Kyle J. Eastman

Applications of Fluorine in Medicinal Chemistry

The role of fluorine in drug design and development is expanding rapidly as we learn more about the unique properties associated with this unusual element and how to deploy it with greater sophistication. The judicious introduction of fluorine into a molecule can productively influence conformation, pKa, intrinsic potency, membrane permeability, metabolic pathways, and pharmacokinetic properties. In addition, (18)F has been established as a useful positron emitting isotope for use with in vivo imaging technology that potentially has extensive application in drug discovery and development, often limited only by convenient synthetic accessibility to labeled compounds. The wide ranging applications of fluorine in drug design are providing a strong stimulus for the development of new synthetic methodologies that allow more facile access to a wide range of fluorinated compounds. In this review, we provide an update on the effects of the strategic incorporation of fluorine in drug molecules and applications in positron emission tomography.

Chemistry in the Pharmaceutical Industry

This chapter discusses the role of chemistry within the pharmaceutical industry [1–3]. Although the focus is upon the industry within the United States, much of the discussion is equally relevant to pharmaceutical companies based in other first-world nations such as Japan and those in Europe. The primary objective of the pharmaceutical industry is the discovery, development, and marketing of safe and efficacious drugs for the treatment of human disease. However, drug companies do not exist as altruistic, charitable organizations. As with other shareholder-owned corporations within a capitalistic society, drug companies must earn profits in order to remain viable. Profits from the enterprise finance the essential research and development that leads to new drugs designed to address unmet medical needs. Thus, there exists a tension between the dual goals of enhancing the quality and duration of human life and that of increasing stockholder equity. Much has been written and spoken in the lay media about the high prices of prescription drugs and the hardships these place upon the elderly and others of limited income. Consequently, some consumer advocate groups support governmental imposition of price controls on ethical pharmaceuticals in the United States, such as those that exist in a number of other countries. However the out-of-pocket dollars spent by patients on prescription drugs must be weighed against the more costly and inherently risky alternatives of surgery and hospitalization, which can often be obviated by drug therapy. Consideration must also be given to the enormous expense associated with the development of new drugs. It typically takes 10 or more years from the inception of a drug in the laboratory to registrational approval and marketing at an overall cost which is now estimated to be in excess of

Phosphocholine conjugation: an unexpected in vivo conjugation pathway associated with hepatitis c ns5b inhibitors featuring a bicyclo[1.1.1]pentane.

800 million and increasing, a figure that includes the opportunity costs of failed development campaigns. Only 1 out of 10,000–20,000 compounds prepared as potential drug candidates ever reach clinical testing in humans and the attrition rate of those that do is >80%, a success rate that has been stubbornly difficult to change despite advances in improving candidate quality and significant increases in investment in research and development. The expense of developing a promising drug grows steadily further through the pipeline it progresses; clinical trials can be several orders of magnitude more costly than the preclinical development of a compound. While the sales of drugs that complete clinical trials and reach the shelves of pharmacies can eventually recoup their developmental expenses many times over if successful, many fail to do so and the cost of the drugs that fail is never recovered.

Tactical Applications of Fluorine in Drug Design and Development

During a medicinal chemistry campaign to identify inhibitors of the hepatitis C virus nonstructural protein 5B (RNA-dependent RNA polymerase), a bicyclo[1.1.1]pentane was introduced into the chemical scaffold to improve metabolic stability. The inhibitors bearing this feature, compound 1 [5-(3-(bicyclo[1.1.1]pentan-1-ylcarbamoyl)-4-fluorophenyl)-2-(4-fluorophenyl)-N-methyl-6-(3,3,3-trifluoropropyl)furo[2,3-b]pyridine-3-carboxamide] and compound 2 [5-(3-(bicyclo[1.1.1]pentan-1-ylcarbamoyl)phenyl)-2-(4-fluorophenyl)-N-methyl-6-(3,3,3-trifluoropropyl)furo[2,3-b]pyridine-3-carboxamide], exhibited low turnover in incubations with liver S9 or hepatocytes (rat, human), with hydroxylation of the bicyclic moiety being the only metabolic pathway observed. In subsequent disposition studies using bile duct–cannulated rats, the metabolite profiles of bile samples revealed, in addition to multiple products of bicyclopentane oxidation, unexpected metabolites characterized by molecular masses that were 181 Da greater than those of compound 1 or 2. Further liquid chromatography/multiple-stage mass spectrometry and nuclear magnetic resonance analysis of the isolated metabolite of compound 1 demonstrated the presence of a phosphocholine (POPC) moiety bound to the methine carbon of the bicyclic moiety through an ester bond. The POPC conjugate of the nonstructural protein 5B inhibitors was assumed to result from two sequential reactions: hydroxylation of the bicyclic methine to a tertiary alcohol and addition of POPC by cytidine-diphosphocholine:1,2-diacylglycerol cholinephosphotransferase, an enzyme responsible for the final step in the biosynthesis of phosphatidylcholine. However, this pathway could not be recapitulated using cytidine-diphosphocholine–supplemented liver S9 or hepatocytes because of inadequate formation of the hydroxylation product in vitro. The observation of this unexpected pathway prompted concerns about the possibility that compounds 1 and 2 might interfere with routine phospholipid synthesis. These results demonstrate the participation in xenobiotic metabolism of a process whose function is ordinarily limited to the synthesis of endogenous compounds.

Identification of a novel series of potent HCV NS5B Site I inhibitors

The increasing utilization of fluorine in drug design parallels advances in understanding the physicochemical attributes of this element and an enhanced appreciation of how these unique properties can be exploited to address the numerous challenges encountered in pharmaceutical candidate optimization. Judicious placement of fluorine in a candidate compound can markedly affect potency, increase metabolic stability and enhance membrane permeability. The powerful electron-withdrawing nature of fluorine serves to modulate the pKa of proximal functionality, particularly basic amines, and can be an important tool for controlling physical properties. Fluorine also exerts a conformation bias that is significant and can be utilized strategically. The 18F isotope is of particular importance in positron emitting tomography (PET), an imaging technique of increasing importance for assessing drug-target engagement in both preclinical and clinical settings. This chapter provides a synopsis of some of the prominent and emerging applications of fluorine in the design and optimization of biologically active molecules.

Improving Metabolic Stability with Deuterium: The Discovery of BMT-052, a Pan-genotypic HCV NS5B Polymerase Inhibitor

Efforts investigating spatially comparative alternates of the ethylene-bridged piperazine in BMS-791325 that would offer a maintained or improved virologic and pharmacokinetic profile have been multifaceted. One foray involved the utilization of various octahydropyrrolo[3,4-c]pyrrole propellanes. Many of the propellane analogs described in this work exhibited better than targeted potency (less than 20 nM). Additionally, improved exposure in rats was achieved through the employment of two newly invented and now readily accessible carbon bridged propellanes as compared to their heteroatom bridged analogs.

Bioactivation of cyclopropyl rings by P450: an observation encountered during the optimisation of a series of hepatitis C virus NS5B inhibitors

Iterative structure-activity analyses in a class of highly functionalized furo[2,3-b]pyridines led to the identification of the second generation pan-genotypic hepatitis C virus NS5B polymerase primer grip inhibitor BMT-052 (14), a potential clinical candidate. The key challenge of poor metabolic stability was overcome by strategic incorporation of deuterium at potential metabolic soft spots. The preclinical profile and status of BMT-052 (14) is described.

The discovery of a pan-genotypic, primer grip inhibitor of HCV NS5B polymerase

Abstract 1. Due to its unique C–C and C–H bonding properties, conformational preferences and relative hydrophilicity, the cyclopropyl ring has been used as a synthetic building block in drug discovery to modulate potency and drug-like properties. During an effort to discover inhibitors of the hepatitis C virus non-structural protein 5B with improved potency and genotype-coverage profiles, the use of a pyrimidinylcyclopropylbenzamide moiety linked to a C6-substituted benzofuran or azabenzofuran core scaffold was explored in an effort to balance antiviral potency and metabolic stability. 2. In vitro metabolism studies of two compounds from this C6-substituted series revealed an NADPH-dependent bioactivation pathway leading to the formation of multiple glutathione (GSH) conjugates. Analysis of these conjugates by LC-MS and NMR demonstrated that the cyclopropyl group was the site of bioactivation. Based on the putative structures and molecular weights of the cyclopropyl-GSH conjugates, a multi-step mechanism was proposed to explain the formation of these metabolites by P450. This mechanism involves hydrogen atom abstraction to form a cyclopropyl radical, followed by a ring opening rearrangement and reaction with GSH. 3. These findings provided important information to the medicinal chemistry team which responded by replacing the cyclopropyl ring with a gem-dimethyl group. Subsequent compounds bearing this feature were shown to avert the bioactivation pathways in question.