Flavin-Dependent Thymidylate Synthase as a New Antibiotic Target

Choi, Michael; Karunaratne, Kalani; Kohen, Amnon

doi:10.3390/molecules21050654

Cited by 23 publications

(23 citation statements)

References 30 publications

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“…Crystallographic structures have agreed on <4 Å gaps between the central ring of FAD's isoalloxazine system and the neighbors it is π-stacked between: the pyrimidine ring of dUMP and the pterin ring of folate (Fig. 2B) [7,11,13,17,18,27–29]. Notably although not catalytically required, His53 ( Tm FDTS) stacks with folate (Fig.…”

Section: Structural Peculiarities Of a Flavoproteinmentioning

confidence: 99%

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Flavin-dependent thymidylate synthase: N5 of flavin as a Methylene carrier

Karunaratne

Luedtke

Quinn

et al. 2017

Archives of Biochemistry and Biophysics

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Thymidylate is synthesized de novo in all living organisms for replication of genomes. The chemical transformation is reductive methylation of deoxyuridylate at C5 to form deoxythymidylate. All eukaryotes including humans complete this well-understood transformation with thymidylate synthase utilizing 6R-N5-N10-methylene-5,6,7,8-tetrahydrofolate as both a source of methylene and a reducing hydride. In 2002, flavin-dependent thymidylate synthase was discovered as a new pathway for de novo thymidylate synthesis. The flavin-dependent catalytic mechanism is different than thymidylate synthase because it requires flavin as a reducing agent and methylene transporter. This catalytic mechanism is not well-understood, but since it is known to be very different from thymidylate synthase, there is potential for mechanism-based inhibitors that can selectively inhibit the flavin-dependent enzyme to target many human pathogens with low host toxicity.

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Section: Structural Peculiarities Of a Flavoproteinmentioning

confidence: 99%

“…Mechanisms b, c, d, and e in Scheme 3 [29] demonstrate proposed mechanisms (up until 2016) for the oxidative half-reaction of FDTS catalyzed thymidylate synthesis. Unlike TSase, FDTS does not have a cysteine in its active site.…”

Section: Chemical Mechanisms Of Fdtsmentioning

confidence: 99%

Flavin-dependent thymidylate synthase: N5 of flavin as a Methylene carrier

Karunaratne

Luedtke

Quinn

et al. 2017

Archives of Biochemistry and Biophysics

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“…[10] Despite this, only al imited number of ThyX inhibitors are known ( Figure 1). [11] Structural variation of the uracil moiety of the natural substrate dUMP afforded as eries of 5-alkynyl dUMP analogues, from which the mostp otent congener (compound 1), displayed an IC 50 value of 0.9 mm against mycobacterial ThyX. [12] However,t he presence of the polar phosphate moiety precludes itsfurtherd evelopment into derivatives with in vitro antimycobacterial activity.2 -Bromo-8-hydroxy-1,4-naphthoquinone (compound 2)a nd 2-hydroxy-3-(4-methoxybenzyl)-1,4naphthoquinone (compound 3)h ave been identified as inhibitors of ThyX from Paramecium bursaria chlorella virus-1 (PBCV-1).…”

Section: Via Reductionmentioning

confidence: 99%

“…The thyX gene is required and essential for mycobacterial growth and survival within macrophages, making ThyX a promising antimycobacterial drug target . Despite this, only a limited number of ThyX inhibitors are known (Figure ) . Structural variation of the uracil moiety of the natural substrate dUMP afforded a series of 5‐alkynyl dUMP analogues, from which the most potent congener (compound 1 ), displayed an IC 50 value of 0.9 μ m against mycobacterial ThyX …”

Section: Introductionmentioning

confidence: 99%

Synthesis and Structure–Activity Relationship Studies of Benzo[b][1,4]oxazin‐3(4H)‐one Analogues as Inhibitors of Mycobacterial Thymidylate Synthase X

Modranka

Parchina

et al. 2019

ChemMedChem

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Since the discovery of a flavin‐dependent thymidylate synthase (ThyX or FDTS) that is absent in humans but crucial for DNA biosynthesis in a diverse group of pathogens, the enzyme has been pursued for the development of new antibacterial agents against Mycobacterium tuberculosis, the causative agent of the widespread infectious disease tuberculosis (TB). In response to a growing need for more effective anti‐TB drugs, we have built upon our previous screening efforts and report herein an optimization campaign of a novel series of inhibitors with a unique inhibition profile. The inhibitors display competitive inhibition toward the methylene tetrahydrofolate cofactor of ThyX, enabling us to generate a model of the compounds bound to their target, thus offering insight into their structure–activity relationships.

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“…Recently, a novel flavin-dependent TS was described as thyX . ( Myllykallio et al, 2002 ), which also has been postulated as an antibacterial target ( Choi, Karunaratne & Kohen, 2016 ).…”

Section: Introductionmentioning

confidence: 99%

A novel thymidylate synthase from theVibrionales,Alteromonadales,Aeromonadales, andPasteurellales(VAAP) clade with altered nucleotide and folate binding sites

López-Zavala

Guevara-Hernández

Vazquez-Lujan

et al. 2018

PeerJ

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Thymidylate synthase (TS, E.C. 2.1.1.45) is a crucial enzyme for de novo deoxythymidine monophosphate (dTMP) biosynthesis. The gene for this enzyme is thyA, which encodes the folate-dependent TS that converts deoxyuridine monophosphate group (dUMP) into (dTMP) using the cofactor 5,10-methylenetetrahydrofolate (mTHF) as a carbon donor. We identified the thyA gene in the genome of the Vibrio parahaemolyticus strain FIM-S1708+ that is innocuous to humans but pathogenic to crustaceans. Surprisingly, we found changes in the residues that bind the substrate dUMP and mTHF, previously postulated as invariant among all TSs known (Finer-Moore, Santi & Stroud, 2003). Interestingly, those amino acid changes were also found in a clade of microorganisms that contains Vibrionales, Alteromonadales, Aeromonadales, and Pasteurellales (VAAP) from the Gammaproteobacteria class. In this work, we studied the biochemical properties of recombinant TS from V. parahemolyticus FIM-S1708+ (VpTS) to address the natural changes in the TS amino acid sequence of the VAAP clade. Interestingly, the Km for dUMP was 27.3 ± 4.3 µM, about one-fold larger compared to other TSs. The Km for mTHF was 96.3 ± 18 µM, about three- to five-fold larger compared to other species, suggesting also loss of affinity. Thus, the catalytic efficiency was between one or two orders of magnitude smaller for both substrates. We used trimethoprim, a common antibiotic that targets both TS and DHFR for inhibition studies. The IC50 values obtained were high compared to other results in the literature. Nonetheless, this molecule could be a lead for the design antibiotics towards pathogens from the VAAP clade. Overall, the experimental results also suggest that in the VAAP clade the nucleotide salvage pathway is important and should be investigated, since the de novo dTMP synthesis appears to be compromised by a less efficient thymidylate synthase.

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Flavin-Dependent Thymidylate Synthase as a New Antibiotic Target

Cited by 23 publications

References 30 publications

Flavin-dependent thymidylate synthase: N5 of flavin as a Methylene carrier

Flavin-dependent thymidylate synthase: N5 of flavin as a Methylene carrier

Synthesis and Structure–Activity Relationship Studies of Benzo[b][1,4]oxazin‐3(4H)‐one Analogues as Inhibitors of Mycobacterial Thymidylate Synthase X

A novel thymidylate synthase from theVibrionales,Alteromonadales,Aeromonadales, andPasteurellales(VAAP) clade with altered nucleotide and folate binding sites

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