My Bibliography

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Nienaber VL, Berliner LJ. Subtle differences in active site structure between bovine and human thrombins: ESR and fluorescence studies. Thromb Haemost. 1991 Jan 23;65(1):40-5. PubMed PMID: 1850875.

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Nienaber VL, Young SL, Birktoft JJ, Higgins DL, Berliner LJ. Conformational similarities between one-chain and two-chain tissue plasminogen activator (t-PA): implications to the activation mechanism on one-chain t-PA. Biochemistry. 1992 Apr 21;31(15):3852-61. doi: 10.1021/bi00130a017. PubMed PMID: 1314651.

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Nienaber V, Breddam K, Birktoft J. A glutamic acid specific series protease utilizes a novel histidine triad in substrate binding. Biochemistry. 1993; 32:11469.

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Nienaber VL, Amparo E. A non-cleavable retro-binding peptide that spans the substrate binding cleft of serine proteases. Atomic structure of Nazumamide A: Human Thrombin. Journal of the American Chemical Society. 1996; 118:6807.

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Urokinase inhibitors. USA patent application US20010049374 A1. 1997.

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Detecting ligand that binds to polypeptide; mix polypeptide and ligands, crystallize, obtain diffraction pattern, detect bound ligand/polypeptide complex. USA US6297021 B1. 1998.

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Highly crystalline urokinase. USA patent application PCT/US1999/004992. 1998.

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Ligand screening and design by x-ray crystallography. USA patent application US20040219607 A1. 1998.

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Bussiere DE, Muchmore SW, Dealwis CG, Schluckebier G, Nienaber VL, Edalji RP, Walter KA, Ladror US, Holzman TF, Abad-Zapatero C. Crystal structure of ErmC', an rRNA methyltransferase which mediates antibiotic resistance in bacteria. Biochemistry. 1998 May 19;37(20):7103-12. doi: 10.1021/bi973113c. PubMed PMID: 9585521.

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Method for automatically aligning a sample in an x-ray diffractometer. USA patent application EP1813935 A3. 1999.

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Automated sample handling for x-ray crystallography. USA US6404849 B1. 1999.

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Hajduk PJ, Dinges J, Schkeryantz JM, Janowick D, Kaminski M, Tufano M, Augeri DJ, Petros A, Nienaber V, Zhong P, Hammond R, Coen M, Beutel B, Katz L, Fesik SW. Novel inhibitors of Erm methyltransferases from NMR and parallel synthesis. J Med Chem. 1999 Sep 23;42(19):3852-9. doi: 10.1021/jm990293a. PubMed PMID: 10508434.

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Napthamidine urokinase inhibitors. USA US 6495562. 2000.

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Nienaber VL, Berliner LJ. Atomic structures of two nitroxide spin labels complexed with human thrombin: comparison with solution studies. J Protein Chem. 2000 Feb;19(2):129-37. doi: 10.1023/a:1007034700573. PubMed PMID: 10945437.

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Nienaber V, Wang J, Davidson D, Henkin J. Re-engineering of human urokinase provides a system for structure-based drug design at high resolution and reveals a novel structural subsite. J Biol Chem. 2000 Mar 10;275(10):7239-48. doi: 10.1074/jbc.275.10.7239. PubMed PMID: 10702294.

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Nienaber VL, Boxrud PD, Berliner LJ. Thrombin inhibitor design: X-ray and solution studies provide a novel P1 determinant. J Protein Chem. 2000 May;19(4):327-33. doi: 10.1023/a:1007055615190. PubMed PMID: 11043938.

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Nienaber VL, Davidson D, Edalji R, Giranda VL, Klinghofer V, Henkin J, Magdalinos P, Mantei R, Merrick S, Severin JM, Smith RA, Stewart K, Walter K, Wang J, Wendt M, Weitzberg M, Zhao X, Rockway T. Structure-directed discovery of potent non-peptidic inhibitors of human urokinase that access a novel binding subsite. Structure. 2000 May 15;8(5):553-63. doi: 10.1016/s0969-2126(00)00136-2. PubMed PMID: 10801494.

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Nienaber VL, Richardson PL, Klighofer V, Bouska JJ, Giranda VL, Greer J. Discovering novel ligands for macromolecules using X-ray crystallographic screening. Nat Biotechnol. 2000 Oct;18(10):1105-8. doi: 10.1038/80319. PubMed PMID: 11017052.

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Hajduk PJ, Boyd S, Nettesheim D, Nienaber V, Severin J, Smith R, Davidson D, Rockway T, Fesik SW. Identification of novel inhibitors of urokinase via NMR-based screening. J Med Chem. 2000 Oct 19;43(21):3862-6. doi: 10.1021/jm0002228. PubMed PMID: 11052791.

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Muchmore SW, Olson J, Jones R, Pan J, Blum M, Greer J, Merrick SM, Magdalinos P, Nienaber VL. Automated crystal mounting and data collection for protein crystallography. Structure. 2000 Dec 15;8(12):R243-6. doi: 10.1016/s0969-2126(00)00535-9. PubMed PMID: 11188700.

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Klinghofer V, Stewart K, McGonigal T, Smith R, Sarthy A, Nienaber V, Butler C, Dorwin S, Richardson P, Weitzberg M, Wendt M, Rockway T, Zhao X, Hulkower KI, Giranda VL. Species specificity of amidine-based urokinase inhibitors. Biochemistry. 2001 Aug 7;40(31):9125-31. doi: 10.1021/bi010186u. PubMed PMID: 11478879.

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Dong J, Swift K, Matayoshi E, Nienaber VL, Weitzberg M, Rockway T, Carey PR. Probing inhibitors binding to human urokinase crystals by Raman microscopy: implications for compound screening. Biochemistry. 2001 Aug 21;40(33):9751-7. doi: 10.1021/bi010955+. PubMed PMID: 11502168.

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Rockway TW, Nienaber V, Giranda VL. Inhibitors of the protease domain of urokinase-type plasminogen activator. Curr Pharm Des. 2002;8(28):2541-58. doi: 10.2174/1381612023392676. Review. PubMed PMID: 12369939.

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Nienaber V. Is X-ray crystallography a viable tool for lead discovery?. Drug Discov Today. 2002 Jun 15;7(12):650. doi: 10.1016/s1359-6446(02)02338-3. PubMed PMID: 12110240.

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Wendt MD, Rockway TW, Geyer A, McClellan W, Weitzberg M, Zhao X, Mantei R, Nienaber VL, Stewart K, Klinghofer V, Giranda VL. Identification of novel binding interactions in the development of potent, selective 2-naphthamidine inhibitors of urokinase. Synthesis, structural analysis, and SAR of N-phenyl amide 6-substitution. J Med Chem. 2004 Jan 15;47(2):303-24. doi: 10.1021/jm0300072. PubMed PMID: 14711304.

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Sanders WJ, Nienaber VL, Lerner CG, McCall JO, Merrick SM, Swanson SJ, Harlan JE, Stoll VS, Stamper GF, Betz SF, Condroski KR, Meadows RP, Severin JM, Walter KA, Magdalinos P, Jakob CG, Wagner R, Beutel BA. Discovery of potent inhibitors of dihydroneopterin aldolase using CrystaLEAD high-throughput X-ray crystallographic screening and structure-directed lead optimization. J Med Chem. 2004 Mar 25;47(7):1709-18. doi: 10.1021/jm030497y. PubMed PMID: 15027862.

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Wendt MD, Geyer A, McClellan WJ, Rockway TW, Weitzberg M, Zhao X, Mantei R, Stewart K, Nienaber V, Klinghofer V, Giranda VL. Interaction with the S1 beta-pocket of urokinase: 8-heterocycle substituted and 6,8-disubstituted 2-naphthamidine urokinase inhibitors. Bioorg Med Chem Lett. 2004 Jun 21;14(12):3063-8. doi: 10.1016/j.bmcl.2004.04.030. PubMed PMID: 15149645.

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Atwell S, Adams JM, Badger J, Buchanan MD, Feil IK, Froning KJ, Gao X, Hendle J, Keegan K, Leon BC, Müller-Dieckmann HJ, Nienaber VL, Noland BW, Post K, Rajashankar KR, Ramos A, Russell M, Burley SK, Buchanan SG. A novel mode of Gleevec binding is revealed by the structure of spleen tyrosine kinase. J Biol Chem. 2004 Dec 31;279(53):55827-32. doi: 10.1074/jbc.M409792200. Epub 2004 Oct 26. PubMed PMID: 15507431.

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Bruncko M, McClellan WJ, Wendt MD, Sauer DR, Geyer A, Dalton CR, Kaminski MA, Weitzberg M, Gong J, Dellaria JF, Mantei R, Zhao X, Nienaber VL, Stewart K, Klinghofer V, Bouska J, Rockway TW, Giranda VL. Naphthamidine urokinase plasminogen activator inhibitors with improved pharmacokinetic properties. Bioorg Med Chem Lett. 2005 Jan 3;15(1):93-8. doi: 10.1016/j.bmcl.2004.10.026. PubMed PMID: 15582418.

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Blaney J, Nienaber V, Burley S. Fragment-based lead discovery and optimization using x-ray crystallography, computational chemistry and high-throughput organic synthesis. In: Jahnke W, Erlanson D, editors. Fragment-based approaches in drug discovery Germany: Wiley; 2006.

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Nienaber V. Start small and stay small. Minimizing attrition in the clinic with a focus on CNS therapeutics. Curr Top Med Chem. 2009;9(18):1688-704. doi: 10.2174/156802609790102374. Review. PubMed PMID: 19929834.

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Mezo AR, Sridhar V, Badger J, Sakorafas P, Nienaber V. X-ray crystal structures of monomeric and dimeric peptide inhibitors in complex with the human neonatal Fc receptor, FcRn. J Biol Chem. 2010 Sep 3;285(36):27694-701. doi: 10.1074/jbc.M110.120667. Epub 2010 Jun 30. PubMed PMID: 20592032; PubMed Central PMCID: PMC2934637.

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Nienaber V. Fragment-based drug discovery for diseases of the central nervous syste. In: Bienstock R, editor. Library design, search method and applications of fragment-based drug design New York: American Chemical Society; 2011. p.179.

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Inhibitors of LRRK2 kinase. USA patent application US14/129099. 2011.

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Badger J, Chie-Leon B, Logan C, Sridhar V, Sankaran B, Zwart PH, Nienaber V. The structure of LpxD from Pseudomonas aeruginosa at 1.3 Å resolution. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2011 Jul 1;67(Pt 7):749-52. doi: 10.1107/S1744309111018811. Epub 2011 Jun 23. PubMed PMID: 21795786; PubMed Central PMCID: PMC3144788.

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Recht MI, Sridhar V, Badger J, Hernandez L, Chie-Leon B, Nienaber V, Torres FE. Fragment-based screening for inhibitors of PDE4A using enthalpy arrays and X-ray crystallography. J Biomol Screen. 2012 Apr;17(4):469-80. doi: 10.1177/1087057111430987. Epub 2012 Jan 5. PubMed PMID: 22223051; PubMed Central PMCID: PMC3745005.

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Badger J, Chie-Leon B, Logan C, Sridhar V, Sankaran B, Zwart PH, Nienaber V. Structure determination of LpxA from the lipopolysaccharide-synthesis pathway of Acinetobacter baumannii. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2012 Dec 1;68(Pt 12):1477-81. doi: 10.1107/S174430911204571X. Epub 2012 Nov 28. PubMed PMID: 23192027; PubMed Central PMCID: PMC3509968.

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Badger J, Chie-Leon B, Logan C, Sridhar V, Sankaran B, Zwart PH, Nienaber V. Structure determination of LpxD from the lipopolysaccharide-synthesis pathway of Acinetobacter baumannii. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2013 Jan 1;69(Pt 1):6-9. doi: 10.1107/S1744309112048890. Epub 2012 Dec 25. PubMed PMID: 23295477; PubMed Central PMCID: PMC3539694.

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Parker AR, Petluru PN, Sridhar V, Leverett BD, Ayala PY, Zhao M, Chei-Leon B, Jair K, Kochat H, Badger J, Hausheer FH. BNP7787 forms novel covalent adducts on human thioredoxin and modulates thioredoxin activity. J Pharmacol Clin Toxicol. 2014; 2:1026.

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Recht MI, Sridhar V, Badger J, Bounaud PY, Logan C, Chie-Leon B, Nienaber V, Torres FE. Identification and optimization of PDE10A inhibitors using fragment-based screening by nanocalorimetry and X-ray crystallography. J Biomol Screen. 2014 Apr;19(4):497-507. doi: 10.1177/1087057113516493. Epub 2013 Dec 27. PubMed PMID: 24375910; PubMed Central PMCID: PMC4007584.

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Parker AR, Petluru PN, Nienaber VL, Zhao M, Ayala PY, Badger J, Chie-Leon B, Sridhar V, Logan C, Kochat H, Hausheer FH. Novel covalent modification of human anaplastic lymphoma kinase (ALK) and potentiation of crizotinib-mediated inhibition of ALK activity by BNP7787. Onco Targets Ther. 2015;8:375-83. doi: 10.2147/OTT.S73690. eCollection 2015. PubMed PMID: 25678804; PubMed Central PMCID: PMC4324543.

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Parker AR, Petluru PN, Nienaber VL, Badger J, Leverett BD, Jair K, Sridhar V, Logan C, Ayala PY, Kochat H, Hausheer FH. Cysteine specific targeting of the functionally distinct peroxiredoxin and glutaredoxin proteins by the investigational disulfide BNP7787. Molecules. 2015 Mar 18;20(3):4928-50. doi: 10.3390/molecules20034928. PubMed PMID: 25793542; PubMed Central PMCID: PMC6272748.