Current Topics in Medicinal Chemistry - Volume 3, Issue 10, 2003

Protein prenylation involves the post-translational modification of specific protein-derived cysteine residues with farnesyl or geranylgeranyl groups through thioether linkages. Because a large number of proteins that participate in signal transduction processes require this modification, there has been intense interest in developing inhibitors of these enzymes and in clarifying the biological function of prenylation. Isoprenoid analogues have proven to be versatile tools for probing the mechanism and structure of prenyltransferases. Mechanistic probes have been created to investigate the stereochemical course and substituent effects in prenyltransferase catalyzed reactions. They have also been used to measure kinetic isotope effects and search for possible cationic intermediates. Photoaffinity labeling analogues containing either diazotrifluoropropionate or benzophenone units have been used to identify the location of isoprenoid binding sites in these enzymes. Biophysical probes incorporating fluorescent moieties or isotopic labels have been used to measure isoprenoid dissociation constants or prenyl group conformation when bound to the enzyme. Analogues containing noncognate alkene isomers or bulky substituents have also contributed to an understanding of isoprenoid recognition. Most recently, photoactive and isomeric isoprenylated analogues are providing insights into the function of protein prenylation.

The development of farnesyltransferase inhibitors, a novel approach to non-cytotoxic anticancer therapy, has been an active area of research over the past decade. Compounds that have advanced to clinical trials were evolved both from substrate-based design efforts and from compound library screening hits. This review focuses on the effort at Merck to evolve inhibitors from the protein substrate of farnesyltransferase, which resulted in the identification of a non-peptide inhibitor for clinical evaluation. X-ray crystal structures of farnesyltransferase complexed with early peptidomimetic as well as later non-peptide inhibitors have validated this design approach. NMR spectroscopic methods for studying enzyme-bound inhibitor structure, in conjunction with the use of conformational constraints, were critical components of subsequent efforts to provide potent inhibitors with varying levels of farnesyltransferase and geranylgeranyltransferase-I inhibitory specificity. Several of these compounds were important tools for investigating the use of prenyltransferase inhibitors to target Ki-Ras-mediated tumor growth.

R115777 (R)-6-amino[(4-chlorophenyl)(1-methyl-1H-imidazol-5-yl)methyl]-4-(3-chlorophenyl )-1- methyl-2(1H)-quinolinone is a potent and selective inhibitor of farnesyl protein transferase with significant antitumor effects in vivo subsequent to oral administration in mice. Taking its roots into Janssen's ketoconazole and retinoic acid catabolism programs, our interest into Ras prenylation process led us stepwise to identify the key structural features of R115777. Methodology, structure activity relationships, and pharmacology will be presented. R115777 is currently in phase III clinical evaluation.

Farnesyl Protein Transferase as a target for therapeutic intervention is currently under investigation in human clinical trials. Sch-66336 (sarasar®), a benzocycloheptapyridyl Farnesyl Transferase Inhibitor (FTI), has been found to be effective in cellular proliferation assays and in in vivo oncology models both as a single agent and in combination with other anti-cancer agents. Clinically, early evidence is being generated that suggests efficacy in humans, particularly in patients with leukemia. Herein, we review the biology of FPT, the discovery of Sch-66336 and other benzocycloheptapyridyl FTIs, and the clinical evaluation of Sch-66336 for the treatment of leukemia and solid tumors.

Inhibition of thrombin receptor (PAR-1) is a promising therapeutic approach for the treatment of various cardiovascular disorders such as unstable angina, acute myocardial infarction, stroke, and restenosis. Since a PAR- 1 antagonist is specific for the cellulalr actions of thrombin, and does not interfere with fibrin generation, it is expected to have less bleeding liability than the currently available treatments. Several peptide and non-peptide PAR-1 antagonists with potent inhibition of platelet aggregation have been reported. Antithrombotic effect of a PAR-1 antibody has been demonstrated in a baboon thrombosis model and the antirestenosis property of a PAR-1 antagonist has been demonstrated in a rat model.

Major reasons preventing many early candidates reaching market are the inappropriate ADME (absorption, distribution, metabolism and excretion) properties and drug-induced toxicity. From a commercial perspective, it is desirable that poorly behaved compounds are removed early in the discovery phase rather than during the more costly drug development phases. As a consequence, over the past decade, ADME and toxicity (ADMET) screening studies have been incorporated earlier in the drug discovery phase. The intent of this review is to introduce the desirable attributes of a new chemical entity (NCE) to the medicinal chemist from an ADMET perspective. Fundamental concepts, key tools, reagents and experimental approaches used by the drug metabolism scientist to aid a modern project team in predicting human pharmacokinetics and assessing the “drug-like”molecule are discussed.

A wide range of neurotransmitters, polypeptides and inflammatory mediators transduce their signals into the interior of cell by specific interactions with cell-surface receptors that are coupled to G-protein. The most familiar G-protein-coupled receptors are muscarinic receptors, adrenergic receptors, dopaminergic receptors and opioid receptors. A single polypeptide chain of 400-500 residues forms most of these receptors. There are seven hydrophobic regions in the receptor and they correspond to transmembrane α-helices, which are membrane spanning domains. This topology is highly conserved among various members of the family of G-protein coupled receptors. The amino-terminal extracellular domain contains potential N-linked glycosylation sites in most receptors. The carboxyl-terminal is involved in the coupling to G-proteins and contains a cysteine site and phosphorylation site (Thr, Ser) and both are involved in receptor desensitization. In this section of the review we will discuss the development of potent, selective, low molecular weight antagonists of two G-protein coupled receptors (M2 muscarinic receptor and CCR5 chemokine receptor) and their potential therapeutic utilities.The initial leads in both antagonist programs came from in house screening of our sample collections. As expected, most of the initial leads for both programs shared a similar pharmacophore and because of this showed strong affinity to many if not few a other G-protein coupled receptors. The initial significant challenge in both programs in terms of structure-activity studies was not only to optimize the structures for potency but also selectivity versus other subtype receptors. In the M2 antagonist program the selectivity versus M1 and other subtypes was a major challenge. Similarly in the CCR5 antagonist program the selectivity versus M2 was a significant issue to overcome. In this review we will discuss in detail the structure activity relationships that resulted in potent and selective antagonists.

Methods for the prediction of octanol / water partition coefficient, aqueous solubility and acid / base dissociation constants are described and discussed. The advantages and limitations of the different approaches are described and an indication of problem areas discussed. Available prediction software is described and listed and attempts are made to assess the likely reliability of the predictions. The concept of “drug-likeness” is introduced and put into context and models for the prediction of ADME properties and toxicity are briefly described and assessed. Software for ADME / toxicity prediction is listed and the impact of these techniques on current drug design efforts is described. Web references are given for both commercial and public domain software which is available for property prediction from chemical structure.