Resume/summaryŁ
Senior Research Scientist
Gilead
Education
1984:
B.S., Physical Chemistry, Department of Chemistry, Xiamen University, Xiamen, Fujian, P.R. China.
Ph.D. in Biophysics/Physical Chemistry with Prof. Robert C. Matthews, Department of Chemistry, the Pennsylvania State University, USA
Postdoctoral Fellow with Prof. Fred Cohen, Department of Pharmaceutical Chemistry, University of California, San Francisco, USA
Professional Experience
1993-1997: Postdoctoral researcher, molecular modeling and structure-based drug discovery,
University of California, San Francisco with Prof. Fred Cohen
Scientist and Sr. Scientist, molecular modeling and structure-based drug discovery, Gilead Sciences, Foster City, California
Membership: American Chemical Society
Patents:
co-inventor of following issued patents
US 5,739,170: Inhibitors of metazoan parasite proteases
US 6,194,421: Inhibitors of metazoan parasite proteases.
US 7,253,180: Pre-organized tricyclic integrase inhibitor compounds.
US 7,407,965: Phosphonate analogs for treating metabolic diseases
US 7,417,055: Kinase inhibitory phosphonate analogs
US 7,427,624: Purine nucleoside phosphorylase inhibitory phosphonate compounds
US 7,427,636: Inosine monophosphate dehydrogenase inhibitory phosphonate compounds
US 7,429,565: Antiviral phosphonate analogs
US 7,432,261: Anti-inflammatory phosphonate compounds
US 7,452,901: Anti-cancer phosphonate analogs
US 7,462,608: Non nucleoside reverse transcriptase inhibitors
US 7,470,724: Phosphonate compounds having immuno-modulatory activity
Oral Presentations
Characterizing Urea-induced Folding Mechanism of the α Subunit of Tryptophan Synthase by
Site-directed Mutagenesis and Kinetics
X. Chen and C.R. Matthews
American Biophysical Society Annual Meeting (1992) San Francisco, USA
Structure-Based Anti-Parasitic Drug Development X. Chen, R. Li, Z. Li, C. Ring, B. Gong, J. Dominquez, E. Davidson, W. Roush, P. Rosenthal, G. Kenyon, J. McKerrow, I. Kuntz, F. Cohen
American Crystallography Union Annual Meeting (1996) Montreal, Canada Discovery of Novel Hydrophobic Interaction Between Influenza Neuraminidase and Oseltamivir and Its implication on Virtual Screening X. Chen, J.M. Chen, S. Swaminathan
SBS 11th Annual Conference & Exhibition: Drug Discovery: From Targets to Candidates (2005) Geneva, Switzerland Structural Basis for Tamiflu’s Role in Influenza Treatment and Prevention X. Chen
CABS (Chinese-American BioPharmaceutial Society) seminar on Avian Flu Research (2006) Mountain View, CA, USA and
CBA (Chinese Bioscience Association) seminar on Avian Flu (2006) Mountain View, CA, USA Tamiflu: Unusual Hydrophobic Interaction and Its Implication on Drug Discovery X. Chen
Theory and Applications of Computational Chemistry 2008 Shanghai, China Chair, session of Cheminformatics and Drug Design Modeling Binding Modes of HIV Integrase Inhibitors X. Chen, S. Swaminathan, J. Chen
The 23rd Annual Meeting of the Groups Studying the Structures of AIDS-Related Systems and Their Application to Targeted Drug Design by NIH (2009) Bethsda, Maryland, USA Modeling Binding Modes of HIV Integrase Inhibitors X. Chen, S. Swaminathan, J. Chen
ACS Fall 2009 National Meeting (2009) Washington, DC, USA Modeling HIV Integrase Inhibition: A Tale of Two Binding Modes X. Chen, S. Swaminathan, J. Chen
NIDDK seminar (2009, hosted by Dr. W. Yang), NIH, Bethesda, Maryland, USA A Tale of Two Drugs: Structure-based Discovery of Neuraminidase Inhibitors Tamiflu (达菲) and Relenza as Anti-Influenza Agents Xiaowu Chen
Seminar (2009, hosted by Prof. Michael Yang), Department of Biology and Chemistry, City University of Hong Kong, Hong Kong, China Modeling Hypothesis and Validation of Scaffold-Dependent SAR of HCV NS3 Protease Inhibition Xiaowu Chen, Chris Sheng, Choung Kim, Huiling Yang, William Delaney, Todd Appleby, S. Swaminathan ACS Spring National Meeting (2010), San Francisco, USA Discovery of A Novel Hydrophobe-Polar π Interaction in Influenza Neuraminidase Inhibition by Tamiflu (达菲) and Implication on Structure-based Drug Development Xiaowu Chen
Seminar (2010, hosted by Prof. Luhua Lai), Department of Chemistry, Peking University, Beijing, China
Publications
1. Mutational analysis of Protein Folding Mechanisms
P. A. Jennings, S. M. Saalau-Bethell, B. E. Finn, X. Chen, and C.R. Matthews
Methods in Enzymology (1991) 202, 113.
2. Analysis of "Toward A Simplification of the Protein Folding Problem: A Stabilizing
Polyalanine α-Helix Engineered in T4 Lysozyme" by Zhang et al. X. Chen and C. R. Matthews
Chemtracts (1991) 2, 260.
3. Principles of Protein Stability I: reversible unfolding of proteins - kinetic and
thermodynamic analysis B. E. Finn, X. Chen, P. A. Jennings, S. M. Saalau-Bethell, and C. R. Matthews
Protein Engineering: A Practical Approach (1992, Rees, A.R., Wetzel, R., & Sternberg, J.E., eds.) IRL Press, Oxford, UK
4. Amino Acid Replacements Can Selectively Affect the Interaction Energy of Autonomous
Folding Units in the α Subunit of Tryptophan Synthase X. Chen, R. Rambo, and C. R. Matthews
Biochemistry (1992, accelerated publication) 31, 2219.
5. Mutagenic Analysis of the Interior Packing of an α/β Barrel Protein. Effects on the Stabilities
and Rates of Interconversion of the Native and Partially Folded Forms of the α Subunit of Tryptophan Synthase T. Tsuji, B. A. Chrunyk, X. Chen, and C. R. Matthews
Biochemistry (1993) 32, 5566.
6. Thermodynamic Properties of the Transition State for the Rate-Limiting Step in the Folding
of the α Subunit of Tryptophan Synthase. X. Chen and C. R. Matthews
Biochemistry (1994) 33, 6356
7. Characterization of a Plasmodium vivax Cysteine Proteinase Gene Identifies Uniquely
Conserved Amino Acids that May Mediate the Substrate Specificity of Malarial Hemoglobinases P. Rosenthal, C. Ring, X. Chen, and F. Cohen
Journal of Molecular Biology (1994) 241, 312
8. Anti-malarial Drug Development Using Models of Enzyme Structure
Z. Li, X. Chen, E. Davidson, O. Zwang, C. Mendis, C. Ring, W. Roush, G. Fegley, R. Li, P. Rosenthal, G. Lee, G. Kenyon, I. Kuntz, and F. Cohen
Chemistry & Biology (1994) 1, 31
9. In Vitro Anti-malarial Activity of Chalcones and Their Derivatives
R. Li, X. Chen, B. Gong, J. Dominguez, E. Davidson, R. Miller, E. Nuzum, J. McKerrow, I. Kuntz, G. Kenyon, and F. Cohen
Journal of Medicinal Chemistry (1995) 38, 5031
10. Structure-based Design of Parasitic Protease Inhibitors
R. Li, X. Chen, B. Gong, Z. Li, E. Davidson, G. Kurzban, R. Miller, E. Nuzum, J.
McKerrow, R. Fletterick, S. Gillmor, C. Craik, I. Kuntz, F. Cohen, and G. Kenyon
Journal of Bioorganic and Medicinal Chemistry (1996)
4, 1421
11. Meeting review: the Second meeting on the Critical Assessment of Techniques for Protein
Structure Prediction (CASP2), Asilomar, California, December 13-16, 1996. R.L. Dunbrack Jr, D.L. Gerloff, M. Bower, X. Chen, O. Lichtarge, F.E. Cohen
Folding and Design (1997) 2:R27
12. Molecular Modeling of Cysteine Proteases from Leishmania major and Development of
Novel, Nonpeptidic Inhibitors P. Selzer, X. Chen, V. Chan, M. Cheng, G. Kenyon, I. Kuntz, J Sakanari, F. Cohen, and J. McKerrow
Experimental Parasitology (1997) 87,212
13. Structure-Activity Relationship Studies of Novel Carbocyclic Influenza Neuraminidase
Inhibitors C. U. Kim, W. Lew, M. A. Williams, H. Wu, L. Zhang, X. Chen, P. A, Escarpe, D. B. Mendel, W. G. Laver, and R. C. Stevens
Journal of Medicinal Chemistry (1998) 41, 2451
14. A new series of C3-aza carbocyclic influenza neuraminidase inhibitors: synthesis and
inhibitory activity. W. Lew, H. Wu, D. B. Mendel, P. A. Escarpe, X. Chen, W. G. Laver, B. J. Graves, and C. U. Kim
Bioorg Med Chem Lett (1998) 8, 3321
15. Synthesis and evaluation of 1,4,5,6-tetrahydropyridazine derivatives as influenza
neuraminidase inhibitors
L. Zhang, M. A. Williams, D. B. Mendel, P. A. Escarpe, X. Chen, K. Y. Wang, B. J.
Graves, G. Lawton, and C. U. Kim
Bioorg Med Chem Lett. (1999)
9,1751
16. Neuraminidase Inhibitors as Anti-Influenza Agents
C. U. Kim, X. Chen, and D. B. Mendel
Antiviral Chemistry & Chemotherapy (1999)
10, 141
17. Chalcone, acyl hydrazide, and related amides kill cultured Trypanosoma brucei brucei
Troeberg, L., X. Chen, T. M. Flaherty, R. E. Morty, M. Cheng, H. Hua, C. Springer, J. H. McKerrow, G. L. Kenyon, J. D. Lonsdale-Eccles, T. H. Coetzer and F. E. Cohen
Mol Med (2000) 6, 660-9.
18. Carbocyclic influenza neuraminidase inhibitors possessing a C3-cyclic amine side chain:
synthesis and inhibitory activity Lew, W., H. Wu, X. Chen, B. J. Graves, P. A. Escarpe, H. L. MacArthur, D. B. Mendel and C. U. Kim
Bioorg Med Chem Lett (2000) 10, 1257-60.
19. Discovery and Development of GS 4104 (oseltamivir): An Orally Active Influenza
Neuraminidase Inhibitor. W. Lew, X. Chen, C. U. Kim
Current Medicinal Chemistry (2000) 7, 663
20. Small molecules VP-14637 and JNJ-2408068 inhibit respiratory syncytial virus fusion by
similar mechanisms
Douglas, J. L., M. L. Panis, E. Ho, K. Y. Lin, S. H. Krawczyk, D. M. Grant, R. Cai, S.
Swaminathan, X. Chen and T. Cihlar
Antimicrob Agents Chemother (2005)
49, 2460-6.

21. Structural Basis of Neuraminidase Inhibitors with Broad Spectrum Activity against Influenza
X. Chen
Trends in Bio/Pharmaceutical Industry (2006) 27-31.
22. Suppression of HIV-1 protease inhibitor resistance by phosphonate-mediated solvent
anchoring
Cihlar, T., G.X. He, X. Liu, J.M. Chen, M. Hatada, S. Swaminathan, M.J. McDermott, Z.Y.
Yang, A. S. Mulato, X. Chen, S.A. Leavitt, K.M. Stray and W. A. Lee
J Mol Biol (2006)
363, 635-47.
23. Design, synthesis, and SAR studies of novel and highly active tri-cyclic HIV integrase
inhibitors Jin, H., R. Z. Cai, L. Schacherer, S. Jabri, M. Tsiang, M. Fardis, X. Chen, J. M. Chen and C. U. Kim
Bioorg Med Chem Lett (2006) 16, 3989-92.
24. Tricyclic HIV integrase inhibitors: potent and orally bioavailable C5-aza analogs.
Jin, H., M. Wright, R. Pastor, M. Mish, S. Metobo, S. Jabri, R. Lansdown, R. Cai, P. Pyun, M. Tsiang, X. Chen and C. U. Kim
Bioorg Med Chem Lett (2008) 18, 1388-91.
25. Modeling, Analysis and Validation of a Novel HIV Integrase Structure Provides Insights into
the Binding Modes of Potent Integrase Inhibitors
X. Chen, M. Tsiang, F. Yu, M. Hung, G.S. Jones, A. Zeynalzadegan, X. Qi, H. Jin, C.U.
Kim, S. Swaminathan and J.M. Chen
Journal of Molecular Biology (2008) 380, 504-19
JMB Top Cited Article 2008-2010
26. Tricyclic HIV integrase inhibitors: VI. SAR studies of 'benzyl flipped' C3-substituted
pyrroloquinolines S. Metobo S, M. Mish, H. Jin, S. Jabri, R. Lansdown, X. Chen, M. Tsiang, M. Wright, C. Kim
Bioorg Med Chem Lett. (2009) 19, 1187-90
27. Tricyclic HIV integrase inhibitors V. SAR studies on the benzyl moiety.
H. Jin, S. Metobo, S. Jabri, M. Mish, R. Lansdown, X. Chen, M. Tsiang, M. Wright, C. Kim
Bioorg Med Chem Lett. (2009) 19, 2263-5
28. Preclinical evaluation of GS-9160, a novel inhibitor of human immunodeficiency virus type 1
integrase GS. Jones, F. Yu, A. Zeynalzadegan, J. Hesselgesser, X. Chen, J. Chen, H. Jin, C. Kim, M. Wright, R. Geleziunas R, M. Tsiang
Antimicrob Agents Chemother. (2009) 53, 1194-203
29. Discovery of novel phosphonate derivatives as hepatitis C virus NS3 protease inhibitors
X. Sheng, H. Pyun, K. Chaudhary, J. Wang, E. Doerffler, M. Fleury, D. McMurtrie, X. Chen, W. Delaney, C. Kim
Bioorg Med Chem Lett. (2009) 19, 3453-7
30. Affinities between the binding partners of the HIV-1 integrase dimer-lens epithelium-derived
M. Tsiang, GS Jones, M. Hung, S. Mukund, B. Han, X. Liu, K. Babaoglu, E. Lansdon, X. Chen, J. Todd, T. Cai, N. Pagratis, R. Sakowicz, R. Geleziunas
J. Biol. Chem. (2009) 248, 33580-99
31. Strand transfer inhibitors of HIV-1 integrase: bringing IN a new era of antiretroviral therapy
Antiviral Research (2010) 85, 101-18
32. Susceptibility of Treatment-Naive HCV Clinical Isolates to HCV Protease Inhibitors
Andrew Bae, Siu-Chi Sun, Xiaoping Qi, Xiaowu Chen, Karin Ku, Angela Worth, Kelly A. Wong, Jeanette Harris, Michael D. Miller and Hongmei Mo
Antimicrobial Agents andChemotherapy (2010) 54:5288-97
33. Novel, potent, and orally bioavailable phosphinic acid inhibitors of the hepatitis C virus NS3
protease. Clarke MO, Chen X, Cho A, Delaney WE 4th, Doerffler E, Fardis M, Ji M, Mertzman M, Pakdaman R, Pyun HJ, Rowe T, Yang CY, Sheng XC, Kim CU.
Bioorg Med Chem Lett. (2011) 21:3568-72
34. Conformationally Constrained Tricyclic HIV Integrase Inhibitors
M. Fardis, H. Jin, X. Chen, M. Tsiang, J.M. Chen, C. Kim, M. Wright
HIV-1 Integrase: Mechanism and Inhibitor Design (2010, N. Nemati, B. Wang eds.), Wiley,
35. Novel, potent and orally bioavailable indolizidinone-derived inhibitors of the hepatitis C virus
NS3 protease. Clarke MO, Byun D, Chen X, Doerffler E, Leavitt SA, Sheng XC, Yang CY, Kim CU.
Bioorg Med Chem Lett. (2012) 22:1095-8
36. Discovery of GS-9256: a novel phosphinic acid derived inhibitor of the hepatitis C virus
NS3/4A protease with potent clinical activity
Sheng XC, Casarez A, Cai R, Clarke MO, Chen X, Cho A, Delaney WE 4th, Doerffler E, Ji M, Mertzman M, Pakdaman R, Pyun HJ, Rowe T, Wu Q, Xu J, Kim CU.
Bioorg Med Chem Lett. (2012) 22:1394-6
37. Discovery of GS-9451: an acid inhibitor of the hepatitis C virus NS3/4A protease
Sheng XC, Appleby T, Butler T, Cai R, Chen X, Cho A, Clarke MO, Cottell J, Delaney WE 4th, Doerffler E, Link J, Ji M, Pakdaman R, Pyun HJ, Wu Q, Xu J, Kim CU.
Bioorg Med Chem Lett. (2012) 22:2629-34
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