Etzkorn Group 2007
L to R: Back Row: Dai Nan, Alexander Rich, Jennifer Przybyla; Front Row: Xingguo Ronald Chen, Ana Y. Mercedes, Guoyan Grace Xu, Jiajia Li
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Etzkorn Group 2007 |
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| L to R: Back Row: Dai Nan, Alexander Rich, Jennifer Przybyla; Front Row: Xingguo Ronald Chen, Ana Y. Mercedes, Guoyan Grace Xu, Jiajia Li |
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Bioorganic Chemistry in the Etzkorn Group
Synthetic organic templates are used to constrain a portion of a peptide in the native conformation. The design process begins with 3D structures available for many proteins and uses chemical intuition together with molecular modeling computer programs. Synthesis efforts focus on control of stereochemistry for amino acid analogs and carbocyclic templates. Bioanalytical techniques used to characterize our mimics include: NMR, mass spectrometry, capillary electrophoresis, circular dichroism, fluorescence and X-ray crystallography. All of our compounds are assayed for biological activity, either enzyme inhibition or DNA-binding activity.
Pin1
Inhibitors | Histone Deacetylase Inhibitors
Environmental
Chemistry | Complete Publications | Patents
| Etzkorn Group Members
Rational Drug Design: Regulation of Mitosis.
We are interested in two enzymes that regulate
mitosis: Pin1, a peptidyl-prolyl isomerase, and histone deacetylase.
Figure 1. Top: Pin1 catalyzes trans-to-cis-Pro amide bond isomerization. The alkene isosteres inhibit Pin1 isomerization, and stop cancer cell growth. X-ray crystal structures of trans and cis alkene inhibitors bound in the active site of Pin1, structures by Yan Zhang and Joseph P. Noel, The Salk Institute, La Jolla, CA.
Pin1 is a key regulator of the cell cycle that may prove to be a good target for anti-cancer therapeutics. Pin1 is essential for mitosis. Proline-containing peptides are substrates for the peptidyl-prolyl isomerase enzymes: Pin1, cyclophilin and FKBP. We have synthesized the Ala and Ser-cis-Pro mimics as inhibitors of cyclophilin and Pin1. L-Amino acid starting materials are used to produce single diastereomeric alcohol intermediates. A Still-Wittig [2,3]-sigmatropic rearrangement is used to set the Z-alkene in the cis isostere, while an Ireland-Claisen rearrangement produces the trans isostere. The phosphoSer-trans- and cis-Pro isosteres have been incorporated into inhibitors of Pin1 with Ki values of 1.74 and 40 mM, respectively. Transition state analogs for Pin1 are in progress. We are also interested in examining the catalysis of protein folding by Pin1 in the cell cycle, especially folding of cdc25 phosphatase and the RNA polymerase C-terminal domain.
Modern rational drug design requires the use of
3D structure-activity relationships. We utilize X-ray crystallography
and computational chemistry to design optimized inhibitors of Pin1. Combinatorial
synthesis, high-throughput screening, and biological evaluation of the designed
inhibitors fuels future refinements to yield potential anti-cancer drugs.
Histone Deacetylase Inhibitors (Back to Top of Page)
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Figure 2. L: Design elements of a potent HDAC inhibitor. R: Computer model of
HDAC inhibitor docked into the active site.
A number of histone deacetylase (HDAC) inhibitors are in the midst of clinical trials for cancer therapy. We have designed and synthesized a potent inhibitor of HDACs (Ki = 46 ± 15 nM). The synthetic route includes a number of strategic steps, including an asymmetric hydrogenation to establish two of the stereocenters, macrocyclization, and unmasking the key hydroxamic acid. The cell cycle is regulated by a number of distinct enzymes; one class of these are histone deacetylases, which remove the acetyl groups from lysine residues of the histone. Histones are the proteins that form a core around which cellular DNA is wrapped to keep it organized. Inhibition of HDACs leads to cancer cell death in vitro. We are currently refining the design of this inhibitor to improve its anti-cancer activity.
Biopolymers: Collagen Inspired Materials (Back to Top of Page)
Figure 3. L: X-ray crystal structure (K.Okuyama,C.Hongo,R.Fukushima,G.Wu,H.Narita, K.Nocuchi,Y.Tanaka,N.Nishino, Biopolymers 2004, 76, 367) of a collagen peptide showing the three strands as: yellow ribbon, spheres and sticks. R: Same image replacing one Gly-Pro with a Gly-trans-Pro conformationally locked alkene isostere in purple. Images were created with MacPyMOL v. 0.99 (http://pymol.sourceforge.net/).
A number of medical problems arise from the breakdown or failure of collagen, including arthritis, wounds, burns, and joint damage. Collagen is the most abundant protein in the human body, and proline is the most common amino acid in collagen. We are synthesizing collagen-inspired polymers with our conformationally locked trans-Pro isosteres. The trans-Pro isosteres are expected to stabilize the polymer to mimic the natural conformation of the collagen triple helix to give a biologically stable material. Standard organic synthesis techniques and a number of polymer and biopolymer characterization techniques are employed, including GPC, MALDI-TOF, CD, and X-ray crystallography.
Environmental and Bioanalytical Chemistry: Neural Tube Defects (Back to Top of Page)
We are studying tap water contaminants that cause neural tube defects in mouse embryos in collaboration with Dr. Terry Hrubec (VA-MD College of Veterinary Medicine). These compounds may be disinfection by-products from water treatment. We use GC-MS and LC-MS to identify suspect compounds, then isolate, purify, and perform structural characterization of the suspect compounds. These compounds are then used in further mouse studies of neural tube defects.
Complete
Publications (Back to Top of Page)
1. Briggs, RW; Etzkorn, FA; Hinton,
JF. Thallium-205 Nuclear Magnetic Resonance Study of the Thallium Complex of
Lasalocid (X537A) J. Magnetic Resonance 1980, 523-528.
2. McEwen, AB; Etzkorn, FA; Maier, WF. Significance of Isotopic Distributions
in Catalytic Reactions of Hydrocarbons with Dideuterium Chimia 1987,
41, 293-297.
3. Villani, AJ; Etzkorn, FA; Rotert, GA; Heys, JR. Synthesis of 13C,
14C and 2H13C Labeled Adrenoceptor Antagonists:
6 Chloro-2,3,4,5 tetrahydro-3 methyl-1H 3 benzazepine Hydrochloride and its
N Desmethyl Analog J. Labelled Compounds and Radiopharmaceuticals 1988,
25, 1339-1347.
4. Bartlett, PA; Etzkorn, FA; Guo, T; Lauri, G; Liu, K; Lipton, M; Morgan, BP;
Shea, GT; Shrader, WD; Waterman, S. Intuitive- and Computer-Assisted Approaches
to the Design of Conformationally Restrained Peptides and Their Mimics Proceedings
of the Robert A. Welch Foundation Conference on Chemical Research, XXXV
Chemistry at the Frontiers of Medicine, 1991, 45-68.
5. Maier, WF; Etzkorn, FA. Hinweise zur thermodynamischen Kontrolle von relativen
Hydriergeschwindigkeiten an Platin. (Indication of Thermodynamic Control in
the Relative Rates of Hydrogenation on Platinum). Zeitschrift für Naturforschung
1992, 47b, 175-178.
6. Benson, TE; Marquardt, JL; Marquardt, AC; Etzkorn, FA; Walsh, CT. Overexpression,
Purification, and Mechanistic Study of UDP-N acetylenolpyruvyl-glucosamine Reductase.
Biochemistry 1992, 32, 2024-2030.
7. Zydowsky, LD; Etzkorn, FA; Chang, H; Ferguson, SB; Stolz, LA; Ho, SI; Walsh,
CT. Active Site Mutants of Human Cyclophilin A Separate Peptidyl-Prolyl Isomerase
Activity from Cyclosporin A Binding and Calcineurin Inhibition Protein Science
1992, 1, 1092-1099.
8. Etzkorn, FA; Stolz, LA; Chang, Z; Walsh, CT. The role of the cyclosporin
A-cyclophilin complex, FK506-FK506 binding protein and calcineurin in the inhibition
of T-cell signal transduction. Current Opinion in Structural Biology
1993, 3, 929-933.
9. Etzkorn, FA; Chang, Z; Stolz, LA; Walsh, CT. Cyclophilin Residues That Affect
Noncompetitive Inhibition of the Protein Serine Phosphatase Activity of Calcineurin
by the Cyclophilin/Cyclosporin A Complex. Biochemistry 1994,
33, 2380-2388.
10. Ke, H, Melrose, D, Belshaw, PJ, Alberg, DG, Schreiber, SL, Chang, Z, Etzkorn,
FA, Ho, S, Walsh, CT Crystal structures of cyclophilin A complexed with cyclosporin
A or N-methyl-4-butenyl-4,4-dimethyl-threonine cyclosporin A. Structure
1994, 2, 33-44.
11. Fejzo, J; Etzkorn, FA; Clubb, RT; Shi, Y; Walsh, CT; Wagner, G. The Mutant
E. coli F112W Cyclophilin Binds Cyclosporin A in Nearly the Identical
Conformation as Human Cyclophilin, Biochemistry 1994,
33, 5711-5720.
12. Etzkorn, FA; Guo, T; Lipton, M; Goldberg, S; Bartlett, PA. Cyclic Hexapeptides
and Chimeric Peptides as Mimics of Tendamistat, J. Am. Chem. Soc. 1994,
116, 10412-10425.
13. Wiederrecht, G; Etzkorn, FA. Immunophilins. In Immunosuppressants
N.H. Sigal and M.J. Wyvratt, Eds.; Perspectives in Drug Discovery and Design
series; ESCOM Science Publishers, B.V.: Leiden, The Netherlands, 1994,
2, 57-84.
14. Travins, JM; Etzkorn, FA. Design and Enantioselective Synthesis of a Peptidomimetic
of the Turn in the Helix-Turn-Helix DNA-Binding Protein Motif. J. Org. Chem.
1997, 62, 8387-8393.
15. Foulds, GJ; Etzkorn, FA. A capillary electrophoresis mobility shift assay
for DNA-binding affinities. Nucleic Acids Res. 1998,
26, 4304-4305.
16. Hart, SA; Sabat, M; Etzkorn, FA. Enantio- and Regio-selective Synthesis
of a (Z)-Alkene cis-Proline Mimic. J. Org. Chem. 1998,
63, 7580-7581.
17. Travins, JM; Etzkorn, FA. Facile synthesis of D-amino acids from an L-serine-derived
aziridine. Tetrahedron Lett. 1998, 39, 9389-9392.
18. Hart, SA; Etzkorn, FA. Cyclophilin Inhibition by a (Z)-Alkene cis-Proline
Mimic. J. Org. Chem. 1999, 64, 2298-2299.
19. Etzkorn, FA; Travins, JM; Hart, SA. Rare Protein Turns: Helix-Turn-Helix,
Gamma-Turn and cis-Proline Mimics. In Advances in Peptidomimetics;
A. Abell, Ed.; JAI Press Inc.: Greenwich, CT, 1999; Vol. 2,
125-163.
20. Foulds, GJ; Etzkorn, FA. DNA-binding affinities of MyoD and E47 homo- and
hetero-dimers by capillary electrophoresis mobility shift assay (CEMSA). J.
Chromatogr. A 1999, 862, 231-236.
21. Etzkorn, FA; Travins, JM. Stereospecific Labeling of proR ?-Protons in the
NMR Structure Determination of a Helix-Turn-Helix Turn Peptidomimetic, J.
Pept. Res. 1999, 55, 436-446.
22. Hart, SA; Etzkorn, FA. (Z)-Alkene PhosphoSer-cis-Pro Substrate Analog for
Pin1, a Phosphorylation-Dependent Peptidyl-Prolyl-Isomerase, Proc. 16th
Am. Pept. Symp. 2000, 478-480.
23. Foulds, GJ; Etzkorn, FA. Protein-DNA affinities by capillary electrophoresis.
In Capillary Electrophoresis of Nucleic Acids; K. Mitchelson and J. Cheng, Eds.;
Methods in Molecular Biology series, J. M. Walker, Ed.; Humana Press:
Totowa, N.J., 2001; 369-378.
24. Hart, SA; Trindle, CO; Etzkorn, FA. Solvent-Dependent Stereoselectivity
in a Still-Wittig Rearrangement: An Experimental and Ab Initio Study. Org.
Lett. 2001, 3, 1789-1791.
25. Wang XJ, Hart SA, Xu B, Mason MD, Goodell JR, Etzkorn FA: Serine-cis- and
-trans-Proline Isosteres: Stereoselective Synthesis of (Z)- and (E)-Alkene Mimics
by Still–Wittig and Ireland–Claisen Rearrangements, J. Org. Chem.,
2003, 62, 2343-2349.
26. Kapustin G, Fejér G, Gronlund JL, Seto E, McCafferty DG, Etzkorn FA: Phosphorus-Based
Transition State Analogues as Histone Deacetylase Inhibitors. Org. Lett.
2003, 5, 3053-3056.
27. Wang XJ, Xu B, Mullins AB, Neiler FK, Etzkorn FA: Conformationally Locked
Isostere of PhosphoSer-cis-Pro Inhibits Pin1 23-Fold Better than PhosphoSer-trans-Pro
Isostere. J. Am. Chem. Soc. 2004, 126, 15533-15542.
28. Wang XJ, Etzkorn FA: Peptidyl-Prolyl Isomerase (PPIase) Inhibitors. Peptide
Science 2006, 84, 125-146.
29. Etzkorn, FA; Noel, JP; Zhang, Y; Wang, XJ, Pin1: Inhibitors and Mechanism. In Understanding Biology Using Peptides, Proc. 19th Am. Pept. Symp., Blondelle, S. E., Ed. Springer, Inc.: San Diego, 2006; 759-762.
30. Etzkorn, FA, Pin1 Flips Alzheimer's Switch. ACS Chem. Biol. 2006, 1, (4), 214-216.
31. Schroeder, O. E.; Carper, E.; Wind, J. J.; Poutsma, J.; Etzkorn, F.; Poutsma, J. C. Theoretical and Experimental Investigation of the Energetics of cis-trans Proline Isomerization in Peptide Models. J. Phys. Chem. A. 2006, 110, 6522-6530.
32. Liu, T.; Kapustin, G.; Etzkorn, F. A. Design and Synthesis of a Potent Histone deacetylase Inhibitor. J. Med. Chem. 2007, 50, 2003-2006. DOI: 10.1021/jm061082q.
32. Dai, N.; Etzkorn, F. A. Cis-Trans Proline Isomerization Effects on Collagen Triple-Helix Stability Are Limited. J Am Chem Soc 2009, 131, 13728–13732. DOI: 10.1021/ja904177k.
Patents
1. Travins, J. M.; Etzkorn, F. A.
Peptidomimetic of Helix-Turn-Helix or Gamma-Turn, University of Virginia Patent
Foundation: US, 08/978,023, 1997.
Etzkorn
Group Members
(Alphabetical within categories)
Please write Dr. Etzkorn <fetzkorn@vt.edu> to update education, employment
and contact information.
Current Members
(3001-3003 Hahn Hall, 226 or 301C Davidson,
540-231-8952)
Xingguo (Ronald) Chen; Graduate 2006- ; B.S./M.S. 2002 Nankai University, China; <xgchen@vt.edu>
Nan Dai; Graduate 2002- ; B.S. 2001 Peking University, China; <ndai@vt.edu>
Ana Mercedes-Camacho; Graduate 2005- ; NIH PREP Scholar 2004-2005; B.S. 2003 Universidad Metropolitana, Puerto Rico; <aymerced@vt.edu>
Jennifer Przybyla; Graduate 2006- ; B.S. 2003, Indiana University; M.S. 2006 Southeast Missouri State University, <przybyla@vt.edu>
Song Zhao; Graduate 2003- ; B.S./M.S. 2002 East China University of Science of Technology, China; <sozhao@vt.edu>
Guoyan (Grace) Xu; Graduate 2004- ; B.S./M.S. 2003 Nankai University, China; <guxu1@vt.edu>
Former Members
Jim Anderson; Graduate 1998-2000; Ph.D. 2003 with Milton Brown, University of Virginia; currently Director of Laboratory Operations, Rivanna Pharmaceuticals, Inc., Charlottesville, VA
Angelina Barron; REU Undergraduate 1998, University of Virginia; B.S. 1999 Hampton University, M.S. 2001 Duke University; Currently Chemist II at Magellan Laboratories, Inhalation Division
Natalie Bischoff; Undergraduate 1998, University of Virginia
Michael Bucy; Undergraduate 2002-2003; B.S. 2004; currently graduate student U. Texas Southwestern Medical School, mbucy@vt.edu
Benjamin Cormier; Undergraduate 2002-2003; B.S. Chemical Engineering May 2004; M.S. Chemical Engineering, Texas A&M expected in December 2005
Tobin (Toby) Dickerson; B.S. 1999 Distinguished Major; M.A. 2000 University of Virginia; Ph.D. 2004 with Kim Janda at The Scripps Research Institute (NIH Predoctoral Fellow, Eli Lilly Fellow); currently Senior Research Associate at Scripps Research Institute, Department of Chemistry, 10550 North Torrey Pines Road, BCC-582, La Jolla, CA 92037, Phone: (858) 784-2522, Fax: (858) 784-2590; tobin@scripps.edu
Andrew Fenley; B.S. 2003 Virginia Tech; currently Graduate Student in Physics at Virginia Tech; afenley@vt.edu
Glenn J. Foulds; Ph.D., AllChemie, Inc., Biotech Startup, Charlottesville, glenn@allchemie.net (434)284-1851.
Stephanie Gaillard; Undergraduate 1996, University of Virginia
John Goodell; REU Undergraduate 1999, University of Virginia; goodelljohn@hotmail.com
Gita Gupta; REU Undergraduate1996, University of Virginia
Allison Hager; SRIP Undergraduate 1996, University of Virginia; Currently Merck & Co. in West Point PA, Staff Biochemist in Vaccine Discovery group; allison_hager@merck.com
Charmagne Harris; REU Undergraduate 1997, University of Virginia
Scott A. Hart; Ph.D. 2000, University of Virginia; 2000-2003 Yale University NIH Postdoctoral Fellow with Alanna Schepartz; Currently Development Scientist II at Amylin Pharmaceuticals, Inc., 9360 Towne Centre Drive, San Diego, CA 92121; Phone: (858) 736-8862, FAX: (858) 754-3001, scott.hart@amylin.com
Vladimir Kalashnikov; NeoMPS, Inc., 9395 Cabot Dr., San Diego, CA 92126; vkalashnikov@mps-sd.com
Galina Kapustina; Postdoctoral Associate 2000-2003; Ph.D. 1989 Leningrad Institute of Chemical Technology; Postdoctoral Associate 1992-1993 Weizmann Institute; Research Scientist at Insight Pharmaceuticals, Peptor Ltd., Rehovot, Israel 1994-2000; 2003-2004 Postdoctoral Associate with Madeleine Joullie, University of Pennsylvania; currently at Provid Pharmaceuticals, Inc., Provid Pharmaceuticals Inc., 671 U.S. Route 1, North Brunswick, NJ 08902; Phone: 732-565-1101 ext 662; FAX: 732-565-3776; galina.kapustin@providpharma.com
Thomas Kurpiers; Visiting Graduate 2001-2002; B.S. University of Marburg, Germany; Currently Graduate Student at University of Marburg.
Michelle Lambert; Undergraduate 2001; B.S. expected 2003.
Marc Lannuzel; Postdoctoral Associate 2001-2003, Virginia Tech; Ph.D. 2000, Université Montpellier and Pierre Fabre Research Institute, France; currently Research Chemist at Syncom BV, Groningen, The Netherlands; marc_lannuzel@hotmail.com
Keith Leung; Graduate 2003-2005; B.S. 2002 University of Virginia; waleung@vt.edu
Julie Lim; REU Undergraduate summer 2004; currently University of Virginia undergraduate; jyl6d@Virginia.EDU
Tao Liu; Ph.D 2002-2007; B.S./M.S. 2001 Nankai University, China; Staff Scientist, 2007-present, American Peptide Company, 1271 Avenida Chelsea, Vista, CA 92081, tao@americanpeptide.com
Eric Lutz; REU Undergraduate 1999, University of Virginia
April Mair; REU Undergraduate 1996, University of Virginia;
Kapil Malshet; Undergraduate 1998, B.S. 2001 School of Commerce, University of Virginia; kvm4z@alumni.virginia.edu
Susan Martin; Ph.D. 1999 with Don Hunt, University of Virginia; Currently Postdoctoral Associate at Furman University, South Carolina
Matt Mason; Undergraduate 2001, 2002-2003; B.S. 2002 Harvey Mudd College; Currently Medical Student at SUNY, Upstate Medical University; masonm@upstate.edu
David May; Undergraduate 2005-; B.S. expected 2007; dkmay@vt.edu
Akshitkumar Mistry; Undergraduate summer 2005; B.S. expected 2007 University of Virginia; amm9x@virginia.edu
Gerald (Gerry) Morgan; REU Undergraduate 1999, University of Virginia
Ashley Mullens; Graduate 2003-2005; B.S. 2002 in Biology, Virginia Tech; asmullin@vt.edu
Elizabeth (Beth) Niehaus; Undergraduate 1999, University of Virginia; Linguistics major; Studied in Spain 2000-2001; ekn5b@virginia.edu
Freda (Katie) Neiler; B.S. 2003, Virginia Tech; Currently 2008 PharmD Candidate, Virginia Commonwealth University/Medical College of Virginia School of Pharmacy; neilerfk@vcu.edu
Boobalan Pachaiyappan; M.S. 2005; B.S. University of Madras; M.S. 2003 Indian Institute of Technology, Bombay; <boobalan@vt.edu>
Jared Peak; B.S. 2003 in Biochemistry, Virginia Tech; currently Scientist II with GlaxoSmithKline; jpeak@vt.edu
Pardha Pyla; Computer Science Graduate 2001-2002; pardha@vt.edu
Nikki Reyer; Undergraduate 1997, University of Virginia
Melinda (Mindy) Richardson; Undergraduate 2001, B.S. 2002 Virginia Tech, Currently Pharmacist's Assistant at Krogers; merichar@vt.edu
David Shonka; B.S. 2000 Distinguished Major, University of Virginia; Currently University of Virginia Medical School; dcs5z@virginia.edu
Matthew Shoulders; Undergraduate 2003-2004; B.S. 2004 Virginia Tech; Currently graduate student with Ron Raines at the University of Wisconsin-Madison; shoulders@wisc.edu
Jennifer (Jenn) Stockdill; Undergraduate 2001-2002; B.S. 2003, Virginia Tech; Graduate at Cal Tech 2003-. Advanced Chemistry Development (ACD) Scholar of the Year Award 2000 3rd Place for "Histone Deacetylase Inhibitors as Potential Anti-Cancer Compounds and a Novel Synthetic Inhibitor"; jstockdi@vt.edu
Jeremy M. Travins; Ph.D. 1999, University of Virginia; Postdoctoral Associate 1999-2001 with Dan Rich, University of Wisconsin, Madison, WI; Currently Scientist – Medicinal Chemistry at Johnson & Johnson Pharmaceutical Research and Development, Spring House, PA; jtravins@prdus.jnj.com
Lucas Tucker; Undergraduate 2006; B.S. expected 2007,
Xiaodong (Jane) Wang; Graduate 2000-2005, Ph.D. 2005; B.S. Nankai University, China; 2005-2006 Postdoctoral Associate with Laurence Hurley at the University of Arizona, Tucson, AZ; 2006-present Staff Scientist Sanofi-Aventis, Phoenix, AZ, jane.wang@sanofi-aventis.com
Luke Wiseman; Undergraduate 2000, B.S. 2000 University of Virginia; Ph.D. 2005 with Jeffrey Kelly at Scripps Research Institute; currently Postdoctoral Associate with David Ron at The Skirball Institute, New York University School of Medicine, NY; Phone: (212) 263-7837; wiseman@saturn.med.nyu.edu
Bailing Xu; Postdoctoral Associate 2002-2003; Ph.D. Institute of Materia Medica, Peking Union Medical College; B.S./M.S. NE Normal University, China; currently Assistant Professor; xubl@imm.ac.cn
Loretta (Lori) Yang; B.S. 1997 Distinguished Major, University of Virginia; Ph.D. 2005 with Alanna Schepartz in Molecular Biophysics and Biochemistry at Yale University, currently Postdoctoral Researcher at La Jolla Bioengineering Institute, 505 Coast Blvd. South #405, La Jolla, CA 92037, PH 858-456-7500 ext 134, FX 858-456-7540; lyang@ljbi.org
Virginia Yo; Undergraduate 1993, University of Virginia
Virginia Yo; Undergraduate
1993, University of Virginia