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Thomas Hermann

TitleAssociate Professor
InstitutionUniversity of California San Diego
DepartmentChemistry and Biochemistry
Address9500 Gilman Drive #0358
La Jolla CA 92093
Phone858-534-4467
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    Collapse Research 
    Collapse Research Activities and Funding
    Chemotherapy targeting human thymidylate synthase messenger RNA
    NIH/NCI R01CA132753Jun 1, 2009 - May 31, 2014
    Role: Principal Investigator
    New Antiviral Therapies for Hepatitis C Infection
    NIH/NIAID R01AI072012Apr 15, 2007 - Mar 31, 2012
    Role: Principal Investigator
    Rational Design of Antibiotics Targeted at the Ribosome
    NIH/NIAID R44AI051104Feb 15, 2002 - Nov 30, 2006
    Role: Co-Principal Investigator
    Rational Design of Antibiotics Targeted at the Ribosome
    NIH/NIAID R43AI051104Feb 15, 2002 - Feb 14, 2003
    Role: Principal Investigator

    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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    1. Boerneke MA, Hermann T. Design and Crystallography of Self-Assembling RNA Nanostructures. Methods Mol Biol. 2017; 1632:135-149. PMID: 28730437.
      View in: PubMed
    2. Charrette BP, Boerneke MA, Hermann T. Ligand Optimization by Improving Shape Complementarity at a Hepatitis C Virus RNA Target. ACS Chem Biol. 2016 12 16; 11(12):3263-3267. PMID: 27775338.
      View in: PubMed
    3. Hermann T. Small molecules targeting viral RNA. Wiley Interdiscip Rev RNA. 2016 11; 7(6):726-743. PMID: 27307213.
      View in: PubMed
    4. Boerneke MA, Dibrov SM, Hermann T. Crystal-Structure-Guided Design of Self-Assembling RNA Nanotriangles. Angew Chem Int Ed Engl. 2016 Mar 14; 55(12):4097-100. PMID: 26914842; PMCID: PMC4824544 [Available on 03/14/17].
    5. Dibrov SM, Hermann T. Structure of the HCV Internal Ribosome Entry Site Subdomain IIa RNA in Complex with a Viral Translation Inhibitor. Methods Mol Biol. 2016; 1320:329-35. PMID: 26227053.
      View in: PubMed
    6. Hermann T. Non-coding RNA: Antibiotic tricks a switch. Nature. 2015 Oct 29; 526(7575):650-1. PMID: 26416738.
      View in: PubMed
    7. Boerneke MA, Hermann T. Conformational flexibility of viral RNA switches studied by FRET. Methods. 2015 Dec; 91:35-39. PMID: 26381686; PMCID: PMC4684784 [Available on 12/01/16].
    8. Boerneke MA, Hermann T. Ligand-responsive RNA mechanical switches. RNA Biol. 2015; 12(8):780-6. PMID: 26158858; PMCID: PMC4615790.
    9. Brunn ND, Dibrov SM, Kao MB, Ghassemian M, Hermann T. Analysis of mRNA recognition by human thymidylate synthase. Biosci Rep. 2014 Dec 23; 34(6):e00168. PMID: 25423174; PMCID: PMC4274661.
    10. Rynearson KD, Charrette B, Gabriel C, Moreno J, Boerneke MA, Dibrov SM, Hermann T. 2-Aminobenzoxazole ligands of the hepatitis C virus internal ribosome entry site. Bioorg Med Chem Lett. 2014 Aug 01; 24(15):3521-5. PMID: 24930829; PMCID: PMC4114401.
    11. Ding K, Wang A, Boerneke MA, Dibrov SM, Hermann T. Aryl-substituted aminobenzimidazoles targeting the hepatitis C virus internal ribosome entry site. Bioorg Med Chem Lett. 2014 Jul 15; 24(14):3113-7. PMID: 24856063; PMCID: PMC4096041.
    12. Dibrov SM, Parsons J, Carnevali M, Zhou S, Rynearson KD, Ding K, Garcia Sega E, Brunn ND, Boerneke MA, Castaldi MP, Hermann T. Hepatitis C virus translation inhibitors targeting the internal ribosomal entry site. J Med Chem. 2014 Mar 13; 57(5):1694-707. PMID: 24138284; PMCID: PMC3954896.
    13. Ding K, Dibrov SM, Hermann T. Synthesis and crystal structure of a phenazine N-oxide. J Chem Crystallogr. 2013 Oct 01; 43(10):550-553. PMID: 24159257.
      View in: PubMed
    14. Dibrov SM, Parker MA, Bergdahl BM, Hermann T. Crystal structure of a benzimidazole hepatitis C virus inhibitor free and in complex with the viral RNA target. J Chem Crystallogr. 2013 May; 43(5):235-239. PMID: 23750099.
      View in: PubMed
    15. Zhou S, Rynearson KD, Ding K, Brunn ND, Hermann T. Screening for inhibitors of the hepatitis C virus internal ribosome entry site RNA. Bioorg Med Chem. 2013 Oct 15; 21(20):6139-44. PMID: 23602522; PMCID: PMC3758467.
    16. Brunn ND, Garcia Sega E, Kao MB, Hermann T. Targeting a regulatory element in human thymidylate synthase mRNA. Chembiochem. 2012 Dec 21; 13(18):2738-44. PMID: 23143777; PMCID: PMC3758747.
    17. Dibrov SM, Ding K, Brunn ND, Parker MA, Bergdahl BM, Wyles DL, Hermann T. Structure of a hepatitis C virus RNA domain in complex with a translation inhibitor reveals a binding mode reminiscent of riboswitches. Proc Natl Acad Sci U S A. 2012 Apr 03; 109(14):5223-8. PMID: 22431596; PMCID: PMC3325719.
    18. Dibrov SM, McLean J, Parsons J, Hermann T. Self-assembling RNA square. Proc Natl Acad Sci U S A. 2011 Apr 19; 108(16):6405-8. PMID: 21464284; PMCID: PMC3080994.
    19. Dibrov S, McLean J, Hermann T. Structure of an RNA dimer of a regulatory element from human thymidylate synthase mRNA. Acta Crystallogr D Biol Crystallogr. 2011 Feb; 67(Pt 2):97-104. PMID: 21245530; PMCID: PMC3045271.
    20. Dibrov S, Carnevali M, Hermann T. (3,4-Dihy-droxy-oxolan-2-yl)methyl 4-methyl-benzene-sulfonate. Acta Crystallogr Sect E Struct Rep Online. 2010 Nov 06; 66(Pt 12):o3088. PMID: 21589395; PMCID: PMC3011728.
    21. Carnevali M, Parsons J, Wyles DL, Hermann T. A modular approach to synthetic RNA binders of the hepatitis C virus internal ribosome entry site. Chembiochem. 2010 Jul 05; 11(10):1364-7. PMID: 20564282; PMCID: PMC3517111.
    22. Dibrov SM, Parsons J, Hermann T. A model for the study of ligand binding to the ribosomal RNA helix h44. Nucleic Acids Res. 2010 Jul; 38(13):4458-65. PMID: 20215440; PMCID: PMC2910043.
    23. Dutta S, Higginson CJ, Ho BT, Rynearson KD, Dibrov SM, Hermann T. 1,3-Diazepanes of natural product-like complexity from cyanamide-induced rearrangement of epoxy-delta-lactams. Org Lett. 2010 Jan 15; 12(2):360-3. PMID: 20028082; PMCID: PMC2810123.
    24. Parsons J, Castaldi MP, Dutta S, Dibrov SM, Wyles DL, Hermann T. Conformational inhibition of the hepatitis C virus internal ribosome entry site RNA. Nat Chem Biol. 2009 Nov; 5(11):823-5. PMID: 19767736; PMCID: PMC2770845.
    25. Dibrov S, Dutta S, Hermann T. 1-Cyclo-hexyl-2-(3-fur-yl)-1H-benzimidazole-5-carboxylic acid. Acta Crystallogr Sect E Struct Rep Online. 2009 Aug 12; 65(Pt 9):o2136. PMID: 21577546; PMCID: PMC2970106.
    26. Hermann T. Aminoglycoside antibiotics: old drugs and new therapeutic approaches. Cell Mol Life Sci. 2007 Jul; 64(14):1841-52. PMID: 17447006.
      View in: PubMed
    27. Hermann T, Tereshko V, Skripkin E, Patel DJ. Apramycin recognition by the human ribosomal decoding site. Blood Cells Mol Dis. 2007 May-Jun; 38(3):193-8. PMID: 17258916.
      View in: PubMed
    28. Dibrov SM, Johnston-Cox H, Weng YH, Hermann T. Functional architecture of HCV IRES domain II stabilized by divalent metal ions in the crystal and in solution. Angew Chem Int Ed Engl. 2007; 46(1-2):226-9. PMID: 17131443.
      View in: PubMed
    29. Hermann T. A-site model RNAs. Biochimie. 2006 Aug; 88(8):1021-6. PMID: 16872733.
      View in: PubMed
    30. Zhao F, Zhao Q, Blount KF, Han Q, Tor Y, Hermann T. Molecular recognition of RNA by neomycin and a restricted neomycin derivative. Angew Chem Int Ed Engl. 2005 Aug 19; 44(33):5329-34. PMID: 16037995.
      View in: PubMed
    31. Blount KF, Zhao F, Hermann T, Tor Y. Conformational constraint as a means for understanding RNA-aminoglycoside specificity. J Am Chem Soc. 2005 Jul 13; 127(27):9818-29. PMID: 15998086.
      View in: PubMed
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