口袋改造策略克服ω-氨基转移酶AtATA对1-乙酰基萘活性和稳定性之间的"trade-off"效应

曹佳仁, 樊芳芳n, 吕常江, 胡升, 赵伟睿, 梅家祺, 邱帅, 梅乐和, 黄俊

工程(英文) ›› 2023, Vol. 30 ›› Issue (11) : 203-214.

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工程(英文) ›› 2023, Vol. 30 ›› Issue (11) : 203-214. DOI: 10.1016/j.eng.2023.04.009
研究论文
Article

口袋改造策略克服ω-氨基转移酶AtATA对1-乙酰基萘活性和稳定性之间的"trade-off"效应

作者信息 +

Pocket Modification of ω-Amine Transaminase AtATA for Overcoming the Trade-Off Between Activity and Stability Toward 1-Acetonaphthone

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摘要

氨基转移酶是一种能够催化前手性酮或醛不对称胺化生成相应的手性胺的生物催化剂。然而,活性和稳定性之间的“trade-off”效应限制了其在工业生产中的应用。因此,开发克服这种相互抵消的“trade-off”效应的普适方法以及获得高效催化的氨基转移酶具有重要意义。对此,我们针对土曲霉属氨基转移酶(AtATA)的底物结合口袋进行共进化改造,以确定控制AtATA对1-乙酰基萘活性和稳定性的关键氨基酸。通过多轮实验筛选,我们发现了一个含四个关键氨基酸位点(R128,V149,L182和L187)的“结构开关”, “最佳”突变体(AtATA_D224K/V149A/L182F/L187F; 命名为M4)。与亲本酶AtATA_D224K(AtATAPa)相比,M4的催化效率(kcat/Km1-乙酰基萘,其中kcat是催化活性常数,为10.1 min-1Km1-乙酰基萘是米氏常数,为1.7 mmol·L-1)和半衰期(t1/2)分别增加59倍和1.6倍。此外,在50 mL反应体系中,M4催化20 mmol·L-1 1-乙酰基萘,反应10 h后可获得产率为78%的目标产物(R)-(+)-1-(1-萘基)乙胺((R)-NEA),对映体纯度达到R > 99.5%。同时,M4还显示出对各种1-乙酰萘酮类似物显著增强的催化活性。通过结构和序列信息分析,进一步发现分子内相互作用的加强以及底物结合口袋和5’-磷酸吡哆醛(PLP)结合口袋之间的角度扩大是AtATA热稳定性和活性同步增强的重要原因。最后,口袋工程策略也将增强的活性和热稳定性成功地转移到其他三个序列相似性介于8%~22%之间的氨基转移酶中。这项研究对于克服ATA活性和热稳定性之间的权衡具有重要意义。

Abstract

Amine transaminases (ATAs) catalyze the asymmetric amination of prochiral ketones or aldehydes to their corresponding chiral amines. However, the trade-off between activity and stability in enzyme engineering represents a major obstacle to the practical application of ATAs. Overcoming this trade-off is important for developing robustly engineered enzymes and a universal approach for ATAs. Herein, we modified the binding pocket of ω-ATA from Aspergillus terreus (AtATA) to identify the key amino acid residues controlling the activity and stability of AtATA toward 1-acetonaphthone. We discovered a structural switch comprising four key amino acid sites (R128, V149, L182, and L187), as well as the “best” mutant (AtATA_D224K/V149A/L182F/L187F; termed M4). Compared to the parent enzyme AtATA_D224K (AtATA-Pa), M4 increased the catalytic efficiency (kcat/Km1-acetonaphthone, where kcat is the constant of catalytic activities and is 10.1 min−1, Km1-acetonaphthone is Michaelis-Menten constant and is 1.7 mmol·L-1) and half-life (t1/2) by 59-fold to 5.9 L·min−1·mmol−1 and by 1.6-fold to 46.9 min, respectively. Moreover, using M4 as the biocatalyst, we converted a 20 mmol·L-1 aliquot of 1-acetonaphthone in a 50 mL scaled-up system to the desired product, (R)-(+)-1(1-naphthyl)ethylamine ((R)-NEA), with 78% yield and high enantiomeric purity (R > 99.5%) within 10 h. M4 also displayed significantly enhanced activity toward various 1-acetonaphthone analogs. The related structural properties derived by analyzing structure and sequence information of robust ATAs illustrated their enhanced activity and thermostability. Strengthening of intramolecular interactions and expansion of the angle between the substrate-binding pocket and the pyridoxal 5′-phosphate (PLP)-binding pocket contributed to synchronous enhancement of ATA thermostability and activity. Moreover, this pocket engineering strategy successfully transferred enhanced activity and thermostability to three other ATAs, which exhibited 8%-22% sequence similarity with AtATA. This research has important implications for overcoming the trade-off between ATA activity and thermostability.

关键词

“trade-off”效应 / 共进化 / 氨基转移酶 / 口袋改造

Keywords

Trade-off / Co-evolution / Amine transaminase / (R)-(+)-1(1-naphthyl)ethylamine

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曹佳仁, 樊芳芳n, 吕常江. 口袋改造策略克服ω-氨基转移酶AtATA对1-乙酰基萘活性和稳定性之间的"trade-off"效应. Engineering. 2023, 30(11): 203-214 https://doi.org/10.1016/j.eng.2023.04.009

参考文献

[1]
T.W. Thorpe, J.R. Marshall, V. Harawa, R.E. Ruscoe, A. Cuetos, J.D. Finnigan, et al.. Multifunctional biocatalyst for conjugate reduction and reductive amination. Nature, 604 (7904) ( 2022), pp. 86-91 DOI: 10.1038/s41586-022-04458-x
[2]
D.J. Newman, G.M. Cragg. Natural products as sources of new drugs over the 30 years from 1981 to 2010. J Nat Prod, 75 (3) ( 2012), pp. 311-335 DOI: 10.1021/np200906s
[3]
W. Zawodny, S.L. Montgomery. Evolving new chemistry: biocatalysis for the synthesis of amine-containing pharmaceuticals. Catalysts, 12 (6) ( 2022), pp. 595-616 DOI: 10.3390/catal12060595
[4]
S. Zhang, J. Del Pozo, F. Romiti, Y. Mu, S. Torker, A.H. Hoveyda. Delayed catalyst function enables direct enantioselective conversion of nitriles to NH2-amines. Science, 364 (6435) ( 2019), pp. 45-51 DOI: 10.1126/science.aaw4029
[5]
M.D. Patil, G. Grogan, A. Bommarius, H. Yun. Oxidoreductase-catalyzed synthesis of chiral amines. ACS Catal, 8 (12) ( 2018), pp. 10985-11015 DOI: 10.1021/acscatal.8b02924
[6]
M. Barniol-Xicota, R. Leiva, C. Escolano, S. Vázquez. Syntheses of cinacalcet: an enantiopure active pharmaceutical ingredient (API). Synthesis, 48 (6) ( 2016), pp. 783-803
[7]
C.Y. Yang, J. Li, Y.Y. Yao, C. Qing, B.C. Shen. Enantioseparation of cinacalcet, and its two related compounds by HPLC with self-made chiral stationary phases and chiral mobile phase additives. Curr Pharm Anal, 15 (2) ( 2019), pp. 200-209 DOI: 10.2174/1573412914666180518105046
[8]
J.A. Barman Balfour, L.J. Scott. Cinacalcet hydrochloride. Drugs, 65 (2) ( 2005), pp. 271-281 DOI: 10.2165/00003495-200565020-00007
[9]
H.U. Blaser. Enantioselective catalysis in fine chemicals production. Chem Commun, 3 (3) ( 2003), pp. 293-296
[10]
T. Yasukawa, R. Masuda, S. Kobayashi. Development of heterogeneous catalyst systems for the continuous synthesis of chiral amines via asymmetric hydrogenation. Nat Catal, 2 (12) ( 2019), pp. 1088-1092 DOI: 10.1038/s41929-019-0371-y
[11]
D. Ghislieri, N.J. Turner. Biocatalytic approaches to the synthesis of enantiomerically pure chiral amines. Top Catal, 57 (5) ( 2014), pp. 284-300 DOI: 10.1007/s11244-013-0184-1
[12]
M. Höhne, U.T. Bornscheuer. Biocatalytic routes to optically active amines. ChemCatChem, 1 (1) ( 2009), pp. 42-51 DOI: 10.1002/cctc.200900110
[13]
D. Ghislieri, A.P. Green, M. Pontini, S.C. Willies, I. Rowles, A. Frank, et al.. Engineering an enantioselective amine oxidase for the synthesis of pharmaceutical building blocks and alkaloid natural products. J Am Chem Soc, 135 (29) ( 2013), pp. 10863-10869 DOI: 10.1021/ja4051235
[14]
V.F. Batista, J.L. Galman, G.A.D.C. Pinto, A.M.S. Silva, N.J. Turner. Monoamine oxidase: tunable activity for amine resolution and functionalization. ACS Catal, 8 (12) ( 2018), pp. 11889-11907 DOI: 10.1021/acscatal.8b03525
[15]
J.S. Völler. Metagenomic imine reductases for synthesis. Nat Catal, 4 (2) ( 2021), p. 2 DOI: 10.1038/s41929-021-00571-8
[16]
P. Yao, J.R. Marshall, Z. Xu, J. Lim, S.J. Charnock, D. Zhu, et al.. Asymmetric synthesis of N-substituted α-amino esters from α-ketoesters via imine reductase-catalyzed reductive amination. Angew Chem Int Ed Engl, 60 (16) ( 2021), pp. 8717-8721 DOI: 10.1002/anie.202016589
[17]
Y.P. Xue, C.H. Cao, Y.G. Zheng. Enzymatic asymmetric synthesis of chiral amino acids. Chem Soc Rev, 47 (4) ( 2018), pp. 1516-1561 DOI: 10.1039/c7cs00253j
[18]
D.H. Wang, Q. Chen, S.N. Yin, X.W. Ding, Y.C. Zheng, Z. Zhang, et al.. Asymmetric reductive amination of structurally diverse ketones with ammonia using a spectrum-extended amine dehydrogenase. ACS Catal, 11 (22) ( 2021), pp. 14274-14283 DOI: 10.1021/acscatal.1c04324
[19]
M.D. Patil, G. Grogan, A. Bommarius, H. Yun. Recent advances in ω-transaminase-mediated biocatalysis for the enantioselective synthesis of chiral amines. Catalysts, 8 (7) ( 2018), pp. 254-278
[20]
Q. Yang, F. Zhao, N. Zhang, M. Liu, H. Hu, J. Zhang, et al.. Mild dynamic kinetic resolution of amines by coupled visible-light photoredox and enzyme catalysis. Chem Commun, 54 (100) ( 2018), pp. 14065-14068 DOI: 10.1039/c8cc07990k
[21]
Z.Q. Rong, Z.Y. Yu, C. Weng, L.C. Yang, S.C. Lu, Y. Lan, et al.. Dynamic kinetic asymmetric amination of alcohols assisted by microwave: stereoconvergent access to tetralin- and indane-derived chiral amines. ACS Catal, 10 (16) ( 2020), pp. 9464-9475 DOI: 10.1021/acscatal.0c02468
[22]
V. Bhat, E.R. Welin, X. Guo, B.M. Stoltz. Advances in stereoconvergent catalysis from 2005 to 2015: transition-metal-mediated stereoablative reactions, dynamic kinetic resolutions, and dynamic kinetic asymmetric transformations. Chem Rev, 117 (5) ( 2017), pp. 4528-4561 DOI: 10.1021/acs.chemrev.6b00731
[23]
F. Steffen-Munsberg, C. Vickers, H. Kohls, H. Land, H. Mallin, A. Nobili, et al.. Bioinformatic analysis of a PLP-dependent enzyme superfamily suitable for biocatalytic applications. Biotechnol Adv, 33 (5) ( 2015), pp. 566-604
[24]
E.Y. Bezsudnova, V.O. Popov, K.M. Boyko. Structural insight into the substrate specificity of PLP fold type IV transaminases. Appl Microbiol Biotechnol, 104 (6) ( 2020), pp. 2343-2357 DOI: 10.1007/s00253-020-10369-6
[25]
L. Zhai, S. Yang, Y. Lai, D. Meng, Q. Tian, Z. Guan, et al.. Effect of residue substitution via site-directed mutagenesis on activity and steroselectivity of transaminase BpTA from Bacillus pumilus W 3 for sitafloxacin hydrate intermediate. Int J Biol Macromol, 137 ( 2019), pp. 732-740
[26]
D.F. Xie, J.X. Yang, C.J. Lv, J.Q. Mei, H.P. Wang, S. Hu, et al.. Construction of stabilized (R)-selective amine transaminase from Aspergillus terreus by consensus mutagenesis. J Biotechnol, 293 ( 2019), pp. 8-16
[27]
K. Fesko, K. Steiner, R. Breinbauer, H. Schwab, M. Schürmann, G.A. Strohmeier. Investigation of one-enzyme systems in the ω-transaminase-catalyzed synthesis of chiral amines. J Mol Catal, B Enzym, 96 ( 2013), pp. 103-110
[28]
K. Deepankumar, M. Shon, S.P. Nadarajan, G. Shin, S. Mathew, N. Ayyadurai, et al.. Enhancing thermostability and organic solvent tolerance of ω-transaminase through global incorporation of fluorotyrosine. Adv Synth Catal, 356 (5) ( 2014), pp. 993-998 DOI: 10.1002/adsc.201300706
[29]
Y.Y. Xie, J.G. Wang, L. Yang, W. Wang, Q.H. Liu, H.L. Wang, et al.. The identification and application of a robust ω-transaminase with high tolerance towards substrates and isopropylamine from a directed soil metagenome. Catal Sci Technol, 12 (7) ( 2022), pp. 2162-2175 DOI: 10.1039/d1cy02032c
[30]
F. Guo, P. Berglund. Transaminase biocatalysis: optimization and application. Green Chem, 19 (2) ( 2017), pp. 333-360
[31]
K.S. Siddiqui. Defying the activity-stability trade-off in enzymes: taking advantage of entropy to enhance activity and thermostability. Crit Rev Biotechnol, 37 (3) ( 2017), pp. 309-322 DOI: 10.3109/07388551.2016.1144045
[32]
S.F. Li, J.Y. Xie, S. Qiu, S.Y. Xu, F. Cheng, Y.J. Wang, et al.. Semirational engineering of an aldo-keto reductase KmAKR for overcoming trade-offs between catalytic activity and thermostability. Biotechnol Bioeng, 118 (11) ( 2021), pp. 4441-4452 DOI: 10.1002/bit.27913
[33]
L. Cui, A.Q. Cui, Q.T. Li, L.Z. Yang, H. Liu, W.G. Shao, et al.. Molecular evolution of an aminotransferase based on substrate-enzyme binding energy analysis for efficient valienamine synthesis. ACS Catal, 12 (21) ( 2022), pp. 13703-13714 DOI: 10.1021/acscatal.2c03784
[34]
S.W. Han, E.S. Park, J.Y. Dong, J.S. Shin. Mechanism-guided engineering of ω-transaminase to accelerate reductive amination of ketones. Adv Synth Catal, 357 (8) ( 2015), pp. 1732-1740 DOI: 10.1002/adsc.201500211
[35]
Q. Meng, N. Capra, C.M. Palacio, E. Lanfranchi, M. Otzen, L.Z. van Schie, et al.. Robust ω-transaminases by computational stabilization of the subunit interface. ACS Catal, 10 (5) ( 2020), pp. 2915-2928 DOI: 10.1021/acscatal.9b05223
[36]
D.F.A.R. Dourado, S. Pohle, A.T.P. Carvalho, D.S. Dheeman, J.M. Caswell, T. Skvortsov, et al.. Rational design of a (S)-selective-transaminase for asymmetric synthesis of (1S)-1-(1,1′-biphenyl-2-yl)ethanamine. ACS Catal, 6 (11) ( 2016), pp. 7749-7759 DOI: 10.1021/acscatal.6b02380
[37]
L. Yang, K. Zhang, M. Xu, Y. Xie, X. Meng, H. Wang, et al.. Mechanism-guided computational design of ω-transaminase by reprograming of high-energy-barrier steps. Angew Chem Int Ed Engl, 61 (52) ( 2022), p. e202212555
[38]
C.K. Savile, J.M. Janey, E.C. Mundorff, J.C. Moore, S. Tam, W.R. Jarvis, et al.. Biocatalytic asymmetric synthesis of chiral amines from ketones applied to sitagliptin manufacture. Science, 329 (5989) ( 2010), pp. 305-309 DOI: 10.1126/science.1188934
[39]
S.J. Novick, N. Dellas, R. Garcia, C. Ching, A. Bautista, D. Homan, et al.. Engineering an amine transaminase for the efficient production of a chiral sacubitril precursor. ACS Catal, 11 (6) ( 2021), pp. 3762-3770 DOI: 10.1021/acscatal.0c05450
[40]
A. Łyskowski, C. Gruber, G. Steinkellner, M. Schürmann, H. Schwab, K. Gruber, et al.. Crystal structure of an (R)-selective ω-transaminase from Aspergillus terreus. PLoS One, 9 (1) ( 2014), p. e87350 DOI: 10.1371/journal.pone.0087350
[41]
J. Huang, D.F. Xie, Y. Feng. Engineering thermostable (R)-selective amine transaminase from Aspergillus terreus through in silico design employing B-factor and folding free energy calculations. Biochem Biophys Res Commun, 483 (1) ( 2017), pp. 397-402
[42]
J.R. Cao, F.F. Fan, C.J. Lv, H.P. Wang, Y. Li, S. Hu, et al.. Improving the thermostability and activity of transaminase from Aspergillus terreus by charge-charge interaction. Front Chem, 9 ( 2021), Article 664156
[43]
D. Baud, N. Ladkau, T.S. Moody, J.M. Ward, H.C. Hailes. A rapid, sensitive colorimetric assay for the high-throughput screening of transaminases in liquid or solid-phase. Chem Commun, 51 (97) ( 2015), pp. 17225-17228
[44]
F.H. Niesen, H. Berglund, M. Vedadi. The use of differential scanning fluorimetry to detect ligand interactions that promote protein stability. Nat Protoc, 2 (9) ( 2007), pp. 2212-2221 DOI: 10.1038/nprot.2007.321
[45]
M. Purmonen, J. Valjakka, K. Takkinen, T. Laitinen, J. Rouvinen.Molecular dynamics studies on the thermostability of family 11 xylanases. Protein Eng Des Sel, 20 (11) ( 2007), pp. 551-559 DOI: 10.1093/protein/gzm056
[46]
S.G. Yuan, H.C.S. Chan, Z.Q. Hu. Using PyMOL as a platform for computational drug design. WIREs Comput Mol Sci, 7 (2) ( 2017), p. e1298
[47]
A. Parvez, Y. Ravikumar, R. Bisht, J. Yun, Y. Wang, S.P. Chandrika, et al.. Functional and structural roles of the dimer interface in the activity and stability of Clostridium butyricum 1,3-propanediol oxidoreductase. ACS Synth Biol, 11 (3) ( 2022), pp. 1261-1271 DOI: 10.1021/acssynbio.1c00555
[48]
X. Yu, X. Wang, P.C. Engel. The specificity and kinetic mechanism of branched-chain amino acid aminotransferase from Escherichia coli studied with a new improved coupled assay procedure and the enzyme’s potential for biocatalysis. FEBS J, 281 (1) ( 2014), pp. 391-400 DOI: 10.1111/febs.12609
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