Structure-guided microbial targeting of antistaphylococcal prodrugs

  1. Justin J Miller
  2. Ishaan T Shah
  3. Jayda Hatten
  4. Yasaman Barekatain
  5. Elizabeth A Mueller
  6. Ahmed M Moustafa
  7. Rachel L Edwards
  8. Cynthia S Dowd
  9. Geoffrey C Hoops
  10. R Jeremy Johnson
  11. Paul J Planet
  12. Florian L Muller
  13. Joseph M Jez
  14. Audrey R Odom John  Is a corresponding author
  1. Department of Pediatrics, Washington University School of Medicine, United States
  2. Department of Biology, Washington University in St. Louis, United States
  3. Department of Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center, United States
  4. Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Children’s Hospital of Philadelphia, United States
  5. Department of Chemistry, The George Washington University, United States
  6. Department of Chemistry and Biochemistry, Butler University, United States
  7. Department of Molecular Microbiology, Washington University School of Medicine, United States
7 figures, 4 videos, 2 tables and 2 additional files

Figures

Prodrug activation model (A) and proposed enzymatic mechanism.

(B) Carboxy ester promoieties highlighted in green.

Figure 2 with 4 supplements
Forward and reverse genetics approaches identify FrmB and GloB as candidate POM-prodrug hydrolases in S. aureus.

(A) Reverse genetics identification of candidate prodrug activating enzymes. (B) POM-HEX susceptibility of identified candidate resistance genes from (A) as determined by IC50. Exact values and error reported in Figure 2—source data 1. (C) Forward genetic screen approach, all mutations listed in Figure 2—source data 2. (D) POM-HEX susceptibility of POM-HEX-resistant S. aureus. (E) Nonsynonymous point mutations identified by whole-genome sequencing in frmB and gloB. In all experiments, GloB is colored green and FrmB orange. Displayed are the means of three independent biological experiments.

Figure 2—source data 1

S. aureus transposon mutants tested and POM-HEX sensitivity.

Half-maximal inhibitory concentration (IC50) values for POM-HEX against predicted prodrug activating esterases. IC50 values are the result of three independent biological experiments with technical duplicates. p-values calculated as a one-way ANOVA with Dunnett’s correction for multiple comparisons.

https://cdn.elifesciences.org/articles/66657/elife-66657-fig2-data1-v3.xlsx
Figure 2—source data 2

S. aureus Newman resistant isolate SNPs and POM-HEX sensitivity.

Genotype and phenotype of POM-HEX resistant S. aureus. Displayed are the whole-genome sequencing mutations that have been verified. Called mutations that were not observed via confirmatory Sanger sequencing are excluded. IC50 values are the result of three independent biologic replicates with technical duplicates.

https://cdn.elifesciences.org/articles/66657/elife-66657-fig2-data2-v3.xlsx
Figure 2—source data 3

S. aureus transposon mutants with genes identified by whole-genome sequencing and POM-HEX sensitivity.

Half-maximal inhibitory concentration (IC50) values for POM-HEX against transposon mutations in genes identified by whole-genome sequencing. Assays performed in biological triplicate with technical duplicates. p-value calculated as a one-way ANOVA with Dunnett correction for multiple comparisons.

https://cdn.elifesciences.org/articles/66657/elife-66657-fig2-data3-v3.xlsx
Figure 2—source data 4

Accession numbers for the isolates used in WhatsGNU analysis.

https://cdn.elifesciences.org/articles/66657/elife-66657-fig2-data4-v3.xlsx
Figure 2—figure supplement 1
Conservation of FrmB and GloB within S. aureus.

(A) WhatsGNU analysis of GloB and FrmB. Control proteins: ArgG, argininosuccinate synthase; Fba, fructose-bisphosphate aldolase; MenD, 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1carboxylate synthase; and MenC, o-succinylbenzoate synthase. GNU stands for gene novelty unit and is a count of how many protein sequences in the database have an exact match to the queried sequence, with higher counts indicating sequence conservation. Strains across the x-axis are representative strains from the 18 s. aureus colony complexes which were used to query the S. aureus database. (B, C) MAFFT alignment of GloB (B) and FrmB (C) protein sequences across the S. aureus sequence database.

Figure 2—figure supplement 2
Phylogenetic tree of FrmB and GloB.

Sequences of GloB, FrmB, and RpoB (encoding the beta subunit of RNA polymerase, included for comparison) were retrieved from NCBI using BlastP against each organism. Sequence alignment performed using MUSCLE and alignment visualized using the interactive Tree of Life (iTOL).

Figure 2—figure supplement 3
Enzymatic characterization of GloB and FrmB.

(A) SDS–PAGE gel of GloB and FrmB protein preparations. Expected molecular weights are 23.3 kDa and 29.5 kDa, respectively. (B) Glyoxalase II activity assay, enzymatic conversion of S-lactoylglutathione releases free glutathione and reacts with DTNB resulting in increased absorbance at 412 nm. (C) 4-Nitrophenyl activation results in increased absorbance at 405 nm. Left to right, activity when supplied 4-nitrophenyl acetate, 4-nitrophenyl butyrate, and 4-nitrophenyl trimethyl acetate. Displayed in points is the mean of two technical replicates for individual experiments, bars indicate mean ± SD of three independent biological experiments performed in technical duplicate.

Figure 2—figure supplement 4
NMR characterization of POM-HEX activation by GloB and FrmB.

Two-dimensional (2D) 1H-31P HSQC NMR spectra of products following incubation of FrmB, GloB, catalytically inactive (boiled) GloB and FrmB, or buffer alone. Also included are the 1H-31P HSQC NMR spectra of POM-HEX and HEX. Displayed are representative traces of three independent experiments. HEMI-POM HEX peak inferred by predicted shift.

Figure 3 with 2 supplements
In vivo activation rates depend on ester promoiety selection.

Time series of activation of various fluorogenic substrates (Figure 3—figure supplement 1). Substrates were added into the microfluidics chamber at t = 10 minutes. On the right, quantification of individual cell or cell cluster fluorescence per area. Faint traces are individual cells and darker traces represent the mean of a given experiment. Each experiment was performed in biological duplicate, and each experiment is displayed in a different color (purple or green). Full movies viewable as Videos 14. Error bars denote SD.

Figure 3—source data 1

(1) Michaelis–Menten parameters for SaFrmB.

Displayed are the results of three independent biological replicates in technical duplicate. (2) Michaelis–Menten parameters for SaGloB. Displayed are the results of three independent biological replicates in technical duplicate.

https://cdn.elifesciences.org/articles/66657/elife-66657-fig3-data1-v3.xlsx
Figure 3—figure supplement 1
Profluorescent substrate library.

Activation of substrates via esterase action results in fluorescence.

Figure 3—figure supplement 2
Catalytic efficiency of GloB (A) and FrmB (B).

Numbers correspond to the structures displayed in Figure S5, compounds in the carbon series denoted in orange, oxygen series in blue, and sulfur series in green.

Figure 4 with 1 supplement
Three-dimensional structure of FrmB.

(A) Overall fold, a-helices colored in orange and β-strands colored in purple. (B) Comparison between SaFrmB (orange) and its closest human ortholog, ESTD (gray). Active site residues denoted in orange spheres. (C, D) Docking of substrate 1O (sticks) in the active site of FrmB. surface view, red indicates highly hydrophobic and white hydrophilic residues. Surface view (C) or stick view with catalytic triad (D).

Figure 4—source data 1

Summary of crystallographic data collection and refinement statistics.

https://cdn.elifesciences.org/articles/66657/elife-66657-fig4-data1-v3.xlsx
Figure 4—figure supplement 1
Structural conservation of FrmB.

(A) Overall structural alignment of FrmB (orange) with S. pneumonia EstA (PDB:2UZ0), B. intestinalis ferulic acid esterase (PDB:5VOL), and deep sea bacteria Est12 (PDB4RGY). (B) Conservation of the serine hydrolase catalytic triad in FrmB and related proteins.

Figure 5 with 1 supplement
Three-dimensional structure of GloB.

(A) Overall fold, a-alpha helices colored in green and β-strands colored in purple. (B) Comparison of SaGloB (green) and human GloB (gray). (C) Docking of the substrate 1O (sticks) in the active site of GloB. Left, partial cartoon view; right, surface view. White represents hydrophilic residues, whereas red represents hydrophobic residues. Zn ions indicated as silver spheres; water indicated as blue sphere.

Figure 5—source data 1

Summary of crystallographic data collection and refinement statistics.

https://cdn.elifesciences.org/articles/66657/elife-66657-fig5-data1-v3.xlsx
Figure 5—figure supplement 1
Structural conservation of GloB.

(A) Overall structural alignment of GloB (green) with S. enterica YcbI (PDB:2XF4), T. thermophilus TTHA1623 (PDB:2ZWR), and A. thaliana glyoxalase II (PDB:1XM8). Zinc coordinating residues are colored in green spheres. (B) Positioning of the zinc coordinating residues (green spheres).

Figure 6 with 3 supplements
Comparison between microbial esterase and serum esterase catalytic efficiency.

(A–D) Volcano plots of catalytic efficiency. Displayed are the means of three independent experiments. p-values calculated as pairwise t-tests with Holm-Sidak correction for multiple comparisons. (A) Comparison between human sera and GloB, (B) human sera and FrmB, (C) mouse sera and GloB, and (D) mouse sera and FrmB. (E) Structures of ester substrates with 210 enrichment in catalytic efficiency for microbial esterases over human serum (left) or 25 enrichment over mouse serum. Dashed line indicates a p-value of 0.05.

Figure 6—source data 1

(1) Michaelis–Menten parameters for human sera.

Displayed are the results of three independent biological replicates in technical duplicate. (2) Michaelis–Menten parameters for mouse sera. Displayed are the results of three independent biological replicates in technical duplicate.

https://cdn.elifesciences.org/articles/66657/elife-66657-fig6-data1-v3.xlsx
Figure 6—figure supplement 1
Comparison of esterase activity between fresh and lyophilized human sera.

Points represent individual experiments; bars represent the mean ± SD of the four replicates.

Figure 6—figure supplement 2
Modified catalytic efficiency (pmol fluorescein produced * min−1*µg−1 protein) of (A) human sera, (B) GloB, (C) FrmB, and (D) mouse sera.

X-axis corresponds to compound identities in Figure S5. Carbon containing compounds indicated in orange, oxygen in blue, and sulfur in green. Displayed are the means ± SD of three independent biological experiments.

Figure 6—figure supplement 3
Comparison of mouse and human sera.

(A) Modified catalytic efficiency (pmol fluorescein produced * min-1*µg-1 protein) of human and mouse sera. Displayed is a linear regression of the fit between mouse and human sera. (B) Volcano plot of catalytic efficiency. Displayed are the means of three independent experiments. p-values calculated as pairwise t-tests with Holm–Sidak correction for multiple comparisons. Dashed line indicates a p-value of 0.05.

Model of antistaphylococcal prodrug activation.

Lipophilic carboxy ester prodrugs transit the cell membrane, are first activated by either GloB or FrmB and at least one additional enzyme, before inhibiting the cellular target.

Videos

Video 1
In vivo activation rates depend on ester promoiety selection.

Time series of fluorogenic ester substrate 1O activation. Substrate added at t = 10 min. Experiments were performed in biological duplicate.

Video 2
In vivo activation rates depend on ester promoiety selection.

Time series of fluorogenic ester substrate 3C activation. Substrate added at t = 10 min. Experiments were performed in biological duplicate.

Video 3
In vivo activation rates depend on ester promoiety selection.

Time series of fluorogenic ester substrate 5O activation. Substrate added at t = 10 min. Experiments were performed in biological duplicate.

Video 4
In vivo activation rates depend on ester promoiety selection.

Time series of fluorogenic ester substrate 9C activation. Substrate added at t = 10 min. Experiments were performed in biological duplicate.

Tables

Table 1
Mutational frequencies of S. aureus.

Newman for POM-HEX and several clinically utilized antibiotics. Experiments performed in technical duplicate and biological triplicate. Displayed are the means ± SD.

Antibiotic (MIC)4× MIC10× MIC
Vancomycin (2 µg/mL)<1 E-10<1 E-10
Clindamycin (0.25 µg/mL)<1 E-10<1 E-10
Rifampicin (7.5 ng/mL)8.96 ± 0.20 E-087.64 ± 2.10 E-08
Nafcillin (0.5 µg/mL)<1 E-10<1 E-10
Linezolid (1.67 µg/mL)<1 E-10<1 E-10
POM-HEX (3.13 µg/mL)5.96 ± 1.60 E-072.92 ± 0.57 E-07
Key resources table
Reagent type
(species) or resource
DesignationSource or referenceIdentifiersAdditional information
Gene (Staphylococcus aureus)GloBGenBankWP_001223008.1GloII
Gene (Staphylococcus aureus)FrmBGenBankestA
Strain, strain background (Staphylococcus aureus)JE2BEI ResourcesNR-46543
Strain, strain background (Staphylococcus aureus)NE64Nebraska Transposon Mutant LibraryHypothetical proteinAvailable from BEI Resources as: NR-48501
Strain, strain background (Staphylococcus aureus)NE145Nebraska Transposon Mutant Libraryprotoporphyrinogen oxidaseAvailable from BEI Resources as: NR-48501
Strain, strain background (Staphylococcus aureus)NE202Nebraska Transposon Mutant LibraryABC transporter, ATP-binding protein, MsbA familyAvailable from BEI Resources as: NR-48501
Strain, strain background (Staphylococcus aureus)NE223Nebraska Transposon Mutant Libraryhydroxyacylglutathione hydrolaseAvailable from BEI Resources as: NR-48501
Strain, strain background (Staphylococcus aureus)NE293Nebraska Transposon Mutant Librarystaphylococcal accessory regulator RotAvailable from BEI Resources as: NR-48501
Strain, strain background (Staphylococcus aureus)NE355Nebraska Transposon Mutant Librarytributyrin esteraseAvailable from BEI Resources as: NR-48501
Strain, strain background (Staphylococcus aureus)NE364Nebraska Transposon Mutant LibraryNAD-dependent epimerase/dehydratase family proteinAvailable from BEI Resources as: NR-48501
Strain, strain background (Staphylococcus aureus)NE377Nebraska Transposon Mutant Librarypyrroline-5-carboxylate reductaseAvailable from BEI Resources as: NR-48501
Strain, strain background (Staphylococcus aureus)NE386Nebraska Transposon Mutant LibraryHypothetical proteinAvailable from BEI Resources as: NR-48501
Strain, strain background (Staphylococcus aureus)NE478Nebraska Transposon Mutant Librarypeptide ABC transporter, permease proteinAvailable from BEI Resources as: NR-48501
Strain, strain background (Staphylococcus aureus)NE503Nebraska Transposon Mutant Libraryconserved hypothetical proteinAvailable from BEI Resources as: NR-48501
Strain, strain background (Staphylococcus aureus)NE520Nebraska Transposon Mutant Librarysensor histidine kinase SaeSAvailable from BEI Resources as: NR-48501
Strain, strain background (Staphylococcus aureus)NE532Nebraska Transposon Mutant LibraryPTS system, mannitol specific IIBC componentAvailable from BEI Resources as: NR-48501
Strain, strain background (Staphylococcus aureus)NE541Nebraska Transposon Mutant Libraryalkaline phosphatase synthesis transcriptional regulatory proteinAvailable from BEI Resources as: NR-48501
Strain, strain background (Staphylococcus aureus)NE621Nebraska Transposon Mutant LibraryHypothetical proteinAvailable from BEI Resources as: NR-48501
Strain, strain background (Staphylococcus aureus)NE812Nebraska Transposon Mutant Librarytetrahydrodipicolinate acetyltransferaseAvailable from BEI Resources as: NR-48501
Strain, strain background (Staphylococcus aureus)NE874Nebraska Transposon Mutant LibraryHypothetical proteinAvailable from BEI Resources as: NR-48501
Strain, strain background (Staphylococcus aureus)NE929Nebraska Transposon Mutant Libraryacetyl-CoA carboxylase, biotin carboxylaseAvailable from BEI Resources as: NR-48501
Strain, strain background (Staphylococcus aureus)NE937Nebraska Transposon Mutant Librarytandem lipoproteinAvailable from BEI Resources as: NR-48501
Strain, strain background (Staphylococcus aureus)NE949Nebraska Transposon Mutant LibraryPutative TransposaseAvailable from BEI Resources as: NR-48501
Strain, strain background (Staphylococcus aureus)NE1039Nebraska Transposon Mutant Libraryexcinuclease ABC, A subunitAvailable from BEI Resources as: NR-48501
Strain, strain background (Staphylococcus aureus)NE1051Nebraska Transposon Mutant LibraryHypothetical proteinAvailable from BEI Resources as: NR-48501
Strain, strain background (Staphylococcus aureus)NE1071Nebraska Transposon Mutant LibraryHypothetical proteinAvailable from BEI Resources as: NR-48501
Strain, strain background (Staphylococcus aureus)NE1118Nebraska Transposon Mutant Librarydihydrolipoamide dehydrogenaseAvailable from BEI Resources as: NR-48501
Strain, strain background (Staphylococcus aureus)NE1127Nebraska Transposon Mutant Librarygamma-hemolysin component BAvailable from BEI Resources as: NR-48501
Strain, strain background (Staphylococcus aureus)NE1173Nebraska Transposon Mutant LibrarytRNA pseudouridine synthase AAvailable from BEI Resources as: NR-48501
Strain, strain background (Staphylococcus aureus)NE1225Nebraska Transposon Mutant LibraryABC transporter, ATP-binding proteinAvailable from BEI Resources as: NR-48501
Strain, strain background (Staphylococcus aureus)NE1238Nebraska Transposon Mutant Librarytranscriptional regulator, TetR familyAvailable from BEI Resources as: NR-48501
Strain, strain background (Staphylococcus aureus)NE1283Nebraska Transposon Mutant LibraryHypothetical proteinAvailable from BEI Resources as: NR-48501
Strain, strain background (Staphylococcus aureus)NE1296Nebraska Transposon Mutant Libraryhydroxyacylglutathione hydrolaseAvailable from BEI Resources as: NR-48501
Strain, strain background (Staphylococcus aureus)NE1486Nebraska Transposon Mutant Libraryphosphonate ABC transporter, permease proteinAvailable from BEI Resources as: NR-48501
Strain, strain background (Staphylococcus aureus)NE1505Nebraska Transposon Mutant Librarytributyrin esteraseAvailable from BEI Resources as: NR-48501
Strain, strain background (Staphylococcus aureus)NE1519Nebraska Transposon Mutant LibraryHypothetical Alkaline PhosphataseAvailable from BEI Resources as: NR-48501
Strain, strain background (Staphylococcus aureus)NE1547Nebraska Transposon Mutant LibraryHypothetical proteinAvailable from BEI Resources as: NR-48501
Strain, strain background (Staphylococcus aureus)NE1610Nebraska Transposon Mutant LibraryHypothetical proteinAvailable from BEI Resources as: NR-48501
Strain, strain background (Staphylococcus aureus)NE1682Nebraska Transposon Mutant LibraryPfkB family kinaseAvailable from BEI Resources as: NR-48501
Strain, strain background (Staphylococcus aureus)NE1723Nebraska Transposon Mutant Librarytype I restriction-modification system, M subunitAvailable from BEI Resources as: NR-48501
Strain, strain background (Escherichia coli)BL21 (DE3)SigmaCMC0014Chemically Competent
Biological sample (Homo sapiens)Fresh Human SerumThis paperWhole blood was collected from a willing volunteer into untreated BD vacutainer tubes (BD, BD366430), allowed to clot, and aggregates were removed via centrifugation
Biological sample (Homo sapiens)Lyophilized Human SerumRockland IncD314-5
Biological sample (Mus musculus)Lyophilized Mouse SerumRockland IncD308-5
Recombinant DNA reagentpET28a-SaFrmBThis paperE. coli expression plasmid for SaFrmB with cleavable HIS tag.
Recombinant DNA reagentpET28a-SaGloBThis paperE. coli expression plasmid for SaGloB with cleavable HIS tag.
Recombinant DNA reagentBG1861-SaGloBThis paperE. coli expression plasmid for SaGloB with HIS tag.
Recombinant DNA reagentBG1861-SaFrmBThis paperE. coli expression plasmid for SaFrmB with HIS tag.
Sequence-based reagentNWMN_0144_FThis paperPCR PrimerTTTTCCTGATCCTGATTCAC
Sequence-based reagentNWMN_0144_RThis paperPCR PrimerATGATGCTTCCATGTTTGTT
Sequence-based reagentNWMN_0306_FThis paperPCR PrimerAATACACCGGGTAACACAAC
Sequence-based reagentNWMN_0306_RThis PaperPCR PrimerCGTTTTGTTGAGCTAATTCC
Sequence-based reagentNWMN_0309_FThis paperPCR PrimerACCATGCTTAAAGGGATTTT
Sequence-based reagentNWMN_0309_RThis PaperPCR PrimerTGTCACCTAAGTCAACACCA
Sequence-based reagentNWMN_0407 (lpl4nm) _FThis paperPCR PrimerCCGTTGGAGATAGGAAGTTA
Sequence-based reagentNWMN_0407 (lpl4nm) _RThis paperPCR PrimerTTTGTGCTTCTTTTGAACCT
Sequence-based reagentNWMN_0654_FThis paperPCR PrimerGAAAATGGAAGACTGATTGC
Sequence-based reagentNWMN_0654_RThis paperPCR PrimerTAATGCATCTGACAAAGTCG
Sequence-based reagentNWMN_0762_FThis paperPCR PrimerGGTGAAGTTTTGGACGATAA
Sequence-based reagentNWMN_0762_RThis paperPCR PrimerTTTTCATCTGTCCGACTTTT
Sequence-based reagentNWMN_1101_FThis paperPCR PrimerTCCACCTATTGGAATTATCG
Sequence-based reagentNWMN_1101_RThis paperPCR PrimerAGACGTTCAATTTCAGTGCT
Sequence-based reagentNWMN_1192 (pgsA) _FThis paperPCR PrimerTGGGACGAAGTAATTACAGTT
Sequence-based reagentNWMN_1192 (pgsA) _RThis paperPCR PrimerATATCCCCCTTGTATCGTTT
Sequence-based reagentNWMN_1308 (dapD) _FThis paperPCR PrimerTCTATTCGTGGAGGTACGAT
Sequence-based reagentNWMN_1308 (dapD) _RThis paperPCR PrimerATCGTATGTGAGCCATTACC
Sequence-based reagentNWMN_1410_FThis paperPCR PrimerCGATAAACCTAAACCACTCG
Sequence-based reagentNWMN_1410_RThis paperPCR PrimerATAAACAATGCTTGCCAAAT
Sequence-based reagentNWMN_1505_FThis paperPCR PrimerTGAAGGTGAATTAAGCGATG
Sequence-based reagentNWMN_1505_RThis paperPCR PrimerTGCTATTCCCAATTTGTTCA
Sequence-based reagentNWMN_1655_FThis paperPCR PrimerGAATTGTTGCAATTTAATGGT
Sequence-based reagentNWMN_1655_RThis paperPCR PrimerAACGTAATCATGCTCCATTC
Sequence-based reagentNWMN_1679_FThis paperPCR PrimerCCATGGGAAAAATTAGACAA
Sequence-based reagentNWMN_1679_RThis paperPCR PrimerAAATATCGCCTCACCTTTTT
Sequence-based reagentNWMN_1723 (hemY) _FThis paperPCR PrimerGCCGAATACACATCCATTAT
Sequence-based reagentNWMN_1723 (hemY) _RThis paperPCR PrimerAACCTTTGTCTCTGCTTCAA
Sequence-based reagentNWMN_1851 (nadC) _FThis paperPCR PrimerAGCCATTTTAGCACCATAAA
Sequence-based reagentNWMN_1851 (nadC)_RThis paperPCR PrimerTAGAATCCTGTCCTCCTGAA
Sequence-based reagentNWMN_2057 (mtlF)_FThis paperPCR PrimerTGTACAACGGTGTTGTTTTG
Sequence-based reagentNWMN_2057 (mtlF)_RThis paperPCR PrimerCGGTGAATAGTACGAGAGGA
Sequence-based reagentNWMN_2528_FThis paperPCR PrimerACTGATGCTTTACCAGAAAC
Sequence-based reagentNWMN_2528_RThis paperPCR PrimerTCAGCGGTAGTAATAAAGGT
Chemical compound, drugPOM-HEXWhite et al., 2018
Chemical compound, drugHemi-HEXLin et al., 2020
Chemical compound, drugHEXLin et al. 2018
Chemical compound, drugFluorescent ProsubstratesWhite et al., 2018
Chemical compound, drugS-D-lactoylglutathioneSigma-AldrichL7140
Chemical compound, drug4-Nitrophenyl acetateSigma-AldrichN8130
Chemical compound, drug4-Nitrophenyl butyrateSigma-AldrichN9876
Chemical compound, drug4-Nitrophenyl trimethyl acetateSigma-Aldrich135046
Software, algorithmWhatsGNUMoustafa and Planet, 2020https://github.com/ahmedmagds/WhatsGNU
Software, algorithmMUSCLELetunic and Bork, 2019https://www.ebi.ac.uk/Tools/msa/muscle/
Software, algorithmiTOLMadeira et al., 2019https://itol.embl.de/
Software, algorithmHKL-3000Minor et al., 2006https://hkl-xray.com/hkl-3000
Software, algorithmPHASERMcCoy et al., 2007
Software, algorithmCOOTEmsley and Cowtan, 2004https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/
Software, algorithmPHENIXAdams et al., 2010http://www.phenix-online.org/
Software, algorithmChemDraw3Dhttps://www.cambridgesoft.com/Ensemble_for_Chemistry/details/Default.aspx?fid=13&pid=668
Software, algorithmAutoDock Tools 1.5.7Morris et al., 2009http://autodock.scripps.edu/resources/adt
Software, algorithmAutoDock VinaTrott and Olson, 2010http://vina.scripps.edu/
Software, algorithmGraphPad Prismhttps://www.graphpad.com/scientific-software/prism/
OtherCellASIC ONIX2 microfluidic plateEMD-MilliporeB04A-03-5PK

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  1. Justin J Miller
  2. Ishaan T Shah
  3. Jayda Hatten
  4. Yasaman Barekatain
  5. Elizabeth A Mueller
  6. Ahmed M Moustafa
  7. Rachel L Edwards
  8. Cynthia S Dowd
  9. Geoffrey C Hoops
  10. R Jeremy Johnson
  11. Paul J Planet
  12. Florian L Muller
  13. Joseph M Jez
  14. Audrey R Odom John
(2021)
Structure-guided microbial targeting of antistaphylococcal prodrugs
eLife 10:e66657.
https://doi.org/10.7554/eLife.66657