Yu Chen, PhD

Assistant Professor, College Of Medicine Molecular Medicine

College Of Medicine Molecular Medicine

Contact Info 12901 Bruce B. Downs Blvd
Tampa, FL 33612

Academic Email: ychen1@health.usf.edu

Academic Phone: (813) 974-7809

View My C.V.


  • PhD, Biochemistry, University Of Chicago, 2002
  • PhD, Biochemistry and Molecular Biology, University of Chicago,, 2002
  • BS, Biochemistry and Molecular Biology, Peking University, 1997

Research Interests

  • The Chen lab focuses on structure-based drug design against proteins involved in infectious diseases and cancer. We utilize a multi-disciplinary approach, combining biochemistry, structural biology and computational chemistry, to investigate the function and inhibition of enzymes related to bacterial cell wall synthesis, the biological process targeted by antibiotics such as penicillin. We also study human signal transduction proteins in collaboration with other laboratories.
  • Our research goals include:
  • Studying molecular interactions at atomic and ultimately subatomic scale through
  • ultra-high resolution X-ray crystallography;
  • Developing fragment-based molecular docking for drug discovery;
  • Identifying novel inhibitors as potential drug leads and chemical probes for proteins of biomedical importance.


  • American Chemical Society (Member, 2009 - Present)

Recent Publications

  • Tomanicek, SJ.Wang, KK.Weiss, KL.Blakeley, MP.Cooper, J.Chen, Y.Coates, L. The active site protonation states of perdeuterated Toho-1 beta-lactamase determined by neutron diffraction support a role for Glu166 as the general base in acylation. FEBS letters. 585(2) : 364-8, 2011. http://www.ncbi.nlm.nih.gov/pubmed/21168411
  • De Leon, JT.Iwai, A.Feau, C.Garcia, Y.Balsiger, HA.Storer, CL.Suro, RM.Garza, KM.Lee, S.Kim, YS.Chen, Y.Ning, YM.Riggs, DL.Fletterick, RJ.Guy, RK.Trepel, JB.Neckers, LM.Cox, MB. Targeting the regulation of androgen receptor signaling by the heat shock protein 90 cochaperone FKBP52 in prostate cancer cells. Proceedings of the National Academy of Sciences. 108(29) : 11878-83, 2011. http://www.ncbi.nlm.nih.gov/pubmed/21730179
  • Tomanicek, SJ.Blakeley, MP.Cooper, J.Chen, Y.Afonine, PV.Coates, L. Neutron diffraction studies of a class A beta-lactamase Toho-1 E166A/R274N/R276N triple mutant. Journal of molecular biology. 396(4) : 1070-80, 2010. http://www.ncbi.nlm.nih.gov/pubmed/20036259
  • Veldkamp, CT.Ziarek, JJ.Peterson, FC.Chen, Y.Volkman, BF. Targeting SDF-1/CXCL12 with a ligand that prevents activation of CXCR4 through structure-based drug design. Journal of the American Chemical Society. 132(21) : 7242-3, 2010. http://www.ncbi.nlm.nih.gov/pubmed/20459090
  • Chen,Y.Pohlhaus, DT. In silico docking and scoring of fragments Drug Discovery Today: Technologies. 7(3) : 149-56, 2010.
  • Chen, Y.McReynolds, A.Shoichet, BK. Re-examining the role of Lys67 in class C beta-lactamase catalysis. Protein Science. 18(3) : 662-9, 2009. http://www.ncbi.nlm.nih.gov/pubmed/19241376
  • Chen, Y.Zhang, W.Shi, Q.Hesek, D.Lee, M.Mobashery, S.Shoichet, BK. Crystal structures of penicillin-binding protein 6 from Escherichia coli. Journal of the American Chemical Society. 131(40) : 14345-54, 2009. http://www.ncbi.nlm.nih.gov/pubmed/19807181
  • Chen, Y.Shoichet, BK. Molecular docking and ligand specificity in fragment-based inhibitor discovery. Nature chemical biology. 5(5) : 358-64, 2009. http://www.ncbi.nlm.nih.gov/pubmed/19305397
  • Delmas, J.Chen, Y.Prati, F.Robin, F.Shoichet, BK.Bonnet, R. Structure and dynamics of CTX-M enzymes reveal insights into substrate accommodation by extended-spectrum beta-lactamases. Journal of molecular biology. 375(1) : 192-201, 2008. http://www.ncbi.nlm.nih.gov/pubmed/17999931
  • Chen, Y.Bonnet, R.Shoichet, BK. The acylation mechanism of CTX-M beta-lactamase at 0.88 a resolution. Journal of the American Chemical Society. 129(17) : 5378-80, 2007. http://www.ncbi.nlm.nih.gov/pubmed/17408273
  • Whiteson, KL.Chen, Y.Chopra, N.Raymond, AC.Rice, PA. Identification of a potential general acid/base in the reversible phosphoryl transfer reactions catalyzed by tyrosine recombinases: Flp H305. Chemistry & biology. 14(2) : 121-9, 2007. http://www.ncbi.nlm.nih.gov/pubmed/17317566
  • Chen, Y.Minasov, G.Roth, TA.Prati, F.Shoichet, BK. The deacylation mechanism of AmpC beta-lactamase at ultrahigh resolution. Journal of the American Chemical Society. 128(9) : 2970-6, 2006. http://www.ncbi.nlm.nih.gov/pubmed/16506777
  • Chen, Y.Shoichet, B.Bonnet, R. Structure, function, and inhibition along the reaction coordinate of CTX-M beta-lactamases. Journal of the American Chemical Society. 127(15) : 5423-34, 2005. http://www.ncbi.nlm.nih.gov/pubmed/15826180
  • Chen, Y.Delmas, J.Sirot, J.Shoichet, B.Bonnet, R. Atomic resolution structures of CTX-M beta-lactamases: extended spectrum activities from increased mobility and decreased stability. Journal of molecular biology. 348(2) : 349-62, 2005. http://www.ncbi.nlm.nih.gov/pubmed/15811373
  • Chen, Y.Rice, PA. New insight into site-specific recombination from Flp recombinase-DNA structures. Annual review of biophysics and biomolecular structure. 32: 135-59, 2003. http://www.ncbi.nlm.nih.gov/pubmed/12598365
  • Chen, Y.Rice, PA. The role of the conserved Trp330 in Flp-mediated recombination. Functional and structural analysis. The Journal of biological chemistry. 278(27) : 24800-7, 2003. http://www.ncbi.nlm.nih.gov/pubmed/12716882
  • Chen, Y.Narendra, U.Iype, LE.Cox, MM.Rice, PA. Crystal structure of a Flp recombinase-Holliday junction complex: assembly of an active oligomer by helix swapping. Molecular cell. 6(4) : 885-97, 2000. http://www.ncbi.nlm.nih.gov/pubmed/11090626

Positions Held

  • Post Doctoral Fellow (Pharmaceutical Chemistry, University of California, San Francisco 2003 - 2009)
  • Post Doctoral Fellow (Biochemistry and Molecular Biology, University of Chicago, 2003 - 2003)