Moving Molecules from the Academic Lab to the Clinic

Past Tides
July 17, 2017 By Wendy Wolfson

In the UCI Cancer Research Institute May 25 symposium, “Moving Molecules from the Academic Lab to the Clinic,” scientists from around the country discussed academic-industry collaborations to commercialize clinical therapies. Post-doctoral students presented their work in a series of poster sessions at the event. The newly-inaugurated UCI Drug Discovery Consortium supports development of therapeutics and offers research teams a $50,000 award for promising drug discovery candidates.


Targeting APC-Mutated Colon Cancer

Jef De Brabander, professor of Biochemistry at the University of Texas Southwestern Medical Center at Dallas, opened the sessions with a talk, “A targeted approach towards APC-Mutated Colon Cancer: Discovery Biology to Pre-Clinical Efficacy.” De Brabander’s lab is investigating the roles of genetics, cholesterol, and insulin signaling in the proliferation of colon cancer cells, with the goal of developing potential drug targets that could selectively arrest the growth of colon cancer cells. De Brabander is also researching APC biology and the role of the destruction complex.

Specifically, De Brabander is studying compounds that can target mutations in the adenomatous polyposis coli (APC) gene which has a regulatory function in intestinal biology. The colon turns over cells in the intestinal lining every six days. For this to occur, multiple cellular programs have to work together precisely. Interestingly, the APC gene is commonly mutated in colon cancer but not in any other cancer. “Nature doesn’t come up with these very complex platforms for just one function,” De Brabander said.


Ligand-targeted imaging and therapeutic agents

Next, Professor Philip Low, director of the Purdue Institute for Drug Discovery, and Ralph C. Corley, distinguished professor of chemistry at Purdue University, described a platform of ligand-targeted imaging and therapeutic agents for cancer, autoimmune, and infectious diseases. Low is also Chief Scientific Officer of Endocyte, On Target Laboratories, HuLow, LLC. and Novosteo, Inc. – companies that developed technology platforms of small molecule drug conjugates for a variety of diseases.

This platform of small molecule drug conjugates comprises a targeting ligand, a spacer/linker, and the payload molecule which can be a drug or an imaging agent. The platform can be customized to facilitate the targeted diagnosis or therapy of a broad range of cancers. For example, Low’s lab uses the conjugate platform to target folate receptors, which are over expressed in many human cancers. Folate receptor B is expressed on tumor-associated macrophages.

The platform can also be used to target a bright fluorescent imaging agent for cancer cells that are otherwise undetectable by the naked eye. Low showed the audience a video of an operation to remove multiple ovarian cancer nodules, during which the targeted dye molecules highlighted cancer cells that were still left over after the surgeon had finished the surgery. “You can see the lesions that the surgeon misses are small,” Low says. “They are no larger than the tip of the forceps, but they can still kill you. hen you turn off the fluorescent lamp, you cannot distinguish these malignant lesions from the normal tissue.”


How the platform works

Low’s lab screens diseased cells for unique receptors. Once they identify a target receptor, they then design a targeting ligand that can bind to the receptor with high affinity. They can then attach a small molecule imaging agent, such as a radionuclide, to the targeting ligand and use existing nuclear imaging equipment to highlight any biological activity. The imaging agent enables them to test preclinical animal models and humans to ascertain whether the drug-ligand conjugant is selectively targeting the diseased cells. This method also enables them to subsequently attach drug payloads comprising extremely potent, highly active molecules that are too toxic to be given in therapeutic doses in their untargeted forms.

Low’s lab has also developed a prostate-specific membrane antigen (PSMA) – targeting technology that uses a targeting ligand to bind to a specific receptor expressed only on the surface of prostate cancer cells.


Saving babies

Jolanta Grembecka, associate professor in the Department of Pathology at the University of Michigan, covered therapeutic targeting of epigenetic regulators in acute leukemia. Her lab is developing small molecules that can block recruitment of epigenetic modifiers of the protein interactions of menin/MLL. Menin, a protein encoded by the Men1 gene, is a scaffold protein involved in the recruitment of multiple proteins to the target gene. Menin is needed to activate gene expression, but this protein is also a key player in a particularly lethal subtype of leukemia called mixed lineage leukemia (MLL), where genes are translocated – that is, a gene is broken off and attached to another gene. From 5% to 10% of acute leukemias in adults, and 70% of acute leukemias in infants, have these abnormal gene fusions which lead to cancers that resist treatment. Patients with these cancers have a poor outlook; only 35% of patients survive five years after diagnosis.

Grembacka’s lab has been developing a small molecule inhibitor of the protein-protein interaction of menin/MLL. The two compounds they developed, ML-503 and ML 463, in in vitro testing on patients’ sample cells and in MLL mice, slow progression of leukemia. Another lab is using their compounds in castration-resistant prostate cancer to inhibit the growth of MLL leukemia cells. This application is now in preclinical testing with San Diego-based biotech, Kura Oncology.


Synergizers for Anti-Fungal Drugs

Next, Aaron Mood, graduate student in chemistry in the Van Vranken Lab at UCI, reviewed the history and biology of azole drugs in “Spiroindolinone Synergizers of Azole Antifungal Drugs.” When fungal infections become systemic and spread throughout the body, they can be lethal. “Forty percent of people who get systemic fungal infections will end up dying,” Mood notes.

Immunocompromised people who are taking drugs to suppress their immune systems after organ transplants are either undergoing chemotherapy, have leukemia, are in the ICU, or have HIV and are particularly vulnerable to fungal infections. Candida albicans, a type of yeast, is a common pathogen in systemic fungal infections. The antifungal fluconazole is the first line of defense, but C. albicans has become increasingly drug-resistant. In the 1990s, companies synthesized drugs that improved upon fluconazole, such as Savuconazole (CresembaTM by Astellas),which was  approved in 2015 and has a projected $500 million market.

Recently, investigators have taken a different approach to azole-resistant fungal infections by using combination drugs that enhance the effects of azoles. According to Mood, the benefits of this strategy are that lower doses are necessary, making treatment less costly and toxic for patients.

Researchers in the Lindquist and Schreiber laboratories at the Broad Institute in Cambridge, Massachusetts screened over 300,000 potential compounds that could be combined with azoles to enhance treatment. Out of three final candidates, none were active below a certain dose range. Using another hit from the Lindquist-Schreiber lab screen, the Van Vranken lab developed a fluconazole analogue, dubbed syanzo-1, which worked synergistically with azoles – even with isavuconazole. Each compound enhanced the effect of the other in vitro and were non-toxic to mammalian cells. Mood’s team has developed some promising Spiroindolinone synergizers of azole antifungal drugs.


Starving Cancer Cells to Death

Dr. Alison McCracken, post doc in the Edinger Laboratory at UCI, presented, “Starving Cancer Cells to Death with Sphingolipids.” Phytosphingosine is a natural sphingolipid that helps heat-stressed yeast take up fewer nutrients. The Edinger team thought that they could use this mechanism to deal with cancer cells, which continually require food to fuel their proliferation. Normal cells can respond to stress by slowing activity, but cut off the food supply of cancer cells and cells enter a bioenergetic crisis and die. Using FTY720, an FDA-approved compound that mimics the effects of phytosphingosine, Edinger’s team achieved the same effect.

But at the anti-cancer dose, FTY720 unacceptably lowered the heart rate in mice. “This means that FTY720 can’t be given to humans at an anti-cancer dose, which is higher than the immunosuppressive dose,” McCracken says.

Working with the Hanessian Lab at UCI, Edinger’s team optimized the compound to develop an analogue for FTY720 that did not show the heart rate effects. The analogue doesn’t target the same receptors, but still retains the ability to starve cancer cells to death, as it blocks both the primary and adaptive nutrient access pathways.

In collaboration with the oncology group of Dr. Dennis Slamon at UCLA, the Edinger team determined that their analogue SH-BC-893 was active against many cancers, and that driver mutations and tissue of origin were not that important in sensitivity. They tested the compound in mouse models of colorectal and prostate cancer and found that the analogue was able to reduce tumors without damaging normal tissue. When tested in prostate cancer organoids, which are clusters of prostate cancer cells that act like a tiny tumor in a dish, they found that the analogue worked better than enzalutamide – the compound administered as the standard of care for prostate cancer. SH-BC-893 is now being commercialized by Obsidio Therapeutics, a startup founded by professors Aimee Edinger and Stephen Hanessian.


A surprisingly good fit

In his talk, “Inhibition of Mediator Kinases as a Therapeutic Approach to Cancer,” Matthew Shair, professor of chemistry and chemical biology at Harvard University, recounted a story about his lab’s work with cortistatin A – a small molecule which inhibits two mediator kinases as a treatment for acute myeloid leukemia (AML). According to Shair, AML is largely a disease of misregulated gene expression.

Over the last ten years, the exomes of many AML patients have been sequenced. “Interestingly, AML has the smallest number of mutations of any type of cancer,” Shair says. “It doesn’t take much to transform a hemapoetic stem cell to a leukemic stem cell that evolves into full-blown acute myeloid leukemia.” Eventually, these tumor cells crowd out the bone marrow, completely blocking hematopoiesis or blood cell production. “It turns out this is one of the worst cancers to have,” Shair says. “The overall five-year survival rate is about 20%.” There had not been a new AML therapy in 25 years until a few weeks ago, when Novartis announced its FLT3 inhibitor for AML.

Many of the mutations in protein-coding sequences of AML patients are associated with proteins that regulate transcription of DNA to RNA, which is then translated to proteins—essentially, how the genome is read out and turned into proteins. But these targets are challenging to directly drug, so Shair’s team took an indirect approach, using small molecules to target the transcriptional machinery of the cancer cells instead.

Shair recounted that he had some cortistatin A in the freezer that his team had synthesized. They were using it as a probe to explore the function of certain kinases, which are enzymes that modify other proteins. Cortistatin A is a small molecule that was originally isolated from an undersea sponge by a Japanese group in a quest for a compound that could inhibit angiogenesis, the proliferation of blood vessels necessary for tumor growth. Shair was aware of cortistatin A’s kinase-inhibiting properties from a paper published by Amgen researchers, but Amgen was not currently pursuing development of the molecule. “One opportunity for academics is looking for molecules that drug companies are too risk-averse to deal with,” Shair says.


Stereochemistry means no rotatable bonds

Shair’s team found that in cells, cortistatin A selectively inhibited a pair of nearly identical kinases, CDK8 and CDK19. “They are the only known enzymes to associate with this behemoth 30-protein mediator complex,” Shair says. Cortistatin A’s selectivity means there is less of a chance for off-target toxicity. “It binds precisely in the ATP-binding site of CDK8,” Shair says. “Nature is pulling out all the stops to make a potent inhibitor for CDK8 (CDK19 is effectively similar).” According to Shair, the key to the perfect fit is stereochemistry, as there are no rotatable bonds in this molecule.

In testing in mice, cortistatin A potently inhibited AML progression. Shair’s team hypothesized that cortistatin A functioned as a “super-regulator,” both up- and down-regulating gene expression. Cortistatin A did not kill the AML cells, but it inhibited their growth in animal tests.