BreakThrough Digest Medical News |
- Moving 3D computer model of key human protein is powerful new tool in fight against cancer
- Inhibitors of shuttle molecule show promise in acute leukemia
- New studies hint at possible approaches to protect those at risk for Huntington’s disease
- UCLA scientists discover how key enzyme involved in aging, cancer assembles
| Moving 3D computer model of key human protein is powerful new tool in fight against cancer Posted: 18 Jun 2012 09:00 PM PDT
A picture is worth 1,000 words when it comes to understanding how things work, but 3D moving pictures are even better. That’s especially true for scientists trying to stop cancer by better understanding the proteins that make some chemotherapies unsuccessful.
Researchers for decades have had to rely at best on static images of the key proteins related to recurring cancers. Now SMU biochemist John G. Wise at Southern Methodist University, Dallas, has brought to life in a moving 3D computer model the structure of human P-glycoprotein, which is thought to contribute to the failure of chemotherapy in many recurring cancers. “This is a very different approach than has been used historically in the field of protein structure biochemistry,” Wise said. “Historically, proteins are very often viewed as static images, even though we know that in reality these proteins move and are dynamic.” The model is a powerful new discovery tool, says Wise, particularly when combined with high-performance supercomputing. The dynamic 3D model already has made it possible for Wise to virtually screen more than 8 million potential drug compounds in the quest to find one that will help stop chemotherapy failure. http://bit.ly/MeUFOo So far, the supercomputer search has turned up a few hundred drugs that show promise, and Wise and SMU biochemist Pia Vogel have begun testing some of those compounds in their wet lab at SMU. “This has been a good proof-of-principle,” said Wise, a research associate professor in the SMU Department of Biological Sciences. “We’ve seen that running the compounds through the computational model is an effective way to rapidly and economically screen massive numbers of compounds to find a small number that can then be tested in the wet lab.” Wise describes his research findings in Biochemistry in the article “Catalytic Transitions in the Human MDR1 P-Glycoprotein Drug Binding Sites” online at http://bit.ly/LBagWA. The research is funded by the National Institute of General Medical Sciences, National Institutes of Health. Seeking new drugs that would allow chemotherapeutic compounds to enter and destroy cancer cells
Since the 1970s it has been known that the so-called multidrug resistance protein, P-gp, is most likely responsible for the failure of many chemotherapy drugs. P-gp is nature’s way of pumping toxins from a cell, but if cancer cells express more P-gp than cells normally would, the chemotherapy is no longer effective because the protein considers it a toxin and pumps it out before it can destroy the cancer. “We’re looking for small molecules that will temporarily inhibit the pump; a new drug that could be co-administered with the chemotherapeutic and that stops the sump pump in the cancer cell so that the cancer chemotherapy can remain in the cell and kill the cancer,” Wise said. High-performance computer enables millions of digital screenings
Wise has run about 10.5 million computational hours since August 2009 and has screened roughly 8 million potential drugs against different protein structures. “We are currently screening about 40,000 compounds per day on SMU’s High Performance Computer,” Wise said. “We found a couple hundred compounds that were interesting, and so far we chose about 30 of those to screen in the lab,” Vogel said. “From those, we found a handful of compounds that do inhibit the protein. We were thrilled. Now we’re going back into the models and looking for other compounds that might be able to throw a stick in the pump’s mechanism.” Massive increases in computational power in recent years have made the screening research possible, Wise said. “Ten years ago you couldn’t have docked 8 million compounds ? there just wasn’t enough computational power.” Human P-gp: “We don’t know what it looks like exactly.”
Every organism has a version of P-gp. Its structure has been previously determined for some organisms ? mostly bacteria, but also in mice ? by studying the arrangement of atoms within protein crystals. However, the exact structure of the human enzyme remains unclear. Wise deduced the structure of human P-gp by relying on evolutionary relationships and scientific understanding of how proteins are put together. He then used computer programs to model the protein in a way that brings the static picture of the human pump to life in the computer. See http://bit.ly/Lncc6T. To develop the model, Wise used freely available simulation software developed by researchers at the University of Illinois, the National Institutes of Health and the Scripps Research Institute. Wise and Vogel use compounds from ZINC, a free database of more than 21 million commercially available compounds for virtual screening. ZINC is provided by the Department of Pharmaceutical Chemistry at the University of California, San Francisco. “We can physically build these molecules in the computer, in silico, and computationally we can model a variety of conditions: We can raise the temperature to 37 degrees Centigrade, we can have the right salts and all the right conditions, just like in a wet-lab experiment. We can watch them thermally move and we can watch them relax,” Wise said. “The software is good enough that the model will move according to the laws of physics and the principles of biochemistry. In this way we can see how these compounds interact with the protein in a dynamic way, not just in a snapshot way.” Even with the 3D dynamic model and a supercomputer, the odds are stiff
Theoretically, if a drug can be found that can temporarily knock out the sump-pump proteins, then all those cancer chemotherapies that don’t work for a patient will work again. “The ultimate goal of our research would be to find a compound that is safe and effective,” Wise said. Even with a supercomputer, however, the odds are steep. “Out of a hundred good inhibitors that we might find, 99 of them might be extremely toxic and can’t be used. In the pharmaceutical industry there are many, many candidates that fall by the wayside for one reason or another,” he said. “They metabolize too quickly, or they’re too toxic, or they’re not soluble enough in the acceptable solvents for humans. There are many different reasons why a drug can fail. Finding a handful has been a great confirmation that we’re on the right track, but I would be totally amazed if one of the first we’ve tested was the one we’re looking for.” Vogel is an associate professor and director of SMU’s Center for Drug Discovery, Design and Delivery. CD4 was launched by SMU’s Biological Sciences and Chemistry departments and has as its mission the search for new drug therapies and delivery methods that can be developed into clinical applications. ### SMU is a nationally ranked private university in Dallas founded 100 years ago. Today, SMU enrolls nearly 11,000 students who benefit from the academic opportunities and international reach of seven degree-granting schools. For more information see www.smuresearch.com. SMU has an uplink facility located on campus for live TV, radio, or online interviews. To speak with an SMU expert or book an SMU guest in the studio, call SMU News & Communications at 214-768-7650. Contact: Margaret Allen |
| Inhibitors of shuttle molecule show promise in acute leukemia Posted: 18 Jun 2012 09:00 PM PDT
COLUMBUS, Ohio ? A novel family of experimental agents that blocks a molecule from shuttling proteins out of the cell nucleus might offer a new treatment for people with acute leukemia, according to a study by researchers at the Ohio State University Comprehensive Cancer Center ? Arthur G. James Cancer Hospital and Richard J. Solove Research Institute. The agents, called KPT-SINEs (selective inhibitors of nuclear export), target a transport protein called CRM1. Using acute myeloid leukemia (AML) cells and an animal model, the researchers showed that these agents inhibited leukemia-cell proliferation, arrested cell division, and induced cell death and differentiation. In the animal model of AML, KPT-SINEs ? described by the researchers as one of the most advanced agents in pre-clinical development ? extended survival by 46 percent compared with controls. KPT-SINEs were particularly effective when the leukemia cells also had mutations in the tumor-suppressor gene NPM1, which are present in about one-third of all adult AML. The findings were published online in the journal Blood. “Our study suggests that these agents might be an effective therapy for AML, particularly for patients with NPM1 mutations,” says principal investigator Dr. Ramiro Garzon, assistant professor of medicine and a researcher with the OSUCCC ? James Molecular Biology and Cancer Genetics Program. “We hope to start a phase I trial using one of these agents soon and to pursue further preclinical studies using this drug in combination with other current chemotherapies,” Garzon says. CRM1 normally transports molecules out of the cell nucleus to the surrounding cytoplasm. In acute leukemia cells, the molecule carries tumor-suppressor, apoptotic and other protective proteins out of the nucleus, thereby contributing to leukemia development. Karyopharm Therapeutics, Inc., developed KPT-SINEs. This study also showed that these agents:
### Other researchers involved with this study were Parvathi Ranganathan, Xueyan Yu, Caroline Na, Ramasamy Santhanam, Alison Walker, Rebecca Klisovic, William Blum, Michael Caligiuri, Carlo M. Croce and Guido Marcucci of Ohio State University; and Sharon Shacham and Michael Kauffman of Karyopharm Therapeutics, Inc. The Ohio State University Comprehensive Cancer Center ? Arthur G. James Cancer Hospital and Richard J. Solove Research Institute strives to create a cancer-free world by integrating scientific research with excellence in education and patient-centered care, a strategy that leads to better methods of prevention, detection and treatment. Ohio State is one of only 41 National Cancer Institute (NCI)-designated Comprehensive Cancer Centers and one of only seven centers funded by the NCI to conduct both phase I and phase II clinical trials. The NCI recently rated Ohio State’s cancer program as “exceptional,” the highest rating given by NCI survey teams. As the cancer program’s 210-bed adult patient-care component, The James is a “Top Hospital” as named by the Leapfrog Group and one of the top 20 cancer hospitals in the nation as ranked by U.S.News & World Report. Contact: Darrell E. Ward |
| New studies hint at possible approaches to protect those at risk for Huntington’s disease Posted: 17 Jun 2012 09:00 PM PDT In Huntington’s disease, abnormally long strands of glutamine in the huntingtin (Htt) protein, called polyglutamines, cause subtle changes in cellular functions that lead to neurodegeneration and death. Studies have shown that the activation of the heat shock response, a cellular reaction to stress, doesn’t work properly in Huntington’s disease. In their research to understand the effects of mutant Htt on the master regulator of the heat shock response, HSF1, researchers have discovered that the targets most affected by stress are not the classic HSF1 targets, but are associated with a range of other important biological functions. Their research is published in the inaugural issue of The Journal of Huntington’s Disease.
In the first genome-wide study of how polyglutamine (polyQ)-expanded Htt alters the activity of HSF1 under conditions of stress, the researchers found that under normal conditions, HSF1 function is very similar in cells carrying either wild-type (natural) or mutant Htt. Upon heat shock, much more dramatic differences emerge in the binding of HSF1. Unexpectedly, the genes no longer regulated by HSF1 were not classical HSF1 targets, such as molecular chaperones and the various genes involved in stress response. The genes that lost binding were associated with a range of other important biological functions, such as GTPase activity, cytoskeletal binding, and focal adhesion. Disorders in many of these functions have been linked to Huntington’s disease in earlier studies; the current research provides a possible mechanism to explain previous observations. Lead investigator Ernest Fraenkel, PhD, Associate Professor, Biological Engineering, MIT, explains that the impaired ability of HSF1 to respond to stress in these cells is consistent with the slow onset of Huntington’s disease. Although polyQ-expanded Htt is expressed throughout the body, it primarily affects striatum and cortex relatively late in life. “An intriguing hypothesis is that polyQ-expanded Htt sensitizes the cells to various stresses, but is not sufficiently toxic on its own to cause cell death,” he notes. “We have shown that polyQ Htt significantly blunts, but does not completely eliminate, the HSF1 mediated stress response. Over time, the reduced response may lead to significant damage and cell death.” The findings raise the possibility that activating HSF1 could be an effective strategy for protecting neurons from stress and damage. However, Dr. Fraenkel notes that such a strategy will have to overcome a number of barriers. “HSF1 is highly regulated, and simply increasing its expression may not increase the levels of the active form of HSF1. Also, increased HSF1 levels may raise the risk of cancer, as tumor cells depend on HSF1 activity. Further analysis of the role of HSF1 in neurodegeneration and cancer are critical to uncovering a safe and effective strategy for using HSF1 activation to treat Huntington’s disease.” In another study published in the inaugural issue of the Journal of Huntington’s Disease, investigators uncover a new biological marker that may be useful in screening antioxidative compounds for the treatment of Huntington’s Disease. Serum 8OHdG is sign of oxidative damage to DNA, and has been shown to be elevated in patients with HD and other neurological disorders. Coenzyme Q (CoQ) is an antioxidant that may slow progression of Huntington’s disease. It is also known to decrease 8OHdG levels in a mouse model of Huntington’s disease. However, it was unknown whether CoQ dosing would reduce 8OHdG in humans. Investigators administered CoQ to 14 Huntington’s disease patients and 6 healthy controls for 20 weeks. Participants started on 1200 mg/day, and the dosage increased at week 8 to 3600 mg/day. CoQ levels were tested at the beginning of the study and at weeks 4, 8, 12, and 20. Four individuals with Huntington’s disease reported that they were taking CoQ at the start of the study. Baseline CoQ levels were elevated in individuals with Huntington’s disease compared with health controls, even when individuals who were taking CoQ at the start of the study were excluded, the investigators found. The researchers suggest that individuals with Huntington’s disease may have naturally high levels of CoQ, or some subjects may have recently discontinued CoQ, as CoQ levels can remain elevated in the system for several weeks. Administration of CoQ led to a reduction of 8OHdG in individuals with Huntington’s disease. While not significant, they found a similar reduction in healthy controls treated with CoQ, suggesting the effect of CoQ on 8OHdG may be non-specific. “Our study supports the hypothesis that CoQ exerts antioxidant effects in patients with Huntington’s disease and therefore is a treatment that warrants further study,” says lead investigator Kevin M. Biglan, MD, MPH, Associate Professor, University of Rochester. “While the current data can’t address the use of 8OHdG as a surrogate marker for the clinical effectiveness of antioxidants in Huntington’s disease, we’ve established that 8OHdG can serve as a marker of the pharmacological activity of an intervention.” Contact: Daphne Watrin ### |
| UCLA scientists discover how key enzyme involved in aging, cancer assembles Posted: 17 Jun 2012 09:00 PM PDT UCLA biochemists have mapped the structure of a key protein?RNA complex that is required for the assembly of telomerase, an enzyme important in both cancer and aging. The researchers found that a region at the end of the p65 protein that includes a flexible tail is responsible for bending telomerase’s RNA backbone in order to create a scaffold for the assembly of other protein building blocks. Understanding this protein, which is found in a type of single-celled organism that lives in fresh water ponds, may help researchers predict the function of similar proteins in humans and other organisms.
The study was published June 14 in the online edition of the journal Molecular Cell and is scheduled for publication in the print edition on July 13. The genetic code of both the single-celled protozoan Tetrahymena and humans is stored within long strands of DNA packaged neatly within chromosomes. The telomerase enzyme helps create telomeres ? protective caps at the ends of the chromosomes that prevent the degradation of our DNA, said Juli Feigon, a UCLA professor of chemistry and biochemistry and senior author of the study. Each time the cell divides, the telomeres shorten, acting like the slow-burning fuse of a time bomb. After many divisions, the telomeres become eroded to a point that can trigger cell death. Cells with abnormally high levels of telomerase activity constantly rebuild their protective chromosomal caps, allowing them to replicate indefinitely and become, essentially, immortal. Yet undying cells generally prove to be more of a curse than a blessing, Feigon said. “Telomerase is not very active in most of our cells because we don’t want them to live forever,” said Feigon, who is also a researcher at UCLA’s Molecular Biology Institute and a member of the National Academy of Sciences. “After many generations, DNA damage builds up and we wouldn’t want to pass those errors on to subsequent cells.” Overactive telomerase has potentially lethal consequences far beyond the propagation of erroneous DNA. The enzyme is particularly lively within cancer cells, which prevents them from dying out naturally. Finding a way to turn off telomerase in cancer cells might help prevent the diseased cells from multiplying. Flipping the switch on telomerase might mean stopping it from forming in the first place, said Feigon. “Any time you want to stop an enzyme, you can target activity, but you can also target assembly,” she said. “If you keep it from assembling, that’s just as good as keeping it from being active, because it never even forms.” While there is enormous interest in telomerase due to its connection to cancer and aging, very little is known about its three-dimensional structure or its formation, Feigon said. Four years ago, UCLA postdoctoral scholar Mahavir Singh set out to determine how a strand of RNA and multiple proteins bind together to form telomerase. He set his sights on the p65 protein, one of the key components of the enzyme. Like many proteins, p65 is a long chain of both stiff and supple links that fold in upon one another in a prescribed pattern. At the very end of the p65 protein is a floppy, disordered tail. “We knew the tail was important for the protein’s function, but it wasn’t clear how or why,” said Singh, first author of the current study. “From the structure, it became evident how it interacts with the telomerase RNA.” When Singh snipped off the flexible tail from p65, he found that the assembly of telomerase became severely limited. The tailless p65 simply couldn’t help put together the enzyme. Using both X-ray crystallography and nuclear magnetic resonance spectroscopy, Singh probed the structure of the protein and its interaction with telomerase RNA. He found that upon assembly, the flexible tail transforms into a rigid crowbar that pries apart the strands of the RNA double helix. The newly altered protein tail bends the RNA into a new shape required for binding an essential component of telomerase, a protein called telomerase reverse transcriptase, or TERT. The p65 protein not only brings two parts of the RNA closer together to allow for the attachment of the TERT protein, but it also folds around the end of the RNA strands to protect them before the telomerase assembles. Without its protein shield, the “naked” RNA is susceptible to degradation and could be chewed up by other enzymes, Singh said. The p65 protein belongs to a family of “La-motif” proteins, molecules that act as “RNA chaperones” in many organisms including humans, said Feigon. “How the p65 protein binds with RNA has never been clear,” Feigon said. “Nobody could figure it out, and that’s partly because they were missing a critical, extra part of the protein which changes from being a completely random coil to being folded and ordered when it interacts with RNA.” Studying p65 within the humble Tetrahymena may help Singh and Feigon better understand its La-motif cousins within the human body, which may also sport protein tails. “A lot of data indicates that the protein tail is important for the binding of all kinds of RNAs in human cells,” Feigon said. “It is particularly critical for the translation of the hepatitis C viral RNA. Now we can potentially predict how those proteins will assemble and interact with their RNAs.” The researchers who first discovered telomerase were awarded the Nobel Prize in 2009. They also used Tetrahymena thermophila, a tiny microorganism with hair-like flagella commonly found in fresh water. ### This research was federally funded by the National Science Foundation and the National Institutes of Health. Other co-authors included UCLA senior staff scientist Duilio Cascio, UCLA postdoctoral scholars Zhongua Wang and Bon-Kyung Koo, UCLA undergraduate researcher Anooj Patel, and UC Berkeley professor of molecular and cell biology Kathleen Collins. UCLA is California’s largest university, with an enrollment of nearly 38,000 undergraduate and graduate students. The UCLA College of Letters and Science and the university’s 11 professional schools feature renowned faculty and offer 337 degree programs and majors. UCLA is a national and international leader in the breadth and quality of its academic, research, health care, cultural, continuing education and athletic programs. Six alumni and five faculty have been awarded the Nobel Prize. For more news, visit the UCLA Newsroom and follow us on Twitter. Contact: Stuart Wolpert |
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