Hermann, Thomas
RNA as a Drug Target and a Material for Nanotechnology
RNA as a Drug Target and a Material for Nanotechnology
Contact Information
Professor of Chemistry and Biochemistry
Founding Co-Director, UCSD Center for Drug Discovery Innovation
Associate Dean for Education and Students, Division of Physical Sciences
Office: Pacific Hall 5222A
Phone: 858-534-4467
Email: tch@ucsd.edu
Web: tch.ucsd.edu
Group: View group members
Founding Co-Director, UCSD Center for Drug Discovery Innovation
Associate Dean for Education and Students, Division of Physical Sciences
Office: Pacific Hall 5222A
Phone: 858-534-4467
Email: tch@ucsd.edu
Web: tch.ucsd.edu
Group: View group members
Education
1996 Ph.D., Max Planck Institute of Biochemistry and Ludwig-Maximilians-Universität München, Germany
1992 Diplom, University of Ulm, Germany
1996 Ph.D., Max Planck Institute of Biochemistry and Ludwig-Maximilians-Universität München, Germany
1992 Diplom, University of Ulm, Germany
Appointments
2018 - current Associate Dean for Education and Students, UC San Diego Division of Physical Sciences
2017 - 2018 Vice Chair of Education, UC San Diego Department of Chemistry and Biochemistry
2014 - current Co-Director, UC San Diego Center for Drug Discovery Innovation
2001-2005 Head, Structural Chemistry Group, Anadys Pharmaceuticals, San Diego
1999-2000 Postdoc, Memorial Sloan Kettering Cancer Center, New York
1996-1998 Postdoc, Institut de Biologie Moleculaire et Cellulaire, CNRS, Strasbourg, France
2018 - current Associate Dean for Education and Students, UC San Diego Division of Physical Sciences
2017 - 2018 Vice Chair of Education, UC San Diego Department of Chemistry and Biochemistry
2014 - current Co-Director, UC San Diego Center for Drug Discovery Innovation
2001-2005 Head, Structural Chemistry Group, Anadys Pharmaceuticals, San Diego
1999-2000 Postdoc, Memorial Sloan Kettering Cancer Center, New York
1996-1998 Postdoc, Institut de Biologie Moleculaire et Cellulaire, CNRS, Strasbourg, France
Awards and Academic Honors
2019
Chair, Gordon Research Conference on RNA Nanotechnology
2017
Vice Chair, Gordon Research Conference on RNA Nanotechnology
1996-1998
EMBO Long-Term Fellow
1996
Otto-Hahn Medal of the Max-Planck Society, Germany
Research Interests
We are exploring structured RNA as (1) a drug target and a material for (2) self-assembling nano-architectures. Our research on RNA is guided by the mantra that what is structure is prologue to function and targeting.
(1) Unique three-dimensional folds enable RNA to participate as key players in cellular processes and provide opportunities to develop selective small molecules as inhibitors and modulators of RNA function. Selective ligands of RNA targets have a potential to expand the existing repertoire of protein-directed therapeutics. We use molecular biology and biochemistry to discover and validate RNA targets, biophysical methods to study their structure and discover interactions with ligands, as well as synthetic organic chemistry to prepare and optimize RNA-binding molecules.
(2) Nucleic acid nanotechnology aims to design and build functional materials and devices that self-assemble through base pairing and folding of DNA or RNA strands. We develop structure-guided design and screening approaches to create complex nucleic acid nano-architectures that self-assemble from RNA motifs as architectural joints and DNA building blocks as functional modules for modification and chemical diversification. To obtain complex composite materials, we devise additive and subtractive manufacturing techniques for self-assembling nucleic acid and protein components.
(1) Unique three-dimensional folds enable RNA to participate as key players in cellular processes and provide opportunities to develop selective small molecules as inhibitors and modulators of RNA function. Selective ligands of RNA targets have a potential to expand the existing repertoire of protein-directed therapeutics. We use molecular biology and biochemistry to discover and validate RNA targets, biophysical methods to study their structure and discover interactions with ligands, as well as synthetic organic chemistry to prepare and optimize RNA-binding molecules.
(2) Nucleic acid nanotechnology aims to design and build functional materials and devices that self-assemble through base pairing and folding of DNA or RNA strands. We develop structure-guided design and screening approaches to create complex nucleic acid nano-architectures that self-assemble from RNA motifs as architectural joints and DNA building blocks as functional modules for modification and chemical diversification. To obtain complex composite materials, we devise additive and subtractive manufacturing techniques for self-assembling nucleic acid and protein components.
Primary Research Area
Organic Chemistry
Organic Chemistry
Interdisciplinary interests
Bioorganic
Macromolecular Structure
Synthesis
Macromolecular Structure
Synthesis
Outreach Activities
Undergraduate research opportunities for underrepresented minorities.
Diversity Plan for the establishment of the Center for Drug Discovery Innovation (CDDI), a cross-campus Organized Research Unit at UC San Diego (since 2014).
Member of the Executive Committee of the US Department of Education Graduate Assistance in Areas of National Need (GAANN) Fellowship Program at UC San Diego.
Mentor in the UC LEADS program (Leadership Excellence through Advanced DegreeS), which prepares promising students for advanced education in the STEM fields and primarily supports undergraduate students who have experienced situations or conditions that have adversely impacted their advancement in their field of study.
Diversity Plan for the establishment of the Center for Drug Discovery Innovation (CDDI), a cross-campus Organized Research Unit at UC San Diego (since 2014).
Member of the Executive Committee of the US Department of Education Graduate Assistance in Areas of National Need (GAANN) Fellowship Program at UC San Diego.
Mentor in the UC LEADS program (Leadership Excellence through Advanced DegreeS), which prepares promising students for advanced education in the STEM fields and primarily supports undergraduate students who have experienced situations or conditions that have adversely impacted their advancement in their field of study.
Image Gallery
Design and Applications of Self-Assembling RNA Nanostructures
Structure Determination of RNA Targets and Ligand Complexes
Design and Synthesis of New Ligands for RNA Targets
Design and Applications of Self-Assembling RNA Nanostructures
Structure Determination of RNA Targets and Ligand Complexes
Design and Synthesis of New Ligands for RNA Targets
Selected Publications
- Chen S,Hermann T "RNA-DNA Hybrid Nanoshape Synthesis by Facile Module Exchange.", J Am Chem Soc, 2021, Vol. 143, Issue 48, 20356-20362 [View]
- Chen S,Xing L,Zhang D,Monferrer A,Hermann T "Nano-sandwich composite by kinetic trapping assembly from protein and nucleic acid.", Nucleic Acids Res, 2021, Vol. 49, Issue 17, 10098-10105 [View]
- Chen S,Zhang Z,Alforque E, Hermann T "Complex RNA-DNA hybrid nanoshapes from iterative mix-and-match screening", Nano Research, 2021, Vol. 14, 46-51 [View]
- Chen S,Hermann T "RNA-DNA hybrid nanoshapes that self-assemble dependent on ligand binding.", Nanoscale, 2020, Vol. 12, Issue 5, 3302-3307 [View]
- Monferrer A,Zhang D,Lushnikov AJ,Hermann T "Versatile kit of robust nanoshapes self-assembling from RNA and DNA modules.", Nat Commun, 2019, Vol. 10, Issue 1, 608 [View]
- Nuthanakanti A,Boerneke MA,Hermann T,Srivatsan SG "Structure of the Ribosomal RNA Decoding Site Containing a Selenium-Modified Responsive Fluorescent Ribonucleoside Probe.", Angew Chem Int Ed Engl, 2017, Vol. 56, Issue 10, 2640-2644 [View]
- Boerneke MA,Dibrov SM,Hermann T "Crystal-Structure-Guided Design of Self-Assembling RNA Nanotriangles.", Angew Chem Int Ed Engl, 2016, Vol. 55, Issue 12, 4097-100 [View]
- Charrette BP,Boerneke MA,Hermann T "Ligand Optimization by Improving Shape Complementarity at a Hepatitis C Virus RNA Target.", ACS Chem Biol, 2016, [View]
- Boerneke MA,Hermann T "Ligand-responsive RNA mechanical switches.", RNA Biol, 2015, Vol. 12, Issue 8, 780-6 [View]
- Boerneke MA, Dibrov SM, Gu J, Wyles DL, Hermann T, "Functional conservation despite structural divergence in ligand-responsive RNA switches.", Proc Natl Acad Sci U S A, 2014, Vol. 111, Issue 45, 15952-7 [View]
- 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, Vol. 57, Issue 5, 1694-707 [View]
- Chou FC, Sripakdeevong P, Dibrov SM, Hermann T, Das R, "Correcting pervasive errors in RNA crystallography through enumerative structure prediction.", Nat Methods, 2013, Vol. 10, Issue 1, 74-6 [View]
- Brunn ND,Garcia Sega E,Kao MB,Hermann T "Targeting a regulatory element in human thymidylate synthase mRNA.", Chembiochem, 2012, Vol. 13, Issue 18, 2738-44 [View]
- 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, Vol. 109, Issue 14, 5223-8 [View]
- Dibrov SM, McLean J, Parsons J, Hermann T, "Self-assembling RNA square.", Proc Natl Acad Sci U S A, 2011, Vol. 108, Issue 16, 6405-8 [View]