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Chemical Synthesis and Purification of a Non-Hydrolyzable CTP Analog Ctpɣs

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Chemical Synthesis and Purification of a Non-Hydrolyzable CTP Analog Ctpɣs bioRxiv preprint doi: https://doi.org/10.1101/2021.01.13.426546; this version posted January 14, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Chemical synthesis and purification of a non-hydrolyzable CTP analog CTPɣS Rejzek M1* and Tung B. K. Le2 1Chemistry Platform John Innes Centre, Norwich, NR4 7UH, United Kingdom 2Department of Molecular Microbiology John Innes Centre, Norwich, NR4 7UH, United Kingdom *For correspondence: [email protected] Abstract Slowly- or non-hydrolyzable analogs of ATP and GTP, for example adenosine 5'-(ɣ-thio)triphosphate (ATPɣS) and guanosine 5'-(γ-thio)triphosphate (GTPɣS), have been widely employed to probe the roles of ATP and GTP in biosystems, and these compounds are readily available from commercial sources. In contrast, cytosine 5'-(ɣ-thio)triphosphate (CTPɣS) is not widely available commercially. The recent discovery of ParB as the founding member of a new class of CTPase enzyme (Osorio- Valeriano et al., 2019; Soh et al., 2019) and the possibility of multiple other undiscovered CTPases necessitate the use of the CTPɣS to elucidate the roles of CTP hydrolysis in these systems. Here, we adapt a procedure for the synthesis of modified phosphoanhydrides (Hofer et al., 2015) to chemically synthesize and purify a milligram-scale of CTPɣS. bioRxiv preprint doi: https://doi.org/10.1101/2021.01.13.426546; this version posted January 14, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Introduction salt was lipophilic enough to dissolve in DMF. A classical approach to the chemical synthesis The coupling was achieved with bis(9H-fluoren- of ɣ-thiophosphate analogs of nucleoside 9-ylmethyl)-diisopropylamidophosphite triphosphates is based on S-2-carbamoylethyl ((iPr)2NP(OFm)2) in the presence of 5- thiophosphate activation by diphenyl (ethylthio)-1H-tetrazole as an activator. The phosphorochloridate (Goody and Eckstein, mixture was stirred for 20 minutes at room 1971). The activated reagent was used to temperature and after that sulfur was added to phosphorylate nucleoside diphosphates. The 2- oxidise the mixed PIII-PV anhydride. The bis- carbamoylethyl protecting group was then fluorenylmethyl-protected intermediate was then removed by hydrolysis with sodium hydroxide obtained by precipitation. Piperidine was used to and the product was purified by DEAE remove the protecting groups and the crude chromatography. This method has not yet been product was precipitated again as a piperidinium applied for preparation of CTPɣS but the isolated salt. The crude product was purified by strong yield for ATPɣS was reported to be 25%. anion exchange chromatography (SAX) on a Poros 50 HQ using a gradient of ammonium A nucleoside diphosphate kinase mediated bicarbonate to give CTPɣS as an ammonium transfer of a thiophosphate group from a salt. The volatile buffer was removed by freeze nucleoside 5′-(ɣ-thio)triphosphate to a drying. The purity of the final product was nucleoside 5′-diphosphate was also reported determined by SAX to be about 88%. The (Goody et al., 1972). This method was applied to principal impurity was CDP formed by partial enzymatically synthesize CTPɣS from ATPɣS decomposition of CTPɣS during the extensive and CDP (Müller et al., 2000). A partially purified freeze-drying procedure. material generated by this transformation was treated with alkaline phosphatase to degrade all CTPɣS promotes the engagement between material devoid of terminal phosphorothioate, N-terminal domains of Caulobacter and with dithiothreitol to reduce any dimeric crescentus ParB (CTPɣS)2. Multistep HPLC purification yielded a Previously, CTPɣS has also been shown to low μmol quantity (about 10% overall yield) of promote the self-dimerization of the N-terminal pure CTPɣS, which was characterized by UV domain (N-engagement) of ParB proteins (Jalal and 31P NMR. et al., 2020; Osorio-Valeriano et al., 2019; Soh et al., 2019). Here, we employed site-specific More recently, a highly versatile synthesis of crosslinking of a purified ParBCcres (D141C nucleoside oligophosphates was reported (Hofer C297S) variant by a sulfhydryl-to-sulfhydryl et al., 2015) based on protected crosslinker bismaleimidoethane (BMOE) to test phosphoramidites coupling to give mixed PIII-PV if our purified CTPɣS can also promote the N- anhydrides. In the case of phosphorothioate engagement of ParB. BMOE can covalently link analogs of nucleotides, the mixed PIII-PV symmetry-related D141C residues together if anhydride was then oxidized by sulfur and the their inter-distance is within 8 Å. Crosslinking protecting group was removed. products in the presence or absence of nucleotides were analyzed by SDS-PAGE Here, we adapt the Hofer et al., (2015) (Figure 1). We observed that CTP and CTPɣS, procedure to synthesize and purify a milligram- but no other nucleotide triphosphate, enhanced scale of CTPɣS. the crosslinking of ParBCcres (D141C C297S) (Figure 1), consistent with the previous findings Results and discussion that CTP hydrolysis is not required for N- Synthesis and purification of CTPɣS engagement (Jalal et al., 2020; Soh et al., 2019). Briefly, the synthesis of CTPɣS (Scheme 1) started from cytidine 5’-diphosphate (CDP) that Conclusions was first converted into the corresponding Here, we report a straightforward procedure for tetrabutylammonium (TBA) salt. Care should be the chemical synthesis and purification of a taken not to add excess tetrabutylammonium milligram-scale of a non-hydrolyzable CTP hydroxide. Ideally, CDP should be provided in a analog (CTPɣS). Improved availability of CTPɣS monoacidic form (2 x TBA). The exact number of will facilitate research by the community into TBA counterion was determined by 1H NMR to ParB/ParB-like proteins and other CTPases be cytidine 5’-diphosphate x 1.44 TBA salt. This enzymes. bioRxiv preprint doi: https://doi.org/10.1101/2021.01.13.426546; this version posted January 14, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Experimental procedures 1 Materials and equipment H NMR (400 MHz, D2O) δ 8.11 (d, J = 7.9 Hz, Sulfur (Cat# 213292-10G) was purchased from 1H), 6.20 (d, J = 7.8 Hz, 1H), 5.90 (d, J = 3.7 Hz, Sigma Aldrich, UK. 5-(Ethylthio)-1H-tetrazole 1H), 4.33-4.28 (m, 2H), 4.26-4.21 (m, 2H), 4.16- (Cat# 493805-2G) was purchased from Sigma 4.11 (m, 1H), 3.17-3.11 (m, 11.5H), 1.63-1.55 Aldrich. Cytidine 5’-diphosphate (Cat# C9755- (m, 11.5H), 1.34-1.25 (m, 11.6H), 0.89 (t, J = 7.4 100MG) was purchased from Sigma Aldrich as a Hz, 17.4H). sodium salt and converted into its + tetrabutylammonium (TBA) salt by ion exchange Next, cytidine 5’-diphosphate x 1.44 nBu4N on Dowex 50WX8 (H+), followed by (10.67 mg, 14.2 μmol) was dissolved in 0.5 mL neutralization with TBA hydroxide (Cat# 178780- of dimethylformamide (DMF). To this solution, 50ML) and subsequent lyophilization. Bis(9H- (iPr)2NP(OFm)2 (13.6 mg, 26.2 μmol) was added fluoren-9-ylmethyl)- and immediately after its dissolution, 5- diisopropylamidophosphite (Cat# SC-0057, (ethylthio)-1H-tetrazole (4.8 mg, 36.8 μmol) was (iPr)2NP(OFm)2) was purchased from SiChem, added. The mixture was stirred for 20 minutes at Germany. Bis-maleimidoethane (BMOE) powder room temperature. After that sulfur (3.0 mg, 94.7 was purchased from ThermoFisher (Cat# μmol) was added and the mixture was mixed 22323) and was dissolved in DMSO to 20 mM. vigorously by vortexing for 2 minutes. The bis- NMR spectra were recorded on a Bruker Fm-protected intermediate was then obtained by Advance III 400 MHz spectrometer. Chemical precipitation with Et2O/hexane 5:1 (7.5 mL) and 1 shifts of H NMR signals were recorded in D2O hexane (2 mL), and pelleted by centrifugation and were reported with respect to residual (184 x g, at 4oC for 5 minutes). The resulting solvent peak at δH 4.79 ppm. 31P{1H} NMR pellet was washed with Et2O and dried under a spectra were recorded with 1H‐decoupling on stream of nitrogen gas and briefly in vacuum. Bruker 162 MHz spectrometer in D2O. High The precipitate was then dissolved in 0.5 mL of resolution accurate mass spectra were obtained DMF. Piperidine (25 μL, 21.55 mg, 253.1 μmol, using a Synapt G2-Si Q-Tof mass spectrometer 5% v/v) was added and the mixture was stirred using negative electrospray ionisation. HPLC for 15 minutes. The final product was purification was performed on a Dionex Ultimate precipitated by adding 3.5 mL of 1:5 DCM/Et2O 3000 instrument equipped with an UV/vis 1:5. The mixture was centrifuged at 184 x g for 5 o detector. Lyophilization was performed with a minutes at 4 C. The pellet was washed with Et2O Labconco FreeZone Benchtop Freeze Dryer and dried under a nitrogen stream to give crude with PTFE Coil. An Eppendorf 5810R benchtop CTPɣS as a piperidinium salt. The sample was centrifuge was used for centrifugation. stored at -80oC, which is stable for approximately 2 months, until the purification step. Synthesis of cytosine 5'-(ɣ-thio)triphosphate 31 1 (CTPɣS) P{ H} NMR (162 MHz, D2O) δ 34.2 (d, J = 29.5 Cytidine 5’-diphosphate (CDP) (8.34 mg, 20.7 Hz), -11.4 (d, J = 19.7 Hz), -23.6 (dd, J = 29.5, μmol) in ultrapure Milli-Q water (1 mL) was 19.7 Hz). The 31P NMR spectrum (Figure S2) is applied on a column containing Dowex 50WX8 in good agreement with data published (H+) (1 mL, pre-washed with HCl and Milli-Q previously, in which CTPɣS was synthesized water to neutral pH).
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