Publications

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

  • Hegde SG, Huang PQ, Bunker KD, Hopkins CD, Slee DH, Kahraman M, Pinchman J, Sit RK, Lee CC, Rutgard M, Samatar AA, Li J, Ma J, Izadi H, Han FQ, Chao A. Discovery of ZN-c5, an Orally Bioavailable Selective Estrogen Receptor Degrader (SERD) with Improved Pharmacokinetics. J Med Chem., 2025, Jul 24;68(14):14740-14755.
  • Wang et al. Identification of MRTX1133, a Noncovalent, Potent, and Selective KRASG12D Inhibitor. J Med Chem., 2022, Feb 24;65(4):3123-3133. (Mirati Therapeutics, first-in-class, clinical phase II)
  • Mao et al. Olgotrelvir, A Dual Inhibitor of SARS-CoV-2 Mpro and Cathepsin L, as a Stand-alone Antiviral Oral Intervention Candidate for COVID-19. Med., 2024, Jan 12;5(1):42-61. (Clinical Phase III)
  • 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.