1. Demonstration of AutoDock as an Educational Tool for Drug Discovery” Helgren, Travis R.; Hagen, Timothy J. Journal of Chemical Education 2017, 94(3), 345–349. DOI:10.1021/acs.jchemed.6b00555
  2. Rickettsia prowazekii methionine aminopeptidase as a promising target for the development of antibacterial agents” Helgren, Travis R.; Chen, Congling; Wangtrakuldee, Phumvadee; Edwards, Thomas E.; Staker, Bart L.; Abendroth, Jan; Sankaran, Banumathi; Housley, Nicole A.; Myler, Peter J.; Audia, Jonathon P.; et al Bioorganic & Medicinal Chemistry 2017, 25(3), 813–824. DOI:10.1016/j.bmc.2016.11.013
  3. Synthesis and biological evaluation of pyrazolopyrimidines as potential antibacterial agents” Goshu, Gashaw M.; Ghose, Debarati; Bain, Joy M.; Pierce, Phillip G.; Begley, Darren W.; Hewitt, Stephen N.; Udell, Hannah S.; Myler, Peter J.; Meganathan, R.; Hagen, Timothy J. Bioorganic & Medicinal Chemistry Letters 2015, 25(24), 5699–5704. DOI:10.1016/j.bmcl.2015.10.096
  4. Advances in Bacterial Methionine Aminopeptidase Inhibition" Travis Helgren, Timothy J. Hagen Current Topics in Medicinal Chemistry 2016, 16(4), 397–414. DOI:10.2174/1568026615666150813145410
  5. "The synthesis, antimalarial activity and CoMFA analysis of novel aminoalkylated quercetin analogs" Helgren, Travis R.; Sciotti, Richard J.; Lee, Patricia; Duffy, Sandra; Avery, Vicky M.; Igbinoba, Osayawemwen; Akoto, Matthew; Hagen, Timothy J. Bioorg. Med. Chem. Lett. 2015, 25(2), 327–332.
  6. "Phthalazines" Helgren, T. R. and Hagen T.J. Science of Synthesis, Knowledge Updates 2015, in press.
  7. "Discovery of triazines as selective PDE4B versus PDE4D inhibitors" Hagen, Timothy J.; Mo, Xuesheng; Burgin, Alex B.; Fox, David; Zhang, Zheng; Gurney, Mark E. Bioorg. Med. Chem. Lett. 2014, 24(16), 4031–4034.
  8. "Cytidine derivatives as IspF inhibitors of Burkolderia pseudomallei." Zhang, Z.; Jakkaraju, S.; Blain, J.; Gogol, K.; Zhao, L.; Hartley, R. C.; Karlsson, C. A.; Staker, B. L.; Edwards, T. E.; Stewart, L. J.; Myler, P. J.; Clare, M.; Begley, D. W.; Horn, J. R.; Hagen, T. J., Bioorg. Med. Chem. Lett. 2013, 23, 6860–6863.
  9. "Discovery of inhibitors of Burkholderia pseudomallei methionine aminopeptidase with antibacterial activity." P. Wangtrakuldee, M.S. Byrd, C.G. Campos, M.W. Henderson, Z. Zhang, A. Masoudi, P.J. Myler, J.R. Horn, P.A. Cotter, T.J. Hagen 2013, ACS Med. Chem. Lett. 2013, 699–703.
  10. "A concise synthesis of biaryl PDE4D allosteric modulators." Dalby, A.; Mo, X.; Stoa, R.; Wroblewski, N.; Zhang, Z.; Hagen, T. J., Tetrahedron Lett. 2013, 54 2737–2739.
  11. "Triazoles and Tetrazoles" Hagen, T.J. and Zhang, Z. Heterocyclic Chemistry in Drug Discovery, Ed. by Jie Jack Li, John Wiley & Sons, 2013, in press, ISBN‐13: 9781118148907.
  12. Recent Trends in Biomarker Research and Development. Hagen, T.J. Biochem Anal Biochem 2012, 1:4 1–3.
  13. 1,2‐diselenins Hagen, T.J., Science of Synthesis 2011, 16, 93–97.
  14. 1,4‐diselenins Hagen, T.J., Science of Synthesis 2011, 16, 99–102.
  15. Optimization of a Pd‐catalyzed intramolecular α‐arylation synthesis of tricyclo‐[,7]‐trideca‐2,4,6‐trien‐13‐ones. Powell, N.A.; Hagen, T.J.; Ciske, F.L.; Cai, C.; Duran, J.E.; Holsworth, D.D.; Leonard, D.; Kennedy, R.M.; Edmunds, J.J. Tet. Lett. 2010 51: 4441–4444.
  16. Design of phosphodiesterase 4D (PDE4D) allosteric modulators for enhancing cognition with improved safety. Burgin, A.B.; Magnusson, O.T.; Singh, J.; Witte, P.; Staker, B.L.; Bjornsson, J.M.; Thorsteinsdottir, M.; Hrafnsdottir, S.; Hagen, T.J.; Kiselyov, A.S.; et al Nature Biotechnology, 2010 28(1), 63–70.
  17. Chirality and Biological Activity Jasbir Singh and Timothy J. Hagen, Burger's Medicinal Chemistry and Drug Discovery, Volume 7, Ed by Donald J. Abraham, John Wiley & Sons, 2010, 127–166.
  18. The Barton Nitrite Photolysis Hagen, Timothy J; Name Reactions for Chain Extension, Ed. by Jie Jack Li, John Wiley & Sons, 2009, 633–647.
  19. The Zaitsev Elimination Hagen, Timothy J; Name Reactions for Functional Group Transformations, Ed. by Jie Jack Li and E. J. Corey, John Wiley & Sons, 2007, 414–421.
  20. The Prilezhaev Reaction, Hagen, Timothy J; Name Reactions for Functional Group Transformations, Ed. by Jie Jack Li and E. J. Corey, John Wiley & Sons, 2007, 274–281.
  21. 5‐Fluorinated L‐Lysine Analogues as Selective Induced Nitric Oxide Synthase Inhibitors. Hallinan, E. Ann; Hagen, Timothy J.; Bergmanis, Arija; Moore, William M.; Jerome, Gina M.; Spangler, Dale P.; Stevens, Anna M.; Shieh, Huey S.; Manning, Pamela T.; Pitzele, Barnett S. J. Med. Chem. 2004, 47(4), 900–906.
  22. 3‐Hydroxy‐4‐methyl‐5‐pentyl‐2‐iminopyrrolidine: A potent and highly selective inducible nitric oxide synthase inhibitor. Tsymbalov, Sofya; Hagen, Timothy J.; Moore, William M.; Jerome, Gina M.; Connor, Jane R.; Manning, Pamela T.; Pitzele, Barnett S.; Hallinan, E. Ann. Bioorg. & Med. Chem. Lett. 2002 12(22), 3337–3339.
  23. Syntheses of new conformationally constrained S‐[2‐[(1‐iminoethyl)amino]ethyl]homocysteine derivatives as potential nitric oxide synthase inhibitors. Wang, Lijuan J.; Grapperhaus, Margaret L.; Pitzele, Barnett S.; Hagen, Timothy J.; Fok, Kam F.; Scholten, Jeffrey A.; Spangler, Dale P.; Toth, Mihaly V.; Jerome, Gina M.; Moore, William M.; Manning, Pamela T.; Sikorski, James A. Hetero. Chem. 2002, 13(1), 77–83.
  24. 2,4‐Disubstituted Oxazoles and Thiazoles as Latent Pharmacophores for Diacylhydrazine of SC‐51089, a Potent PGE2 Antagonist. Hallinan, E.A.; Hagen, T.J.; Tsymbalov, S.; Husa, Staplefeld, A.; Savage, M.A. Biorgan. and Med. Chem., 2001, 1–6.
  25. "Specific Inhibitors of Inducible Nitric Oxide Synthase: Efficacy in a Rodent Model of Sepsis." Fretland, D.J.; Widomski, D.L.; Anglin, C.P.; Moore, W.M.; Jerome, G.; Kornmeier, C.; Connor, J.; Branson, L.; Wyatt, P.; Manning, P.; Toth, M.; Webber, R.K.; Hansen, D.W.; Hallinan, E.A.; Hagen, T.J.; Bergmanis, A.; Pitzele, B.; and Currie, M.G.; Inflamm. Res. 48. Supplement 2 1999, 796–797.
  26. 2‐Iminopyrrolidines as Potent and Selective Inhibitors of Human Inducible Nitric Oxide Synthase. Hagen, T.J.; Bergmanis, A.A.; Kramer, S.W.; Fok, K.F.; Schmelzer, A.E.; Pitzele, B.S.; Swenton, L.; Jerome, G.M.; Kornmeier, C.M.; Moore, W.M.; Connor, J.R.; Branson, L.F.; Manning, P.T.; Currie, M.G. and Hallinan, E.A. J. Med. Chem. 1998, 41, 3675–3683.
  27. Substituted 2‐Iminopiperidines as Inhibitors of Human Nitric Oxide Synthase Isoforms. Webber, R.K.; Metz, S.; Moore, W.M.; Connor, J.R.; Currie, M.G.; Fok, K.F.; Hagen, T.J.; Hansen, Jr., D.W.; Jerome, G.M.; Manning, P.T.; Pitzele,B.S.; Toth, M.V.; Trivedi, M.; Zupec, M.E.; Tjoeng, F. S. J. Med. Chem. 1998, 41, 96–101.
  28. Aminoacetyl Moiety as a Potential Surrogate for Diacylhydrazine Group of SC‐51089, a Potent PGE2 Antagonist, and Its Analogs. Hallinan, E.A.; Hagen, T.J.; Tsymbalov, S.; Husa, R.K.; Lee, A.C.; Stapelfeld, A.; Savage, M.A. J. Med. Chem. 1996, 39, 609–613.
  29. Structure‐activity Relationships in Antagonist and Inverse Agonist ligands for the Benzodiazepine Receptor. Codding, P.W.; Roszak, A.W.; Szkaradzinska, M.B.; Cook, J.M.; Hagen, T.J.; Allen, M.S. Can. J. Chem. 1995, 73, 499–512.
  30. BZ1 Receptor Selective Specific Ligands. Synthesis and Biological Properties of BCCt, a BZ1 Receptor Subtype Specific Antagonist. Cox, E.D.; Hagen, T.J.; McKernan, R.M.; Cook, J.M. Med. Chem. Res. 1995, 5, 710–718.
  31. Lithiation and Electrophilic Substitution of 8‐Chlorodibenz[b,f][1,4]‐oxaze[ine‐10‐tertbuty]carbamate: The preparation of Novel Fused Heterocyclic Derivatives of 8‐Chlorodibenzoxazepine. Li, J.J.; Hagen, T.J.; Chrusciel, R.A.; Norton, M.B.; Tsymbalov, S.; Hallinan, E.A.; Reitz, D.B. J. Heterocyclic. Chem., 31, 1994, 1689–96.
  32. The N‐Boc Group as an Activator for the α‐Lithiation of Carbamates: Synthesis of 11‐Substituted Dibenzoxazepines. Hagen, T.J.; Rafferty, M.F.; Collins, J.T.; Garland, D.J.; Li, J.J.; Norton, M.B.; Reitz, D.B.; Tsymbalov, S.; Pitzele, B.S.; Hallinan, E.A. Heterocycles 1994, 38, 601–611.
  33. N‐Substituted Dibenzoxazepines as analgesic PGE2 Antagonists. Hallinan, E.A.; Hagen, T.J.; Husa, R.K.; Tsymbalov, S.; Rao, S.N.; vanHoeck, J.P.; Rafferty, M.F.; Stapelfeld, A.; Savage, M.A.; Reichman, M. J. Med. Chem. 1993, 36, 3293–9.
  34. Predictive Binding of β‐Carboline Inverse Agonists and Antagonists via the CoMFA Approach. Allen, M.S.; LaLoggia, J.; Dorn, L.J.; Martin, M.J.; Constantino, G.; Hagen, T.J.; Koehler, K.F.; Skolnick, P.; Cook, J.M. J. Med. Chem. 1992, 35, 4001–10.
  35. Synthetic and Computer Assisted Analysis of the Pharmacophore for Agonists at Benzodiazepine Receptors. Diaz‐Arauzo,H; Koehler, K.F.; Hagen, T.J.; Cook, J.M. Life Sci. 1991, 49, 207–16.
  36. Synthetic and Computer Assisted Approaches to the Pharmacophore of the Benzodiazepine Receptor Inverse Agonist Site. Allen, M.S.; Yun‐C,T.; Trudell, M.L.; Narayanan, K.; Schindler, L.R.; Martin, M.; Hagen, T.J.; Koehler, K.F.; Codding, P.W.; Skolnick, P.;Cook, J.M. J. Med. Chem. 1990, 33, 2343–57.
  37. Regioselective Functionalization of Medium Ring Lactams. Hagen, T.J. Synlett 1990, 1, 63.
  38. DDQ Oxidations in the Indole Area; The Total Synthesis of 1‐Methoxycanthin‐6‐one and an Improved Synthesis of Crenatine. Hagen, T.J.; Narayanan, K.; Cook, J.M. J. Org. Chem. 1989, 54, 2170–8.
  39. Inhibition of Sleep and Benzodiazepine Receptor Binding by a β‐Carboline Derivative. Martin, J.J.; Cook, J.M.; Hagen, T.J.; Mendelson, W.B. Pharmacol. Biochem. Behav. 1989, 34, 37–42.
  40. Behaviorial effects of benzodiazepine antagonists in chlordiazepoxide tolerant and non‐tolerant rats. Takada,K.; Suzuki, T.; Hagen, T.; Cook, J.M.; Katz, J.L. Life Sci. 1989, 44, 289–99.
  41. Structure‐activity Studies of β‐Carbolines. 4. Crystal and molecular structures of t‐butyl β‐carboline‐3‐carboxylate and 2‐(methoxycarbonyl)canthin‐6‐one. Codding, P.; Szkaradzinska, M.B.; Roszak, A.; Hagen, T.J.; Cook, J.M. Can. J. Chem. 1988,66(12), 2981.
  42. 3‐Ethoxy‐β‐Carboline: A High Affinity Benzodiazepine Receptor Ligand with Partial Inverse Agonist Properties. Trullas, R.; Ginter, H.; Jackson, B.; Skolnick, P.; Allen, M.; Hagen, T.; Cook, J.M. Life Sci. 1988, 43, 1189–97.
  43. Synthesis of 1‐Methoxycanthin‐6‐one. Hagen T.J.; Cook, J.M. Tetrahedron Lett. 1988, 29, 2421–4.
  44. β‐Carbolines as Antagonists of the Discriminative Stimulus Effects of Diazepam in Rats. Shannon, H.E.; Hagen, T.J.; Guzman, F.; Cook, J.M. J. Pharm. Exp. Ther. 1988, 246, 275–81.
  45. Synthesis of Novel 3‐Substituted β‐Carbolines as Benzodiazepine Receptor Ligands: Probing the Benzodiazepine Receptor Pharmacophore. Cook, J.M.; Allen, M.S.; Hagen, T.J.; Trudell, M.L.; Codding, P.; Skolnick, P. J. Med. Chem. 1988, 31, 1854–61.
  46. Discriminative Stimulus Effects of Intravenous Nicotine in Squirrel Monkeys. Takada, K.; Hagen, T.J.; Cook, J.M.; Goldberg, S.A.; Katz, J.L. Pharmacol. Biochem. Behav. 1988, 30, 243–7.
  47. Synthesis of 6‐substituted β‐Carbolines That Behave as Benzodiazepine Receptor Antagonists an Inverse Agonists. Hagen, T.J.; Skolnick, P.; Cook, J.M. J. Med. Chem. 1987, 30, 750–3.
  48. Synthesis of 3,6‐Disubstituted β‐Carbolines Which Possess Either Benzodiazepine Antagonist or Agonist Activity. Hagen, T.J.; Guzman, F.; Schultz, C.; Skolnick, P.; Cook, J.M. Heterocycles 1986, 24, 2845–55.
  49. Cerebrovascular and Cerebral Metabolic Effects of Physostigmine, Midazolam, and a Benzodiazepine Agonist. Hoffman, W.E.; Albrecht, R.F.; Miletich, D.J.; Hagen, T.J.; Cook J.M. Anesth. Analg. 1986, 65, 639–44.
  50. Biomimetic Approach to Potential Benzodiazepine Agonists and Antagonists. Guzman, F.; Cain,M.; Larschied, P.; Hagen, T.J.; Cook, J.M.; Schweri, M.; Skolnick, P.; Paul, S.M. J. Med. Chem. 1984, 27, 564–70.
  51. Photochemical Aromatic Cyanomethylation: Aromatic substitution by way of radical cations. Kurz, M.E.; Lapin, S.C.; Miriam, K.; Hagen T.J.; Qain, X.Q. J. Org. Chem. 1984,49, 2728–33.

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