A Non-Competitive Inhibitor of VCP/p97 and VPS4 Reveals Conserved Allosteric Circuits in Type I and II AAA ATPases

AAA ATPases have pivotal functions in diverse cellular processes essential for survival and proliferation. Revealing strategies for chemical inhibition of this class of enzymes is therefore of great interest for the development of novel chemotherapies or chemical tools. Here, we characterize the compound MSC1094308 as a reversible, allosteric inhibitor of the type II AAA ATPase human ubiquitin-directed unfoldase (VCP)/p97 and the type I AAA ATPase VPS4B. Subsequent proteomic, genetic and biochemical studies indicate that MSC1094308 binds to a previously characterized drugable hotspot of p97, thereby inhibiting the D2 ATPase activity. Our results furthermore indicate that a similar allosteric site exists in VPS4B, suggesting conserved allosteric circuits and drugable sites in both type I and II AAA ATPases. Our results may thus guide future chemical tool and drug discovery efforts for the biomedically relevant AAA ATPases.

Cell survival and protein secretion associated with Golgi integrity in response to Golgi stress-inducing agents

The Golgi apparatus is part of the secretory pathway and of central importance for modification, transport and sorting of proteins and lipids. ADP-ribosylation factors, whose activation can be blocked by brefeldin A (BFA), play a major role in functioning of the Golgi network and regulation of membrane traffic and are also involved in proliferation and migration of cancer cells. Due to high cytotoxicity and poor bioavailability, BFA has not passed the preclinical stage of drug development. Recently, AMF-26 and golgicide A have been described as novel inhibitors of the Golgi system with antitumor or bactericidal properties. We provide here further evidence that AMF-26 closely mirrors the mode of action of BFA but is less potent. Using several human cancer cell lines, we studied the effects of AMF-26, BFA and golgicide A on cell homeostasis including Golgi structure, endoplasmic reticulum (ER) stress markers, secretion and viability, and found overall a significant correlation between these parameters. Furthermore, modulation of ADP-ribosylation factor expression has a profound impact on Golgi organization and survival in response to Golgi stress inducers.

Functional analysis of Hsp70 inhibitors

The molecular chaperones of the Hsp70 family have been recognized as targets for anti-cancer therapy. Since several paralogs of Hsp70 proteins exist in cytosol, endoplasmic reticulum and mitochondria, we investigated which isoform needs to be down-regulated for reducing viability of cancer cells. For two recently identified small molecule inhibitors, VER-155008 and 2-phenylethynesulfonamide (PES), which are proposed to target different sites in Hsp70s, we analyzed the molecular mode of action in vitro. We found that for significant reduction of viability of cancer cells simultaneous knockdown of heat-inducible Hsp70 (HSPA1) and constitutive Hsc70 (HSPA8) is necessary. The compound VER-155008, which binds to the nucleotide binding site of Hsp70, arrests the nucleotide binding domain (NBD) in a half-open conformation and thereby acts as ATP-competitive inhibitor that prevents allosteric control between NBD and substrate binding domain (SBD). Compound PES interacts with the SBD of Hsp70 in an unspecific, detergent-like fashion, under the conditions tested. None of the two inhibitors investigated was isoform-specific.

Fragment-based discovery of hydroxy-indazole-carboxamides as novel small molecule inhibitors of Hsp90

Inhibitors of the Hsp90 molecular chaperone are showing considerable promise as potential molecular therapeutic agents for the treatment of cancer. Here we describe the identification of novel small molecular weight inhibitors of Hsp90 using a fragment based approach. Fragments were selected by docking, tested in a biochemical assay and the confirmed hits were crystallized. Information gained from X-ray structures of these fragments and other chemotypes was used to drive the fragment evolution process. Optimization of these high μM binders resulted in 3-benzylindazole derivatives with significantly improved affinity and anti-proliferative effects in different human cancer cell lines.

Abstract 2639: Discovery of novel small molecule inhibitors of Hsp90 for oral treatment

Hsp90 is a molecular chaperone that plays an important role in the folding and function of client protein substrates in the cell. Many of these client proteins are well known oncogenes that are often over-expressed and mutated in tumor cells and association of Hsp90 with these client proteins maintains their ability to function in the deregulated state. Therefore Hsp90 inhibitors target tumor growth by multiple parallel mechanisms involving several oncogenes, which are critically involved in cell cycle, tumor growth, angiogenesis and apoptosis.

Here we will present HTS and structure based design efforts to identify novel chemotypes that show potent binding to HSP90. In particular a 5-methyl-1H-pyrazol-3-yl-benzene-1,3-diol derivative (1) was identified during an HTS as a potent starting point for further optimization. This initial hit already showed an IC50 of 240nM in a HSP90 binding assay. The HSP90 co-crystal structure of this initial HTS hit revealed its binding mode to the N-terminal ATPase pocket and thus guided subsequent optimization of this structural series towards potency and oral bioavailability. Especially the identification of a new binding pocket for the ethyl group in (1) opened the route for the introduction of a broad variety of substituents. In addition to these variations the pyrazole core in (1) was replaced by a triazolone system. Although the SAR with respect to in vitro potency is comparable for both series, this fine tuning led to compounds with improved bioavailability and in vivo potency.

The most promising candidates from both series were screened for selectivity against other ATPases, kinases and ion channels where they turned out to be completely HSP90 selective. In vivo tumor xenografts using prostate cancer cell line PC3, colon carcinoma HCT116 (KRAS mutation: mechanism of resistance against EGFR inhibitor in mCRC) and NSCLC tumor H1975 (EGFR-T790M mutation: mechanism of resistance against EGFR TKI) demonstrated excellent anti-tumor activity under different schedules after oral and iv administration. Biomarker analysis demonstrated efficient dose and time-dependent down-regulation of EGFR, phospho-Erk, cyclin D1 and up-regulation of Hsp70 as well as induction of apoptosis as determined by the increase of cleaved PARP and cleaved caspase 3. Favorably PK/PD studies revealed extraordinary long lasting compound levels in tumor tissue and long lasting pharmacodynamic effects (for more than 5 days in the tumors), indicating prolonged Hsp90 inhibition in tumor tissue in contrast to healthy tissue, from which the triazolones were rapidly cleared. The overall profile of the triazolones including synthesis, structure activity relationships, X-ray structures as well as a comprehensive pharmacological in vitro and in vivo characterization, together with potential pharmacodynamic and predictive biomarkers will be presented.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 2639.