Publications

A list of peer reviewed publications from Scientist at Structure Based Design, Inc.

  • Han, Q.; Zhao, Q.; Simonsen, K.B.; Yuefen, Z.; Webber, S.; Hermann, T.; Kissinger, C. Co-crystal Structure of the Minimum Pharmacophore of Apromycin with Decoding A-site RNA. (to be submitted)
  • Reich, S.H.; Sprengeler, P.A.; Chiang, G.G.; Appleman, J.R.; Chen, J.; Clarine, J.; Eam, B.; Ernst, J.T.; Han, Q.; Goel, V.K.; Han, E.Z.R.; Huang, V.; Hung, I.N.J.; Jemison, A.; Jessen, K.A.; Molter, J.; Murphy, D.; Neal, M.; Parker, G.S.; Shaghafi, M.; Sperry, S.; Staunton, J.; Stumpf, C.R.; Thompson, P.A.; Tran, C.; Webber, S.E.; Wegerski, C.J.; Zheng, H.; Webster, K.R. Structure-based Design of Pyridone--Aminal eFT508 Targeting Dysregulated Translation by Selective Mitogen-activated Protein Kinase Interacting Kinases 1 and 2 (MNK1/2) Inhibition. J. Med. Chem., 2018,, 61(8), 3516-40. (Cover story)
    PDB code: 6CJ5, 6CJE, 6CJH, 6CJW, 6CJY, 6CK3, 6CK6, 6CKI
  • Jankun J.; Yang J.; Zheng H.; Han F.Q.; Al-Senaidy A.; Skrzypczak-Jankun E. Remarkable extension of PAI-1 half-life surprisingly brings no changes to its structure. Int. J. Mol. Med., 2012, 29(1), 61-4.
    PDB code: 3R4L
  • Lack, N.A.; Axerio-Cilies, P.; Tavassoli, P.; Han, F.Q.; Chan, K.H.; Feau, C.; Leblanc, E.; Guns E.T.; Guy, R.K.; Rennie, P.S.; Cherkasov A. Targeting the Binding Function 3 (BF3) Site of the Human Androgen Receptor through Virtual Screening. J. Med. Chem., 2011, 54(24), 8563-73.
    PDB code: 2YLQ, 2YLP, 2YLO
  • Axerio-Cilies, P.; Lack, N.A.; Nayana, M.R.; Chan, K.H.; Yeung, A.; Leblanc, E.; Guns, E.S.; Rennie, P.S.; Cherkasov, A. Inhibitors of androgen receptor activation function-2 (AF2) site identified through virtual screening. J. Med. Chem. 2011, 54(18), 6197-205.
    PDB code: 2YHD
  • Akula, N.; Zheng, H.; Han, F.Q.; Wang, N. Discovery of novel SecA inhibitors of Candidatus Liberibacter asiaticus by structure based design. Bioorg. Med. Chem. Lett. 2011, 21(14), 4183-8.
  • Zhao, Q.; Han, Q.; Kissinger, C.; Hermann, T.; Thompson, P. Crystal Structure of Hepatitis C Virus IRES Subdomain IIa. Acta Crystallogr. D Biol. Crystallogr. 2008, 64(4), 436-43. (Cover Story)
  • 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.A.; 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′λ6-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, 5635-9.
  • 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.F.; Han, Q.; Zhao, Q.; Kissinger, C.; Showalter, R.E.; Lardy, M.; Shah, A.; Tsan, M.; Patel, R.; LeBrun, L.; Kamran, R.; Sergeeva, M.V.; Kirkovsky, L. Pyrrolo[1,2-b]pyridazin-2-ones as potent inhibitors of HCV NS5B polymerase. Bioorg. Med. Chem. Lett. 2008, 18(12), 3616-21.
  • Ellis, D.A.; Blazel, J.K.; Webber, S.E.; Tran, C.V.; Dragovich, P.S.; Sun, Z.X.; Ruebsam, F.; McGuire, H.M.; Xiang, A.X.; Zhao, J.; Li, L.-S.; Zhou, Y.F.; Han, Q.; Kissinger, C.R.; Showalter, R.E.; Lardy, M.; Amit, M.; Shah, A.M.; Tsan, M.; Patel, R.; Laurie, A.; LeBrun, L.A.; Kamran, R.; Darian, M.; Bartkowski, D.B.; Thomas, G.; Nolan, T.G.; Daniel, A.; Norris, D.A.; Maria, V.; Sergeeva, M.V.; Kirkovsky, L. 4-(1,1-Dioxo-1,4-dihydro-1λ6-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(16), 4628-32.
  • Zhou, Y.F.; Li, L.-S., Dragovich, P.S.; Murphy, D.E.; Tran, C.; Ruebsam, F.; Webber, S.; Shah, A.; Tsan, M.; Averill, A.; Showalter, R.; Patel, R.; Han, Q.; Zhao, Q.; Hermann, T.; Kissinger, C.; LeBrun, L.; Sergeeva, M. Novel HCV NS5B polymerase inhibitors derived from 4-(1′,1′-dioxo-1′,4′-dihydro-1′λ6-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(4), 1419-24.
  • 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.F.; 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(14), 4181-5
  • Zhou, Y.F.; Webber, S.; Murphy, D.E.; Li, L.-S.; Dragovich, P.S.; Tran, C.; Sun, Z.X.; Ruebsam F.; Shah, A.; Tsan, M.; Showalter, R.; Patel, R.; Li, B.; Zhao, Q.; Han, Q.; Hermann, T.; Kissinger, C.; LeBrun, L.; Sergeeva, M.; Kirkovsky, L. Novel HCV NS5B polymerase inhibitors derived from 4-(1',1'-dioxo-1',4'-dihydro-1'λ6-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(4), 1413-8.
  • Han, Q.; Zhao, Q.; Fish, S.; Simonsen, K.B.; Vourloumis, D.; Froelich, J.M.; Wall, D.; Hermann, T. Molecular recognition by glycoside pseudo base pairs and triples in an apramycin-RNA complex.. Angew. Chem. Int. Ed. Engl. 2005, 44(18), 2694-700.
  • Zhao, F.; Zhao, Q.; Blount, K.F.; Han, Q.; Tor, Y.; Herman, T. Molecular recognition of RNA by neomycin and a restricted neomycin derivative. Angew. Chem. Int. Ed. Engl. 2005, 44, 5329-34.
  • Vourloumis, D.; Winters, G.C.; Simonsen, K.B.; Takahashi, M.; Ayida, B.K.; Shandrick, S.; Zhao, Q.; Han, Q.; Hermann, T. Aminoglycoside-hybrid ligands targeting the ribosomal decoding site. Chembiochem. 2005, 6(1), 58-65.
  • Shandrick, S.; Zhao, Q.; Han, Q.; Ayida, B.K.; Takahashi, M.; Winters, G.C.; Simonsen, K.B.; Vourloumis, D.; Hermann, T. Monitoring molecular recognition of the ribosomal decoding site. Angew. Chem. Int. Ed. Engl. 2004, 43(24), 3177-82.
  • Barluenga, S.; Simonsen, K.B.; Littlefield, E.S.; Ayida, B.K.; Vourloumis, D.; Winters, G.C.; Takahashi, M.; Shandrick, S.; Zhao, Q.; Han, Q.; Hermann, T. Rational design of azepane-glycoside antibiotics targeting the bacterial ribosome. Bioorg. Med. Chem. Lett. 2004, 14(3), 713-8.
  • Mi, L.Z.; Devarakonda, S.; Harp, J.M.; Han, Q.; Pellicciari, R.; Willson, T.M.; Khorasanizadeh, S.; Rastinejad, F. Structural basis for bile acid binding and activation of the nuclear receptor FXR. Mol. Cell. 2003, 11(4), 1093-100.
  • Han, Q.; Campbell, R.L.; Gangloff, A.; Huang, Y.-W.; Lin, S.-X. DHEA and DHT Recognition by Human Estrogenic 17β-Hydroxysteroid Dehydrogenase: C18/C19 Steroid Discrimination and Enzyme Induced Strain. J. Biol. Chem. 2000, 275(2), 1105-11.
  • Han, Q.; Lin, S.-X. The Study of Crystallization of Estrogenic 17β-Hydroxysteroid Dehydrogenase with DHEA and DHT at Elevated Temperature. Biochem. and Biophys. Res. Commun. 2000, 277(1), 100-6.
  • Jia, J.#, Han, Q.#, Lollike, K.; Borregaard, N.; Cygler, M. Crystal Structure of Human Grancalcin, a Member of the Penta-EF-hand Protein Family. J. Mol. Biol. 2000, 300(5), 1261-71. (# The two authors contributed equality to this paper)
  • Han, Q.; Jia, J.; Lollike, K.; Borregaard, N.; Cygler, M. Crystallization and Preliminary X-ray Anlysis of Human Grancalcin, a Novel Cytosolic-binding Protein Present in Leukocytes. Acta Crystallogr. D Biol. Crystallogr. 2000, 56(6), 772-4.
  • Feng, Y.; Leavitt, M.; Triz, R.; Duarte, E.; Kang, D.; Mamounas, M.; Gilles, P.; Wong-Staal, F.; Kennedy, S.; Meron, J.; Yu, M.; and Barber, J.R. Inhibition of CCR5-dependent HIV-1 infection by hairpin ribozyme gene therapy against CC-chemokine receptor 5. Virology 2000, 276(2), 271-8.
  • Carroll, R.G.; Riley, J.L.; Levine, B.L.; Feng, Y. , Kaushal, S.; Ritchey, D.W.; Bernstein, W.; Weislow, O.S.; Brown, C.R.; Berger, E.A.; June, C.H.; Louis, D.C. Differential regulation of HIV-1 fusion cofactor expression by CD28 costimulation of CD4+ T cells. Science 1997, 276(5310), 273-6.
  • Alkhatib, G.; Combadiere, C.; Broder, C.C.; Feng, Y.; Kennedy, P.E.; Murphy, P.M.; Berger, E.A. CC CKR5: A RANTES, MIP-1α, MIP-1 Receptor as a Fusion Cofactor for Macrophage-Tropic HIV-1. Science 1996, 272(5270), 1955-1958.
  • Feng, Y.; Broder, C.C.; Kennedy, P.E.; E.A.; Berger, E.A. HIV-1 entry cofactor: functional cDNA cloning of a seven-transmembrane, G protein-coupled receptor. Science 1996, 272(5263), 872-7.
  • Lin, S.-X.; Han, Q.; Azzi, A.; Zhu, D.-W., Gangloff, A., Campbell, R.L. 3D-structure of human estrogenic 17β-HSD1: binding with various steroids. J. Steroid Biochem. Mol. Biol. 1999, 69(1-6), 425-9.
  • Zhu, D.-W.; Han, Q.; Qiu, W.; Campbell, R.L.; Xie, B.-X.; Azzi, A.; Lin, S.-X. Human 17β-hydroxysteroid dehydrogenase-ligand complexes: crystals of different space groups with various cations and combined seeding and co-crystallization. J. Crystal Growth 1999, 196(2-4), 356-64.
  • Han, Q.; Lin, S.-X. A Microcrystal Selection Technique in Protein Crystallization. J. Crystal Growth 1995, 168, 181-4.
  • Han, Q.; Lin, S.-X. A Technique of Protein Addition for Repeated Enlargement of Protein Crystal in Solution, Techniques in Protein Chemistry VII, Ed. D.R. Marshak (Academic Press, New York, 1996) pp. 361-371.
  • Wang, Y.-P.; Pan, J.-L.; Nui, X.-T.; Zhou, Y.-C.; Hua, Z.-Q.; Xu, Q.; Wu, S.; Han, Q.; Li, H.-M.; Liu, Y.-S.; Teng M.-K.; He H.-H.; Lin S.-X.; Bi Y.-C.; The Second Experiment of Growing Protein Crystal in Space. Sci. China (Series B) (1995).
  • Bi, R.-C.; Gui, L.-L.; Han, Q.; Wang, Y.-P.; Chen, S.-Z.; Shi, K.; Hu, Y.-L.; Shen, F.-L.; Niu, X.-T. Protein Crystallization in Space. Microgravity Sci. Technol. VII/2, (1994) pp. 203-206.
  • Han, Q.; Shen, F.-L.; Gui, L.-L.; & Bi, R.-C.; Application of the Gel Technique to Lysozyme and Acidic Phospholipase A2 Crystal Growth. Acta Biophysica Sinica, 9, (1993) pp. 515-519.
  • Bi, R.-C. Gui, L-L.; Shi, K.; Wang, Y.-P.; Chen, S.-Z.; Han, Q.; Hu, Y.-L.; Shen F.-L.; Niu, X.-T.; Hua, Z.-Q.; Lu, G.-Y.; Chang, J.; Li, S.-L.; Gong, W.-M.; Niu, L.-W.; Protein Crystal Growth Under Microgravity. Science China (Series B), 23, (1993) pp. 1154-1157.