1
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Li R, Lichstrahl MS, Zandi TA, Kahlert L, Townsend CA. Erratum: The dabABC operon is a marker of C4-alkylated monobactam biosynthesis and responsible for (2S,3R)-diaminobutyrate production. iScience 2024; 27:109572. [PMID: 38600972 PMCID: PMC11004980 DOI: 10.1016/j.isci.2024.109572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2024] Open
Abstract
[This corrects the article DOI: 10.1016/j.isci.2024.109202.].
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2
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Patel KD, Oliver RA, Lichstrahl MS, Li R, Townsend CA, Gulick AM. The structure of the monobactam-producing thioesterase domain of SulM forms a unique complex with the upstream carrier protein domain. bioRxiv 2024:2024.04.06.588331. [PMID: 38617275 PMCID: PMC11014566 DOI: 10.1101/2024.04.06.588331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Nonribosomal peptide synthetases (NRPSs) are responsible for the production of important biologically active peptides. The large, multidomain NRPSs operate through an assembly line strategy in which the growing peptide is tethered to carrier domains that deliver the intermediates to neighboring catalytic domains. While most NRPS domains catalyze standard chemistry of amino acid activation, peptide bond formation and product release, some canonical NRPS catalytic domains promote unexpected chemistry. The paradigm monobactam antibiotic sulfazecin is produced through the activity of a terminal thioesterase domain that catalyzes an unusual β-lactam forming reaction in which the nitrogen of the C-terminal N-sulfo-2,3-diaminopropionate residue attacks its thioester tether to release the β-lactam product. We have determined the structure of the thioesterase domain as both a free-standing domain and a didomain complex with the upstream holo peptidyl-carrier domain. The structure illustrates a constrained active site that orients the substrate properly for β-lactam formation. In this regard, the structure is similar to the β-lactone forming thioesterase domain responsible for the production of obafluorin. Analysis of the structure identifies features that are responsible for this four-membered ring closure and enable bioinformatic analysis to identify additional, uncharacterized β-lactam-forming biosynthetic gene clusters by genome mining.
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Affiliation(s)
- Ketan D. Patel
- Department of Structural Biology, University at Buffalo, SUNY, Buffalo, NY, 14203, USA
| | - Ryan A. Oliver
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD, 21218 USA
| | - Michael S. Lichstrahl
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD, 21218 USA
| | - Rongfeng Li
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD, 21218 USA
| | - Craig A. Townsend
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD, 21218 USA
| | - Andrew M. Gulick
- Department of Structural Biology, University at Buffalo, SUNY, Buffalo, NY, 14203, USA
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3
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Li R, Lichstrahl MS, Zandi TA, Kahlert L, Townsend CA. The dabABC operon is a marker of C4-alkylated monobactam biosynthesis and responsible for ( 2S, 3R)-diaminobutyrate production. iScience 2024; 27:109202. [PMID: 38433893 PMCID: PMC10906522 DOI: 10.1016/j.isci.2024.109202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/12/2024] [Accepted: 02/07/2024] [Indexed: 03/05/2024] Open
Abstract
Non-ribosomal peptide synthetases (NRPSs) assemble metabolites of medicinal and commercial value. Both serine and threonine figure prominently in these processes and separately can be converted to the additional NRPS building blocks 2,3-diaminopropionate (Dap) and 2,3-diaminobutyrate (Dab). Here we bring extensive bioinformatics, in vivo and in vitro experimentation to compose a unified view of the biosynthesis of these widely distributed non-canonical amino acids that both derive by pyridoxal-mediated β-elimination of the activated O-phosphorylated substrates followed by β-addition of an amine donor. By examining monobactam biosynthesis in Pseudomonas and in Burkholderia species where it is silent, we show that (2S,3R)-Dab synthesis depends on an l-threonine kinase (DabA), a β-replacement reaction with l-aspartate (DabB) and an argininosuccinate lyase-like protein (DabC). The growing clinical importance of monobactams to both withstand Ambler Class B metallo-β-lactamases and retain their antibiotic activity make reprogrammed precursor and NRPS synthesis of modified monobactams a feasible and attractive goal.
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Affiliation(s)
- Rongfeng Li
- Department of Chemistry, The Johns Hopkins University, 3400 N Charles St, Baltimore, MD, USA
| | - Michael S. Lichstrahl
- Department of Chemistry, The Johns Hopkins University, 3400 N Charles St, Baltimore, MD, USA
| | - Trevor A. Zandi
- T. C. Jenkins Department of Biophysics, The Johns Hopkins University, Baltimore, MD, USA
| | - Lukas Kahlert
- Department of Chemistry, The Johns Hopkins University, 3400 N Charles St, Baltimore, MD, USA
| | - Craig A. Townsend
- Department of Chemistry, The Johns Hopkins University, 3400 N Charles St, Baltimore, MD, USA
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4
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Han EJ, Lee SR, Townsend CA, Seyedsayamdost MR. Targeted Discovery of Cryptic Enediyne Natural Products via FRET-Coupled High-Throughput Elicitor Screening. ACS Chem Biol 2023; 18:1854-1862. [PMID: 37463302 PMCID: PMC11062413 DOI: 10.1021/acschembio.3c00281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Abstract
Enediyne antibiotics are a striking family of DNA-cleaving natural products with high degrees of cytotoxicity and structural complexity. Microbial genome sequences, which have recently accumulated, point to an untapped trove of "cryptic" enediynes. Most of the cognate biosynthetic gene clusters (BGCs) are sparingly expressed under standard growth conditions, making it difficult to characterize their products. Herein, we report a fluorescence-based DNA cleavage assay coupled with high-throughput elicitor screening for the rapid, targeted discovery of cryptic enediyne metabolites. We applied the approach to Streptomyces clavuligerus, which harbors two such BGCs with unknown products, identified steroids as effective elicitors, and characterized 10 cryptic enediyne-derived natural products, termed clavulynes A-J with unusual carbonate and terminal olefin functionalities, with one of these congeners matching the recently reported jejucarboside. Our results contribute to the growing repertoire of enediynes and provide a blueprint for identifying additional ones in the future.
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Affiliation(s)
- Esther J Han
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Seoung Rak Lee
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Craig A Townsend
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Mohammad R Seyedsayamdost
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
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5
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Pal P, Wessely SML, Townsend CA. Normal and Aberrant Methyltransferase Activities Give Insights into the Final Steps of Dynemicin A Biosynthesis. J Am Chem Soc 2023; 145:12935-12947. [PMID: 37276497 PMCID: PMC10985829 DOI: 10.1021/jacs.3c04393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The naturally occurring enediynes are notable for their complex structures, potent DNA cleaving ability, and emerging usefulness in cancer chemotherapy. They can be classified into three distinct structural families, but all are thought to originate from a common linear C15-heptaene. Dynemicin A (DYN) is the paradigm member of anthraquinone-fused enediynes, one of the three main classes and exceptional among them for derivation of both its enediyne and anthraquinone portions from this same early biosynthetic building block. Evidence is growing about how two structurally dissimilar, but biosynthetically related, intermediates combine in two heterodimerization reactions to create a nitrogen-containing C30-coupled product. We report here deletions of two genes that encode biosynthetic proteins that are annotated as S-adenosylmethionine (SAM)-dependent methyltransferases. While one, DynO6, is indeed the required O-methyltransferase implicated long ago in the first studies of DYN biosynthesis, the other, DynA5, functions in an unanticipated manner in the post-heterodimerization events that complete the biosynthesis of DYN. Despite its removal from the genome of Micromonospora chersina, the ΔdynA5 strain retains the ability to synthesize DYN, albeit in reduced titers, accompanied by two unusual co-metabolites. We link the appearance of these unexpected structures to a substantial and contradictory body of other recent experimental data to advance a biogenetic rationale for the downstream steps that lead to the final formation of DYN. A sequence of product-forming transformations that is in line with new and existing experimental results is proposed and supported by a model reaction that also encompasses the formation of the crucial epoxide essential for the activation of DYN for DNA cleavage.
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Affiliation(s)
- Paramita Pal
- Department of Chemistry, The Johns Hopkins University, 3400 N. Charles Street, Baltimore, Maryland 21218, United States
| | - Serena M L Wessely
- Department of Chemistry, The Johns Hopkins University, 3400 N. Charles Street, Baltimore, Maryland 21218, United States
| | - Craig A Townsend
- Department of Chemistry, The Johns Hopkins University, 3400 N. Charles Street, Baltimore, Maryland 21218, United States
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6
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Kahlert L, Lichstrahl MS, Townsend CA. Colorimetric Determination of Adenylation Domain Activity in Nonribosomal Peptide Synthetases by Using Chrome Azurol S. Chembiochem 2023; 24:e202200668. [PMID: 36511946 PMCID: PMC10041650 DOI: 10.1002/cbic.202200668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/12/2022] [Accepted: 12/13/2022] [Indexed: 12/15/2022]
Abstract
Adenylation domains are the main contributor to structural complexity among nonribosomal peptides due to their varied but stringent substrate selection. Several in vitro assays to determine the substrate specificity of these dedicated biocatalysts have been implemented, but high sensitivity is often accompanied by the cost of laborious procedures, expensive reagents or the requirement for auxiliary enzymes. Here, we describe a simple protocol that is based on the removal of ferric iron from a preformed chromogenic complex between ferric iron and Chrome Azurol S. Adenylation activity can be rapidly followed by a decrease in absorbance at 630 nm, visualized by a prominent color change from blue to orange.
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Affiliation(s)
- Lukas Kahlert
- Department of Chemistry, The Johns Hopkins University, 3400 N. Charles Street, Baltimore, Maryland, 21218, USA
| | - Michael S Lichstrahl
- Department of Chemistry, The Johns Hopkins University, 3400 N. Charles Street, Baltimore, Maryland, 21218, USA
| | - Craig A Townsend
- Department of Chemistry, The Johns Hopkins University, 3400 N. Charles Street, Baltimore, Maryland, 21218, USA
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7
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Pal P, Alley JR, Townsend CA. Examining Heterodimerization by Aryl C-N Coupling in Dynemicin Biosynthesis. ACS Chem Biol 2023; 18:304-314. [PMID: 36696117 DOI: 10.1021/acschembio.2c00709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Distinct among the enediyne antitumor antibiotics, the dynemicin subgroup is comprised of two discrete halves, an enediyne and an anthraquinone, but each is ultimately derived from the same linear β-hydroxyhexaene precursor. The linkage of these two halves by an aryl C-N bond is examined here using a variety of experimental approaches. We demonstrate that this heterodimerization is specific for anthracenyl iodide as the corresponding bromo- and amino-substituted anthracenes do not support dynemicin biosynthesis. Furthermore, biochemical experiments and chemical model reactions support an SRN1 mechanism for the aryl C-N coupling in which electron transfer occurs to the iodoanthracene, followed by loss of an anthracenyl iodide and partition of the resulting aryl radical between C-N coupling and reduction by hydrogen abstraction. An enzyme pull-down experiment aiming to capture the protein(s) involved in the coupling reaction is described in which two proteins, Orf14 and Orf16, encoded by the dynemicin biosynthetic gene cluster, are specifically isolated. Deletion of orf14 from the genome abolished dynemicin production accompanied by a 3-fold increased accumulation of the iodoanthracene coupling partner, indicating the plausible involvement of this protein in the heterodimerization process. On the other hand, the deletion of orf16 only reduced dynemicin production to 55%, implying a noncatalytic, auxiliary role of the protein. Structural comparisons using AlphaFold imply key similarities between Orf14 and X-ray crystal structures of several proteins from enediyne BGCs believed to bind hydrophobic polyene or enediyne motifs suggest Orf14 templates aryl C-N bond formation during the central heterodimerization in dynemicin biosynthesis.
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Affiliation(s)
- Paramita Pal
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Jamie R Alley
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Craig A Townsend
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
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8
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Lichstrahl MS, Kahlert L, Li R, Zandi TA, Yang J, Townsend CA. Synthesis of Functionalized 2,3-Diaminopropionates and Their Potential for Directed Monobactam Biosynthesis. Chem Sci 2023; 14:3923-3931. [PMID: 37035696 PMCID: PMC10074443 DOI: 10.1039/d2sc06893a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 03/14/2023] [Indexed: 03/22/2023] Open
Abstract
The N-sulfonated monobactams harbor considerable potential to combat emerging bacterial infections that are problematic to treat due to their metallo-β-lactamase mediated resistance against conventional β-lactam antibiotics. Herein, we report a...
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Affiliation(s)
- Michael S Lichstrahl
- Department of Chemistry, The Johns Hopkins University 3400 N Charles St Baltimore MD USA
| | - Lukas Kahlert
- Department of Chemistry, The Johns Hopkins University 3400 N Charles St Baltimore MD USA
| | - Rongfeng Li
- Department of Chemistry, The Johns Hopkins University 3400 N Charles St Baltimore MD USA
| | - Trevor A Zandi
- Novartis Institutes for Biomedical Research Cambridge MA USA
- Chemical Biology and Therapeutics Science Program, Broad Institute Cambridge MA USA
- T. C. Jenkins Department of Biophysics, Johns Hopkins University Baltimore MD USA
| | - Jerry Yang
- Department of Chemistry, The Johns Hopkins University 3400 N Charles St Baltimore MD USA
| | - Craig A Townsend
- Department of Chemistry, The Johns Hopkins University 3400 N Charles St Baltimore MD USA
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9
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Sinner EK, Li R, Marous DR, Townsend CA. ThnL, a B12-dependent radical S-adenosylmethionine enzyme, catalyzes thioether bond formation in carbapenem biosynthesis. Proc Natl Acad Sci U S A 2022; 119:e2206494119. [PMID: 35969793 PMCID: PMC9407657 DOI: 10.1073/pnas.2206494119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 07/19/2022] [Indexed: 11/18/2022] Open
Abstract
Complex carbapenems are important clinical antibiotics used to treat recalcitrant infections. Their biosynthetic gene clusters contain three essential B12-dependent radical S-adenosylmethionine (rSAM) enzymes. The majority of characterized enzymes in this subfamily catalyze methyl transfer, but only one is required to sequentially install all methionine-derived carbons in complex carbapenems. Therefore, it is probable that the other two rSAM enzymes have noncanonical functions. Through a series of fermentation and in vitro experiments, we show that ThnL uses radical SAM chemistry to catalyze thioether bond formation between C2 of a carbapenam precursor and pantetheine, uniting initial bicycle assembly common to all carbapenems with later tailoring events unique to complex carbapenems. ThnL also catalyzes reversible thiol/disulfide redox on pantetheine. Neither of these functions has been observed previously in a B12-dependent radical SAM enzyme. ThnL expands the known activity of this subclass of enzymes beyond carbon-carbon bond formation or rearrangement. It is also the only radical SAM enzyme currently known to catalyze carbon-sulfur bond formation with only an rSAM Fe-S cluster and no additional auxiliary clusters.
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Affiliation(s)
- Erica K. Sinner
- Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218
| | - Rongfeng Li
- Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218
| | - Daniel R. Marous
- Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218
| | - Craig A. Townsend
- Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218
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10
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Wheadon MJ, Townsend CA. Accurate Substrate-Like Probes for Trapping Late-Stage Intermediates in Nonribosomal Peptide Synthetase Condensation Domains. ACS Chem Biol 2022; 17:2046-2053. [PMID: 35914245 PMCID: PMC10029145 DOI: 10.1021/acschembio.2c00474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nonribosomal peptide synthetases (NRPSs) are a family of multidomain enzymes dedicated to the production of peptide natural products. Central to NRPS function are condensation (C) domains, which catalyze peptide bond formation and a number of specialized transformations including dehydroamino acid and β-lactam synthesis. Structures of C domains in catalytically informative states are limited due to a lack of clear strategies for stabilizing C domain interactions with their substrates and client domains. Inspired by a β-lactam forming C domain, we report herein the synthesis and application of 1, which forms irreversible cross-links with engineered thiol nucleophiles in a C domain active site. Deployment of 1 demonstrates the synthetic tractability of trapping late-stage nascent peptides in C domains and provides a readily adaptable tactic for stabilizing C domain interactions in multidomain NRPS fragments.
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Affiliation(s)
- Michael J Wheadon
- Johns Hopkins University, 3400 N Charles St., Baltimore, Maryland 21218, United States
| | - Craig A Townsend
- Johns Hopkins University, 3400 N Charles St., Baltimore, Maryland 21218, United States
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11
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Batchelder HR, Zandi TA, Kaushik A, Naik A, Story-Roller E, Maggioncalda EC, Lamichhane G, Nuermberger EL, Townsend CA. Structure-Activity Relationship of Penem Antibiotic Side Chains Used against Mycobacteria Reveals Highly Active Compounds. ACS Infect Dis 2022; 8:1627-1636. [PMID: 35916356 PMCID: PMC10029149 DOI: 10.1021/acsinfecdis.2c00229] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The rise of antibiotic-resistant Mycobacterium tuberculosis and non-tuberculous mycobacterial infections has placed ever-increasing importance on discovering new antibiotics to treat these diseases. Recently, a new penem, T405, was discovered to have strong antimicrobial activity against M. tuberculosis and Mycobacteroides abscessus. Here, a penem library of C2 side-chain variants was synthesized, and their antimicrobial activities were evaluated against M. tuberculosis H37Rv and M. abscessus ATCC 19977. Several new penems with antimicrobial activity stronger than the standard-of-care carbapenem antibiotics were identified with some candidates improving on the activity of the lead compound, T405. Moreover, many candidates showed little or no increase in the minimum inhibitory concentration in the presence of serum compared to the highly protein-bound T405. The penems with the strongest activity identified in this study were then biochemically characterized by reaction with the representative l,d-transpeptidase LdtMt2 and the representative penicillin-binding protein d,d-carboxypeptidase DacB2.
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Affiliation(s)
- Hunter R Batchelder
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Trevor A Zandi
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Amit Kaushik
- Center for Tuberculosis Research, Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, United States
| | - Akul Naik
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Elizabeth Story-Roller
- Center for Tuberculosis Research, Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, United States
| | - Emily C Maggioncalda
- Center for Tuberculosis Research, Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, United States
| | - Gyanu Lamichhane
- Center for Tuberculosis Research, Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, United States
| | - Eric L Nuermberger
- Center for Tuberculosis Research, Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, United States
| | - Craig A Townsend
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
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12
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Lichstrahl MS, Townsend CA, Sinner EK. Stereochemical course of cobalamin-dependent radical SAM methylation by TokK and ThnK. RSC Chem Biol 2022; 3:1028-1034. [PMID: 36042702 PMCID: PMC9358933 DOI: 10.1039/d2cb00113f] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 06/06/2022] [Indexed: 11/21/2022] Open
Abstract
Complex carbapenems are important clinical antibiotics for difficult-to-treat infections. An essential step in the biosyntheses of these natural products is stereospecific methylation at C6 and subsequent alkylations by cobalamin-dependent radical SAM methylases such as TokK and ThnK. We have prepared isotopically labeled substrates in a stereospecific manner and found that both homologous enzymes selectively abstract the 6-pro-S hydrogen, followed by methyl transfer to the opposite face to give the (6R)-methyl carbapenam product proceeding, therefore, by inversion of absolute configuration at C6. These data clarify an unexpected ambiguity in the recently solved substrate-bound crystal structure of TokK and have led to a stereochemically complete mechanistic proposal for both TokK and ThnK.
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Affiliation(s)
- Michael S Lichstrahl
- Department of Chemistry, The Johns Hopkins University 3400 N Charles St Baltimore Maryland USA
| | - Craig A Townsend
- Department of Chemistry, The Johns Hopkins University 3400 N Charles St Baltimore Maryland USA
| | - Erica K Sinner
- Department of Chemistry, The Johns Hopkins University 3400 N Charles St Baltimore Maryland USA
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13
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Li F, Lin Z, Torres JP, Hill EA, Li D, Townsend CA, Schmidt EW. Sea Urchin Polyketide Synthase SpPks1 Produces the Naphthalene Precursor to Echinoderm Pigments. J Am Chem Soc 2022; 144:9363-9371. [PMID: 35588530 DOI: 10.1021/jacs.2c01416] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Nearly every animal species on Earth contains a unique polyketide synthase (PKS) encoded in its genome, yet no animal-clade PKS has been biochemically characterized, and even the chemical products of these ubiquitous enzymes are known in only a few cases. The earliest animal genome-encoded PKS gene to be identified was SpPks1 from sea urchins. Previous genetic knockdown experiments implicated SpPks1 in synthesis of the sea urchin pigment echinochrome. Here, we express and purify SpPks1, performing biochemical experiments to demonstrate that the sea urchin protein is responsible for the synthesis of 2-acetyl-1,3,6,8-tetrahydroxynaphthalene (ATHN). Since ATHN is a plausible precursor of echinochromes, this result defines a biosynthetic pathway to the ubiquitous echinoderm pigments and rewrites the previous hypothesis for echinochrome biosynthesis. Truncation experiments showed that, unlike other type I iterative PKSs so far characterized, SpPks1 produces the naphthalene core using solely ketoacylsynthase (KS), acyltransferase, and acyl carrier protein domains, delineating a unique class of animal nonreducing aromatic PKSs (aPKSs). A series of amino acids in the KS domain define the family and are likely crucial in cyclization activity. Phylogenetic analyses indicate that SpPks1 and its homologs are widespread in echinoderms and their closest relatives, the acorn worms, reinforcing their fundamental importance to echinoderm biology. While the animal microbiome is known to produce aromatic polyketides, this work provides biochemical evidence that animals themselves also harbor ancient, convergent, dedicated pathways to carbocyclic aromatic polyketides. More fundamentally, biochemical analysis of SpPks1 begins to define the vast and unexplored biosynthetic space of the ubiquitous animal PKS family.
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Affiliation(s)
- Feng Li
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, P. R. China.,Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Zhenjian Lin
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Joshua P Torres
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Eric A Hill
- Department of Chemistry, The Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Dehai Li
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, P. R. China
| | - Craig A Townsend
- Department of Chemistry, The Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Eric W Schmidt
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
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14
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Abstract
While bioinformatic evidence of cobalamin-dependent radical S-adenosylmethionine (SAM) enzymes has existed since the naming of the radical SAM superfamily in 2001, none were biochemically characterized until 2011. In the past decade, the field has flourished as methodological advances have facilitated study of the subfamily. Because of the ingenuity and perseverance of researchers in this field, we now have functional, mechanistic, and structural insight into how this class of enzymes harnesses the power of both the cobalamin and radical SAM cofactors to achieve catalysis. All of the early characterized enzymes in this subfamily were methylases, but the activity of these enzymes has recently been expanded beyond methylation. We anticipate that the characterized functions of these enzymes will become both better understood and increasingly diverse with continued study.
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Affiliation(s)
- Erica
K. Sinner
- Department
of Chemistry, Johns Hopkins University, 3400 N Charles St., Baltimore, Maryland 21218, United States
| | - Daniel R. Marous
- Department
of Chemistry, Wittenberg University, 200 W Ward St., Springfield, Ohio 45504, United States
| | - Craig A. Townsend
- Department
of Chemistry, Johns Hopkins University, 3400 N Charles St., Baltimore, Maryland 21218, United States
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15
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Abstract
The carbapenem family of β-lactam antibiotics displays a remarkably broad spectrum of bactericidal activity, exemplified by meropenem's phase II clinical trial success in patients with pulmonary tuberculosis, a devastating disease for which β-lactam drugs historically have been notoriously ineffective. The discovery and validation of l,d-transpeptidases (Ldts) as critical drug targets of bacterial cell-wall biosynthesis, which are only potently inhibited by the carbapenem and penem structural classes, gave an enzymological basis for the effectiveness of the first antitubercular β-lactams. Decades of study have delineated mechanisms of β-lactam inhibition of their canonical targets, the penicillin-binding proteins; however, open questions remain regarding the mechanisms of Ldt inhibition that underlie programs in drug design, particularly the optimization of kinetic behavior and potency. We have investigated critical features of mycobacterial Ldt inhibition and demonstrate here that the covalent inhibitor meropenem undergoes both reversible reaction and nonhydrolytic off-loading reactions from the cysteine transpeptidase LdtMt2 through a high-energy thioester adduct. Next-generation carbapenem optimization strategies should minimize adduct loss from unproductive mechanisms of Ldt adducts that reduce effective drug concentration.
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Affiliation(s)
- Trevor A Zandi
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218
| | - Craig A Townsend
- Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218
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16
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Long DH, Townsend CA. Acyl Donor Stringency and Dehydroaminoacyl Intermediates in β-Lactam Formation by a Non-ribosomal Peptide Synthetase. ACS Chem Biol 2021; 16:806-812. [PMID: 33847484 DOI: 10.1021/acschembio.1c00117] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Condensation (C) domains in non-ribosomal peptide synthetases catalyze peptide elongation steps whereby activated amino acid or peptidyl acyl donors are coupled with specific amino acid acceptors. In the biosynthesis of the β-lactam antibiotic nocardicin A, an unusual C domain converts a seryl tetrapeptide into its pentapeptide product containing an integrated β-lactam ring. While indirect evidence for the intermediacy of a dehydroalanyl species has been reported, here we describe observation of the elusive enzyme-bound dehydroamino acyl intermediate generated from the corresponding allo-threonyl tetrapeptide and partitioned into pentapeptide products containing either a dehydrobutyrine residue or an embedded β-lactam. Contrary to trends in the literature where condensation domains have been deemed flexible as to acyl donor structure, this β-lactam synthesizing domain is highly discriminating. The observation of dehydrobutyrine formation links this C domain to related clades associated with natural products containing dehydroamino acid and d-configured residues, suggesting a common mechanistic link.
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Affiliation(s)
- Darcie H. Long
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Craig A. Townsend
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
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17
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Batchelder HR, Story-Roller E, Lloyd EP, Kaushik A, Bigelow KM, Maggioncalda EC, Nuermberger EL, Lamichhane G, Townsend CA. Development of a penem antibiotic against Mycobacteroides abscessus. Commun Biol 2020; 3:741. [PMID: 33288821 PMCID: PMC7721803 DOI: 10.1038/s42003-020-01475-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 11/05/2020] [Indexed: 01/24/2023] Open
Abstract
β-lactams are the most widely used antibiotic class to treat bacterial infections in humans. Mycobacteroides abscessus is an emerging pulmonary pathogen resistant to most antibiotics, including penicillins and cephalosporins. With no current FDA-approved treatment and cure rates <50%, there is a pressing need for effective therapies. Here we report T405, a new β-lactam of the penem subclass that exhibits potent activity against M. abscessus and a panel of drug-resistant strains isolated from cystic fibrosis patients. Additionally, in combination with the β-lactamase inhibitor avibactam, the rate of spontaneous resistance of M. abscessus to T405 approached the limit of detection. Lastly, we show the favorable pharmacokinetic profile of T405 in mice and the absence of toxicity at elevated dosage, which support the clinical potential of this compound. Batchelder et al. report a new penem class antibiotic, T405, which exhibits potent activity against M. abscessus and clinical isolates from cystic fibrosis patients. The development of resistance to T405 is inhibited with the addition of a β-lactamase inhibitor, avibactam. Its clinical potential is further demonstrated by T405 displaying a favourable pharmacokinetic profile in mice with an absence of toxicity.
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Affiliation(s)
- Hunter R Batchelder
- Department of Chemistry, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Elizabeth Story-Roller
- Center for Tuberculosis Research, Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Evan P Lloyd
- Department of Chemistry, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Amit Kaushik
- Center for Tuberculosis Research, Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Kristina M Bigelow
- Center for Tuberculosis Research, Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Emily C Maggioncalda
- Center for Tuberculosis Research, Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Eric L Nuermberger
- Center for Tuberculosis Research, Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Gyanu Lamichhane
- Center for Tuberculosis Research, Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Craig A Townsend
- Department of Chemistry, Johns Hopkins University, Baltimore, MD, 21218, USA.
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18
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Abstract
The biosynthesis of the three structural subclasses of enediyne antitumor antibiotics remains largely unknown beyond a common C16 -hexaene precursor. For the anthraquinone-fused subtype, however, an unexpected iodoanthracene γ-thiolactone was established to be a mid-pathway intermediate to dynemicin A. Having deleted a putative flavin-dependent oxidoreductase from the dynemicin biosynthetic gene cluster, we can now report four metabolites that incorporate the iodoanthracene and reveal the formation of the C-N bond linking the anthraquinone and enediyne halves emblematic of this structural subclass. The coupling of an aryl iodide and an amine is familiar from organometallic chemistry, but has little or no precedent in natural product biosynthesis. These metabolites suggest further that enediyne formation occurs early in the overall biosynthesis, and that even earlier events might convert the C16 -hexaene to a common C15 intermediate that partitions to enediyne and anthraquinone building blocks for the heterodimerization.
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Affiliation(s)
- Douglas R Cohen
- Department of Chemistry, The Johns Hopkins University, 3400 North Charles Street, Baltimore, MD, 21218, USA
| | - Craig A Townsend
- Department of Chemistry, The Johns Hopkins University, 3400 North Charles Street, Baltimore, MD, 21218, USA
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19
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Sinner EK, Lichstrahl MS, Li R, Marous DR, Townsend CA. Methylations in complex carbapenem biosynthesis are catalyzed by a single cobalamin-dependent radical S-adenosylmethionine enzyme. Chem Commun (Camb) 2019; 55:14934-14937. [PMID: 31774078 DOI: 10.1039/c9cc07197k] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Complex carbapenem β-lactam antibiotics contain diverse C6 alkyl substituents constructed by cobalamin-dependent radical SAM enzymes. TokK installs the C6 isopropyl chain found in asparenomycin. Time-course analyses of TokK and its ortholog ThnK, which forms the C6 ethyl chain of thienamycin, indicate that catalysis occurs through a sequence of discrete, non-processive methyl transfers.
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Affiliation(s)
- Erica K Sinner
- Department of Chemistry, Johns Hopkins University, 3400 N Charles St., Baltimore, MD 21218, USA.
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20
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Abstract
Polyketide C-methylation occurs during a programmed sequence of dozens of reactions carried out by multidomain polyketide synthases (PKSs). Fungal PKSs perform these reactions iteratively, where a domain may be exposed to and act upon multiple enzyme-tethered intermediates during biosynthesis. We surveyed a collection of C-methyltransferase (CMeT) domains from nonreducing fungal PKSs to gain insight into how different methylation patterns are installed. Our in vitro results show that control of methylation resides primarily with the CMeT, and CMeTs can intercept and methylate intermediates from noncognate nonreducing PKS domains. Furthermore, the methylation pattern is likely imposed by a competition between methylation or ketosynthase-catalyzed extension for each intermediate. Understanding site-specific polyketide C-methylation may facilitate targeted C-C bond formation in engineered biosynthetic pathways.
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Affiliation(s)
- Philip A. Storm
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Paramita Pal
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Callie R. Huitt-Roehl
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Craig A. Townsend
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
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21
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Abstract
Covering: up to mid of 2018 Type I fatty acid synthases (FASs) are giant multienzymes catalyzing all steps of the biosynthesis of fatty acids from acetyl- and malonyl-CoA by iterative precursor extension. Two strikingly different architectures of FAS evolved in yeast (as well as in other fungi and some bacteria) and metazoans. Yeast-type FAS (yFAS) assembles into a barrel-shaped structure of more than 2 MDa molecular weight. Catalytic domains of yFAS are embedded in an extensive scaffolding matrix and arranged around two enclosed reaction chambers. Metazoan FAS (mFAS) is a 540 kDa X-shaped dimer, with lateral reaction clefts, minimal scaffolding and pronounced conformational variability. All naturally occurring yFAS are strictly specialized for the production of saturated fatty acids. The yFAS architecture is not used for the biosynthesis of any other secondary metabolite. On the contrary, mFAS is related at the domain organization level to major classes of polyketide synthases (PKSs). PKSs produce a variety of complex and potent secondary metabolites; they either act iteratively (iPKS), or are linked via directed substrate transfer into modular assembly lines (modPKSs). Here, we review the architectures of yFAS, mFAS, and iPKSs. We rationalize the evolution of the yFAS assembly, and provide examples for re-engineering of yFAS. Recent studies have provided novel insights into the organization of iPKS. A hybrid crystallographic model of a mycocerosic acid synthase-like Pks5 yielded a comprehensive visualization of the organization and dynamics of fully-reducing iPKS. Deconstruction experiments, structural and functional studies of specialized enzymatic domains, such as the product template (PT) and the starter-unit acyltransferase (SAT) domain have revealed functional principles of non-reducing iterative PKS (NR-PKSs). Most recently, a six-domain loading region of an NR-PKS has been visualized at high-resolution together with cryo-EM studies of a trapped loading intermediate. Altogether, these data reveal the related, yet divergent architectures of mFAS, iPKS and also modPKSs. The new insights highlight extensive dynamics, and conformational coupling as key features of mFAS and iPKS and are an important step towards collection of a comprehensive series of snapshots of PKS action.
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Affiliation(s)
- Dominik A Herbst
- Department Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland.
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22
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Barajas JF, Finzel K, Valentic TR, Shakya G, Gamarra N, Martinez D, Meier JL, Vagstad AL, Newman AG, Townsend CA, Burkart MD, Tsai SC. Structural and Biochemical Analysis of Protein-Protein Interactions Between the Acyl-Carrier Protein and Product Template Domain. Angew Chem Int Ed Engl 2018; 55:13005-13009. [PMID: 27653519 DOI: 10.1002/anie.201605401] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 08/18/2016] [Indexed: 11/08/2022]
Abstract
In fungal non-reducing polyketide synthases (NR-PKS) the acyl-carrier protein (ACP) carries the growing polyketide intermediate through iterative rounds of elongation, cyclization and product release. This process occurs through a controlled, yet enigmatic coordination of the ACP with its partner enzymes. The transient nature of ACP interactions with these catalytic domains imposes a major obstacle for investigation of the influence of protein-protein interactions on polyketide product outcome. To further our understanding about how the ACP interacts with the product template (PT) domain that catalyzes polyketide cyclization, we developed the first mechanism-based crosslinkers for NR-PKSs. Through in vitro assays, in silico docking and bioinformatics, ACP residues involved in ACP-PT recognition were identified. We used this information to improve ACP compatibility with non-cognate PT domains, which resulted in the first gain-of-function ACP with improved interactions with its partner enzymes. This advance will aid in future combinatorial biosynthesis of new polyketides.
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Affiliation(s)
- Jesus F Barajas
- Department of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, 92697, USA
| | - Kara Finzel
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Timothy R Valentic
- Department of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, 92697, USA
| | - Gaurav Shakya
- Department of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, 92697, USA
| | - Nathan Gamarra
- Department of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, 92697, USA
| | - Delsy Martinez
- Department of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, 92697, USA
| | - Jordan L Meier
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Anna L Vagstad
- Department of Chemistry, The Johns Hopkins University, 3400 North Charles Street, Baltimore, MD, 21218, USA
| | - Adam G Newman
- Department of Chemistry, The Johns Hopkins University, 3400 North Charles Street, Baltimore, MD, 21218, USA
| | - Craig A Townsend
- Department of Chemistry, The Johns Hopkins University, 3400 North Charles Street, Baltimore, MD, 21218, USA
| | - Michael D Burkart
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093, USA.
| | - Shiou-Chuan Tsai
- Department of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, 92697, USA.
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23
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Jakob R, Herbst DA, Huitt-Roehl CR, Kravetz JM, Storm PA, Alley JR, Townsend CA, Maier T. The structural organization of substrate loading in iterative polyketide synthases. Acta Crystallogr A Found Adv 2018. [DOI: 10.1107/s2053273318094792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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24
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Abstract
Despite the identification of a β-hydroxyhexaene produced by the enediyne polyketide synthases (PKSs), the post-PKS biosynthetic steps to the individual members of this antitumor and antibiotic family remain largely unknown. The massive biosynthetic gene clusters (BGCs) that direct the formation of each product caution that many steps could be required. It was recently demonstrated that the enediyne PKS in the dynemicin A BGC from Micromonospora chersina gives rise to both the anthraquinone and enediyne halves of the molecule. We now present the first evidence for a mid-pathway intermediate in dynemicin A biosynthesis, an iodoanthracene bearing a fused thiolactone, which was shown to be incorporated selectively into the final product. This unusual precursor reflects just how little is understood about these biosynthetic pathways, yet constrains the mechanisms that can act to achieve the key heterodimerization to the anthraquinone-containing subclass of enediynes.
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Affiliation(s)
- Douglas R Cohen
- Department of Chemistry, The Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA
| | - Craig A Townsend
- Department of Chemistry, The Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA
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25
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Cohen DR, Townsend CA. Rücktitelbild: Characterization of an Anthracene Intermediate in Dynemicin Biosynthesis (Angew. Chem. 20/2018). Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201803006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Douglas R. Cohen
- Department of Chemistry; The Johns Hopkins University; 3400 North Charles Street Baltimore MD 21218 USA
| | - Craig A. Townsend
- Department of Chemistry; The Johns Hopkins University; 3400 North Charles Street Baltimore MD 21218 USA
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26
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Affiliation(s)
- Douglas R. Cohen
- Department of Chemistry; The Johns Hopkins University; 3400 North Charles Street Baltimore MD 21218 USA
| | - Craig A. Townsend
- Department of Chemistry; The Johns Hopkins University; 3400 North Charles Street Baltimore MD 21218 USA
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27
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Cohen DR, Townsend CA. Back Cover: Characterization of an Anthracene Intermediate in Dynemicin Biosynthesis (Angew. Chem. Int. Ed. 20/2018). Angew Chem Int Ed Engl 2018. [DOI: 10.1002/anie.201803006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Douglas R. Cohen
- Department of Chemistry; The Johns Hopkins University; 3400 North Charles Street Baltimore MD 21218 USA
| | - Craig A. Townsend
- Department of Chemistry; The Johns Hopkins University; 3400 North Charles Street Baltimore MD 21218 USA
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28
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Abstract
Modular nonribosomal peptide synthetases (NRPSs) are large, multidomain engines of bioactive natural product biosynthesis that function as molecular "assembly lines" in which monomer units are selectively bound, modified, and linked in a specific order and number dictated by their mega-enzyme templates. Recently, a condensation domain in an NRPS was discovered to carry out the synthesis of an integrated β-lactam ring from a substrate seryl residue during antibiotic biosynthesis. We report here a series of experiments supporting a mechanism that involves C-N bond formation by stepwise elimination/addition reactions followed by canonical NRPS-catalyzed amide bond synthesis to achieve β-lactam formation. Partitioning of reactive intermediates formed during the multistep catalytic cycle provided insight into the ability of the NRPS to overcome the reversibility of corresponding reactions in solution and enforce directionality during synthesis.
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Affiliation(s)
- Darcie H Long
- Department of Chemistry , Johns Hopkins University , Baltimore , Maryland 21218 , United States
| | - Craig A Townsend
- Department of Chemistry , Johns Hopkins University , Baltimore , Maryland 21218 , United States
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29
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Saraiva RG, Huitt-Roehl CR, Tripathi A, Cheng YQ, Bosch J, Townsend CA, Dimopoulos G. Chromobacterium spp. mediate their anti-Plasmodium activity through secretion of the histone deacetylase inhibitor romidepsin. Sci Rep 2018; 8:6176. [PMID: 29670144 PMCID: PMC5906607 DOI: 10.1038/s41598-018-24296-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 03/19/2018] [Indexed: 12/03/2022] Open
Abstract
The Chromobacterium sp. Panama bacterium has in vivo and in vitro anti-Plasmodium properties. To assess the nature of the Chromobacterium-produced anti-Plasmodium factors, chemical partition was conducted by bioassay-guided fractionation where different fractions were assayed for activity against asexual stages of P. falciparum. The isolated compounds were further partitioned by reversed-phase FPLC followed by size-exclusion chromatography; high resolution UPLC and ESI/MS data were then collected and revealed that the most active fraction contained a cyclic depsipeptide, which was identified as romidepsin. A pure sample of this FDA-approved HDAC inhibitor allowed us to independently verify this finding, and establish that romidepsin also has potent effect against mosquito stages of the parasite's life cycle. Genomic comparisons between C. sp. Panama and multiple species within the Chromobacterium genus further demonstrated a correlation between presence of the gene cluster responsible for romidepsin production and effective antiplasmodial activity. A romidepsin-null Chromobacterium spp. mutant loses its anti-Plasmodium properties by losing the ability to inhibit P. falciparum HDAC activity, and romidepsin is active against resistant parasites to commonly deployed antimalarials. This independent mode of action substantiates exploring a chromobacteria-based approach for malaria transmission-blocking.
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Affiliation(s)
- Raúl G Saraiva
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | | | - Abhai Tripathi
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Yi-Qiang Cheng
- UNT System College of Pharmacy, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - Jürgen Bosch
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
- InterRayBio, LLC, Baltimore, Maryland, USA
| | - Craig A Townsend
- Department of Chemistry, Johns Hopkins University, Baltimore, MD, USA
| | - George Dimopoulos
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA.
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30
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Herbst DA, Huitt-Roehl CR, Jakob RP, Kravetz JM, Storm PA, Alley JR, Townsend CA, Maier T. The structural organization of substrate loading in iterative polyketide synthases. Nat Chem Biol 2018; 14:474-479. [PMID: 29610486 DOI: 10.1038/s41589-018-0026-3] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 02/07/2018] [Indexed: 11/09/2022]
Abstract
Polyketide synthases (PKSs) are microbial multienzymes for the biosynthesis of biologically potent secondary metabolites. Polyketide production is initiated by the loading of a starter unit onto an integral acyl carrier protein (ACP) and its subsequent transfer to the ketosynthase (KS). Initial substrate loading is achieved either by multidomain loading modules or by the integration of designated loading domains, such as starter unit acyltransferases (SAT), whose structural integration into PKS remains unresolved. A crystal structure of the loading/condensing region of the nonreducing PKS CTB1 demonstrates the ordered insertion of a pseudodimeric SAT into the condensing region, which is aided by the SAT-KS linker. Cryo-electron microscopy of the post-loading state trapped by mechanism-based crosslinking of ACP to KS reveals asymmetry across the CTB1 loading/-condensing region, in accord with preferential 1:2 binding stoichiometry. These results are critical for re-engineering the loading step in polyketide biosynthesis and support functional relevance of asymmetric conformations of PKSs.
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Affiliation(s)
- Dominik A Herbst
- Department of Biozentrum, University of Basel, Basel, Switzerland
| | | | - Roman P Jakob
- Department of Biozentrum, University of Basel, Basel, Switzerland
| | - Jacob M Kravetz
- Department of Chemistry, Johns Hopkins University, Baltimore, MD, USA
| | - Philip A Storm
- Department of Chemistry, Johns Hopkins University, Baltimore, MD, USA
| | - Jamie R Alley
- Department of Chemistry, Johns Hopkins University, Baltimore, MD, USA
| | - Craig A Townsend
- Department of Chemistry, Johns Hopkins University, Baltimore, MD, USA
| | - Timm Maier
- Department of Biozentrum, University of Basel, Basel, Switzerland.
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31
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Abstract
Polyketide synthases (PKSs) have several known editing mechanisms to ensure that non-productive intermediates are removed from the acyl carrier protein (ACP). We demonstrate that CitA, a putative hydrolase in the citrinin biosynthetic gene cluster, removes ACP-bound acyl intermediates. We propose that it serves an editing role in trans.
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Affiliation(s)
- Philip A Storm
- Department of Chemistry, Johns Hopkins University, 3400 N Charles St, Baltimore, MD 21218, USA.
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32
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Horsman ME, Marous DR, Li R, Oliver RA, Byun B, Emrich SJ, Boggess B, Townsend CA, Mobashery S. Whole-Genome Shotgun Sequencing of Two β-Proteobacterial Species in Search of the Bulgecin Biosynthetic Cluster. ACS Chem Biol 2017; 12:2552-2557. [PMID: 28937735 PMCID: PMC5653948 DOI: 10.1021/acschembio.7b00687] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
We
have produced draft whole-genome sequences for two bacterial
strains reported to produce the bulgecins as well as NRPS-derived
monobactam β-lactam antibiotics. We propose classification of
ATCC 31363 as Paraburkholderia acidophila. We further
reaffirm that ATCC 31433 (Burkholderia ubonensis subsp. mesacidophila) is a taxonomically distinct producer of bulgecins with notable
gene regions shared with Paraburkholderia acidophila. We use RAST multiple-gene comparison and MASH distancing with published
genomes to order the draft contigs and identify unique gene regions
for characterization. Forty-eight natural-product gene clusters are
presented from PATRIC (RASTtk) and antiSMASH annotations. We present
evidence that the 10 genes that follow the sulfazecin and isosulfazecin
pathways in both species are likely involved in bulgecin A biosynthesis.
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Affiliation(s)
| | | | - Rongfeng Li
- Department
of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Ryan A. Oliver
- Department
of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | | | | | | | - Craig A. Townsend
- Department
of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
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33
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Mattoo R, Lloyd EP, Kaushik A, Kumar P, Brunelle JL, Townsend CA, Lamichhane G. Ldt Mav2, a nonclassical transpeptidase and susceptibility of Mycobacterium avium to carbapenems. Future Microbiol 2017; 12:595-607. [PMID: 28555497 PMCID: PMC5619143 DOI: 10.2217/fmb-2016-0208] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Aim: Mycobacterium avium infections, especially in immune-compromised individuals, present a significant challenge as therapeutic options are limited. In this study, we investigated if M. avium genome encodes nonclassical transpeptidases and if newer carbapenems are effective against this mycobacteria. Materials & methods: Biochemical and microbiological approaches were used to identify and characterize a nonclassical transpeptidase, namely L,D-transpeptidase, in M. avium. Results & conclusion: We describe the biochemical and physiological attributes of a L,D-transpeptidase in M. avium, LdtMav2. Suggestive of a constitutive requirement, levels of LdtMav2, a L,D-transpeptidase in M. avium, remain constant during exponential and stationary phases of growth. Among β-lactam antibacterials, only a subset of carbapenems inhibit LdtMav2 and tebipenem, a new oral carbapenem, inhibits growth of M. avium.
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Affiliation(s)
- Rohini Mattoo
- Department of Medicine, Center for Tuberculosis Research, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Evan P Lloyd
- Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Amit Kaushik
- Department of Medicine, Center for Tuberculosis Research, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Pankaj Kumar
- Department of Medicine, Center for Tuberculosis Research, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Julie L Brunelle
- Howard Hughes Medical Institute, Department of Molecular Biology & Genetics, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Craig A Townsend
- Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218, USA.,Department of Medicine, Taskforce to Study Resistance Emergence & Antimicrobial Development Technology, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Gyanu Lamichhane
- Department of Medicine, Center for Tuberculosis Research, Johns Hopkins University, Baltimore, MD 21231, USA.,Department of Medicine, Taskforce to Study Resistance Emergence & Antimicrobial Development Technology, Johns Hopkins University, Baltimore, MD 21231, USA
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Bianchet MA, Pan YH, Basta LAB, Saavedra H, Lloyd EP, Kumar P, Mattoo R, Townsend CA, Lamichhane G. Structural insight into the inactivation of Mycobacterium tuberculosis non-classical transpeptidase Ldt Mt2 by biapenem and tebipenem. BMC Biochem 2017; 18:8. [PMID: 28545389 PMCID: PMC5445500 DOI: 10.1186/s12858-017-0082-4] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 05/09/2017] [Indexed: 05/29/2023]
Abstract
Background The carbapenem subclass of β-lactams is among the most potent antibiotics available today. Emerging evidence shows that, unlike other subclasses of β-lactams, carbapenems bind to and inhibit non-classical transpeptidases (L,D-transpeptidases) that generate 3 → 3 linkages in bacterial peptidoglycan. The carbapenems biapenem and tebipenem exhibit therapeutically valuable potencies against Mycobacterium tuberculosis (Mtb). Results Here, we report the X-ray crystal structures of MtbL,D-transpeptidase-2 (LdtMt2) complexed with biapenem or tebipenem. Despite significant variations in carbapenem sulfur side chains, biapenem and tebipenem ultimately form an identical adduct that docks to the outer cavity of LdtMt2. We propose that this common adduct is an enzyme catalyzed decomposition of the carbapenem adduct by a mechanism similar to S-conjugate elimination by β-lyases. Conclusion The results presented here demonstrate biapenem and tebipenem bind to the outer cavity of LdtMt2, covalently inactivate the enzyme, and subsequently degrade via an S-conjugate elimination mechanism. We discuss structure based drug design based on the findings and propose that the S-conjugate elimination can be leveraged to design novel agents to deliver and locally release antimicrobial factors to act synergistically with the carbapenem carrier. Electronic supplementary material The online version of this article (doi:10.1186/s12858-017-0082-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mario A Bianchet
- Department of Neurology, Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, MD, 21205, USA. .,Department of Biophysics and Biophysical Chemistry, Structural Enzymology and Thermodynamics Group, Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, MD, 21205, USA.
| | - Ying H Pan
- Department of Neurology, Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, MD, 21205, USA
| | | | - Harry Saavedra
- Department of Neurology, Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, MD, 21205, USA
| | - Evan P Lloyd
- Department of Chemistry, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Pankaj Kumar
- Division of Infectious Diseases, Center for Tuberculosis Research, Taskforce to study Resistance Emergence & Antimicrobial development Technology (TREAT), Johns Hopkins University School of Medicine, Baltimore, MD, 21231, USA
| | - Rohini Mattoo
- Division of Infectious Diseases, Center for Tuberculosis Research, Taskforce to study Resistance Emergence & Antimicrobial development Technology (TREAT), Johns Hopkins University School of Medicine, Baltimore, MD, 21231, USA
| | - Craig A Townsend
- Department of Chemistry, Johns Hopkins University, Baltimore, MD, 21218, USA.,Division of Infectious Diseases, Taskforce to study Resistance Emergence & Antimicrobial development Technology (TREAT), Johns Hopkins University School of Medicine, 1503 E. Jefferson Street, Baltimore, MD, 21231, USA
| | - Gyanu Lamichhane
- Division of Infectious Diseases, Center for Tuberculosis Research, Taskforce to study Resistance Emergence & Antimicrobial development Technology (TREAT), Johns Hopkins University School of Medicine, Baltimore, MD, 21231, USA. .,Division of Infectious Diseases, Taskforce to study Resistance Emergence & Antimicrobial development Technology (TREAT), Johns Hopkins University School of Medicine, 1503 E. Jefferson Street, Baltimore, MD, 21231, USA.
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35
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Storm PA, Herbst DA, Maier T, Townsend CA. Functional and Structural Analysis of Programmed C-Methylation in the Biosynthesis of the Fungal Polyketide Citrinin. Cell Chem Biol 2017; 24:316-325. [PMID: 28238725 DOI: 10.1016/j.chembiol.2017.01.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 11/30/2016] [Accepted: 01/30/2017] [Indexed: 01/09/2023]
Abstract
Fungal polyketide synthases (PKSs) are large, multidomain enzymes that biosynthesize a wide range of natural products. A hallmark of these megasynthases is the iterative use of catalytic domains to extend and modify a series of enzyme-bound intermediates. A subset of these iterative PKSs (iPKSs) contains a C-methyltransferase (CMeT) domain that adds one or more S-adenosylmethionine (SAM)-derived methyl groups to the carbon framework. Neither the basis by which only specific positions on the growing intermediate are methylated ("programming") nor the mechanism of methylation are well understood. Domain dissection and reconstitution of PksCT, the fungal non-reducing PKS (NR-PKS) responsible for the first isolable intermediate in citrinin biosynthesis, demonstrates the role of CMeT-catalyzed methylation in precursor elongation and pentaketide formation. The crystal structure of the S-adenosyl-homocysteine (SAH) coproduct-bound PksCT CMeT domain reveals a two-subdomain organization with a novel N-terminal subdomain characteristic of PKS CMeT domains and provides insights into co-factor and ligand recognition.
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Affiliation(s)
- Philip A Storm
- Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Dominik A Herbst
- Department Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland
| | - Timm Maier
- Department Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland
| | - Craig A Townsend
- Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218, USA.
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36
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Li R, Oliver RA, Townsend CA. Identification and Characterization of the Sulfazecin Monobactam Biosynthetic Gene Cluster. Cell Chem Biol 2016; 24:24-34. [PMID: 28017601 DOI: 10.1016/j.chembiol.2016.11.010] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 10/18/2016] [Accepted: 11/17/2016] [Indexed: 11/16/2022]
Abstract
The monobactams, exemplified by the natural product sulfazecin, are the only class of β-lactam antibiotics not inactivated by metallo-β-lactamases, which confer bacteria with extended-spectrum β-lactam resistance. We screened a transposon mutagenesis library from Pseudomonas acidophila ATCC 31363 and isolated a sulfazecin-deficient mutant that revealed a gene cluster encoding two non-ribosomal peptide synthetases (NRPSs), a methyltransferase, a sulfotransferase, and a dioxygenase. Three modules and an aberrant C-terminal thioesterase (TE) domain are distributed across the two NRPSs. Biochemical examination of the adenylation (A) domains provided evidence that L-2,3-diaminopropionate, not L-serine as previously thought, is the direct source of the β-lactam ring of sulfazecin. ATP/PPi exchange assay also revealed an unusual substrate selectivity shift of one A domain when expressed with or without the immediately upstream condensation domain. Gene inactivation analysis defined a cluster of 13 open reading frames sufficient for sulfazecin production, precursor synthesis, self-resistance, and regulation. The identification of a key intermediate supported a proposed NRPS-mediated mechanism of sulfazecin biosynthesis and β-lactam ring formation distinct from the nocardicins, another NRPS-derived subclass of monocyclic β-lactam. These findings will serve as the basis for further biosynthetic research and potential engineering of these important antibiotics.
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Affiliation(s)
- Rongfeng Li
- Department of Chemistry, The Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA
| | - Ryan A Oliver
- Department of Chemistry, The Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA
| | - Craig A Townsend
- Department of Chemistry, The Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA.
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37
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Barajas JF, Finzel K, Valentic TR, Shakya G, Gamarra N, Martinez D, Meier JL, Vagstad AL, Newman AG, Townsend CA, Burkart MD, Tsai SC. Structural and Biochemical Analysis of Protein-Protein Interactions Between the Acyl-Carrier Protein and Product Template Domain. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201605401] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Jesus F. Barajas
- Department of Molecular Biology and Biochemistry; Chemistry, and Pharmaceutical Sciences; University of California, Irvine; Irvine CA 92697 USA
| | - Kara Finzel
- Department of Chemistry and Biochemistry; University of California, San Diego; La Jolla CA 92093 USA
| | - Timothy R. Valentic
- Department of Molecular Biology and Biochemistry; Chemistry, and Pharmaceutical Sciences; University of California, Irvine; Irvine CA 92697 USA
| | - Gaurav Shakya
- Department of Molecular Biology and Biochemistry; Chemistry, and Pharmaceutical Sciences; University of California, Irvine; Irvine CA 92697 USA
| | - Nathan Gamarra
- Department of Molecular Biology and Biochemistry; Chemistry, and Pharmaceutical Sciences; University of California, Irvine; Irvine CA 92697 USA
| | - Delsy Martinez
- Department of Molecular Biology and Biochemistry; Chemistry, and Pharmaceutical Sciences; University of California, Irvine; Irvine CA 92697 USA
| | - Jordan L. Meier
- Department of Chemistry and Biochemistry; University of California, San Diego; La Jolla CA 92093 USA
| | - Anna L. Vagstad
- Department of Chemistry; The Johns Hopkins University; 3400 North Charles Street Baltimore MD 21218 USA
| | - Adam G. Newman
- Department of Chemistry; The Johns Hopkins University; 3400 North Charles Street Baltimore MD 21218 USA
| | - Craig A. Townsend
- Department of Chemistry; The Johns Hopkins University; 3400 North Charles Street Baltimore MD 21218 USA
| | - Michael D. Burkart
- Department of Chemistry and Biochemistry; University of California, San Diego; La Jolla CA 92093 USA
| | - Shiou-Chuan Tsai
- Department of Molecular Biology and Biochemistry; Chemistry, and Pharmaceutical Sciences; University of California, Irvine; Irvine CA 92697 USA
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38
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Abstract
Five naturally-occurring families of β-lactams have inspired a class of drugs that constitute >60% of the antimicrobials used in human medicine. Their biosynthetic pathways reveal highly individualized synthetic strategies that yet converge on a common azetidinone ring assembled in structural contexts that confer selective binding and inhibition of d,d-transpeptidases that play essential roles in bacterial cell wall (peptidoglycan) biosynthesis. These enzymes belong to a single 'clan' of evolutionarily distinct serine hydrolases whose active site geometry and mechanism of action is specifically matched by these antibiotics for inactivation that is kinetically competitive with their native function. Unusual enzyme-mediated reactions and catalytic multitasking in these pathways are discussed with particular attention to the diverse ways the β-lactam itself is generated, and more broadly how the intrinsic reactivity of this core structural element is modulated in natural systems through the introduction of ring strain and electronic effects.
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Affiliation(s)
- Craig A Townsend
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA.
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39
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Zhou J, Outlaw VK, Townsend CA, Bragg AE. Quenching of pH-Responsive Luminescence of a Benzoindolizine Sensor by an Ultrafast Hydrogen Shift. Chemistry 2016; 22:15212-15215. [PMID: 27549912 DOI: 10.1002/chem.201603284] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Indexed: 11/12/2022]
Abstract
Fluorescent-sensor design requires consideration of how photochemical dynamics control properties of a sensing state. Transient absorption (TA) spectroscopy reveals an ultrafast net [1,3]-hydrogen shift following excitation of a protonated methoxy benzoindolizine (bzi) sensor in solution. These photochemical dynamics explain a quenched pH-responsive fluorescence shift and dramatically reduced fluorescence quantum yield relative to other (e. g. methyl) bzi compounds that do not tautomerize. Calculations predict the energetic and structural feasibility for rearrangement in protonated bzi compounds, such that interaction between the pi-network and strongly electron-donating methoxyl must lower the barrier for suprafacial H or H+ shift across an allylic moiety. As bzi compounds broadly exhibit pH-responsive emission shifts, chemical interactions that modulate this electronic interaction and suppress tautomerization could be used to facilitate binding- or surface-specific acid-responsive sensing.
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Affiliation(s)
- Jiawang Zhou
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD, 21218, USA
| | - Victor K Outlaw
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD, 21218, USA
| | - Craig A Townsend
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD, 21218, USA
| | - Arthur E Bragg
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD, 21218, USA.
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40
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Outlaw VK, Zhou J, Bragg AE, Townsend CA. Unusual Blue-Shifted Acid-Responsive Photoluminescence Behavior in 6-Amino-8-cyanobenzo[1,2- b]indolizines. RSC Adv 2016; 6:61249-61253. [PMID: 28580137 DOI: 10.1039/c6ra10605f] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
6-Amino-8-cyanobenzo[1, 2-b]indolizines, a new class of photoluminescent materials, exhibit reversible pH-dependent optical properties characterized by an uncommon and dramatic blue shift in fluorescence emission when protonated. Acid titration and NMR spectroscopy experiments reveal that, rather than the anticipated N-protonation, C-protonation and loss of aromaticity is responsible for the observed photophysical changes. Efficient synthesis from indole-2-carboxaldehydes makes variously substituted versions of this nucleus readily available to tune optical and pH effects.
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Affiliation(s)
- Victor K Outlaw
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Jiawang Zhou
- Department of Chemistry, The Johns Hopkins University, Remsen Hall, 3400 N. Charles Street, Baltimore, MD 21218, USA
| | - Arthur E Bragg
- Department of Chemistry, The Johns Hopkins University, Remsen Hall, 3400 N. Charles Street, Baltimore, MD 21218, USA
| | - Craig A Townsend
- Department of Chemistry, The Johns Hopkins University, Remsen Hall, 3400 N. Charles Street, Baltimore, MD 21218, USA
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41
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Newman AG, Townsend CA. Molecular Characterization of the Cercosporin Biosynthetic Pathway in the Fungal Plant Pathogen Cercospora nicotianae. J Am Chem Soc 2016; 138:4219-28. [PMID: 26938470 DOI: 10.1021/jacs.6b00633] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Perylenequinones are a class of photoactivated polyketide mycotoxins produced by fungal plant pathogens that notably produce reactive oxygen species with visible light. The best-studied perylenequinone is cercosporin-a product of the Cercospora species. While the cercosporin biosynthetic gene cluster has been described in the tobacco pathogen Cercospora nicotianae, little is known of the metabolite's biosynthesis. Furthermore, in vitro investigations of the polyketide synthase central to cercosporin biosynthesis identified the naphthopyrone nor-toralactone as its direct product-an observation in conflict with published biosynthetic proposals. Here, we present an alternative biosynthetic pathway to cercosporin based on metabolites characterized from a series of biosynthetic gene knockouts. We show that nor-toralactone is the key polyketide intermediate and the substrate for the unusual didomain protein CTB3. We demonstrate the unique oxidative cleavage activity of the CTB3 monooxygenase domain in vitro. These data advance our understanding of perylenequinone biosynthesis and expand the biochemical repertoire of flavin-dependent monooxygenases.
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Affiliation(s)
- Adam G Newman
- Department of Chemistry, Johns Hopkins University , Baltimore, Maryland 21218, United States
| | - Craig A Townsend
- Department of Chemistry, Johns Hopkins University , Baltimore, Maryland 21218, United States
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42
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Brammer Basta LA, Ghosh A, Pan Y, Jakoncic J, Lloyd EP, Townsend CA, Lamichhane G, Bianchet MA. Loss of a Functionally and Structurally Distinct ld-Transpeptidase, LdtMt5, Compromises Cell Wall Integrity in Mycobacterium tuberculosis. J Biol Chem 2015; 290:25670-85. [PMID: 26304120 DOI: 10.1074/jbc.m115.660753] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Indexed: 11/06/2022] Open
Abstract
The final step of peptidoglycan (PG) biosynthesis in bacteria involves cross-linking of peptide side chains. This step in Mycobacterium tuberculosis is catalyzed by ld- and dd-transpeptidases that generate 3→3 and 4→3 transpeptide linkages, respectively. M. tuberculosis PG is predominantly 3→3 cross-linked, and LdtMt2 is the dominant ld-transpeptidase. There are four additional sequence paralogs of LdtMt2 encoded by the genome of this pathogen, and the reason for this apparent redundancy is unknown. Here, we studied one of the paralogs, LdtMt5, and found it to be structurally and functionally distinct. The structures of apo-LdtMt5 and its meropenem adduct presented here demonstrate that, despite overall architectural similarity to LdtMt2, the LdtMt5 active site has marked differences. The presence of a structurally divergent catalytic site and a proline-rich C-terminal subdomain suggest that this protein may have a distinct role in PG metabolism, perhaps involving other cell wall-anchored proteins. Furthermore, M. tuberculosis lacking a functional copy of LdtMt5 displayed aberrant growth and was more susceptible to killing by crystal violet, osmotic shock, and select carbapenem antibiotics. Therefore, we conclude that LdtMt5 is not a functionally redundant ld-transpeptidase, but rather it serves a unique and important role in maintaining the integrity of the M. tuberculosis cell wall.
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Affiliation(s)
- Leighanne A Brammer Basta
- From the Taskforce to study Resistance Emergence and Antimicrobial development Technology (TREAT) and Division of Infectious Diseases, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21231
| | - Anita Ghosh
- Structural Enzymology and Thermodynamics Group, Department of Biophysics and Biophysical Chemistry and
| | - Ying Pan
- Structural Enzymology and Thermodynamics Group, Department of Biophysics and Biophysical Chemistry and
| | - Jean Jakoncic
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, New York 11973, and
| | - Evan P Lloyd
- Department of Chemistry, The Johns Hopkins University, Baltimore, Maryland 21218
| | - Craig A Townsend
- Department of Chemistry, The Johns Hopkins University, Baltimore, Maryland 21218
| | - Gyanu Lamichhane
- From the Taskforce to study Resistance Emergence and Antimicrobial development Technology (TREAT) and Division of Infectious Diseases, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21231,
| | - Mario A Bianchet
- Structural Enzymology and Thermodynamics Group, Department of Biophysics and Biophysical Chemistry and Department of Neurology, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205,
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43
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Conradt D, Schätzle MA, Haas J, Townsend CA, Müller M. New Insights into the Conversion of Versicolorin A in the Biosynthesis of Aflatoxin B1. J Am Chem Soc 2015; 137:10867-9. [PMID: 26266881 DOI: 10.1021/jacs.5b06770] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A crucial and enigmatic step in the complex biosynthesis of aflatoxin B1 is the oxidative rearrangement of versicolorin A to demethylsterigmatocystin. This step is thought to proceed by an oxidation-reduction-oxidation sequence, in which the NADPH-dependent oxidoreductase AflM catalyzes the enclosed reduction step. AflM from Aspergillus parasiticus, after heterologous production in E. coli and purification, however, catalyzed the reduction of the hydroquinoid form of the starting compound versicolorin A (25% conversion) to a so far unknown product of aflatoxin biosynthesis. The asymmetric reduction of emodin hydroquinone to (R)-3,8,9,10-tetrahydroxy-6-methyl-3,4-dihydroanthracen-1(2H)-one (up to 82% for AflM) has also been observed in previous studies using MdpC from Aspergillus nidulans (monodictyphenone biosynthetic gene cluster). The first (nonenzymatic) reduction of emodin to emodin hydroquinone, for example with sodium dithionite, is obligatory for the enzymatic reduction by AflM or MdpC. These results imply an unprecedented role of AflM in the complex enzymatic network of aflatoxin biosynthesis.
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Affiliation(s)
- David Conradt
- Institut für Pharmazeutische Wissenschaften, Albert-Ludwigs-Universität Freiburg , Albertstr. 25, 79104 Freiburg, Germany
| | - Michael A Schätzle
- Institut für Pharmazeutische Wissenschaften, Albert-Ludwigs-Universität Freiburg , Albertstr. 25, 79104 Freiburg, Germany
| | - Julian Haas
- Institut für Pharmazeutische Wissenschaften, Albert-Ludwigs-Universität Freiburg , Albertstr. 25, 79104 Freiburg, Germany
| | - Craig A Townsend
- Department of Chemistry, The Johns Hopkins University , 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Michael Müller
- Institut für Pharmazeutische Wissenschaften, Albert-Ludwigs-Universität Freiburg , Albertstr. 25, 79104 Freiburg, Germany
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44
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Huitt-Roehl CR, Hill EA, Adams MM, Vagstad AL, Li JW, Townsend CA. Starter unit flexibility for engineered product synthesis by the nonreducing polyketide synthase PksA. ACS Chem Biol 2015; 10:1443-9. [PMID: 25714897 DOI: 10.1021/acschembio.5b00005] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nonreducing polyketide synthases (NR-PKSs) are unique among PKSs in their domain structure, notably including a starter unit:acyl-carrier protein (ACP) transacylase (SAT) domain that selects an acyl group as the primer for biosynthesis, most commonly acetyl-CoA from central metabolism. This clan of mega-enzymes resembles fatty acid synthases (FASs) by sharing both their central chain elongation steps and their capacity for iterative catalysis. In this mode of synthesis, catalytic domains involved in chain extension exhibit substrate plasticity to accommodate growing chains as small as two carbons to 20 or more. PksA is the NR-PKS central to the biosynthesis of the mycotoxin aflatoxin B1 whose SAT domain accepts an unusual hexanoyl starter from a dedicated yeast-like FAS. Explored in this paper is the ability of PksA to utilize a selection of potential starter units as substrates to initiate and sustain extension and cyclization to on-target, programmed polyketide synthesis. Most of these starter units were successfully accepted and properly processed by PksA to achieve biosynthesis of the predicted naphthopyrone product. Analysis of the on-target and derailment products revealed trends of tolerance by individual PksA domains to alternative starter units. In addition, natural and un-natural variants of the active site cysteine were examined and found to be capable of biosynthesis, suggesting possible direct loading of starter units onto the β-ketoacyl synthase (KS) domain. In light of the data assembled here, the predictable synthesis of unnatural products by NR-PKSs is more fully defined.
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Affiliation(s)
- Callie R. Huitt-Roehl
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles
Street, Baltimore, Maryland 21218, United States
| | - Eric A. Hill
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles
Street, Baltimore, Maryland 21218, United States
| | - Martina M. Adams
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles
Street, Baltimore, Maryland 21218, United States
| | - Anna L. Vagstad
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles
Street, Baltimore, Maryland 21218, United States
| | - Jesse W. Li
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles
Street, Baltimore, Maryland 21218, United States
| | - Craig A. Townsend
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles
Street, Baltimore, Maryland 21218, United States
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Abstract
An efficient route to substituted N-fused aromatic heterocycles, including indolizines, imidazo[1,2-a]pyridines, and imidazo[1,5-a]pyridines from azole aldehydes, is reported. Wittig olefination of the aldehydes with fumaronitrile and triethylphosphine affords predominantly E-alkenes that undergo rapid cyclization upon treatment with a mild base. Substituent control of the 1-, 2-, and 3-positions of the resulting heteroaromatic bicycles is shown. Alternatively, the isolable E-alkene undergoes selective alkylation with electrophiles, followed by in situ annulation to indolizines additionally substituted at the 6-position.
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Affiliation(s)
- Victor K. Outlaw
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Felipe B. d’Andrea
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Craig A. Townsend
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
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46
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Gaudelli NM, Long DH, Townsend CA. β-Lactam formation by a non-ribosomal peptide synthetase during antibiotic biosynthesis. Nature 2015; 520:383-7. [PMID: 25624104 PMCID: PMC4401618 DOI: 10.1038/nature14100] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2014] [Accepted: 11/19/2014] [Indexed: 01/23/2023]
Abstract
Non-ribosomal peptide synthetases (NRPSs) are giant enzymes comprised of modules that house repeated sets of functional domains, which select, activate and couple amino acids drawn from a pool of nearly 500 potential building blocks.1 The structurally and stereochemically diverse peptides generated in this manner underlie the biosynthesis of a large sector of natural products. Many of their derived metabolites are bioactive such as the antibiotics vancomycin, bacitracin, daptomycin and the β-lactam-containing penicillins, cephalosporins and nocardicins. Although penicillins and cephalosporins are synthesised from a classically derived NRPS tripeptide (from ACVS, δ-(L-α-aminoadipyl)–L-cysteinyl–D-valine synthetase)2, we now report an unprecedented NRPS activity to both assemble a serine-containing peptide and mediate its cyclisation to the critical β-lactam ring of the nocardicin family of antibiotics. A histidine-rich condensation (C) domain, which typically carries out peptide bond formation during product assembly, was found to also synthesise the embedded 4-membered ring. Here, a mechanism is proposed and supporting experiments are described, which is distinct from the pathways that have evolved to the three other β-lactam antibiotic families: penicillin/cephalosporins, clavams and carbapenems. These findings raise the possibility that β-lactam rings can be regio- and stereospecifically integrated into engineered peptides for application as, for example, targeted protease inactivators.3,4
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Affiliation(s)
- Nicole M Gaudelli
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Darcie H Long
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Craig A Townsend
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, USA
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47
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Abstract
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Among
privileged structures, indoles occupy a central place in
medicinal chemistry and alkaloid research. Here we report a flexible
and efficient conversion of pyrrole-3-carboxaldehydes to substituted
7-amino-5-cyanoindoles. Phosphine addition to fumaronitrile proceeds
with prototropic rearrangement of the initially formed zwitterion
to the thermodynamically favored phosphonium ylide, which is poised
for in situ Wittig olefination. The predominantly E-alkene product positions the allylic nitrile for facile intramolecular
Hoeben–Hoesch reaction in the presence of BF3·OEt2. Syntheses of 2,5- and 3,5-disubstituted 7-aminoindoles are
illustrated. Additionally, dianion alkylation of the allylic nitrile
is demonstrated to furnish, after cyclization, 5,6-disubstituted 7-aminoindoles
to further exemplify this scalable and high-yielding method.
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Affiliation(s)
- Victor K Outlaw
- Department of Chemistry, Johns Hopkins University , 3400 North Charles Street, Baltimore, Maryland 21218, United States
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48
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Abstract
In this viewpoint highlights are drawn from a deep analysis of the multifaceted problem of aflatoxin biosynthesis, one of the most highly rearranged polyketide natural products known. Fundamental chemical insights have emerged into how cytochrome P450-mediated skeletal rearrangements occur through probable cationic intermediates and oxidative dearomatizations, which are applicable more widely in natural product catabolism. So to where current experimental methods have failed in our hands, bioinformatic tools and fresh experimental strategies have been developed to identify linker regions in large, polydomain proteins and guide the dissection and reassembly of their component parts. It has been possible to deduce individual catalytic roles, how overall synthesis is coordinated and how these enzymes can be re-engineered in a rational manner to prepare non-natural products. These insights and innovations were often not planned or anticipated, but sprung from the inability to answer fundamental questions. Advances in science can take place by chance favoring the prepared mind, other times by refusing to give up and devising new solutions to address hard questions. Both ways forward played important roles in the investigation of aflatoxin biosynthesis. For these contributions I am pleased to share this special issue of NPR with John Vederas and Tom Simpson, who have been leaders in this field for the last third of a century.
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Affiliation(s)
- Craig A Townsend
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA.
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Buller AR, Freeman MF, Schildbach JF, Townsend CA. Exploring the role of conformational heterogeneity in cis-autoproteolytic activation of ThnT. Biochemistry 2014; 53:4273-81. [PMID: 24933323 PMCID: PMC4095933 DOI: 10.1021/bi500385d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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In
the past decade, there have been major achievements in understanding
the relationship between enzyme catalysis and protein structural plasticity.
In autoprocessing systems, however, there is a sparsity of direct
evidence of the role of conformational dynamics, which are complicated
by their intrinsic chemical reactivity. ThnT is an autoproteolytically
activated enzyme involved in the biosynthesis of the β-lactam
antibiotic thienamycin. Conservative mutation of ThnT results in multiple
conformational states that can be observed via X-ray crystallography,
establishing ThnT as a representative and revealing system for studing
how conformational dynamics control autoactivation at a molecular
level. Removal of the nucleophile by mutation to Ala disrupts the
population of a reactive state and causes widespread structural changes
from a conformation that promotes autoproteolysis to one associated
with substrate catalysis. Finer probing of the active site polysterism
was achieved by EtHg derivatization of the nucleophile, which indicates
the active site and a neighboring loop have coupled dynamics. Disruption
of these interactions by mutagenesis precludes the ability to observe
a reactive state through X-ray crystallography, and application of
this insight to other autoproteolytically activated enzymes offers
an explanation for the widespread crystallization of inactive states.
We suggest that the N → O(S) acyl shift in cis-autoproteolysis might occur through a si-face attack,
thereby unifying the fundamental chemistry of these enzymes through
a common mechanism.
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Affiliation(s)
- Andrew R Buller
- Department of Biophysics, Johns Hopkins University , Baltimore, Maryland 21218, United States
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50
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Outlaw VK, Wydysh EA, Vadlamudi A, Medghalchi SM, Townsend CA. Design, Synthesis, and Evaluation of 4- and 5-Substituted o-(Octanesulfonamido)benzoic Acids as Inhibitors of Glycerol-3-Phosphate Acyltransferase. Medchemcomm 2014; 5:826-830. [PMID: 25068033 PMCID: PMC4109893 DOI: 10.1039/c4md00126e] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Despite a rising demand for anti-obesity therapeutics, few effective pharmacological options are clinically available that target the synthesis and accumulation of body fat. Moderate inhibition of mammalian glycerol-3-phosphate acyltransferase (GPAT) with 2-(alkanesulfonamido)benzoic acids has recently been described in vitro, accompanied by promising weight loss in vivo. In silico docking studies with 2-(octanesulfonamido)benzoic acid modeled into the active site of squash GPAT revealed an unoccupied volume lined with hydrophobic residues proximal to C-4 and C-5 of the benzoic acid ring. In an effort to produce more potent GPAT inhibitors, a series of 4- and 5-substituted analogs were designed, synthesized, and evaluated for inhibitory activity. In general, compounds containing hydrophobic substituents at the 4- and 5-positions, such as biphenyl and alkylphenyl hydrocarbons, exhibited an improved inhibitory activity against GPAT in vitro. The most active compound, 4-([1,1'-biphenyl]-4-carbonyl)-2-(octanesulfonamido)benzoic acid, demonstrated an IC50 of 8.5 µM and represents the best GPAT inhibitor discovered to date. Conversely, further substitution with hydroxyl or fluoro groups, led to a 3-fold decrease in activity. These results are consistent with the presence of a hydrophobic pocket and may support the binding model as a potential tool for developing more potent inhibitors.
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Affiliation(s)
- Victor K Outlaw
- Department of Chemistry, The Johns Hopkins University, Remsen Hall, 3400 N. Charles Street, Baltimore, MD 21218, USA
| | - Edward A Wydysh
- Department of Chemistry, The Johns Hopkins University, Remsen Hall, 3400 N. Charles Street, Baltimore, MD 21218, USA
| | - Aravinda Vadlamudi
- FASGEN, Inc., UMB Research Park, Building One, 800 W. Baltimore St., Suite 150, Baltimore, MD 21201, USA
| | - Susan M Medghalchi
- FASGEN, Inc., UMB Research Park, Building One, 800 W. Baltimore St., Suite 150, Baltimore, MD 21201, USA
| | - Craig A Townsend
- Department of Chemistry, The Johns Hopkins University, Remsen Hall, 3400 N. Charles Street, Baltimore, MD 21218, USA
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