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Chemistry and Chemical Biology
Graduate Program

 

Chemistry-Biology Interface
NIH Training Grant

Research Training in Chemistry and Chemical Biology

The NIH NIGMS Chemistry-Biology Interface (CBI) Predoctoral Training Grant is a major source of support for UCSF's Chemistry and Chemical Biology Graduate Program. This training grant provides stipend and fee support for our nine CBI trainees. The CBI trainees meet for regularly scheduled "CBI Student Forum" meetings. These biweekly lunch meetings provide an environment for CBI students to exchange ideas, post questions, offer answers, and offer help on relevant subjects. The students meet to discuss chemical biology-focused scientific interests and to share experiences of the journey through graduate school. The form of the meeting can differ depending on the topic of interest. Sometimes faculty may be invited to participate, other times the forum may take the shape of a workshop.

All students in our Chemistry and Chemical Biology Graduate Program can participate in CBI activities, although not all students are funded by a traineeship in the NIH CBI training grant. Other methods of support include central campus support, departmental support, PIBS support, extramural predoctoral fellowships, and faculty mentor support.

Current CBI trainees in the Chemistry and Chemical Biology Graduate Program

Jee

Noel Jee

Noel received his undergraduate degree in Biochemistry and Physiology Neurobiolgy from University of Maryland.
Kaemmerer

Daniel Kaemmerer

Daniel received his undergraduate degree in Chemistry and Biochemistry from Stanford University.
Karpiak

Joel Karpiak

Joel received his undergraduate degree in Chemistry from Yale University.
Lee

Melody Lee

Melody received her undergraduate degree in Molecular & Cellular Biology and Immunology from University of California, Berkeley and her Masters degree in Biomedical Sciences from Eastern Virginia Medical School.
Mendez

Aaron Mendez

Aaron received his undergraduate degree in Biochemistry and Molecular Biology from University of California, Irvine.
Myers

Samuel Myers

Samuel is a second-year graduate student in the lab of Al Burlingame. Samuel received his undergraduate degree in biochemistry from the California Polytechnic State University.
Nyitray

Crystal Nyitray

Crystal received her undergraduate degree in Biochemistry and Molecular Biology from University of California, Santa Cruz.

Rettenmaier

Justin Rettenmaier

Justin received his undergraduate degree in Chemistry from University of California, Santa Cruz.
Riel-Mehan

Megan Riel-Mehan

Megan is a second-year graduate student in the lab of Kevan Shokat. Megan received her undergraduate degree in from UC Berkeley.
Silber

Amanda Silber

Amanda received her undergraduate degree in Biochemistry from Colorado College.

 

Past CBI trainees who have Graduated

Alan Marnett: Alan received his PhD in Chemistry and Chemical Biology from UCSF in 2005. Alan's research here in the labs of Charles Craik and Paul Ortiz de Montellano was on the inhibition of Kaposi’s Sarcoma-associated herpesvirus protease. Alan is currently doing postdoctoral research in Elly Nedivi's lab at MIT.
Publications:

  1. Shimba N, Nomura AM, Marnett AB, Craik CS. Herpesvirus protease inhibition by dimer disruption. J Virol. 78(12):6657-65 (2004).
  2. Marnett AB, Nomura AM, Shimba N, Ortiz de Montellano PR, Craik CS. Communication between the active sites and dimer interface of a herpesvirus protease revealed by a transition-state inhibitor. Proc Natl Acad Sci U S A. 101(18):6870-5 (2004).
  3. Marnett AB and Craik CS. Papa’s got a brand new tag: Recent advances in identification of proteases and their natural substrates. Trends Biotechnol. 2005 Feb;23(2):59-64
  4. Marnett AB, Nomura AM, Shimba N, Dotsch V, Craik CS. Induced structure of a helical switch as a mechanism to regulate enzymatic activity. Nat Struct Mol Biol. 2005 Oct 23.
  5. Nomura AM, Marnett AB, Shimba N, Dotsch V, Craik CS. One functional switch mediates reversible and irreversible inactivation of a herpesvirus protease. Biochemistry. 2006 Mar 21;45(11):3572-9.

Brian Feng: Brian received his PhD in Chemistry and Chemical Biology from UCSF in 2007. Brian's research here in the lab of Brian Shoichet was on the application of a detergent-based counter screen for aggregation in a high-throughput screen. Brian is currently doing postdoctoral research in James Chen's lab at Stanford.
Publications:

  1. Feng BY, Simeonov A, Jadhav A, Babaoglu K, Inglese J, Shoichet BK, Austin CP. A high-throughput screen for aggregation-based inhibition in a large compound library. J Med Chem. 2007 May 17;50(10):2385-90.
  2. Feng BY, Shoichet BK. A detergent-based assay for the detection of promiscuous inhibitors. Nat Protoc. 2006;1(2):550-3.
  3. Feng BY, Shoichet BK. Synergy and antagonism of promiscuous inhibition in multiple-compound mixtures. J Med Chem. 2006 Apr 6;49(7):2151-4. Erratum in: J Med Chem. 2007 Jun 14;50(12):2930.
  4. Feng BY, Shelat A, Doman TN, Guy RK, Shoichet BK. High-throughput assays for promiscuous inhibitors. Nat Chem Biol. 2005 Aug;1(3):146-8.
  5. McGovern SL, Helfand BT, Feng B, Shoichet BK. A specific mechanism of nonspecific inhibition. J Med Chem. 2003 Sep 25;46(20):4265-72.

Nicholas Mills: Nicholas received his PhD in Chemistry and Chemical Biology from UCSF in 2007. Nick's research in the lab of Kip Guy focused on chemical and structural components of specific RNA recognition. Nicholas is currently working for McKinsey Consulting in New Jersey.
Publications:

  1. Laurie NA, Donovan SL, Shih CS, Zhang J, Mills N, Fuller C, Teunisse A, Lam S, Ramos Y, Mohan A, Johnson D, Wilson M, Rodriguez-Galindo C, Quarto M, Francoz S, Mendrysa SM, Guy RK, Marine JC, Jochemsen AG, Dyer MA. Inactivation of the p53 pathway in retinoblastoma. Nature. 2006 Nov 2;444(7115):61-6.
  2. Mills NL, Daugherty MD, Frankel AD, Guy RK. An alpha-helical peptidomimetic inhibitor of the HIV-1 Rev-RRE interaction. J Am Chem Soc. 2006 Mar 22;128(11):3496-7.

Nathan Sallee: Nathan received his PhD in Chemistry and Chemical Biology from UCSF in 2007.  Nathan’s research at UCSF in the lab of Wendell Lim focused on rewiring the regulatory mechanisms of signaling proteins.  Nathan is currently working as a scientist in the protein chemistry group at FivePrime Therapeutics.
Publications:

  1. Sallee NA, Rivera GM, Dueber JE, Vasilescu D, Mullins RD, Mayer BJ, Lim WA.  The pathogen protein EspF(U) hijacks actin polymerization using mimicry and multivalency.  Nature. 2008 Aug 21;454(7207):1005-8.
  2. Sallee NA, Yeh BJ, Lim WA.  Engineering modular protein interaction switches by sequence overlap.  J Am Chem Soc. 2007 Apr 18;129(15):4606-11.

Edwin Tan:  Edwin received his PhD in Chemistry and Chemical Biology from UCSF in 2007.  Edwin’s research in Tom Scanlan’s lab was on Understanding the Molecular Basis of Trace Amine-Associated Receptor 1 Activation by Thyronamines and Related Analogs.
Publications:

  1. Snead AN, Miyakawa M, Tan ES, Scanlan TS. Trace amine-associated receptor 1 (TAAR(1)) is activated by amiodarone metabolites. Bioorg Med Chem Lett. 2008 Aug 9.
  2. Tan ES, Groban ES, Jacobson MP, Scanlan TS. Toward deciphering the code to aminergic G protein-coupled receptor drug design. Chem Biol. 2008 Apr;15(4):343-53.
  3. Tan ES, Miyakawa M, Bunzow JR, Grandy DK, Scanlan TS. Exploring the structure-activity relationship of the ethylamine portion of 3-iodothyronamine for rat and mouse trace amine-associated receptor 1.  J Med Chem. 2007 Jun 14;50(12):2787-98.