Structure Based Design, Inc.

Peer-Reviewed Journal Articles

  • Reich SH, Sprengeler PA, Chiang GG, Appleman JR, Chen J, Clarine J, Eam B1, Ernst JT, Han Q, Goel VK, Han EZR, Huang V, Hung INJ, Jemison A, Jessen KA, Molter J, Murphy D, Neal M, Parker GS, Shaghafi M, Sperry S, Staunton J, Stumpf CR, Thompson PA, Tran C, Webber SE, Wegerski CJ, Zheng H, Webster KR (2018) 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. 61(8):3516-3540. (Cover story)
    PDB code: 6CJ5, 6CJE, 6CJH, 6CJW, 6CJY, 6CK3, 6CK6, 6CKI
  • Jankun J, Yang J, Zheng H, Han FQ, Al-Senaidy A, Skrzypczak-Jankun E. (2012 Jan) Remarkable extension of PAI-1 half-life surprisingly brings no changes to its structure, Int J Mol Med. 29(1):61-4.
    PDB code: 3R4L
  • Lack NA, Axerio-Cilies P, Tavassoli P, Han FQ, Chan KH, Feau C, Leblanc E, Guns ET, Guy RK, Rennie PS, Cherkasov A. (2011)Targeting the Binding Function 3 (BF3) Site of the Human Androgen Receptor through Virtual Screening, J Med Chem. 54(24):8563-73
    PDB code: 2YLQ, 2YLP, 2YLO
  • Axerio-Cilies P, Lack NA, Nayana MR, Chan KH, Yeung A, Leblanc E, Guns ES, Rennie PS, Cherkasov A. (2011 Sep 22)Inhibitors of androgen receptor activation function-2 (AF2) site identified through virtual screening, J Med Chem. 54(18):6197-205.
    PDB code: 2YHD
  • Akula N, Zheng H, Han FQ, Wang N. (2011 Jul 15) Discovery of novel SecA inhibitors of Candidatus Liberibacter asiaticus by structure based design, Bioorg Med Chem Lett. 21(14):4183-87.
  • Han Q.,  Zhao Q., Simonsen KB., Yuefen Zhou., Webber S., Hermann T., Kissinger C., Co-crystal Structure of the Minimum Pharmacophore of Apromycin with Decoding A-site RNA,  (to be submitted)
  • Zhao Q., Han Q., Kissinger C., Hermann T., Thompson P. (2008) Crystal Structure of Hepatitis C Virus
    IRES Subdomain IIa
    , Acta Cryst. D64, 436-443 (cover page of Journal)
  • Dragovich PS, Blazel JK, Ellis DA, Han Q, Kamran R, Kissinger CR, LeBrun LA, Li LS, Murphy DE, Noble M, Patel RA, Ruebsam F, Sergeeva MV, Shah AM, Showalter RE, Tran CV, Tsan M, Webber SE, Kirkovsky L, Zhou Y. (2008) Novel HCV NS5B polymerase inhibitors derived from 4-(1',1'-dioxo-1',4'-dihydro-1'lambda(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 . 18, 5635-9
  • Ruebsam F., Webber SE., Tran MT., Tran CV., Murphy DE., Zhao J., Dragovich PS., Kim SH., Li LS, Zhou YF., Han Q., Zhao Q., Kissinger C., Showalter RE., Lardy M., Shah A., Tsan M., Patel R., LeBrun L., Kamran R., Sergeeva MV., and Kirkovsky L., Pyrrolo[1,2-b]pyridazin-2-ones as potent inhibitors of HCV NS5B polymerase, Bioorg. Med. Chem. Lett  18, 3616-21.
  • Ellis DA., Blazel JK, Webber SE,Tran CV., Dragovich PS., Sun ZX., Ruebsam F., McGuire HM., Xiang AX., Zhao J., Li LS., Zhou YF., Han Q., Kissinger CR., Showalter RE., Lardy M., Amit M. Shah AM., Tsan M., Patel R., Laurie A. LeBrun LA., Kamran R., Darian M., Bartkowski DB., Thomas G., Nolan TG., Daniel A. Norris DA., Maria V. Sergeeva MV., Kirkovsky L., 4-(1,1-Dioxo-1,4-dihydro-1k6-benzo[1,4]thiazin-3-yl)-5-hydroxy-2H-pyridazin-3-ones as potent inhibitors of HCV NS5B polymerase, Bioorg. Med. Chem. Lett  (in press)
  • Zhou YF., Li LS, Dragovich PS., Murphy DE., 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. and Sergeeva M., 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 2. Variation of the 2- and 6-pyridazinone substituents, Bioorg. Med. Chem. Lett. 18, 1419-24
  • Kim SH., Tran MT, Ruebsam F., Xiang AX., Ayida B., McGuire H., Ellis D., Blazel J., Tran CV., Murphy DE., Webber SE., Zhou YF., Shah AM., Tsan M., Showalter RE., Patel R., Gobbi A., LeBrun LA., Bartkowski DM., Nolan TG., Norris DA., Sergeeva MV., Kirkovsky L., Zhao Q., Han Q., Kissinger CR., 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. 18, 4181-5
  • Zhou YF, Webber S., Murphy DE, Li LS., Dragovich PS., Tran C., Sun ZX., Ruebsam F., Shah A., Tsan M., Showalter R., Patel R., Li B., Zhao Q., Han Q., Hermann T., Kissinger C., LeBrun L., Sergeeva M. and  Kirkovsky L., 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 1. Exploration of 7’-substitution of benzothiadiazine, Bioorg. Med. Chem. Lett. 18, 1413-8.
  • Han Q, Zhao Q, Fish S, Simonsen KB, Vourloumis D, Froelich JM, Wall D, Hermann T. (2005) Molecular recognition by glycoside pseudo base pairs and triples in an apramycin-RNA complex. Angew Chem. Int . Ed. Engl.   44, 2694-700.
  • Zhao F, Zhao Q., Blount KF, Han Q, Tor Y, Herman T. (2005) Molecular recognition of RNA by neomycin and a restricted neomycin derivative. Angew Chem. Int. Ed. Engl. 44, 5329-34.
  • Vourloumis D, Winters GC, Simonsen KB, Takahashi M, Ayida BK, Shandrick S, Zhao Q, Han Q, Hermann T. (2005) Aminoglycoside-hybrid ligands targeting the ribosomal decoding site. Chembiochem. 6, 58-65.
  • Shandrick S, Zhao Q, Han Q, Ayida BK, Takahashi M, Winters GC, Simonsen KB, Vourloumis D, Hermann T. (2004) Monitoring molecular recognition of the ribosomal decoding site. Angew Chem. Int. Ed. Engl. 43, 3177-82.
  • Barluenga S, Simonsen KB, Littlefield ES, Ayida BK, Vourloumis D, Winters GC, Takahashi M, Shandrick S, Zhao Q, Han Q, Hermann T. (2004) Rational design of azepane-glycoside antibiotics targeting the bacterial ribosome. Bioorg. Med. Chem. Lett. 14, 713-8.
  • Mi LZ, Devarakonda S, Harp JM, Han Q, Pellicciari R, Willson TM, Khorasanizadeh S, Rastinejad F. (2003) Structural basis for bile acid binding and activation of the nuclear receptor FXR. Mol.  Cell. 11, 1093-100.
  • Han Q, Campbell LR, Gangloff A, Lin SX (2000)  DHEA and DHT Recognition by Human Estrogenic 17ß-Hydroxysteroid Dehydrogenase: C18/C19 Steroid Discrimination and Enzyme Induced Strain. J. Biol. Chem. 275, 1105-11.
  • Han Q, Lin SX (2000) The Study of Crystallization of Human 17ß-Hydroxysteroid Dehydrogenase Type 1 in Complex with DHEA and DHT at Elevated Temperature. Biochem. and Biophys.  Res. Commun. 277, 100-6.
  • Jia J#, Han Q#, Lollike K, Borregaard N, Cygler M (# The two authors contributed equality to this paper) (2000) Crystal Structure of Human Grancalcin, a Member of the Penta-EF-hand Protein Family. J. Mol. Biol. 300, 1261-71.
  • Han Q, Jia J, Lollike K, Borregaard N, Cygler M (2000) Crystallization and Preliminary X-ray Anlysis of Human Grancalcin, a Novel Cytosolic-binding Protein Present in Leukocytes. Acta Crystallogr. D Biol. Crystallogr. 56, 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. (2000) Inhibition of CCR5-dependent HIV-1 infection by hairpin ribozyme gene therapy against CC-chemokine receptor 5. Virology 276: 271-278.
  • Carroll RG, Riley JL, Levine BL, Feng Y , Kaushal S, Ritchey DW, Bernstein W, Weislow OS, Brown CR, Berger EA, June CH, and Louis DC(1997) Differential regulation of HIV-1 fusion cofactor expression by CD28 costimulation of CD4+ T cells. Science 276, 273-276.
  • Alkhatib G., Feng Y , Combadiere C, Broder CC, Kennedy PE, Murphy PM and Berger EA(1996) Fusion cofactor for macrophage-tropic HIV-1 isolates: a receptor for RANTES, MIP-1 a and MIP-1 b. Science 272, 1955-1958.
  • Feng Y, Broder CC, Kennedy PE, and E.A. Berger EA (1996) Cofactor for HIV-1 entry: functional cDNA cloning of a 7-transmembrane G protein-coupled receptor. Science 272, 872.
  • Lin SX, Han Q, Azzi A. Campbell RL (1999) 3D-Structure of 17b-HSD1 with Various Steroids. J. Steroid Biochem. Mol. Biol. 69, 425-9.
  • Zhu DW, Han Q, Campbell RL, Lin SX (1999) Molecule Packing and Modification of Crystal Space Group of Human Estrogenic 17ß-Hydroxysteroid Dehydrogenase Using Cations. J. Crystal Growth, 196, 356-64.
  • Han Q, Lin SX (1996) A Microcrystal Selection Technique in Protein Crystallization. J. Crystal Growth 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.