Discovery and substrate specificity engineering of nucleotide halogenases.
Journal
Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555
Informations de publication
Date de publication:
19 Jun 2024
19 Jun 2024
Historique:
received:
23
09
2023
accepted:
24
05
2024
medline:
20
6
2024
pubmed:
20
6
2024
entrez:
19
6
2024
Statut:
epublish
Résumé
C2'-halogenation has been recognized as an essential modification to enhance the drug-like properties of nucleotide analogs. The direct C2'-halogenation of the nucleotide 2'-deoxyadenosine-5'-monophosphate (dAMP) has recently been achieved using the Fe(II)/α-ketoglutarate-dependent nucleotide halogenase AdaV. However, the limited substrate scope of this enzyme hampers its broader applications. In this study, we report two halogenases capable of halogenating 2'-deoxyguanosine monophosphate (dGMP), thereby expanding the family of nucleotide halogenases. Computational studies reveal that nucleotide specificity is regulated by the binding pose of the phosphate group. Based on these findings, we successfully engineered the substrate specificity of these halogenases by mutating second-sphere residues. This work expands the toolbox of nucleotide halogenases and provides insights into the regulation mechanism of nucleotide specificity.
Identifiants
pubmed: 38898020
doi: 10.1038/s41467-024-49147-7
pii: 10.1038/s41467-024-49147-7
doi:
Substances chimiques
Nucleotides
0
Deoxyguanine Nucleotides
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
5254Subventions
Organisme : National Natural Science Foundation of China (National Science Foundation of China)
ID : 22173077
Organisme : Natural Science Foundation of Guangdong Province (Guangdong Natural Science Foundation)
ID : 2023B1515020052
Informations de copyright
© 2024. The Author(s).
Références
Moir, M., Danon, J. J., Reekie, T. A. & Kassiou, M. An overview of late-stage functionalization in today’s drug discovery. Expert Opin. Drug Discov. 14, 1137–1149 (2019).
doi: 10.1080/17460441.2019.1653850
Castellino, N. J., Montgomery, A. P., Danon, J. J. & Kassiou, M. Late-stage functionalization for improving drug-like molecular properties. Chem. Rev. 123, 8127–8153 (2023).
doi: 10.1021/acs.chemrev.2c00797
Romero, E. et al. Enzymatic late-Stage modifications: better late than never. Angew. Chem. Int. Ed. 60, 16824–16855 (2021).
doi: 10.1002/anie.202014931
Ainsley, J. et al. Structural insights from molecular dynamics simulations of tryptophan 7-halogenase and tryptophan 5-halogenase. ACS Omega 3, 4847–4859 (2018).
doi: 10.1021/acsomega.8b00385
Karabencheva-Christova, T. G., Torras, J., Mulholland, A. J., Lodola, A. & Christov, C. Z. Mechanistic insights into the reaction of chlorination of tryptophan catalyzed by tryptophan 7-halogenase. Sci. Rep. 7, 17395 (2017).
doi: 10.1038/s41598-017-17789-x
Hegarty, E., Büchler, J. & Buller, R. M. Halogenases for the synthesis of small molecules. Curr. Opin. Green. Sustain. Chem. 41, 100784 (2023).
doi: 10.1016/j.cogsc.2023.100784
Tao, H. & Abe, I. Oxidative modification of free-standing amino acids by Fe(II)/αKG-dependent oxygenases. Eng. Microbiol. 3, 2667–3703 (2023).
doi: 10.1016/j.engmic.2022.100062
Latham, J., Brandenburger, E., Shepherd, S. A., Menon, B. R. K. & Micklefield, J. Development of halogenase enzymes for use in synthesis. Chem. Rev. 118, 232–269 (2018).
doi: 10.1021/acs.chemrev.7b00032
Voss, M., Honda Malca, S. & Buller, R. Exploring the biocatalytic potential of Fe/α-ketoglutarate-dependent halogenases. Chem. Eur. J. 26, 7336–7345 (2020).
doi: 10.1002/chem.201905752
Galonić Fujimori, D. et al. Spectroscopic evidence for a high-spin Br-Fe(IV)-oxo intermediate in the α-ketoglutarate-dependent halogenase CytC3 from streptomyces. J. Am. Chem. Soc. 129, 13408–13409 (2007).
doi: 10.1021/ja076454e
Krebs, C., Galonić Fujimori, D., Walsh, C. T. & Bollinger, J. M. Jr. Non-heme Fe(IV)–oxo intermediates. Acc. Chem. Res. 40, 484–492 (2007).
doi: 10.1021/ar700066p
Vaillancourt, F. H., Yeh, E., Vosburg, D. A., O’Connor, S. E. & Walsh, C. T. Cryptic chlorination by a non-haem iron enzyme during cyclopropyl amino acid biosynthesis. Nature 436, 1191–1194 (2005).
doi: 10.1038/nature03797
Vaillancourt, F. H., Yin, J. & Walsh, C. T. SyrB2 in syringomycin E biosynthesis is a nonheme FeII α-ketoglutarate- and O
doi: 10.1073/pnas.0504412102
Galonic, D. P., Vaillancourt, F. H. & Walsh, C. T. Halogenation of unactivated carbon centers in natural product biosynthesis: trichlorination of leucine during barbamide biosynthesis. J. Am. Chem. Soc. 128, 3900–3901 (2006).
doi: 10.1021/ja060151n
Ueki, M. et al. Enzymatic generation of the antimetabolite γ,γ-dichloroaminobutyrate by NRPS and mononuclear iron halogenase action in a Streptomycete. Chem. Biol. 13, 1183–1191 (2006).
doi: 10.1016/j.chembiol.2006.09.012
Khare, D. et al. Conformational switch triggered by α-ketoglutarate in a halogenase of curacin A biosynthesis. Proc. Natl Acad. Sci. USA 107, 14099–14104 (2010).
doi: 10.1073/pnas.1006738107
Pratter, S. M. et al. More than just a halogenase: modification of fatty acyl moieties by a trifunctional metal enzyme. ChemBioChem 15, 567–574 (2014).
doi: 10.1002/cbic.201300345
Hillwig, M. L. & Liu, X. A new family of iron-dependent halogenases acts on freestanding substrates. Nat. Chem. Biol. 10, 921–923 (2014).
doi: 10.1038/nchembio.1625
Hillwig, M. L., Zhu, Q., Ittiamornkul, K. & Liu, X. Discovery of a promiscuous non-heme iron halogenase in ambiguine alkaloid biogenesis: Implication for an evolvable enzyme family for late-stage halogenation of aliphatic carbons in small molecules. Angew. Chem. Int. Ed. 55, 5780–5784 (2016).
doi: 10.1002/anie.201601447
Zhu, Q. & Liu, X. Characterization of non-heme iron aliphatic halogenase WelO5* from Hapalosiphon welwitschii IC-52-3: Identification of a minimal protein sequence motif that confers enzymatic chlorination specificity in the biosynthesis of welwitindolelinones. Beilstein J. Org. Chem. 13, 1168–1173 (2017).
doi: 10.3762/bjoc.13.115
Voss, M. et al. Enzyme engineering enables inversion of substrate stereopreference of the halogenase WelO5*. ChemCatChem 14, 1867–3880 (2022).
Buchler, J. et al. Algorithm-aided engineering of aliphatic halogenase WelO5* for the asymmetric late-stage functionalization of soraphens. Nat. Commun. 13, 371 (2022).
doi: 10.1038/s41467-022-27999-1
Mitchell, A. J. et al. Structural basis for halogenation by iron- and 2-oxo-glutarate-dependent enzyme WelO5. Nat. Chem. Biol. 12, 636–640 (2016).
doi: 10.1038/nchembio.2112
Kim, C. Y. et al. The chloroalkaloid (-)-acutumine is biosynthesized via a Fe(II)- and 2-oxoglutarate-dependent halogenase in Menispermaceae plants. Nat. Commun. 11, 1867 (2020).
doi: 10.1038/s41467-020-15777-w
Neugebauer, M. E. et al. A family of radical halogenases for the engineering of amino-acid-based products. Nat. Chem. Biol. 15, 1009–1016 (2019).
doi: 10.1038/s41589-019-0355-x
Neugebauer, M. E. et al. Reaction pathway engineering converts a radical hydroxylase into a halogenase. Nat. Chem. Biol. 18, 171–179 (2022).
doi: 10.1038/s41589-021-00944-x
Zhao, C. et al. An Fe
doi: 10.1002/anie.201914994
Dai, L. et al. Structural and functional insights into a nonheme iron- and α-ketoglutarate-dependent halogenase that catalyzes chlorination of nucleotidesubstrates. Appl. Environ. Microbiol. 88, e02497–02421 (2022).
doi: 10.1128/aem.02497-21
Yates, M. K. & Seley-Radtke, K. L. The evolution of antiviral nucleoside analogues: a review for chemists and non-chemists. Part II: Complex modifications to the nucleoside scaffold. Antivir. Res. 162, 5–21 (2019).
doi: 10.1016/j.antiviral.2018.11.016
Lin, X. et al. Advance of structural modification of nucleosides scaffold. Eur. J. Med. Chem. 214, 113233 (2021).
doi: 10.1016/j.ejmech.2021.113233
Pruijssers, A. J. & Denison, M. R. Nucleoside analogues for the treatment of coronavirus infections. Curr. Opin. Virol. 35, 57–62 (2019).
doi: 10.1016/j.coviro.2019.04.002
Jordheim, L. P., Durantel, D., Zoulim, F. & Dumontet, C. Advances in the development of nucleoside and nucleotide analogues for cancer and viral diseases. Nat. Rev. Drug Discov. 12, 447–464 (2013).
doi: 10.1038/nrd4010
Gao, M., Zhang, Q., Feng, X. H. & Liu, J. Synthetic modified messenger RNA for therapeutic applications. Acta Biomater. 131, 1–15 (2021).
doi: 10.1016/j.actbio.2021.06.020
Liang, Y., Smerznak, E. & Wnuk, S. F. Construction of quaternary stereocenters at carbon 2′ of nucleosides. Carbohydr. Res. 528, 108814 (2023).
doi: 10.1016/j.carres.2023.108814
Flamme, M., McKenzie, L. K., Sarac, I. & Hollenstein, M. Chemical methods for the modification of RNA. Methods 161, 64–82 (2019).
doi: 10.1016/j.ymeth.2019.03.018
Rajapaksha, D. G., Mondal, S., Wang, J. W. & Meanwell, M. W. A guide for the synthesis of key nucleoside scaffolds in drug discovery. Med. Chem. Res. 32, 1315–1333 (2023).
doi: 10.1007/s00044-023-03096-w
Meanwell, M. et al. A short de novo synthesis of nucleoside analogs. Science 369, 725–730 (2020).
doi: 10.1126/science.abb3231
Peifer, M., Berger, R., Shurtleff, V. W., Conrad, J. C. & MacMillan, D. W. C. A general and enantioselective approach to pentoses: a rapid synthesis of PSI-6130, the nucleoside core of Sofosbuvir. J. Am. Chem. Soc. 136, 5900–5903 (2014).
doi: 10.1021/ja502205q
Zhai, G. et al. Structural insight into the catalytic mechanism of non-heme iron halogenase AdaV in 2′-chloropentostatin biosynthesis. ACS Catal. 12, 13910–13920 (2022).
doi: 10.1021/acscatal.2c04608
Hayashi, T. et al. Evolved aliphatic halogenases enable regiocomplementary C-H functionalization of a pharmaceutically relevant compound. Angew. Chem. Int. Ed. 58, 18535–18539 (2019).
doi: 10.1002/anie.201907245
Tamura, T., Hayakawa, M. & Hatano, K. A new genus of the order Actinomycetales, Virgosporangium gen. nov., with descriptions of Virgosporangium ochraceum sp. nov. and Virgosporangium aurantiacum sp. nov. Int. J. Syst. Evol. Microbiol. 51, 1809–1816 (2001).
doi: 10.1099/00207713-51-5-1809
Yang, Y. et al. Catellatospora tritici sp. nov., a novel cellulase-producing actinobacterium isolated from rhizosphere soil of wheat (Triticum aestivum L.) and emended description of the genus Catellatospora. Int. J. Syst. Evol. Microbiol. 72, 005420 (2022).
doi: 10.1099/ijsem.0.005420
Wilson, R. H., Chatterjee, S., Smithwick, E. R., Dalluge, J. J. & Bhagi-Damodaran, A. Role of secondary coordination sphere residues in halogenation catalysis of non-heme iron enzymes. ACS Catal. 12, 10913–10924 (2022).
doi: 10.1021/acscatal.2c00954
Zhang, X., Wang, Z., Gao, J. & Liu, W. Chlorination versus hydroxylation selectivity mediated by the non-heme iron halogenase WelO5. Phys. Chem. Chem. Phys. 22, 8699–8712 (2020).
doi: 10.1039/D0CP00791A
Knecht, W. et al. A few amino acid substitutions can convert deoxyribonucleoside kinase specificity from pyrimidines to purines. EMBO J. 21, 1873–1880 (2002).
doi: 10.1093/emboj/21.7.1873
Toh, J. D. W. et al. A strategy based on nucleotide specificity leads to a subfamily-selective and cell-active inhibitor of N(6)-methyladenosine demethylase FTO. Chem. Sci. 6, 112–122 (2015).
doi: 10.1039/C4SC02554G
Vashisht, K. et al. Engineering nucleotide specificity of succinyl-CoA synthetase in blastocystis: the emerging role of gatekeeper residues. Biochemistry 56, 534–542 (2017).
doi: 10.1021/acs.biochem.6b00098
Nobeli, I., Laskowski, R. A., Valdar, W. S. J. & Thornton, J. M. On the molecular discrimination between adenine and guanine by proteins. Nucleic Acids Res. 29, 4294–4309 (2001).
doi: 10.1093/nar/29.21.4294
Rogne, P. et al. Molecular mechanism of ATP versus GTP selectivity of adenylate kinase. Proc. Natl Acad. Sci. USA 115, 3012–3017 (2018).
doi: 10.1073/pnas.1721508115
Kissman, E. N. et al. Biocatalytic control of site-selectivity and chain length-selectivity in radical amino acid halogenases. Proc. Natl Acad. Sci. USA 120, e2214512120 (2023).
doi: 10.1073/pnas.2214512120
Duewel, S. et al. Directed evolution of an feii-dependent halogenase for asymmetric C(sp3)–H chlorination. ACS Catal. 10, 1272–1277 (2019).
doi: 10.1021/acscatal.9b04691
Madeira, F. et al. Search and sequence analysis tools services from EMBL-EBI in 2022. Nucleic Acids Res. 50, W276–W279 (2022).
doi: 10.1093/nar/gkac240
Letunic, I. & Bork, P. Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Res. 49, W293–W296 (2021).
doi: 10.1093/nar/gkab301
Waterhouse, A. et al. SWISS-MODEL: homology modelling of protein structures and complexes. Nucleic Acids Res. 46, 296–303 (2018).
doi: 10.1093/nar/gky427
Jumper, J. et al. Highly accurate protein structure prediction with AlphaFold. Nature 596, 583–589 (2021).
doi: 10.1038/s41586-021-03819-2
Eberhardt, J., Santos-Martins, D., Tillack, A. F. & Forli, S. Autodock Vina 1.2.0: New docking methods, expanded force field, and python bindings. J. Chem. Inf. Model. 61, 3891–3898 (2021).
doi: 10.1021/acs.jcim.1c00203
Mehmood, R., Vennelakanti, V. & Kulik, H. J. Spectroscopically guided simulations reveal distinct strategies for positioning substrates to achieve selectivity in nonheme Fe(II)/α-ketoglutarate-dependent halogenases. ACS Catal. 11, 12394–12408 (2021).
doi: 10.1021/acscatal.1c03169
Kastner, D. W., Nandy, A., Mehmood, R. & Kulik, H. J. Mechanistic insights into substrate positioning that distinguish non-heme Fe(II)/α-ketoglutarate-dependent halogenases and hydroxylases. ACS Catal. 13, 2489–2501 (2023).
doi: 10.1021/acscatal.2c06241
Anandakrishnan, R., Aguilar, B. & Onufriev, A. V. H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations. Nucleic Acids Res. 40, 537–541 (2012).
doi: 10.1093/nar/gks375
Wang, J., Wolf, R. M., Caldwell, J. W., Kollman, P. A. & Case, D. A. Development and testing of a general amber force field. J. Comput. Chem. 25, 1157–1174 (2004).
doi: 10.1002/jcc.20035
Bayly, C. I., Cieplak, P., Cornell, W. D. & Kollman, P. A. A Well-Behaved Electrostatic Potential Based Method Using Charge Restraints for Deriving Atomic Charges - the Resp Model. J. Phys. Chem. 97, 10269 (1993).
doi: 10.1021/j100142a004
Li, P. & Merz, K. M. Jr MCPB.py: A python based metal center parameter builder. J. Chem. Inf. Model. 56, 599–604 (2016).
doi: 10.1021/acs.jcim.5b00674
Ivani, I. et al. Parmbsc1: a refined force field for DNA simulations. Nat. Methods 13, 55–58 (2016).
doi: 10.1038/nmeth.3658
Case, D. A. et al. AMBER 2020 (University of California, San Francisco, 2020).
Maier, J. A. et al. ff14SB: Improving the accuracy of protein side chain and backbone parameters from ff99SB. J. Chem. Theory Comput. 11, 3696–3713 (2015).
doi: 10.1021/acs.jctc.5b00255
Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W. & Klein, M. L. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79, 926–935 (1983).
doi: 10.1063/1.445869
Salomon-Ferrer, R., Götz, A. W., Poole, D., Le Grand, S. & Walker, R. C. Routine microsecond molecular dynamics simulations with AMBER on GPUs. 2. explicit solvent particle mesh ewald. J. Chem. Theory Comput. 9, 3878–3888 (2013).
doi: 10.1021/ct400314y
Roe, D. R. & Cheatham, T. E. PTRAJ and CPPTRAJ: Software for processing and analysis of molecular dynamics trajectory data. J. Chem. Theory Comput. 9, 3084 (2013).
doi: 10.1021/ct400341p
Vennelakanti, V., Qi, H. W., Mehmood, R. & Kulik, H. J. When are two hydrogen bonds better than one? Accurate first-principles models explain the balance of hydrogen bond donors and acceptors found in proteins. Chem. Sci. 12, 1147–1162 (2021).
doi: 10.1039/D0SC05084A
Rodriguez, A. & Laio, A. Clustering by fast search and find of density peaks. Science 344, 1492–1496 (2014).
doi: 10.1126/science.1242072
Grant, B. J., Rodrigues, A. P. C., ElSawy, K. M., McCammon, J. A. & Caves, L. S. D. Bio3d: an R package for the comparative analysis of protein structures. Bioinformatics 22, 2695–2696 (2006).
doi: 10.1093/bioinformatics/btl461
Chaturvedi, S. S. et al. Can second coordination sphere and long-range interactions modulate hydrogen atom transfer in a non-heme Fe(II)-dependent histone demethylase? JACS Au 2, 2169–2186 (2022).
doi: 10.1021/jacsau.2c00345
Waheed, S. O., Varghese, A., Chaturvedi, S. S., Karabencheva-Christova, T. G. & Christov, C. Z. How human TET2 enzyme catalyzes the oxidation of unnatural cytosine modifications in double-stranded DNA. ACS Catal. 12, 5327–5344 (2022).
doi: 10.1021/acscatal.2c00024