Allan M. Jordan

The Medicinal Chemist’s Toolbox: An Analysis of Reactions Used in the Pursuit of Drug Candidates

Industrial medicinal chemistry departments the world over are charged with the rapid delivery of small molecule new chemical entities (NCEs) into the screening process to facilitate the discovery of novelmedicines to allow for the prevention,management, or cure of disease. While this headline aim seems straightforward on paper, the reliable, timely, and dependable synthesis of NCEs remains an unpredictable art that calls for the application of robust and reliable chemical transformations to best ensure chances of success and to help alleviate the bottlenecks often caused by synthetic tractability issues within a drug discovery program. It is little wonder that chemists have therefore developed a repertoire of transformations that, to a greater or lesser extent, can be relied upon to furnish the desired derivatives across a variety of chemotypes and in the presence of varied pendent functionalities. This collection of amassed knowledge and experience of robust transformations is often referred to as the “chemist’s toolbox”, into which they can delve to select the best synthetic strategy to furnish the desired chemical transformation. However, the exact contents of this “toolbox” naturally vary between individual chemists, based largely upon personal experience. In a recent publication, we noted that “while a recent review has surveyed the reaction types most commonly used in the large scale manufacture of pharmaceuticals, no such review exists for those reactions favored in the small-scale synthesis of drug candidates. However, informal discussions between the authors and a small number of practicing medicinal chemists defined a number of key reaction types that were almost universally considered to be essential in the rapid synthesis of compounds for bio-assay”. While this small survey was useful for the intended purpose, we wondered how representative the findings would be of the work being conducted within the wider context of pharmaceutical R&D laboratories around the world. More interestingly, we considered whether this analysis would support many commonly expressed beliefs regarding the nature of this work. In our experiences, there are several statements frequently expressed by those both outside and within the medicinal chemistry community. For example, discussions with other chemists have revealed that many of our drug discovery colleagues outside the synthetic community perceive our syntheses to consist of typically six steps, predominantly composed of amine deprotections to facilitate amide formation reactions and Suzuki couplings to produce biaryl derivatives. These “typical” syntheses invariably result in large, flat, achiral derivatives destined for screening cascades. We believed these statements to be misconceptions, or at the very least exaggerations, but noted there was little if any hard evidence in the literature to support our case. To this end, we determined to analyze the reaction types used in the pursuit of novel drug candidates and evaluate their frequency of occurrence, alongside other factors such as drug likeness, chirality, and the number of steps to each derivative. Such a survey can never be truly comprehensive because of a multitude of factors. For example, company confidentiality means a substantial proportion of intellectual output remains within the confines of the organization and never enters the public domain through publication. Furthermore, the wealth of information in the literature is too great to wholly encompass in an analysis such as this. To this end, we elected to analyze a representative subset of the literature that we felt offered a sensible and manageable snapshot of the types of chemistries being applied to medicinal chemistry problems within the pharmaceutical industry. In parallel with the related analysis of reactions used to produce drug candidates themselves on large scale, we elected to analyze the published output from the medicinal chemistry departments of GlaxoSmithKline, Pfizer, and AstraZeneca, assuming that this would offer a wide summary of different therapeutic areas and chemical transformations and allowing a direct and meaningful comparison between the two ends of the chemistry effort in drug discovery and development. We determined that a survey of the three highest impact dedicated medicinal chemistry journals would best represent this output [Journal of Medicinal Chemistry (“JMC”; American Chemical Society, impact factor 4.898), Bioorganic and Medicinal Chemistry (“BMC”; Elsevier, impact factor 3.075), and Bioorganic andMedicinal Chemistry Letters (“BMCL”; Elsevier, Impact factor 2.822)] and chose to focus our analysis upon publications dating from 2008, the latest year for which the entire output was available at the start of the analysis process in late 2009. During the preparation of this manuscript, workers at GSK published a related analysis covering 4800 reactions performed specifically during the lead-optimization phase in the Respiratory CEDD at GSK, including reactions performed in the high-throughput parallel array synthesis of compound libraries. While offering only a representative overview of the reaction types employed and the products produced, this perspective article offers some insight into the chemistries regularly employed in pharmaceutical R&D laboratories around the world. Not only may this analysis prove or dispel some of the many myths and preconceptions that surround the work but we feel it may also prompt areas of further synthetic research, suggesting chemistries that are at present under-represented and in clear need of robust,

Tubulin as a target for anticancer drugs: agents which interact with the mitotic spindle.

Tubulin is the biochemical target for several clinically used anticancer drugs, including paclitaxel and the vinca alkaloids vincristine and vinblastine. This review describes both the natural and synthetic agents which are known to interact with tubulin. Syntheses of the more complex agents are referenced and the potential clinical use of the compounds is discussed. This review describes the biochemistry of tubulin, microtubules, and the mitotic spindle. The agents are discussed in relation to the type of binding site on the protein with which they interact. These are the colchicine, vinca alkaloid, rhizoxin/maytansine, and tubulin sulfhydryl binding sites. Also included are the agents which either bind at other sites or unknown sites on tubulin. The literature is reviewed up to October 1997.

Combining Hit Identification Strategies: Fragment- Based and in Silico Approaches to Orally Active 2-Aminothieno[2,3-D]Pyrimidine Inhibitors of the Hsp90 Molecular Chaperone.

Inhibitors of the Hsp90 molecular chaperone are showing considerable promise as potential molecular therapeutic agents for the treatment of cancer. Here we describe novel 2-aminothieno[2,3-d]pyrimidine ATP competitive Hsp90 inhibitors, which were designed by combining structural elements of distinct low affinity hits generated from fragment-based and in silico screening exercises in concert with structural information from X-ray protein crystallography. Examples from this series have high affinity (IC50 = 50-100 nM) for Hsp90 as measured in a fluorescence polarization (FP) competitive binding assay and are active in human cancer cell lines where they inhibit cell proliferation and exhibit a characteristic profile of depletion of oncogenic proteins and concomitant elevation of Hsp72. Several examples (34a, 34d and 34i) caused tumor growth regression at well tolerated doses when administered orally in a human BT474 human breast cancer xenograft model.

Drug-like annotation and duplicate analysis of a 23-supplier chemical database totalling 2.7 million compounds

We have implemented five drug-like filters, based on 1D and 2D molecular descriptors, and applied them to characterize the drug-like properties of commercially available chemical compounds. In addition to previously published filters (Lipinski and Veber), we implemented a filter for medicinal chemistry tractability based on lists of chemical features drawn up by a panel of medicinal chemists. A filter based on the modeling of aqueous solubility (>1 microM) was derived in-house, as well as another based on the modeling of Caco-2 passive membrane permeability (>10 nm/s). A library of 2.7 million compounds was collated from the 23 compound suppliers and analyzed with these filters, highlighting a tendency toward highly lipophilic compounds. The library contains 1.6 M unique structures, of which 37% (607,223) passed all five drug-like filters. None of the 23 suppliers provides all the members of the drug-like subset, emphasizing the benefit of considering compounds from various compound suppliers as a source of diversity for drug discovery.

Antagonists of the human adenosine A2A receptor. Part 3 Design and synthesis of pyrazolo[3,4-d]pyrimidines, pyrrolo[2,3-d]pyrimidines and 6-arylpurines

A series of pyrazolo[3,4-d]pyrimidine, pyrrolo[2,3-d]pyrimidine and 6-arylpurine adenosine A(2A) antagonists is described. Many examples were highly selective against the human A(1) receptor sub-type and were active in an in vivo model of Parkinsons disease.

Fragment-based hit identification: thinking in 3D

The identification of high-quality hits during the early phases of drug discovery is essential if projects are to have a realistic chance of progressing into clinical development and delivering marketed drugs. As the pharmaceutical industry goes through unprecedented change, there are increasing opportunities to collaborate via pre-competitive networks to marshal multifunctional resources and knowledge to drive impactful, innovative science. The 3D Fragment Consortium is developing fragment-screening libraries with enhanced 3D characteristics and evaluating their effect on the quality of fragment-based hit identification (FBHI) projects.

Antagonists of the human A(2A) adenosine receptor. 4. Design, synthesis, and preclinical evaluation of 7-aryltriazolo[4,5-d]pyrimidines.

Antagonism of the human A(2A) receptor has been implicated as a point of therapeutic intervention in the alleviation of the symptoms associated with Parkinsons disease. This is thought to occur, at least in part, by increasing the sensitivity of the dopaminergic neurons to the residual, depleted levels of striatal dopamine. We herein describe a novel series of functionalized triazolo[4,5-d]pyrimidine derivatives that display functional antagonism of the A(2A) receptor. Optimization of these compounds has resulted in improvements in potency, selectivity, and the pharmacokinetic properties of key derivatives. These efforts have led to the discovery of 60 (V2006/BIIB014), which demonstrates strong oral activity in commonly used models of Parkinsons disease. Furthermore, this derivative has shown excellent preclinical pharmacokinetics and has successfully completed phase I clinical studies. This compound is presently undergoing further clinical evaluation in collaboration with Biogen Idec.

Reversible inhibitors of LSD1 as therapeutic agents in acute myeloid leukemia: clinical significance and progress to date

In the 10 years since the discovery of lysine‐specific demethylase 1 (LSD1), this epigenetic eraser has emerged as an important target of interest in oncology. More specifically, research has demonstrated that it plays an essential role in the self‐renewal of leukemic stem cells in acute myeloid leukemia (AML). This review will cover clinical aspects of AML, the role of epigenetics in the disease, and discuss the research that led to the first irreversible inhibitors of LSD1 entering clinical trials for the treatment of AML in 2014. We also review recent achievements and progress in the development of potent and selective reversible inhibitors of LSD1. These compounds differ in their mode of action from tranylcypromine derivatives and could facilitate novel biochemical studies to probe the pathways mediated by LSD1. In this review, we will critically evaluate the strengths and weaknesses of published series of reversible LSD1 inhibitors. Overall, while the development of reversible inhibitors to date has been less fruitful than that of irreversible inhibitors, there is still the possibility for their use to facilitate further research into the roles and functions of LSD1 and to expand the therapeutic applications of LSD1 inhibitors in the clinic.

Development and evaluation of selective, reversible LSD1 inhibitors derived from fragments

Two series of aminothiazoles have been developed as reversible inhibitors of lysine specific demethylase 1 (LSD1) through the expansion of a hit derived from a high concentration biochemical fragment based screen of 2466 compounds. The potency of the initial fragment hit was increased 32-fold through synthesis, with one series of compounds showing clear structure–activity relationships and inhibitory activities in the range of 7 to 187 μM in a biochemical assay. This series also showed selectivity against the related FAD-dependent enzyme mono-amine oxidase A (MAO-A). Although a wide range of irreversible inhibitors of LSD1 have been reported with activities in the low nanomolar range, this work represents one of the first reported examples of a reversible small molecule inhibitor of LSD1 with clear SAR and selectivity against MAO-A, and could provide a platform for the development of more potent reversible inhibitors. Herein, we also report the use of a recently developed cell-based assay for profiling LSD1 inhibitors, and present results on our own compounds as well as a selection of recently described reversible LSD1 inhibitors.

Toxoflavins and Deazaflavins as the First Reported Selective Small Molecule Inhibitors of Tyrosyl-DNA Phosphodiesterase II

The recently discovered enzyme tyrosyl-DNA phosphodiesterase 2 (TDP2) has been implicated in the topoisomerase-mediated repair of DNA damage. In the clinical setting, it has been hypothesized that TDP2 may mediate drug resistance to topoisomerase II (topo II) inhibition by etoposide. Therefore, selective pharmacological inhibition of TDP2 is proposed as a novel approach to overcome intrinsic or acquired resistance to topo II-targeted drug therapy. Following a high-throughput screening (HTS) campaign, toxoflavins and deazaflavins were identified as the first reported sub-micromolar and selective inhibitors of this enzyme. Toxoflavin derivatives appeared to exhibit a clear structure-activity relationship (SAR) for TDP2 enzymatic inhibition. However, we observed a key redox liability of this series, and this, alongside early in vitro drug metabolism and pharmacokinetics (DMPK) issues, precluded further exploration. The deazaflavins were developed from a singleton HTS hit. This series showed distinct SAR and did not display redox activity; however low cell permeability proved to be a challenge.