Accounts in Drug Discovery describes recent case studies in medicinal chemistry with a particular emphasis on how the inevitable problems that arise during any project can be surmounted or overcome. The Editors cover a wide range of therapeutic areas and medicinal chemistry strategies, including lead optimization starting from high-throughput screening "hits" as well as rational, structure-based design. The chapters include "follow-ons" and "next generation" compounds that aim to improve upon first-generation agents. This volume surveys the range of challenges commonly faced by medicinal chemistry researchers, including the optimization of metabolism and pharmacokinetics, toxicology, pharmaceutics and pharmacology, including proof-of-concept in the clinic for novel biological targets. The case studies include medicinal chemistry stories on recently approved and marketed drugs, but also chronicle "near-misses", i.e. exemplary compounds that may have proceeded well into the clinic but for various reasons did not result in a successful registration. As the vast majority of projects fail prior to registration, much can be learned from such narratives. By sharing a wide range of drug discovery experiences and information across the community of medicinal chemists in both industry and academia, the Editors believe that these accounts will provide insights into the art of medicinal chemistry as it is currently practiced and will help to serve the needs of active medicinal chemists.

Joel C. Barrish was awarded his Ph.D. in Organic Chemistry from Columbia University; spent 25 years as a medicinal chemist in Drug Discovery Research; co-inventor of the anti-cancer agent SPRYCEL and is currently Vice President in Discovery Chemistry responsible for multiple programs across therapeutic areas. Percy H. Carter was awarded his Ph.D. in Organic Chemistry from Harvard University; 10 years as a medicinal chemist in Drug Discovery Research and is currently Group Director in Discovery Chemistry responsible for multiple programs Inflammation Research. Peter T. W. Cheng was awarded Ph.D. in Organic Chemistry from the University of Toronto; approximately 20 yrs as a medicinal chemist in Drug Discovery Research and is currently a Research Fellow in Metabolic Diseases Chemistry. Robert Zahler gained his Ph.D. in Organic Chemistry from the California Institute of Technology; approximately 30 yrs experience as a medicinal chemist in Drug Discovery Research and is the inventor of the anti-infective agent Entecavir.

Accounts in Drug Discovery

Case Studies in Medicinal Chemistry

By Joel C. Barrish, Percy H. Carter, Peter T. W. Cheng, Robert Zahler

The Royal Society of Chemistry

Copyright © 2011 Royal Society of Chemistry
All rights reserved.
ISBN: 978-1-84973-126-3

Contents

Chapter 1 The Discovery of the Dipeptidyl Peptidase-4 (DPP4) Inhibitor Onglyza™: From Concept to Market Jeffrey A. Robl and Lawrence G. Hamann, 1,
Chapter 2 The Discovery of Vorapaxar (SCH 530348), a Thrombin Receptor (Protease Activated Receptor-1) Antagonist with Potent Antiplatelet Effects Samuel Chackalamannil, 25,
Chapter 3 The Discovery of Piragliatin, a Glucokinase Activator Ramakanth Sarabu, Jefferson W. Tilley and Joseph Grimsby, 51,
Chapter 4 The Discovery of OSI-906, a Small-molecule Inhibitor of the Insulin-like Growth Factor-1 and Insulin Receptors Mark J. Mulvihill and Elizabeth Buck, 71,
Chapter 5 The Genesis of the Antibody Conjugate Gemtuzumab Ozogamicin (Mylotarg®) for Acute Myeloid Leukemia Philip R. Hamann, 103,
Chapter 6 Novel Androgen Receptor Antagonists for the Treatment of Prostate Cancer Ashvinikumar V. Gavai, William R. Foster, Aaron Balog and Gregory D. Vite, 120,
Chapter 7 The Discovery of UK-390957: the Challenge of Targeting a Short Half-life, Rapid Tmax SSRI Mark D. Andrews and Donald S. Middleton, 142,
Chapter 8 The Discovery of the Long-acting PDE5 Inhibitor PF-489791 for the Treatment of Pulmonary Hypertension Andrew S. Bell and Michael J. Palmer, 166,
Chapter 9 From HTS to Market: the Discovery and Development of Maraviroc, a CCR5 Antagonist for the Treatment of HIV Chris Barber and David Pryde, 183,
Chapter 10 The Discovery of GS-9131, an Amidate Prodrug of a Novel Nucleoside Phosphonate HIV Reverse Transcriptase Inhibitor Richard Mackman, 215,
Chapter 11 2'-F-2'-C-Methyl Nucleosides and Nucleotides for the Treatment of Hepatitis C Virus: from Discovery to the Clinic Michael J. Sofia, Phillip A. Furman and William T. Symonds, 238,
Chapter 12 A Case History on the Challenges of Central Nervous System and Dual Pharmacology Drug Discovery Paul V. Fish, Anthony Harrison, Florian Wakenhut and Gavin A. Whitlock, 267,
Chapter 13 The Discovery of TRPV1 Antagonists: Turning up the Heat Mark H. Norman, 287,
Chapter 14 Uncoupling Neuroprotection from Immunosuppression: the Discovery of ILS-920 Edmund I. Graziani, 316,
Chapter 15 Identification of α7 Nicotinic Acetylcholine Receptor Agonists for their Assessment in Improving Cognition in Schizophrenia Bruce N. Rogers, E. Jon Jacobsen, Christopher J. O'Donnell, Christopher L. Shaffer, Daniel P. Walker and Donn G. Wishka, 332,
Subject Index, 363,

CHAPTER 1

The Discovery of the Dipeptidyl Peptidase-4 (DPP4) Inhibitor Onglyza™: From Concept to Market

JEFFREY A. ROBL AND LAWRENCE G. HAMANN

Bristol-Myers Squibb Research & Development, Department of Discovery Chemistry – Metabolic Diseases, P.O. Box 5400, Princeton, NJ 08543, USA

1.1 Introduction

The prevalence of diabetes in developed and now emerging countries represents a significant health burden to a large portion of the world's population. Type-2 diabetic patients, characterized in part by elevated fasting plasma glucose of > 125 mg dL-1 (7.0 mmol L-1) and glycosylated hemoglobin (HbA1c) ≥ 6%, are at increased risk for the development of both microvascular (retinopathy, neuropathy, nephropathy) as well as macrovascular complications (myocardial infarction, stroke). As such, diabetes is the leading cause of blindness, kidney failure, and limb amputation worldwide. Diabetes is a progressive disease, with morbidity and mortality risk increasing with both duration and severity of hyperglycemia. Additionally, diabetes is also now impacting different population sectors (adolescents, developing countries) not typically associated with the disease 30 years ago. Consequently, the continually increasing diabetes prevalence is placing greater strain on both health care systems and economies on a global scale. In 2007 alone, studies have shown that diabetes cost the US economy $174 billion in medical expenses and lost productivity. While death rates related to heart disease, stroke, and cancer have all decreased since 1987, the death rate due to diabetes has increased by 45% during this same period. Thus, the discovery and development of new therapies for treating and preventing diabetes continue to be a major emphasis of health care companies.

In response to this landscape, the Discovery organization at Bristol-Myers Squibb (BMS) made the strategic decision to refocus efforts in the late 1990's towards identifying and progressing novel targets for the treatment of diabetes. This was in part aimed at building upon BMS's already established presence in the anti-diabetes market through the Glucophaget™ franchise and in recognition of the significant unmet medical need for novel, more efficacious, and well tolerated treatments for the disease. It was from these efforts that advanced clinical candidates such as muraglitazar (1, Pargluvat™, dual PPAR agonist), dapagliflozin (2, SGLT2 inhibitor), and saxagliptin (3, Onglyzat™, DPP4 inhibitor) were discovered within the BMS Discovery organization (Figure 1.1).

1.2 Modulation of GLP-1 in the Treatment of Diabetes

At the start of this effort, several oral anti-diabetic agents (OADs) were available to patients suffering from type-2 diabetes. These included hepatic glucose suppressors (e.g. metformin), insulin secretagogues (e.g. sulfonylureas), glucose absorption inhibitors (e.g. acarbose), and insulin sensitizers (e.g. thiazolidinediones or TZDs such as rosiglitazone and pioglitazone). While all have shown utility in lowering HbA1c levels in diabetic patients, current OADs come with a variety of safety and/or tolerability issues. The biguanindes such as metformin, currently the most widely prescribed therapy for diabetes, have issues related to gastrointestinal (GI) tolerability and lactic acidosis. Sulfonylurea treatment is often accompanied by higher incidences of hypoglycemia and weight gain, while glucose absorption inhibitors exhibit modest efficacy and GI disturbance. Finally, TZDs have been associated with edema, worsening of congestive heart failure, negative effects on bone fracture rate, and, in recent studies, mixed results regarding cardiovascular (CV) safety profiles. With this background in mind, we sought to identify new targets which would not only provide an efficacious alternative mechanism for lowering blood glucose and HbA1c levels, but would also present an opportunity for achieving a superior safety and tolerability profile when compared to current standards of care. Ideally, such a drug would be suitable for combination with existing agents, as poly-pharmacology with multiple OADs is emerging as the standard treatment paradigm for type-2 diabetes therapy.

Glucagon like peptide-1 (GLP-1) is a 30-amino acid peptide incretin hormone derived from processing of pro-glucagon and is secreted by the L-cells of the intestinal mucosa in response to glucose stimulation. Since the early 1990's, GLP-1 had been known to be a potent insulin secretagogue and glucagon suppressor, with robust anti-diabetic and pro-satiety effects in diabetic humans, but efforts to advance GLP-1 itself as a pharmaceutical agent were hampered by its extremely short pharmacokinetic half-life in vivo (plasma t1/2 ≈ 2 min). As a result, considerable effort in the drug discovery community was expended toward the identification of small-molecule GLP-1 receptor agonists that would capture the beneficial effects of GLP-1 while exhibiting oral bioavailability and a superior pharmacokinetic duration of action. Unfortunately, efforts to identify such small-molecule agonists have to date been unsuccessful, due in part to a dearth of viable bona fide screening hits. In light of this shortcoming, a number of pharmaceutical and biotech companies have advanced subcutaneously administered, peptide GLP-1 receptor agonists with superior duration of action in vivo. Among the most advanced agents are exenatide (Byetta™) and liraglutide (Victoza™), both of which have been approved by regulatory agencies for the treatment of type-2 diabetes. While these drugs are effective in lowering HbA1c and demonstrate a net beneficial effect on weight gain and other CV risk factors, they require parenteral administration (once or twice daily dosing), and patient uptake of these agents has been limited despite their robust efficacy and promising safety profile.

1.3 Dipeptidyl Peptidase-4 as a Target for Diabetes Treatment

While the advancement of orally active, small-molecule GLP-1 receptor agonists remains elusive, another opportunity to modulate GLP-1 receptor activity in vivo focused on preventing the degradation of endogenous GLP-1 with smallmolecule inhibitors of the primary peptidase responsible for the in vivo degradation of GLP-1, dipeptidyl peptidase-4 (DPP4), a non-classical serine protease. Our initial interest in DPP4 inhibitors was piqued by a report from Holst and Deacon, wherein the authors outlined a compelling argument for the utility of DPP4 inhibition in the treatment of diabetes, primarily via the potentiation of endogenous GLP-1. DPP4 belongs to a family of aminodipeptidases and is both a cell surface and circulating enzyme. Historically, it had also been identified as the lymphocyte cell surface marker CD26, and as such DPP4/CD26 exhibits pharmacology related to cell membrane-associated activation of intracellular signal transduction pathways and cell–cell interaction in addition to its peptidase enzymatic activity. It is widely believed that the signaling function of DPP4/CD26 is distinct from its enzymatic function.

The concept of generating targeted protease/peptidase inhibitors as therapeutic agents is well documented in the literature. In the majority of cases, selective enzyme inhibitors have been used to prevent the conversion of an endogenous "non-functional" peptide/protein precursor (e.g. angiotensin I) to a physiologically active peptide/protein (e.g. angiotensin II), thereby attenuating formation of the protagonist bio-active enzyme product to effect amelioration of the disease state. Use of such approaches has led to marketed drugs for numerous indications, including ACE and renin inhibitors for hypertension, HIV protease inhibitors for AIDS, and thrombin inhibitors for DVT. Less prevalent are approaches targeting proteases/peptidases that degrade endogenous substrates which are known to exert a beneficial effect. For example, neutral endopeptidase (NEP) proteolytically degrades the endogenous vasodilator atrial natriuretic peptide (ANP) to inactive fragments. By retarding this degradation, NEP inhibitors have found use in the treatment of hypertension. In common with NEP, where inhibition of protease mediated protein degradation was the pharmacological objective, BMS and several other research groups engaged in the search for DPP4 inhibitors to maximize the beneficial effects of endogenously released GLP-1.

1.4 Early Inhibitors of DPP4

To jump-start the BMS DPP4 chemistry program, the group was able to capitalize on groundwork laid in the mid-late 1990's when several potent inhibitors of DPP4/CD26 were reported that could be classified as either "irreversible" or "reversible", depending on the mechanism of inhibition (Figures 1.2 and 1.3). Hydroxamates such as 4 were proposed to be both substrates and inhibitors of DPP4, presumably via direct covalent modification of the enzyme through the active-site serine residue (Ser630). Phosphatebased inhibitors such as 5 were also reported to undergo covalent addition to DPP4 but exhibited weak potency. The interesting boronate-based inhibitors (e.g.6), originally advanced by the Tufts University and Boehringer Ingelheim groups, exhibited exceptionally high inhibitory activity in vitro, presenting themselves as "transition-state" inhibitors which presumably form tetrahedral boronate esters involving the Ser630 hydroxyl group. As such, many of these compounds exhibited slow tight-binding kinetics with Koff rates of several days (versus seconds/minutes with non-covalently bound inhibitors). However, these compounds also suffered from poor solution stability arising from intramolecular cyclization of the terminal primary amine with the boronate, affording an inactive product (e.g.7). The propensity of compounds of this chemotype to undergo internal cyclization limited their viability as drug candidates.

Due to the uncertain risks associated with advancing irreversible inhibitors as drug candidates, the team viewed the reversible inhibitors exploited by the Mount Sinai, Probiodrug, Ferring Research, and Novartis scientific teams as more attractive starting points for a lead finding effort (Figure 1.3). Probiodrug had described simple Ile-pyrrolidides (8) and Ile-thiazolidides (9, later advanced to the clinic by Merck and Probiodrug as P32/98) which exhibited in vitro potency in the nanomolar range, were chemically stable, and, in the case of 9, demonstrated glucose area under the curve (AUC) reductions in Zuckerfa/fa rats in an oral glucose tolerance test (oGTT). Reports from Li et al. at Mount Sinai highlighted early examples of nitrilopyrrolidines specifically designed as inhibitors of DPP4. Equally intriguing was the work described by Ferring in which nitrilo-pyrrolidines such as 10 were identified as exceptionally potent inhibitors of the enzyme. Initially targeted as agents for immunomodulation (via CD26 inhibition), these compounds represented "drug-like" scaffolds and exhibited exceptional inhibitory potency. Additionally, a contemporaneous patent application from Novartis described the structure of compound 11 (a related analogue 12 would later be disclosed as Novartis' first clinical compound, DPP-728) and its ability to increase plasma insulin in fasted, high-fat fed rats in an oGTT. The inhibitors represented by compounds 8–12 provided useful insights for the design of DPP4 inhibitors at BMS.

At the initiation of the program, there were still many unknown factors related to the pharmacology and safety of DPP4 inhibition. It was clear from earlier work that Fischer 344 rats possessing a naturally occurring loss-of-function mutation of the DPP4 gene were healthy, viable, and free of serious immunological complications. It was later shown that these rats also exhibited a favorable metabolic phenotype on a high-fat diet and demonstrated improved glucose tolerance and GLP-1 secretion. Thus, complete ablation of DPP4 did not appear to represent a serious safety concern in rats, but rather the Fischer rat provided support for the concept that inhibition of DPP4 could be both safe and efficacious. Others questions still remained. Was high selectivity for DPP4 versus other related peptidases (e.g. DPP8, DPP9, FAP, etc.) an absolute requirement for this target? Would inhibition of DPP4 potentiate other endogenous peptides, leading to unintended deleterious (or beneficial) consequences? Would potentiating endogenous GLP-1 (versus exogenous administration) be sufficient to affect a robust anti-diabetic response in humans? Finally, what potential mechanism-based toxicological effects, if any, would be seen upon chronic administration of a DPP4 inhibitor?

In light of limited literature in the field, and with no reports of a compound having advanced to clinical trials, these questions would ultimately need to be addressed during the execution of our discovery and subsequent clinical development programs. Despite the unknowns, the positive aspects of this target were numerous. Potent small-molecule inhibitors with systemic exposure upon oral dosing were known. Although limited, DPP4 inhibitors had demonstrated pharmacodynamic efficacy in genetic animal models of type 2 diabetes in preliminary pharmacological studies. Preclinical proof-of-concept for the anti-diabetic actions of GLP-1 was already established and suggested a low potential for hypoglycemia. In vitro assays and several in vivo models were already described in the literature, enabling rapid program initiation. It was against this backdrop that significant medicinal chemistry and biology resources at BMS were deployed on this newly emerging target in the early months of 1999.

1.5 Design of BMS's DPP4 Medicinal Chemistry Program

Given the attractiveness of DPP4 as a therapeutic target, it was anticipated that this field would soon become highly competitive, and we therefore sought to accelerate the program. High-throughput screening (HTS), routinely a key component of drug discovery programs, was deemed as too time consuming to rapidly afford a chemical starting point. Thus, we decided to initially adopt a design optimization approach, improving upon the leads reported by the Probiodrug, Ferring, and Novartis research groups; HTS would later be used to provide leads for a second-generation effort. From a potency perspective, the nitrilo-pyrrolidines were deemed to be highly attractive, but were reported to exhibit modest pharmacokinetic duration of action and suffered from chemical instability. In solution, the proximal amino group attacks the nitrile functionality (see Figure 1.3), eventually leading to the intermediate cyclic imidate 13 and ultimately the diketopiperzine 14, both of which are inactive versus DPP4. Addressing this issue was viewed as a critical component of the medicinal chemistry effort due to considerations regarding both the half-life of the compound in vivo, and for high purity processing of the active pharmaceutical ingredient (API) on large scale in a drug manufacturing setting.

(Continues...)Excerpted from Accounts in Drug Discovery by Joel C. Barrish, Percy H. Carter, Peter T. W. Cheng, Robert Zahler. Copyright © 2011 Royal Society of Chemistry. Excerpted by permission of The Royal Society of Chemistry.
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