What a failed drug does (and is there hope for latrepirdine?)

Latrepirdine (Dimebon) was initially used as an antihistamine drug in Russia. It was later found to be neuroprotective, and entered phase II clinical trials in the US for both Alzheimer’s disease and Huntington’s disease. However, Dimebon failed in a US-based phase II replication trial of a prior successful Russian phase II trial of mild-to-moderate AD. Given the initial promise of the drug and split results,  as well as the lack of treatments for neurodegenerative diseases, there in is significant interest in understanding the underlying molecular mechanism(s) for the drug’s effects.

In a paper appearing this week in Molecular Psychiatry, Brandeis researchers in the Petsko-Ringe lab, including postdoc Shulin Ju and undergraduate Jessica Liken ’11, used yeast models of neurodegenerative disease associated proteins to show that Dimebon specifically protects yeast from the cytotoxiciy of α-synuclein, a protein involved in Parkinson’s disease. They further showed that protection is mediated through its up-regulation of autophagy pathway. In collaboration with Sam Gandy‘s group at Mount Sinai School of Medicine, these findings were further confirmed and validated in neuronal cell and animal models.

Given these observations, disparities in the contribution of α-synuclein to the neuropathology between the Russian and US Dimebon studies might also explain, at least in part, the inconsistency of the cognitive benefit in the two trials. If this speculation is correct, then it may be interesting to test for benefits of Dimebon in treating synucleinopathies such as Parkinson’s disease, Lewy body dementia, REM sleep disorder and/or multiple system atrophy.

see also: press release from Mt. Sinai Alzheimer’s Diesease Research Center

Steele JW (*), Ju S(*), Lachenmayer ML(*), Liken J, Stock A, Kim SH, Delgado LM, Alfaro IE, Bernales S, Verdile G, Bharadwaj P, Gupta V, Barr R, Friss A, Dolios G, Wang R, Ringe D, Protter AA, Martins RN, Ehrlich ME, Yue Z, Petsko GA, Gandy S. Latrepirdine stimulates autophagy and reduces accumulation of alpha-synuclein in cells and in mouse brain. Molecular psychiatry. 2012.

Steele JW(*), Lachenmayer ML(*), Ju S, Stock A, Liken J, Kim SH, Delgado LM, Alfaro IE, Bernales S, Verdile G, Bharadwaj P, Gupta V, Barr R, Friss A, Dolios G, Wang R, Ringe D, Fraser P, Westaway D, St George-Hyslop PH, Szabo P, Relkin NR, Buxbaum JD, Glabe CG, Protter AA, Martins RN, Ehrlich ME, Petsko GA, Yue Z, Gandy S. Latrepirdine improves cognition and arrests progression of neuropathology in an Alzheimer’s mouse model. Molecular psychiatry. 2012.

What is α-synuclein when it’s not aggregated?

In a recent paper in PNAS, co-lead authors Wei Wang (Indiana U. School of Medicine) and Iva Perovic (Chemistry Ph. D. program, Brandeis), together with researchers from Brandeis, Indiana, Scripps, NIH, Washington State, and Harvard, investigated the structure of the abundant small neuronal protein α-synuclein. α-Synuclein has been strongly associated with the disease process in Parkinson disease, both from histology (found in aggregates in Lewy bodies associated with disease) and from genetics (mutations in the gene associated with a rare familial form of Parkinson disease). The structure and function of α-synuclein is not well understood. It is an abundant neuronal protein, and appears to bind to lipids, vesicles, and plasma membrane. Heterologously expressed α-synuclein is often observed to be unfolded, and the biochemical role of the protein is still unidentified.

In this new study, α-synuclein was expressed as a GST fusion protein in E. coli and proteolytically cleaved to form α-synuclein with a 10 amino acid N-terminal extension. This protein was shown to form a stable tetrameter with alpha-helical content in the absence of lipids, using a combination of many techniques, including NMR spectroscopy, electron microscopy, circular dichroism and mass spectroscopy of cross-linked products. The authors combined this information to propose a model for the structure of native α-synuclein when it is not aggregated that is a tetramer based on amphipathic central helices.

Researchers in the Pochapsky, Petsko-Ringe and Agar labs at Brandeis participated in the study. Future work is aimed at understanding the function of this tetrameric form of the protein, with the hope of developing techniques to stabilize it and determine its function. For more information and interview with the authors, see the story at BrandeisNOW.


Sprout Grant Winners 2011

Entrepreneurship is alive and well at Brandeis.

Last week, fourteen teams of Brandeis scientists presented their research to a panel of industry experts to compete for funding from the Brandeis University Virtual Incubator Sprout Grant Program.  The Virtual Incubator seeks to nurture and support entrepreneurial scientists at Brandeis by providing education, mentoring, networking and seed grants to help move their discoveries from the laboratory to the market.

Judges were impressed by the team presentations. The teams ranged from biologists who have projects that could be ready for licensing as early as next year, to computer science / IT entrepreneurship students with a web application that already has 1200 users.

“We were overwhelmed by the phenomenal proposals we received” says Irene Abrams, Associate Provost for Innovation.  “The response was incredible – with only a few weeks notice, 23 teams applied for Sprout Grants and 14 presented their proposals to the panel of judges.  I was impressed by the level of creativity among the applicants, and by the hard work the teams put into the presentations.  We only had $50,000, so we had to turn down many excellent applications, which we would have funded if we had more money.”

The 2011 winning projects are:

  • Generation Of A Rapid And Efficient Protein Knockout System, Lead Scientist:  Erin Jonasson (with Satoshi Yoshida)
  • Identification Of Molecules For Stabilizing DJ-1, A Protein Involved In Parkinson And Alzheimer Diseases. Lead Scientist: Joey Salisbury (with Brian Williams, Ala Nassar, Jeff Agar and Greg Petsko)
  • Targeting Oncogenic Ras For Protein Degradation, A Novel Approach To Therapy. Lead Scientist: Rory Coffey (with Marcus Long, Ruibao Ren, and Liz Hedstrom)
  • Identifying Pharmacological Chaperones that Promote Survival in Mouse Models of ALS, Lead Scientist: Jared Auclair (with Joey Salisbury, Dagmar Ringe, Greg Petsko, and Jeff Agar)
  • A Novel, Low Cost, Highly Sensitive Form Of Suppression PCR, Lead Scientist: Ken Sugino (with Sean O’Toole and Sacha Nelson)
  • Zen.Do, Team: Bill DeRusha, Joshua Silverman, Jason Urton (Computer Science)

see also: Brandeis NOW

Mapping hydrogens in chymotrypsin structures with neutron diffraction

In a new paper “Time-of-flight neutron diffraction study of bovine γ-chymotrypsin at the Protein Crystallography Station” published in this month’s edition of the journal Acta Cryst F, Biochemistry grad student Louis Lazar and co-workers from the Petsko-Ringe lab report progress on their project to determine exact hydrogen positions in proteins using neutron diffraction.

Neutron diffraction was chosen, as opposed to X-ray diffraction, because one can visualize hydrogen species directly using neutrons, while it is extremely difficult and in most cases impossible to do so using X-ray diffraction. They chose the protein γ-chymotrypsin in order to determine hydrogen positions, as it fills the necessary requirements to be suitable for a neutron diffraction experiment. These requirements include a very large crystal size (> 1 mm3), moderately sized unit cell axes (no dimension greater than 100 Å), and it must be very stable as well as well-characterized. γ-chymotrypsin is the stereotypical serine protease, cleaving C-terminal to aliphatic and aromatic residues and containing a catalytic triad of serine, histidine, and aspartate. This information on hydrogen placement can then be applied to improve computational methods in which said placement is paramount, such as molecular modeling and rational drug design.

The paper details the collection of neutron data at pD (pH*) 7.1, with the help of the scientists at the Los Alamos National Laboratory. In particular, from the initial maps, they note that the catalytic histidine is doubly protonated, while the serine and aspartate making up the catalytic triad do not show density for the presence of deuterium. In order to complete the study of γ-chymotrypsin, data at a variety of pH values must be collected; data at pD (pH*) 5.6 has already been collected (Acta Cryst F65, 317-320), and data at pD (pH*) 9.0 will be collected in the future.

see also: full text of article (Brandeis users)

Yeast genetics and familial ALS

In a recent paper in PLoS Biology, “A Yeast Model of FUS/TLS-Dependent Cytotoxicity“, Brandeis postdoc Shulin Ju and coworkers applied yeast genetics to examine the function of the human protein FUS/TLS. The gene for FUS/TLS is mutated in 5-10$ of cases of Familial ALS. The yeast model expressing the mutant protein recapitulates many important features of the pathology.

A particular feature of interest is that  FUS/TLS form cytoplasmic inclusions of this protein which is normally localized to the nucleus. Over-expression of a number of yeast proteins rescues the cells from the toxic effect without removing the inclusions. The results are suggested to implicate RNA processing or RNA quality control in the mechanism of toxicity, which I find really interesting in light of the talk Susan Lindquist (an author on this paper) gave at Brandeis about yeast prions and regulatory proteins earlier this month.

Other authors on the paper include Brandeis professors Dagmar Ringe and Gregory Petsko, and Brandeis alumni Dan Tardiff (PhD, Mol. Cell. Biol.,  ’07), currently a postdoc in the Lindquist lab at the Whitehead Institute,  and Daryl Bosco (PhD, Bioorganic Chem, ’03), currently on the faculty at U. Mass. Medical School.

For more information, please see the paper itself or the longer article about the research on Brandeis NOW.

Biochemistry Senior Research Talks on April 29

The Department of Biochemistry presents senior research talks by the 2010/2011 Biochemistry Honor and BS/MS Candidates on Friday, April 29, 11:30-1:30pm in Gerstenzang 121.

Benjamin D. Hornstein – BS/MS
Seq A: construction and analysis of mutants
Advisor: Sue Lovett

Marcus R. Kelly– BS/MS
Replacement Matrices for Transmembrane Proteins
Advisor: Douglas Theobald

Yuliya Y. Mints – BS/MS
Inosine Monophosphate Dehydrogenase and Transcription: a mechanism for retinitis pigmentosa?
Advisor: Liz Hedstrom

Sarah Naomi Olsen – BS/MS
Isolation, Purification, and Characterization of (+)-4R-limonene synthase
Advisor: Dan Oprian

Benjamin M. Whitlock – BS/MS
PABPN1 and SKIIP: A putative mechanism for the onset of Oculopharyngeal Muscular Dystrophy
Advisor: Dagmar Ringe

Philip D. Lessans – BS
Developing a Method of Extracting Native U snRNPs from eukaryotic cells using Snurportin 1 constructs
Advisor: Daniel Pomeranz Krummel

Jessica P. Liken – BS
Deletion Library Screen for Enhancers and Suppressors of ALS-associated FUS/TLS Toxicity in Yeast
Advisor: Greg Petsko

Everyone is welcome and encouraged to come. Pizza will be provided.

Two more NSF GRFP fellowship winners

Brandeis had 1 current undergraduate, 7 undergraduate alunmi, and 1 incoming graduate student win NSF graduate research fellowships this year. In addition to those cited below, Richard Stefan Isaac ’10 and Orly Wapinski ’09 were also selected. Isaac graduated magna cum laude with a BS/MS degree with high honors in Biochemistry. His thesis work “Functional Characterization of Regulators of Bacterial Pathogenicity and
” was done in the Petsko/Ringe lab. His work teaching in the Biology laboratory also resulted in a paper  in CBE Life Science Education. Isaac is currently a graduate student at Univ. of California, San Francisco. Wapinsky received a BS degree with Highest Honors in Biology, doing in her thesis work “Characterization of Interferon Regulatory Factor-4 mutants” with Professor Ruibao Ren. Wapinski is currently studying at Stanford.

Life is a Ponzi Scheme (and more)

Greg Petsko, Gyula and Katica Tauber Professor of Biochemistry & Chemistry, has been writing a monthly column in the journal Genome Biology since its inception 10 years ago. To honor the journal’s 10th anniversary, these columns have now been released as an e-book.

These columns are wide-ranging and rarely fail to amuse and inform. Some examples:

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