Courtney Aldrich - Research

The central theme of our research is the development of novel antibiotics to treat drug-resistant pathogenic bacteria. Two general approaches are taken. The first is to design new antibacterial agents based on novel mechanisms of action. The second approach involves the redesign of existing natural product-based antibiotics to regain activity towards bacteria that have developed resistance to the parent antibiotic. We leverage our expertise in enzymology, medicinal chemistry and molecular biology with collaborators who have expertise in computational chemistry (Dr. Eric Bennett), microbiology (Dr. Clifton E. Barry III), pharmacology (Prof. Rory Remmel), and structural biology (Prof. Andrew Gulick).

Identification of Novel Bacterial Targets

A primary objective of our research is to design new antibacterial agents based on novel mechanisms of action. Currently, all clinically used antibiotics act by one of a limited number of mechanisms (e.g. inhibition of protein synthesis, DNA synthesis, cell-wall synthesis, and RNA transcription). The identification of novel bacterial enzymes as potential targets for the development of new antibiotics is greatly aided by the availability of over 100 genome sequences to some of the most notorious human pathogens. We utilize available data from experimental genetic approaches (random transposon mutagenesis, targeted genetic disruptions) as well as comparison to the human proteome to identify candidate bacterial targets. In cases where the structure and enzymology of the bacterial enzyme is known we rationally design substrate mimics to generate competitive enzyme inhibitors. However, for many potential targets there is inadequate structural information available to permit such a structure-based drug design approach. In these cases we develop high-throughput-screening (HTS) assays that allow us to rapidly screen >10,000 compounds to identify a lead candidate molecule.

Once a small molecule inhibitor is identified against the targeted enzyme we then apply medicinal chemistry efforts to methodically optimize the inhibitor scaffold. Structure- and/or ligand-based computational approaches are employed to rationalize activity data in order to refine inhibitor design. At an early stage we also test for antibacterial activity against the targeted organism(s) since whole-cell activity is a composite of binding affinity, membrane permeability, and stability. Additionally drug properties of our inhibitors are evaluated using a variety of in vitro assays to examine toxicity, absorption, and metabolism. Using this approach we developed a new class of antibiotics that act by disruption of bacterial iron acquisition. We identified a previously unexplored target (an enzyme known as MbtA involved in biosynthesis of the mycobactins, which are small-molecule iron-chelators produced by Mycobacterium tuberculosis) and described the design, synthesis, and biochemical evaluation of subnanomlar inhibitors effective against MbtA that also possess potent in vivo activity against Mycobacterium tuberculosis. Since tuberculosis is the leading cause of bacterial infectious disease mortality this research is expected to have a positive impact on human health and may additionally validate a new class of antibiotics that target siderophore biosynthesis.

Redesign of Existing Antibiotics

The development of bacterial resistance to existing antibiotics is a major health problem. The rational redesign of an antibiotic to restore activity towards resistant organisms requires knowledge of the antibiotic-receptor interaction in conjunction with knowledge of the resistance-conferring mutation (Note: the term receptor herein is used in the sense of any target molecule - protein, DNA, RNA, or other biopolymer - to which the drug binds). The glycopeptide antibiotic vancomycin represents an exemplary case wherein the molecular details of the ligand-receptor interaction are well established. Additionally, the resistance conferring mutation for high-level vancomycin resistance involves the acquisition of a plasmid that encodes for five genes that coordinatively reprogram the biosynthesis of the bacterial receptor (the peptidoglycan precursor to the cell wall). Boger and co-workers (Boger et al. J. Am. Chem. Soc. 2006, 128, 2885-2892) recently described the synthesis of a vancomycin analogue that partially restores activity against vancomycin resistant bacteria. The approximately 100-step chemical synthesis unfortunately limits practical access to this new antibiotic. We propose to prepare a related vancomycin analogue by fermentation rather than through chemical synthesis utilizing a strategy known as precursor directed biosynthesis. While precursor directed biosynthesis has been utilized to prepare novel side-chain analogues of vancomycin (see Süssmth et al. J. Am. Chem. Soc. 2004, 126, 5942-5943), our strategy will allow access to analogues with modifications to the core peptide backbone of vancomycin. This hybrid chemo-biosynthetic approach will allow us to redesign vancomycin to bind both the mutant (D-Ala-D-Lac termini of the peptidoglycan cell wall precursor) and wild-type (D-Ala-D-Ala termini of the peptidoglycan cell wall precursor) receptor by replacing one of the key residues of vancomycin involved in the molecular recognition of both receptors. This project involves molecular modeling to examine the binding energies of the proposed analogues, chemical synthesis, in vitro biochemical investigation of the relevant enzymes, genetic disruption of a key biosynthetic building block, and natural product isolation and characterization along with testing of the analogues against a representative panel of pathogenic bacterial strains. We expect our fermentation-based route to vancomycin analogues as a practical and economical means to prepare these antibiotics. This research draws upon a wide array of disciplines and provides an ideal training ground for scientists interested in gaining exposure to methods in enzymology, microbiology, molecular biology, and synthetic chemistry.

Publications
 

A Mechanism-Based Aryl Carrier Protein/Thiolation Domain Affinity Probe. Qiao C, Wilson DJ, Bennett EM, Aldrich CC. J. Am. Chem. Soc. 2007 129(20): 6350-51. Abstract

Characterization and Analysis of Early Enzymes for Petrobactin Biosynthesis in Bacillus anthracis. Pfleger BF, Lee JY, Somu RV, Aldrich CC, Hanna PC, Sherman DH. Biochemistry 2007; 46(13): 4147-57. Abstract

Biosynthetic Analysis of the Petrobactin Siderophore Pathway from Bacillus anthracis Lee JY, Janes BK, Passalacqua KD, Pfleger B, Bergman NH, Liu H, Hakansson K, Somu RV, Aldrich CC, Cendrowski S, Hanna PC, Sherman DH. J Bacteriol 189: 1675-88 (2007). Abstract

Antitubercular nucleosides that inhibit siderophore biosynthesis: SAR of the glycosyl domain. Somu RV, Wilson DJ, Bennett EM, Boshoff HI, Celia L, Beck BJ, Barry CE 3rd, Aldrich CC. J Med Chem 49(26), 7623-25 (2006). Abstract

Design, Synthesis, and Biological Evaluation of Beta-Ketosulfonamide Adenylation Inhibitors as Potential Antitubercular Agents. Vannada J, Bennett EM, Wilson DJ, Boshoff HI, Barry CE 3rd, Aldrich CC. Org Lett 2006 Oct 12; 8(21):4707-10. Abstract

Rationally designed nucleoside antibiotics that inhibit siderophore biosynthesis of Mycobacterium tuberculosis. Somu RV, Boshoff H, Qiao C, Bennett EM, Barry CE 3rd, Aldrich CC. J. Med. Chem. 49(1), 31-4 (2006). Abstract

Chemoenzymatic synthesis of cryptophycin/arenastatin natural products. Beck ZQ, Aldrich CC, Magarvey NA, Georg GI, Sherman DH. Biochemistry. 44(41), 13457-66 (2005). Abstract
 

Chemoenzymatic Synthesis of the Polyketide 10-Deoxymethynolide. Aldrich CC, Fecik RA, Lakshmanan V, and Sherman DH. J. Am. Chem. Soc. 2005 127(25), 8910-1 (2005). Abstract

Biochemical Investigation of Pikromycin Biosynthesis Employing Native Penta- and Hexaketide Chain Elongation Intermediates. Aldrich CC, Beck BJ, Fecik RA, and Sherman DH. J. Am. Chem. Soc. 127(23), 8441-52 (2005). Abstract

Formal total synthesis of the polyketide macrolactone narbonolide. Venkatraman L, Aldrich CC, Sherman DH, Fecik RA. J. Org. Chem. 70(18), 7267-72 (2005). Abstract

Molecular analysis of the rebeccamycin L-amino acid oxidase from Lechevalieria aerocolonigenes ATCC 39243. Nishizawa T, Aldrich CC, and Sherman DH. J. Bacteriol. 187(6), 2084-92 (2005). Abstract

Synthesis of GTP-derived Ras ligands. Soulere L, Aldrich C, Daumke O, Gail R, Kissau L, Wittinghofer A, and Waldmann H. Chembiochem 5(10), 1448-1453 (2004). Abstract

Substrate recognition and channeling of monomodules from the pikromycin polyketide synthase. Beck BJ, Aldrich CC, Fecik RA, Reynolds KA, and Sherman DH. J. Am. Chem. Soc. 125(41), 12551-7 (2003). Abstract

Iterative chain elongation by a pikromycin monomodular polyketide synthase. Beck BJ, Aldrich CC, Fecik RA, Reynolds KA, and Sherman DH. J. Am. Chem. Soc. 125(16), 4682-3 (2003). Abstract

Total synthesis of the calphostins: application of fischer carbene complexes and thermodynamic control of atropisomers. Merlic CA, Aldrich CC, Albaneze-Walker J, Saghatelian A, and Mammen J. J .Org. Chem. 66(4), 1297-309 (2001). Abstract

Acylamino Chromium Carbene Complexes: Direct Carbonyl Insertion, Formation of M|nchnones, and Trapping with Dipolarophiles. Merlic CA, Baur A, and Aldrich CC. J. Am. Chem. Soc. 122 (30), 7398-7399 (2000). Article link (subscription required; no abstract)

Carbene Complexes in the Synthesis of Complex Natural Products: Total Synthesis of the Calphostins. Merlic CA, Aldrich CC, Albaneze-Walker J, and Saghatelian A. J. Am. Chem. Soc. 122(13), 3224-3225 (2000). Article link (subscription required; no abstract)