SAR study of novel iminothiadiazolo-pyrimidinone
A Paudel et al
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ice water and acidified with acetic acid. The precipitate was collected and 371C in MHB was diluted 1000 times with MHB medium and cultured for 2 h
washed with water to afford 0001-03-KK in 64% yield as a yellow solid and at 371C. For daptomycin, MHB was supplemented with 50mg lꢀ1 Ca2 þ
0005-08-KK in 97% yield as a colorless solid.
Synthesis of compounds 0002-04-KK, 0019-25-KK, 0021-27-KK, 0027-56- added to 1 ml of the culture and incubated at 371C for 0–24 h. Culture
.
Compounds 1, 2 (5ꢁ MIC), or daptomycin (5ꢁ MIC; MIC: 1 mg mlꢀ1) was
KK, 0006-09-KK, 0017-22-KK, 0023-37-KK and 0026-59-KK:
Aldehyde (0.86 mmol) and one drop of Et3N were added to a solution of
aliquots were collected at the indicated times, diluted and spread on Luria
Bertani agar plates and incubated at 371C for 24h. Cell viability was
thiadiazolopyrimidine 0001-03-KK or 0005-08-KK (0.82 mmol) in dimethyl- determined by the colony-forming units per ml. The lower limit of detection
formamide (0.82 ml) and ethanol (0.82 ml). The reaction mixture was heated was 104 colony-forming units per ml.
at 50–601C for 3 h and then kept standing at 251C for 12 h to obtain a
precipitate. The resulting precipitate was collected by filtration and washed
with dry diethyl ether to give products (0002-04-KK (1), 0019-25-KK, 0021-
27-KK, 0027-56-KK (4), 0006-09-KK (3), 0017-22-KK, 0023-37-KK and 0026-
Toxicity tests in silkworms
Fifth instar silkworm larvae were injected into the hemolymph with 0–400mg
of each compound and observed for 3 days. The LD50 was determined as the
amount of chemical (mg gꢀ1) that killed 50% of the larvae.
59-KK (2)) of 28–70% yield. The physicochemical properties and structure
elucidation details for the compounds are shown in the Supplementary
Information.
Incorporation of [3H]N-acetylglucosamine into cell wall
peptidoglycans
CONFLICT OF INTEREST
The authors declare no conflict of interest.
Measurement of incorporated [3H]N-acetylglucosamine was performed as
previously described by Paudel et al.12 Briefly, S. aureus NCTC8325-4 was
cultured at 37 1C overnight in CGPY broth (Na2HPO4, 6 g; NaCl, 3 g;
MgCl2.6H2O, 0.1 g; NH4Cl, 2 g; Na2SO4, 0.15g; KH2PO4, 3 g; bactopeptone,
10 g; yeast extract, 0.1 g and glucose, 5 g lꢀ1, pH 7.0). The culture was diluted
100-fold with the same medium and further cultured until an optical density
(OD)660 of 0.2 was reached. The culture was centrifuged at 8000 g for 10min
and the pellet was suspended in modified cell wall synthesis medium
(KH2PO4, 6 g; K2HPO4, 6 g; NH4Cl, 2 g; MgSO4. 7H2O, 5 mg; FeSO4, 5 mg;
glucose, 100mg; uracil, 40mg; L-alanine, 50 mg; L-glutamic acid, 120 mg;
L-lysine, 50 mg and chloramphenicol, 100 mglꢀ1), pH 6.8) to obtain
OD660 ¼ 0.1. In the presence of 35mCi [3H]N-acetyl glucosamine, 1, 2,
vancomycin, or norfloxacin (5ꢁ MIC) was added to 1 ml of the cell
suspension at time zero and incubated at 37 1C with shaking at 150 r.p.m.
Samples were collected at the indicated times and an equal volume of 10%
trichloroacetic acid was added. The mixture was incubated at 901C for 15min,
placed on ice for 30 min and filtered with a membrane filter (0.45mm HA,
Millipore, County Cork, Ireland) followed by washing with 5% trichloroacetic
acid. Radioactivity was counted on a liquid scintillation counter (LS6000SE,
Beckman Coulter, Brea, CA, USA) and expressed as c.p.m.
ACKNOWLEDGEMENTS
We thank the Chemical Library in the Open Innovation Center for Drug
Discovery at the University of Tokyo for providing the compounds used in this
study. We also thank Ms Matsuzawa, Ms Noguchi (Yoshino) and Ms
Kyougoku for technical assistance. This study was supported by the Program
for Promotion of Fundamental Studies in Health Sciences of the National
Institute of Biomedical Innovation (NIBIO) and partly supported by JSPS
Grant-in-Aid for Young Scientists (A) (24689008) from JSPS (HH) and
Grant-in-Aid for Scientific Research on Innovative Areas (24102510) from
MEXT (KS), and Platform for Drug Discovery, Informatics (MS).
1
2
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antibiotic era. Nat. Rev. Microbiol. 7, 629–641 (2009).
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(2010).
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animal to evaluate drug candidate toxicity and metabolism. Comp. Biochem. Physiol.
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Clinical and Laboratory Standards Institute. Reference method for Broth Dilution
Antifungal Susceptibility Testing of Yeasts: Approved Standard M27-A (Clinical and
Laboratory Standards Institute, Wayne, PA, USA, 1997).
Incorporation of radiolabeled thymidine, uridine and methionine
Incorporation of thymidine, uridine, and methionine was measured as
described previously.10 Briefly, S. aureus NCTC8325-4 was grown overnight
in Luria Bertani medium at 371C. The culture was diluted 200-fold in Luria
Bertani medium and incubated at 371C until an OD600 of 0.3 was reached.
Either 7 mCi [3H]uridine, 70mCi [3H]thymidine or 20 mCi [35S]methionine was
added to the culture. Rifampicin, norfloxacin and chloramphenicol at a
concentration of 5 ꢁ MIC were used to inhibit RNA, DNA and protein
synthesis, respectively; and vancomycin or ampicillin (5ꢁ MIC) was used
as a negative control. Compounds 1 and 2 (5ꢁ MIC) were used for all the
assays. The MICs of rifampicin, norfloxacin, chloramphenicol, vancomycin
and ampicillin were 0.004 mg mlꢀ1, 0.5 mg mlꢀ1, 4 mg mlꢀ1, 1 mg mlꢀ1 and
0.03 mg mlꢀ1, respectively. At time zero, agents were added to exponentially
growing cultures. Aliquots were collected at the indicated times, diluted twice
with 5% trichloroacetic acid and the acid-insoluble fraction was obtained by
filtration through glass fiber filters (Whatman, GE Healthcare, Maidstone,
Kent, UK). Radioactivity retained on the filters was measured on a liquid
scintillation counter and expressed as c.p.m.
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10 Paudel, A et al. Identification of novel deoxyribofuranosyl indole antimicrobial agents.
J. Antibiot. (Tokyo) 65, 53–57 (2012).
11 National Committee for Clinical Laboratory Standards. Methods for Determining
Bactericidal Activity of Antimicrobial Agents; Approved Guideline NCCLS Document
M26-A, Vol. 19. (National Committee for Clinical Laboratory Standards, Wayne, PA,
USA, 1999).
12 Clinical and Laboratory Standards Institute. Methods for Dilution Antimicrobial
Susceptibility Tests for Bacteria that Grow Aerobically; Approved Standard, CLSI
document M07-A8, 8th edn, Vol. 29 (Clinical and Laboratory Standards Institute,
Wayne, PA, USA, 2009).
Killing assay
The killing assay was performed as per the National Committee for Clinical
Laboratory Standards.11 Briefly, an overnight culture of S. aureus MSSA1 at
The Journal of Antibiotics