intracellular collagen accumulation compared to balicatib and the pan-cathepsin inhibitor relacatib J. Gauthier et. al. BMCL 2008, 18, 923 38 Odanacatib Inhibits Bone Resorption with Less Reduction of Bone Formation Bone formation factors IGF-1, TGF-BMP. Wnt 10b Bisphosphonates and denosumab reduce the number of osteoclasts −Fewer resorption pits, reduced new bone formation Osteoblast (Ob) Ob progenitor Osteoclast Odanacatib reduces the activity of Cat K in the osteoclast Vehicle −Same number of, but shallower resorption pits −Allows new bone formation Odanacatib O O C C P P O O C C OC: Osteoclast P: Resorption Pit Leung et al. Bone 2011, 49, 623 39 P P Differential Effects on Bone Turnover Markers Odanacatib inhibits bone resorption (uNTx) while exhibiting less reduction of bone formation (BSAP) than observed with alendronate. Historical Comparison to Alendronate Urinary NTx Serum BSAP 1 Binkley et al., ASBMR 2011 2 Merck data on file Geometric Mean Percent Change from Baseline (SE) Odanacatib Phase IIB1 20 0 20 Year 1 2 3 Alendronate Phase III2 4 5 0 -20 -20 -40 -40 -60 -60 -80 -80 -100 2 3 1 2 1 2 -100 Year 1 Year 4 5 20 20 0 0 -20 -20 -40 -40 -60 -60 -80 -80 -100 -100 40 3 4 5 4 5 Year 3 Odanacatib: Phase IIb Study 5-Year Data Bone Mineral Density (DXA) Odanacatib progressively increases BMD over 5 years at lumbar spine, femoral neck and total hip Historical Comparison to Alendronate Lumbar Spine Femoral Neck Total Hip Mean Percent Change from Baseline (±SE) Odanacatib Phase IIB1 Alendronate Phase III2 15 15 10 10 5 5 0 1 2 3 Year 4 5 0 10 10 5 5 0 1 2 10 3 Year 4 5 2 1 2 1 2 10 3 Year 4 5 3 4 5 3 4 5 Year 5 5 0 0 1 1 2 3 Year 4 0 5 41 Year Summary Early inhibitors were found to accumulate in lysosomes thereby lowering their selectivity towards related cathepsins in functional assays Optimized leads produced selective non-basic inhibitors Optimized non-basic leads reduced metabolism and improved pharmacokinetic properties In post-menopausal women, odanacatib treatment: − Demonstrates less suppression of markers of bone formation than has been observed with alendronate* − Progressively increases BMD over 5 years at lumbar spine, femoral neck, and total hip * Historical comparison 42
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