Research: Elusive drug targets; cell demolition enzymes; useful pharmacogenomics info

Predicting difficult-to-detect drug binding sites

Most drugs are comprised of small molecules that pass through cell membranes and are designed to bind to much larger protein molecules at exposed concave pockets. But in many disease-associated proteins, these binding sites are difficult to detect. Concave pockets may form only in the immediate presence of small molecules that bind to them (natural ligands or drugs) or are open only for brief periods during protein shape-shifting.

UCSF School of Pharmacy faculty member and associate dean of research Andrej Sali, PhD, senior-authored an article in a February issue of the Journal of Molecular Biology, describing the creation of a new computer tool that predicts the locations of these so-called cryptic sites. The work by Sali and co-authors, published in a special journal issue devoted to eight “important computational resources” for researchers, compared experimentally identified cryptic sites—before and after pocket formation and ligand binding—to create predictive algorithms. The new tool, CryptoSite, was then tested and found 96 percent accurate at localizing cryptic sites in a set of benchmark proteins.

To further demonstrate the tool’s usefulness, it was employed to predict a cryptic site on the enzyme protein-tyrosine phosphatase 1B, a target of major interest to diabetes drug researchers. The results were then validated via physical experiments. Indeed, Sali and colleagues estimated that use of this new tool—now available to the research community online—increases the percentage of disease-associated human proteins that can potentially be targeted with drugs from about 40 percent to nearly 80 percent.

The Sali Lab is based in the Department of Bioengineering and Therapeutic Sciences, a joint department of the UCSF Schools of Pharmacy and Medicine.

Journal Citation: Cimermancic, Weinkam P, Rettenmaier TJ, Bichmann L, Keedy DA, Woldeyes RA, Schneidman-Duhovny D, Demerdash ON, Mitchell JC, Wells JA, Fraser JS, Sali A, “CryptoSite: Expanding the Druggable Proteome by Characterization and Prediction of Cryptic Binding Sites,” Journal of Molecular Biology,” Vol. 428, p. 709-719.


Andrej Sali, PhD


James Wells, PhD

UCSF School of Pharmacy

Jaekyu Shin, PharmD

Determining the preferred targets of cell demolition enzymes

Humans have more than 600 types of protease enzymes—protein molecules that act like chemical scissors, cleaving the peptide bonds that link amino acids in other proteins. One family of a dozen proteases called caspases plays a crucial role in apoptosis, the programmed self-destruction of cells that is dysregulated in many neurodegenerative diseases, such as Alzheimer’s disease, and fails to occur in cancers.

As with most protease enzymes, it has been difficult to parse which caspases (numbered 1-12) cleave which proteins (substrates) in this crucial process. Indeed, studies have found lots of overlap among hundreds of different caspase substrates. Knowing each caspase’s preferred substrates (specificities) could clarify their roles and aid the design of drugs to precisely inhibit or activate them in cellular demolition.

James Wells, PhD, senior-authored a paper in the Proceedings of the National Academy of Sciences in April that used a combination of protein engineering and mass spectrometry developed by the Wells Lab to label, identify, and quantify the cleaved substrates of lesser-known apoptotic family members—caspase-2 and caspase-6. Wells and his co-authors discovered more than a thousand protein substrates for these two enzymes in cell extracts. Wells is a faculty member in the Department of Pharmaceutical Chemistry, and holds the Harry Wm. and Diana V. Hind Distinguished Professorship in Pharmaceutical Sciences I.

But, most significantly, the study found that the rate at which these caspases cleaved particular substrates varied more than 500-fold. Further, comparing them with three other caspases that are also involved in apoptosis showed that each enzyme had a unique set of preferred substrates based on these major variations in catalytic efficiency and thus more specialized roles than was previously understood.

Journal Citation: Julien O, Zhuang M, Wiita AP, O’Donoghue AJ, Knudsen GM, Craik CS, Wells JA, “Quantitative MS-based enzymology of caspases reveals distinct protein substrate specificities, hierarchies, and cellular roles,” Proceedings of the National Academy of Sciences, Vol 113, p. 2001-2010.

Evaluating pharmacogenomics information in drug information resources

Screening is increasingly available to determine how a patient’s genetics will affect their response to a medication. But is such clinically useful pharmacogenomics information—including peer-reviewed guidelines that help clinicians interpret genetic test results to optimize drug therapy—available via the drug information resources routinely used by clinicians?

This question was addressed in a paper senior-authored by Jaekyu Shin, PharmD, faculty member in the Department of Clinical Pharmacy, in the January issue of the Journal of the Medical Library Association. Shin and his colleagues evaluated four popular drug information resources—Lexicomp, Micromedex 2.0, Epocrates, and U.S. Food and Drug Administration-approved package inserts—for their pharmacogenomics information on 27 drugs, including the biological effect of a genetic biomarker, its population prevalence, testing recommendations, and interpretation of the test results.

Their analysis found wide variations. And while Lexicomp was the most useful for pharmacogenomics information, none of the resources were sufficiently complete. Shin and his co-authors were “surprised and alarmed” to find that only a few of the peer-reviewed guidelines for translating lab test results into clinical action from the Clinical Pharmacogenomics Implementation Consortium were incorporated in the resources; thus, clinicians would need to directly consult those guidelines online.

Journal Citation: Chang JS, Pham DA, Dang MT, Lu Y, VanOsdol S, Shin J, “Evaluation of popular drug information resources on clinically useful and actionable pharmacogenomic information,” Journal of the Medical Library Association, Vol. 104, p. 58-61.


School of Pharmacy, Department of Pharmaceutical Chemistry, Department of Bioengineering and Therapeutic Sciences, Department of Clinical Pharmacy, PharmD Degree Program

About the School: The UCSF School of Pharmacy aims to solve the most pressing health care problems and strives to ensure that each patient receives the safest, most effective treatments. Our discoveries seed the development of novel therapies, and our researchers consistently lead the nation in NIH funding. The School’s doctor of pharmacy (PharmD) degree program, with its unique emphasis on scientific thinking, prepares students to be critical thinkers and leaders in their field.