Kinases as Targets for Drug Discovery in an Academic Setting

August 01, 2011

Drug discovery at its most basic is the creation or discovery of a compound that will modify a biological process to ameliorate an unwanted condition. As such, almost every drug has its roots in academic research. While the drug in question can span myriad diseases and biological target areas, the basic biology underlying its discovery usually came to light in an academic research lab. That being said, the process of converting the conceptual knowledge into a human therapeutic has remained primarily the domain of the pharmaceutical industry for the last 50 years.

But the pharmaceutical industry is undergoing sweeping changes. Bottom line-driven cuts in pharmaceutical research combined with a continued desire for novel treatments at lower costs are fundamentally rearranging drug discovery and leading to the creation of more and more academic and government-based programs. These range from major initiatives such as the proposal to create a new translational research center within the NIH [1,2] and the National Cancer Institute’s (NCI) re-entry into drug development [3,4] to academic centers like the University of North Carolina’s Center for Integrative Chemical Biology and Drug Discovery (CICBDD). These programs are recruiting experienced staff and have access to higher quality chemical libraries than at any time in the past[5].

The CICBDD typifies the “new breed” of academic drug discovery centers; groups that include faculty with extensive experience in medicinal chemistry, assay development, computational chemistry and high throughput screening, as well as staff that support each of these functions [6].

The CICBDD was created with the mission of bringing dedicated medicinal chemistry expertise to bear on biological targets of therapeutic relevance under investigation by UNC faculty. Synthetic chemists, assay development and compound profiling scientists work in the Center and create dedicated, multidisciplinary project teams with other groups on campus in order to progress targets through the drug discovery and development process. In addition to targets developed in collaboration with UNC faculty, the CICBDD is a Chemical Biology Center in the NCI Experimental Therapeutics Program (NExT) and pursues a research program to develop chemical probes for epigenetic targets [7,8].

The target portfolio of the CICBDD mimics the diversity of this broad research base (Figure 1). What differentiates the academic portfolio from a comparable pipeline in industry is the targets themselves. Academic discovery groups generally try to avoid direct competition with big pharma and also have access to target biology at earlier stages of validation, that is, targets where a disease association has only recently been demonstrated. Targets in the CICBDD portfolio also tend to contain a higher percentage of orphan diseases.

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Figure 1: Target distribution at the CICBDD. Kinases of all types represent >25% of all targets in the portfolio with protein kinases accounting for 22%. Excluding internal programs in epigenetics, the total kinase percentage increases to 33%.

Interestingly, once the epigenetic targets are removed, kinase targets make up one third of the portfolio. Kinases are a well-validated target class with a wellunderstood, tractable mechanism, a well-mapped genomic family [9,10] and available structural data on many members [11] that has produced several marketed drugs so this is not surprising [12-14]. Even so, a large portion of the human kinome remains untapped for drug discovery [15]. Three examples of kinase targets currently in the CICBDD portfolio follow that typify attractive kinase groups for academic drug discovery: 1) neglected or overlooked kinases, 2) novel orphan kinases, and 3) near neighbors to well-prosecuted targets (Figure 2).

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The UNC CICBDD protein kinase portfolio as compared to industry patents. The number of patents per target is reflected by the size and color of the dot. UNC targets are represented by blue arrows. Generously supplied by Knapp, S. and adapted with permission from the author (15).

Mer Kinase

Mer receptor tyrosine kinase is an example of a neglected target with clear disease validation [16], but of little interest to pharma due to the small target population and the possible need for combination therapy. Mer is part of the TAM (Tyro-3, Axl, Mer) family, whose over-expression in a wide range of human cancers points to a role in oncogenesis. While TAM’ kinases are largely nonessential for early development, their distribution in adults is widespread, with a distinct expression profile for each. Mer’s profile is more restricted, and is not expressed in normal lymphocytes, but over-expressed in 60% of childhood acute lymphoblastic leukemias (ALL). Sadly, this ectopic expression of Mer correlates with a poor clinical outcome [17]. In addition, Mer may play a role in other cancers: Mer is involved in the ingestion of apoptotic cells by monocytes and can suppress cytokine synthesis in stimulated monocytes [18], Mer is present in tumor associated macrophages and may play a role in breast cancer [19]; and Mer activates the intracellular kinase Ack1 which causes the androgen receptor to become ligand independent leading to prostate neoplasia in mouse models [20]. Thus, small molecule Mer inhibitors may have utility beyond chemoresistant pediatric ALL in blocking cell survival, migration, invasion, metastasis and and chemoresistance [21].

The TAM kinases have a unique tyrosine kinase domain sequence, which improves the chances of developing a selective inhibitor, although no potent and selective inhibitors were reported prior to our efforts. Additionally, a crystal structure of Mer bound to a small molecule was available as a starting point for docking studies and virtual screening [22]. With support from the NCI NeXT Program, the CICBDD has successfully developed nanomolar type II Mer inhibitors with greater than 10-fold selectivity over family members Axl and Tyro-3 with good structure activity relationship (SA R) data. These inhibitors are currently in lead optimization.

The success of this program is due in no small part to our ability to combine the drug discovery capabilities of the CICBDD with extensive onsite basic science expertise. We were fortunate to collaborate with Dr. Shelton Earp, Director of the Lineberger Comprehensive Cancer Center at UNC, on this target. Dr. Earp’s lab first cloned and sequenced Mer, and he is a worldrenown expert in TAM kinases and acute lymphocytic leukemia (ALL) with over 40 publications in this field alone. Further, as a clinician who still sees patients, Dr. Earp is well-positioned to understand the needs of the patient community.

Ror2 Kinase

Ror2 is a novel orphan kinase target and was one of the first targets to enter the CICBDD portfolio. Ror2 is a transmembrane receptor tyrosine kinase containing an extracellular Frizzled (Fz) domain and has been implicated in the Wnt/β-catenin signaling pathway. Ror2’s upregulation in many renal cell carcinomas (RCC) and human tumors was discovered only recently by Dr. Kimryn Rathmell, our collaborator for this project [23]. Dr. Rathmell, who is also a clinician, and her lab identified the requirement of inactivation of the tumor suppressor von Hippel-Lindau (VHL) and/or stabilization of hypoxia inducible factor (HIF) for expression of Ror2 in RCC, both common events in the pathogenesis of RCC [24]. Assay development efforts were funded by UNC’s TraCS Institute in 2010.

Although Ror2 entered the CICBDD portfolio early, difficulties in the production of active protein combined with limited funding have made progress slow and it is still in the screening stage. This is not atypical for novel kinases. Timelines for these targets tend to be long and funding for these projects tends to be limited. However, unlike pharma, academic centers are ideally suited to the job of progressing these targets where time to market is less important than novel disease mechanisms and lower levels of funding can partially support efforts through the use of postdoctoral fellows and graduate students.

BK/IKKε

TBK1 and IKKε are examples of near neighbor targets. Close family members IKKα and IKKβ have been considered major drug targets for some time [25] but IKKε and TBK1 have been relegated to the status of counterscreens so no potent and selective inhibitors for either kinase currently exist. Yet, IKKε is over-expressed in breast and ovarian cancers and is associated with tumor progression and cancer therapy resistance. Further, IKKε has been shown to activate the transcription factor NF-κB in cancers via p65/RelA ser536 phosphorylation in cancer cells. However, neither IKKε nor TBK1 contribute to the activation of NF-κB regulation downstream of TNF, IL-1 or LPS induced signaling [26]. Blocking this activation suppresses in situ oncogenesis in several animal models [27,28]. TBK1 is activated by the RalB-GTPase, an important downstream effector in the Ras pathway [29]. Making use of a novel substrate identified by our collaborator for this project [30], we have taken a target family approach and successfully screened these targets and IKKα in parallel to identify selective hits of each.

So while the jury is still out on the ultimate success of Academic Drug Discovery, it is clear that the immediate goal of bringing resources to bear on neglected, novel and simply difficult targets is being met. While most will fail on the long road to market, at least in the academic arena they will still contribute to our collective scientific knowledge because their academic origins will mean that all of the related results will be made public in peer-reviewed journals and the compounds will be available as chemical probes.

Acknowledgements

Work for Mer Kinase was supported by federal funds from the National Cancer Institute, under Contract No. HHSN261200800001E.

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