Scientific Publications

1. Ruebsam, F.; Tran, C. V.; Li, L.-S.; Kim, S. H.; Xiang, A. X.; Zhou, Y.; Blazel, J. K.; Sun, Z.; Dragovich, P. S.; Zhao, J.; McGuire, H.; Murphy, D. E.; Tran, M. T.; Stankovic, N.; Ellis, D. A.; Gobbi, A.; Showalter, R. E.; Webber, S. E.; Shah, A. M.; Tsan, M.; Patel, R. A.; LeBrun, L. A.; Hou, H. J.; Kamran, R.; Sergeeva, M. V.; Bartkowski, D. M.; Nolan, T. G.; Norris, D. A.; Kirkovsky, L. "5,6-Dihydro-1H-pyridin-2-ones as potent inhibitors of HCV NS5B polymerase." Bioorg. Med. Chem. Lett. 2009, 19, 451-458.

2. Zhao, Q.; Han, Q.; Kissinger, C. R.; Hermann, T.; Thompson, P. A. "Structure of Hepatitis C Virus IRES Subdomain IIa" Acta Cryst. 2008, D64, 436-443.

3. Belogurov GA, Vassylyeva MN, Sevostyanova A, Appleman JR, Xiang AX, Lira R, Webber SE, Klyuyev S, Nudler E, Artsimovitch I, Vassylyev DG. Transcription inactivation through local refolding of the RNA polymerase structure. Nature. 2008 Oct 22. [Epub ahead of print] PMID: 18946472 [PubMed - as supplied by publisher]

4. Ruebsam, F.; Sun, Z.; Ayida, B. K.; Webber, S. E.; Zhou, Y.; Zhao, Q.; Kissinger, C. R.; Showalter, R. E.; Shah, A. M.; Tsan, M.; Patel, R.; LeBrun, L. A.; Kamran, R.; Sergeeva, M. V.; Bartkowski, D. M.; Nolan, T. G.; Norris D. A.; Kirkovsky, L. "Hexahydro-pyrrolo- and hexahydro-1H-pyrido[1,2-b]pyridazin-2-ones as potent inhibitors of HCV NS5B polymerase." Bioorg. Med. Chem. Lett. 2008, 18, 5002-5005.

5. Dragovich, P. S.; Blazel, J. K.; Ellis, D. A.; Han, Q.; Kamran, R.; Kissinger, C. R.; LeBrun, L. A.; Li, L.-S.; Murphy, D. E.; Noble, M.; Patel, R.; Ruebsam, F.; Sergeeva, M. V.; Shah, A. M.; Showalter, R. E.; Tran, C. V.; Tsan, M.; Webber, S. E.; Kirkovsky, L.; Zhou, Y. "Novel HCV NS5B polymerase inhibitors derived from 4-(1',1'-dioxo-1',4'-dihydro-1' 6-benzo[1',2',4']thiadiazin-3'-yl)-5-hydroxy-2H-pyridazin-3-ones: Part 5. Exploration of pyridazinones containing 6-amino-substituents." Bioorg. Med. Chem. Lett. 2008, 18, 5635-5639.

6. Dragovich, P. S.; Murphy, D. E.; Tran, C. V.; Ruebsam, F. "An Efficient Large-Scale Synthesis of 2-Amino-5-methanesulfonylaminobenzenesulfonamide." Synth. Commun. 2008, 38, 1909-1916.

7. Ellis, D. A.; Blazel, J. K.; Webber, S. E.; Tran, C. V.; Dragovich, P. S.; Sun, Z.; Ruebsam, F.; McGuire, H. M.; Xiang, A. X.; Zhao, J.; Li, L.-S.; Zhou, Y.; Han, Q.; Kissinger, C. R.; Showalter, R. E.; Lardy, M.; Shah, A. M.; Tsan, M.; Patel, R.; LeBrun, L. A.; Kamran, R.; Bartkowski, D. M.; Nolan, T. G.; Norris, D. A.; Sergeeva, M. V.; Kirkovsky, L. "4-(1,1-Dioxo-1,4-dihydro-1?6 -benzo[1,4]thiazin-3-yl)-5-hydroxy-2H -pyridazin-3-ones as potent inhibitors of HCV NS5B polymerase." Bioorg. Med. Chem. Lett. 2008, 18, 4628-4632.

8. Ruebsam, F.; Webber, S. E.; Tran, M. T.; Tran, C. V.; Murphy, D. E.; Zhao, J.; Dragovich, P. S.; Kim, S. H.; Li, L.-S.; Zhou, Y.; Han, Q.; Kissinger, C. R.; Showalter, R. E.; Lardy, M.; Shah, A. M.; Tsan, M.; Patel, R.; LeBrun, L. A.; Kamran, R.; Sergeeva, M. V.; Bartkowski, D. M.; Nolan, T. G.; Norris D. A.; Kirkovsky, L. "Pyrrolo[1,2-b]pyridazin-2-ones as potent inhibitors of HCV NS5B polymerase." Bioorg. Med. Chem. Lett. 2008, 18, 3616-3621.

9. Kim, S. H.; Tran, M. T.; Ruebsam, F.; Xiang, A. X.; Ayida, B.; McGuire, H.; Ellis, D.; Blazel, J.; Tran, C. V.; Murphy, D. E.; Webber, S. E.; Zhou, Y.; Shah, A. M.; Tsan, M.; Showalter, R. E.; Patel, R.; Gobbi, A.; LeBrun, L. A.; Bartkowski, D. M.; Nolan, T. G.; Norris, D. A.; Sergeeva, M. V.; Kirkovsky, L.; Zhao, Q.; Han, Q.; Kissinger, C. R. "Structure-based design, synthesis and biological evaluation of 1,1-dioxoisothiazole and benzo[b]thiophene-1,1-dioxide derivatives as novel inhibitors of hepatitis C virus NS5B polymerase." Bioorg. Med. Chem. Lett. 2008, 18, 4181-4185.

10. Sergeeva, M. V.; Zhou, Y.; Bartkowski, D. M.; Nolan, T. G.; Norris, D. A.; Okamoto, E.; Kirkovsky, L.; Kamran, R.; LeBrun, L. A.; Tsan, M.; Patel, R.; Shah, A. M.; Lardy, M.; Gobbi, A.; Li, L.-S.; Zhao, J.; Bertolini, T.; Stankovic, N.; Sun, Z.; Murphy D. E.; Webber, S. E.; Dragovich, P. S. "Novel HCV NS5B polymerase inhibitors derived from 4-(1',1'-dioxo-1',4'-dihydro-1' 6-benzo[1',2',4']thiadiazin-3'-yl)-5-hydroxy-2H-pyridazin-3-ones: Part 4. Optimization of DMPK properties." Bioorg. Med. Chem. Lett. 2008, 18, 3421-3426.

11. Li, L.-S.; Zhou, Y.; Murphy, D. E.; Stankovic, N.; Zhao, J.; Dragovich, P. S.; Bertolini, T.; Sun, Z.; Ayida, B.; Tran, C. V.; Ruebsam, F.; Webber, S. E.; Shah, A. M.; Tsan, M.; Showalter, R. E.; Patel, R.; LeBrun, L.; Bartkowski, D.; Nolan, T.; Norris, D.; Kamran, R.; Brooks, J.; Sergeeva, M. V.; Kirkovsky, L.; Zhao, Q.; Kissinger, C. R. "Novel HCV NS5B Polymerase Inhibitors Derived From 4-(1',1'-Dioxo-1',4'-dihydro-1'l6-benzo[1',2',4']thiadiazin-3'-yl)-5-hydroxy-2H-pyridazin-3-ones: Part 3. Further Optimization of the 2-, 6-, and 7'-Substituents and Initial Pharmacokinetic Assessments." Bioorg. Med. Chem. Lett. 2008, 18, 3446-3455.

12. Thompson PA, Wang S, Howett LJ, Wang MM, Patel R, Averill A, Showalter RE, Li B, Appleman JR. Identification of ligand binding by protein stabilization: comparison of ATLAS with biophysical and enzymatic methods.
Assay Drug Dev Technol. 2008 Feb;6(1):69-81. PMID: 18336087 [PubMed - indexed for MEDLINE]

13. Patel R, Lebrun LA, Wang S, Howett LJ, Thompson PA, Appleman JR, Li B. ATLAS--a high-throughput affinity-based screening technology for soluble proteins: technology application using p38 MAP kinase.
Assay Drug Dev Technol. 2008 Feb;6(1):55-68. PMID: 18336086 [PubMed - indexed for MEDLINE]

14. Murphy, D. E.; Dragovich, P. S.; Ayida, B. K.; Bertolini, T. M.; Li, L.-S.; Ruebsam, F.; Stankovic, N. S.; Sun, Z.; Zhou, J.; Zhou. Y. "Efficient Synthesis of 2,6-Disubstituted-5-hydroxy-3-oxo-2,3-dihydro-pyridazine-4-carboxylic Acid Ethyl Esters." Tetrahedron Lett. 2008, 49, 811-815.

15. Dragovich, P. S.; Blazel, J. K.; Dao, K.; Ellis, D. A.; Li, L.-S.; Murphy, D. E.; Ruebsam, F.; Tran, C. V.; Zhou, Y. "Regiospecific Synthesis of Novel 6-Amino-5-hydroxy-3(2H)-pyridazinones." Synthesis 2008, 610-616.

16. Zhou, Y.; Webber, S. E.; Murphy, D. E.; Li, L.-S.; Dragovich, P. S.; Tran, C.; Sun, Z.; Ruebsam, F.; Shah, A. M.; Tsan, M.; Showalter, R. E.; Patel, R.; Li, B.; Zhao, Q.; Han, Q.; Hermann, T.; Kissinger, C. R.; LeBrun, L.; Sergeeva, M. V.; Kirkovsky, L. "Novel HCV NS5B polymerase inhibitors derived from 4-(1',1'-dioxo-1',4'-dihydro-1' 6-benzo[1',2',4']thiadiazin-3'-yl)-5-hydroxy-2H-pyridazin-3-ones: Part 1. Exploration of 7'-substitution of benzothiadiazine." Bioorg. Med. Chem. Lett. 2008, 18, 1413-1418.

17. Zhou, Y.; Li, L.-S.; Dragovich, P. S.; Murphy, D. E.; Tran, C.; Ruebsam, F.; Webber, S. E.; Shah, A. M.; Tsan, M.; Averill, A.; Showalter, R. E.; Patel, R.; Han, Q.; Zhao, Q.; Hermann, T.; Kissinger, C. R.; LeBrun, L.; Sergeeva, M. V. "Novel HCV NS5B polymerase inhibitors derived from 4-(1',1'-dioxo-1',4'-dihydro-1' 6-benzo[1',2',4']thiadiazin-3'-yl)-5-hydroxy-2H-pyridazin-3-ones: Part 2. Variation of the 2- and 6-pyridazinone substituents." Bioorg. Med. Chem. Lett. 2008, 18, 1419-1424.

18. Bullard, Drew; Gobbi, Alberto; Lardy, Mathew A.;Perkins, Charles; Little, Zach. Hydra: A Self Regenerating High Performance Computing Grid for Drug Discovery, J. Chem. Inf. Model., 2008, 48 (4), pp 811–816.

19. Averett DR, Fletcher SP, Li W, Webber SE, Appleman JR.The pharmacology of endosomal TLR agonists in viral disease. Biochem Soc Trans. 2007 Dec;35(Pt 6):1468-72. Review. PMID: 18031247 [PubMed - indexed for MEDLINE]

20. Lira R, Xiang AX, Doundoulakis T, Biller WT, Agrios KA, Simonsen KB, Webber SE, Sisson W, Aust RM, Shah AM, Showalter RE, Banh VN, Steffy KR, Appleman JR. Syntheses of novel myxopyronin B analogs as potential inhibitors of bacterial RNA polymerase.
Bioorg Med Chem Lett. 2007 Dec 15;17(24):6797-800. Epub 2007 Oct 17.
PMID: 17980587 [PubMed - indexed for MEDLINE]

21. Li, L.-S.; Zhou, Y.; Zhao, J.; Dragovich, P. S.; Stankovic, N.; Bertolini, T. M.; Murphy, D. E.; Sun, Z.; Tran, C. V.; Ayida, B. K.; Ruebsam, F.; Webber, S. E. "Synthesis of New Pyridazinone Derivatives: 2,6-Disubstituted-5-hydroxy-3(2H)-pyridazinone-4-carboxylic Acid Ethyl Esters." Synthesis, 2007,3301-3308.

22. Xiang AX, Webber SE, Kerr BM, Rueden EJ, Lennox JR, Haley GJ, Wang T, Ng JS, Herbert MR, Clark DL, Banh VN, Li W, Fletcher SP, Steffy KR, Bartkowski DM, Kirkovsky LI, Bauman LA, Averett DR. Discovery of ANA975: an oral prodrug of the TLR-7 agonist isatoribine. Nucleosides Nucleotides Nucleic Acids. 2007;26(6-7):635-40.

23. Dragovich, P. S., Bertolini, T. M.; Ayida, B. K.; Li, L.-S.; Murphy, D. E.; Ruebsam, F.; Sun, Z.; Zhou, Y. "Regiospecific Synthesis of 1,5-Disubstituted-1H-pyrazoles Containing Differentiated 3,4-Dicarboxylic Acid Esters via Suzuki Coupling of the Corresponding 5-Trifluoromethane Sulfonates." Tetrahedron 2007, 63, 1154-1166.

24. Fletcher, Simon P.; Steffy, Kevin R.; Averett, Devon R. Masked Oral Prodrugs of Toll-Like Receptor 7 Agonists: A New Approach for the Treatment of Infectious Diseases, Current Opinion in Investigational Drugs, 2006, 2006 7(8): 702-708.

25. Horsmans, Yves; Berg, Thomas; Desager, Jean-Pierre; Mueller, Tobias; Schott, Eckart; Fletcher, Simon P.; Steffy, Kevin R.; Bauman Lisa A.; Kerr, Bradley M.; Averett, Devron R. Isatoribine, an Agonist of TLR7, Reduces Plasma Virus Concentration in Chronic Hepatitis C Infection, Hepatology 2005, 42(2), 724-731.

26. Hermann, Thomas. Drugs targeting the ribosome, Current Opinion in Structural Biology 2005, 15(3), 355-366.

27. Hewitt, Robin; Gobbi, Alberto; Lee, Man-ling. A Searching and Reporting System for Relational Databases Using a Graph-Based Metadata Representation, Journal of Chemical Information Model. 2005, 45, 863-869

28. Han, Qing; Zhao, Qiang; Fish, Sarah; Simonsen, Klaus B.; Vourloumis, Dionisios; Froelich, Jamie M.; Wall, Daniel; Hermann, Thomas. Molecular recognition by glycoside pseudo base pairs and triples in an apramycin-RNA complex, Angewandte Chemie International Edition 2005, 44(18), 2694-2700.

29. Ayida, Benjamin K.; Simonsen, Klaus B.; Vourloumis, Dionisios; Hermann, Thomas. Synthesis of dehydroalanine fragments as thiostrepton side chain mimetics, Bioorganic & Medicinal Chemistry Letters 2005, 15(10), 2457-2460.

30. Yaroshevsky-Glanville, Mary. Conflict resolution in the biotech industry, Nature Biotechnology 2005, 23(3), 391-392.

31. Hermann, Thomas; Tor, Yitzhak. RNA as a target for small-molecule therapeutics, Expert Opinion on Therapeutic Patents 2005, 15(1), 49-62.

32. Vourloumis, Dionisios; Winters, Geoffrey C.; Simonsen, Klaus B.; Takahashi, Masayuki; Ayida, Benjamin K.; Shandrick, Sarah; Zhao, Qiang; Han, Qing; Hermann, Thomas. Aminoglycoside-hybrid ligands targeting the ribosomal decoding site, ChemBioChem 2005, 6(1), 8-65.

33. Doundoulakis, Thomas; Xiang, Alan X.; Lira, Ricardo; Agrios, Konstantinos A.; Webber, Stephen E.; Sisson, Wes; Aust, Robert M.; Shah, Amit M.; Showalter, Richard E.; Appleman, James R.; Simonsen, Klaus B. Myxopyronin B analogs as inhibitors of RNA polymerase, synthesis and biological evaluation, Bioorganic & Medicinal Chemistry Letters 2004, 14(22), 5667-5672.

34. Zhou, Yuefen; Murphy, Douglas E.; Sun, Zhongxiang; Gregor, Vlad E. Novel parallel synthesis of N-(4-oxo-2-substituted-4H-quinazolin-3-yl)-substituted sulfonamides, Tetrahedron Letters 2004, 45(43), 8049-8051.

35. Yaroshevsky-Glanville, Mary. Careers and recruitment: Strategic HR for today's biotechnology companies, Nature Biotechnology 2004, 22(9), 1189.

36. Ovenden, Simon P.B; Sberna, Gian; Tait, R. Murray; Wildman, Howard G.; Patel, Rupal; Li, Bin; Steffy, Kevin; Nguyen, Natalie; Meurer-Grimes, Barbara M. A Diketopiperazine Dimer from a Marine-Derived Isolate of Aspergillus niger, Journal of Natural Products 2004, 67, 2093-2095.

37. Shandrick, Sarah; Zhao, Qiang; Han, Qing; Ayida, Benjamin K.; Takahashi, Masayuki; Winters, Geoffrey C.; Simonsen, Klaus B.; Vourloumis, Dionisios; Hermann, Thomas. Monitoring molecular recognition of the ribosomal decoding site, Angewandte Chemie International Edition 2004, 43(24), 3177-3182.

38. Gobbi, Alberto; Funeriu, Sandra; Ioannou, John; Wang, Jinyi; Lee, Man-Ling; Palmer, Chris; Bamford, Bob; Hewitt, Robin. Process-Driven Information Management System at a Biotech Company: Concept and Implementation, Journal of Chemical Information and Computer Sciences 2004, 44(3), 964-975.

39. Barluenga, Sofia; Simonsen, Klaus B.; Littlefield, Ethel S.; Ayida, Benjamin K.; Vourloumis, Dionisios; Winters, Geoffrey C.; Takahashi, Masayuki; Shandrick, Sarah; Zhao, Qiang; Han, Qing; Hermann, Thomas. Rational design of azepane-glycoside antibiotics targeting the bacterial ribosome, Bioorganic & Medicinal Chemistry Letters 2004, 14(3), 713-718.