Douglas A. Mitchell
Assistant Professor of Chemistry
Faculty, Institute for Genomic Biology:
Mining Microbial Genomes for Novel Antibiotics
Affiliate, Department of Microbiology
Professor Mitchell received his undergraduate degree in chemistry from Carnegie Mellon University in 2002. After a short internship in medicinal chemistry at Merck Research Laboratories, he obtained his Ph.D. from the University of California, Berkeley in 2006. For postdoctoral studies, he worked with Jack Dixon at the University of California, San Diego. Professor Mitchell joined the University of Illinois faculty in 2009 and has research interests that span the interface of chemistry and biology.
Our primary objective is to employ chemical methods to better address the issue of antibiotic resistance and, more generally, to obtain a more comprehensive understanding of the molecular underpinnings of bacterial virulence. By understanding these processes in greater detail, we seek to develop strategies for the next generation of antimicrobial drugs. The Mitchell laboratory is a multidisciplinary research team that draws methodology from the fields of chemical biology, organic chemistry, pharmacology, structural biology, bioinformatics, and microbiology.
The focus of our current studies is centered on a recently recognized, burgeoning class of natural product: the thiazole/oxazole-modified microcins (TOMMs). Genome mining has identified that over 20% of all sequenced bacteria and archaea have the genetic capacity to biosynthesize a TOMM natural product. While only a small fraction of the known TOMMs have been characterized, these ribosomally produced products harbor a structural and functional diversity that rivals that of any non-ribosomal (NRPS, PKS, terpene) biosynthetic system. Examples include microcin B17 (DNA gyrase inhibitor), patellamide A (anti-cancer), thiostrepton (50S ribosome inhibitor; antibiotic), streptolysin S (disease-promoting cytolysin), and plantazolicin (ultra-narrow spectrum antibiotic). Given their functional relevance to human health, and the fact that the majority of all medicines are natural products or simple derivatives thereof, we view the TOMM family as a treasure trove of bioactive molecules awaiting further exploration.
Current research in the Mitchell Laboratory can be broadly divided into two categories. I.) We aim to characterize the structure and function of unique TOMM natural products and the enzymes that produce them. To achieve this, we employ chemical and biological approaches including high-resolution mass spectrometry, nuclear magnetic resonance spectroscopy, X-ray crystallography, in vitro reconstitution, and genetic manipulation techniques. II.) We aim to utilize what we have learned about TOMM natural product structure and function to exploit biosynthetic weakness or promiscuity. In the cases where a human pathogen produces a TOMM natural product that promotes virulence (i.e. streptolysin S), the development of small molecule biosynthetic inhibitors not only aids the study of toxin maturation but could also be clinically useful. In the event the TOMM natural product itself holds promise as a therapeutic, identification of enzymatic promiscuity can be harnessed to generate combinatorial libraries of natural product variants. The proper tailoring of small molecule probes and interception of engineered biosynthetic pathways are both expected to produce novel compounds that hold pharmacological value.
Zhang, Z., et al., “HIV integrase inhibitor-inspired antibacterials targeting isoprenoid biosynthesis”, ACS Med. Chem. Lett. (2012)
Dunbar, K.L; Melby, J.O.; Mitchell, D.A.*, “YcaO domains use ATP to activate amide backbones during peptide cyclodehydrations”, Nat. Chem. Biol., (2012)
Melby, J.O.; Dunbar, K.L.; Trinh, N; Mitchell, D.A.*, “Selectivity, directionality, and promiscuity in peptide processing from the Bacillus sp. Al Hakam cyclodehydratase”, J. Am. Chem. Soc., 134:5309 (2012)
Molohon, K.J.; Melby, J.O.; Lee, J.; Evans, B.S.; Dunbar, K.L.; Bumpus, S.B.; Kelleher, N.L.; Mitchell, D.A.*, “Structure determination and interception of biosynthetic intermediates for the plantazolicin class of highly discriminating antibiotics”, ACS Chem. Biol., 6:1307 (2011)
Pei, J.; Mitchell, D.A.; Dixon, J.E.; Grishin, N.V., “Expansion of type II CAAX proteases reveals evolutionary origin of g-secretase subunit APH-1”, J. Mol. Biol., 410:18 (2011)
Molloy, E.; Cotter, P.D.; Hill, C.; Mitchell, D.A.; Ross, R.P, “Streptolysin S-like virulence factors: the continuing saga ”, Nat. Rev. Microbiol., 9:670 (2011)Scholz, R.; Molohon, K.J.; Nachtigall, J.; Vater, J.; Markley, A.L.; Sussmuth, R.D.; Mitchell, D.A.*; Borriss, R.*, “Plantazolicin, a novel microcin B17/streptolysin S-like natural product from Bacillus amyloliquefaciens FZB42”, J. Bacteriol., 193:215 (2011)
Haft, D.*; Basu, M.; Mitchell, D.A.*, “Expansion of ribosomally produced natural products: A nitrile hydratase- and Nif11-related precursor family”, BMC Biol., 8:70 (2010)
Tomorrow's PI: Genome Technology magazine
Packard Fellowship in Science and Engineering
NIH Director's New Innovator Award
- Hartwell Foundation Biomedical Research Fellowship
- American Heart Association Predoctoral Fellowship
- American Society of Pharmacology and Experimental Therapeutics Research Fellowship
News and Views: Kelly, W.L., "Biosynthesis: Ringing in a new view" Nat. Chem. Biol., 8:505 (2012)
Schmidt, E.W.; "The hidden diversity of ribosomal peptide natural products" BMC Biol., 8:83 (2010)
Walsh, C.T.; Nolan, E.M., "Morphing Peptide Backbones into Heterocycles" Proc. Natl. Acad. Sci. USA, 105: 5655-5656 (2008)
Tannenbaum, S.R. and White, F.M., "Regulation and Specificity of S-Nitrosylation and Denitrosylation" ACS Chem. Biol., 1: 615-618 (2006)
Tannenbaum, S.R. and Kim, J., "Controlled S-Nitrosation" Nat. Chem. Biol., 1: 126-127 (2005)