Structure-based design of novel human Pin1 inhibitors (III): optimizing affinity beyond the phosphate recognition pocket.

The design of potent Pin1 inhibitors has been challenging because its active site specifically recognizes a phospho-protein epitope. The de novo design of phosphate-based Pin1 inhibitors focusing on the phosphate recognition pocket and the successful replacement of the phosphate group with a carboxylate have been previously reported. The potency of the carboxylate series is now further improved through structure-based optimization of ligand-protein interactions in the proline binding site which exploits the H-bond interactions necessary for Pin1 catalytic function. Further optimization using a focused library approach led to the discovery of low nanomolar non-phosphate small molecular Pin1 inhibitors. Structural modifications designed to improve cell permeability resulted in Pin1 inhibitors with low micromolar anti-proliferative activities against cancer cells.

Novel isoquinolone PDK1 inhibitors discovered through fragment-based lead discovery.

Phosphoinositide-dependent kinase-1 (PDK1) is a critical enzyme in the PI3K/AKT pathway and to the activation of AGC family protein kinases, including S6K, SGK, and PKC. Dysregulation of this pathway plays a key role in cancer cell growth, survival and tumor angiogenesis. As such, inhibitors of PDK1 offer the promise of a new therapeutic modality for cancer treatment. Fragment based drug screening has recently become a viable entry point for hit identification. In this work, NMR spectroscopy fragment screening of PDK1 afforded novel chemotypes as orthogonal starting points from HTS screening hits. Compounds identified as hits by NMR spectroscopy were tested in a biochemical assay, and fragments with activity in both assays were clustered. The Pfizer compound file was mined via substructure and 2D similarity search, and the chemotypes were prioritized by ligand efficiency (LE), SAR mining, chemical attractiveness, and chemical enablement of promising vectors. From this effort, an isoquinolone fragment hit, 5 (IC(50) 870 µM, LE = 0.39), was identified as a novel, ligand efficient inhibitor of PDK1 and a suitable scaffold for further optimization. Initially in the absence of crystallographic data, a fragment growing approach efficiently explored four vectors of the isoquinolone scaffold via parallel synthesis to afford a compound with crystallographic data, 16 (IC(50) 41.4 µM, LE = 0.33). Subsequent lead optimization efforts provided 24 (IC(50) 1.8 µM, LE = 0.42), with greater than fivefold selectivity against other key pathway kinases.

Structure-based design of novel human Pin1 inhibitors (II).

Following the discovery of a novel series of phosphate-containing small molecular Pin1 inhibitors, the drug design strategy shifted to replacement of the phosphate group with an isostere with potential better pharmaceutical properties. The initial loss in potency of carboxylate analogs was likely due to weaker charge-charge interactions in the putative phosphate binding pocket and was subsequently recovered by structure-based optimization of ligand-protein interactions in the proline binding site, leading to the discovery of a sub-micromolar non-phosphate small molecular Pin1 inhibitor.

Structure-based design of novel human Pin1 inhibitors (I).

Pin1 is a member of the cis-trans peptidyl-prolyl isomerase family with potential anti-cancer therapeutic value. Here we report structure-based de novo design and optimization of novel Pin1 inhibitors. Without a viable lead from internal screenings, we designed a series of novel Pin1 inhibitors by interrogating and exploring a protein crystal structure of Pin1. The ligand efficiency of the initial concept molecule was optimized with integrated SBDD and parallel chemistry approaches, resulting in a more attractive lead series.

Dihydroxylphenyl amides as inhibitors of the Hsp90 molecular chaperone.

Information from X-ray crystal structures were used to optimize the potency of a HTS hit in a Hsp90 competitive binding assay. A class of novel and potent small molecule Hsp90 inhibitors were thereby identified. Enantio-pure compounds 31 and 33 were potent in PGA-based competitive binding assay and inhibited proliferation of various human cancer cell lines in vitro, with IC(50) values averaging 20 nM.

Synthesis and Reactions of 3-(Nosyloxy)-2-keto Esters.

A series of 3-(nosyloxy)-2-keto esters 7a-j were prepared from the corresponding alpha-keto esters by conversion to the trimethylsilyl enol ether and reaction with p-nitrobenzenesulfonyl peroxide. Conversion of these materials to 1,2,3-trifunctionalized compounds is described, and comparison of their properties with isomeric 2-(nosyloxy)-3-keto esters is discussed.

Discovery of pyrroloaminopyrazoles as novel PAK inhibitors.

The P21-activated kinases (PAK) are emerging antitumor therapeutic targets. In this paper, we describe the discovery of potent PAK inhibitors guided by structure-based drug design. In addition, the efflux of the pyrrolopyrazole series was effectively reduced by applying multiple medicinal chemistry strategies, leading to a series of PAK inhibitors that are orally active in inhibiting tumor growth in vivo.

Design, synthesis, and biological evaluation of novel human 5'-deoxy-5'-methylthioadenosine phosphorylase (MTAP) substrates.

The structure-based design, chemical synthesis, and biological evaluation of novel MTAP substrates are described. These compounds incorporate various C5'-moieties and are shown to have different k(cat)/K(m) values compared with the natural MTAP substrate (MTA).

Synthesis of 2-oxazolone-4-carboxylates from 3-nosyloxy- and 3-bromo-2-ketoesters.

New methods for the synthesis of 2-oxazolone-4-carboxylates from 3-nosyloxy- and 3-bromo-2-ketoesters are described. Condensation of 3-nosyloxy-2-ketoesters with methyl carbamate in refluxing toluene in the presence of p-TSA provided 2-oxazolone-4-carboxylates in good yields (41-80%). Alternatively, bromination of alpha-ketoesters with CuBr2 provided 3-bromo-2-ketoesters which condensed with methyl carbamate in the presence of p-TSA and AgOTf under similar conditions to provide 2-oxazolone-4-carboxylates in comparable yields (30-79%). The 2-oxazolone-4-carboxylates bear functionality that can be elaborated to a variety of potentially useful compounds. For example, some of these heterocycles were readily N-acylated, reduced to alcohols, or saponified and coupled with amino acids.