蛋白质功能化新策略:嵌入非天然氨基酸

天然蛋白质由20种天然氨基酸组成,这些蛋白质的构筑基元包含功能基团:羧基、氨基、巯基、硫醚、羟基、碱性胺、烷基和芳基。然而,这些有限的功能基团却不足以完成生物体内所有的生物学功能。为了更好地让生命的体现者--蛋白质完成更加精确和多样的生物学功能,自然界会对蛋白质进行翻译后的修饰,包括:磷酸化,甲基化,乙酰化或者羟基化,甚至在某些情况下,进化出一种新型的翻译机制以便插入硒代半胱氨酸或者吡咯霉素。受此启发,生物化学家发展出各种生物或化学方法来改变或插入新的蛋白质构筑基元,使天然蛋白质完成其相应的生物学功能或者使其具有某些特殊的性质,甚至是创造一种新酶。该文将简单介绍这些蛋白质修饰策略以及该领域的最新进展。     

Applications of Unnatural Amino Acids in Protease Probes

Since proteases are involved in a wide range of physiological and disease states, the development of novel tools for imaging proteolytic enzyme activity is attracting increasing interest from scientists. Peptide substrates containing proteinogenic amino acids are often the first line of defining enzyme specificity. This Minireview outlines examples of major recent advances in probing proteases using unnatural amino acid residues, which greatly expands the possibilities for designing substrate probes and inhibitory activity‐based probes. This approach already yielded innovative probes that selectively target only one active protease within the group of enzymes exhibiting similar specificity both in cellular assays and in bioimaging research.     

Proximity‐Enabled Protein Crosslinking through Genetically Encoding Haloalkane Unnatural Amino Acids

The selective generation of covalent bonds between and within proteins would provide new avenues for studying protein function and engineering proteins with new properties. New covalent bonds were genetically introduced into proteins by enabling an unnatural amino acid (Uaa) to selectively react with a proximal natural residue. This proximity‐enabled bioreactivity was expanded to a series of haloalkane Uaas. Orthogonal tRNA/synthetase pairs were evolved to incorporate these Uaas, which only form a covalent thioether bond with cysteine when positioned in close proximity. By using the Uaa and cysteine, spontaneous covalent bond formation was demonstrated between an affibody and its substrate Z protein, thereby leading to irreversible binding, and within the affibody to increase its thermostability. This strategy of proximity‐enabled protein crosslinking (PEPC) may be generally expanded to target different natural amino acids, thus providing diversity and flexibility in covalent bond formation for protein research and protein engineering.     

Asymmetric Synthesis of Unnatural Amino Acids and Tamsulosin Chiral Intermediate

An efficient and enantioselective hydrogenation of N-acetylamino phenyl acrylic acids was successfully developed by using ruthenium catalyst. This methodology is important in the field of pharmaceuticals and provides a new process for the preparation of unnatural amino acids and tamsulosin chiral intermediate.

[Supplementary materials are available for this article. Go to the publisher's online edition of Synthetic Communications® for the following free supplemental resource: Full experimental and spectral details.]     

In Situ Deprotection and Incorporation of Unnatural Amino Acids during Cell‐Free Protein Synthesis

The S30 extract from E. coli BL21 Star (DE3) used for cell‐free protein synthesis removes a wide range of α‐amino acid protecting groups by cleaving α‐carboxyl hydrazides; methyl, benzyl, tert‐butyl, and adamantyl esters; tert‐butyl and adamantyl carboxamides; α‐amino form‐, acet‐, trifluoroacet‐, and benzamides; and side‐chain hydrazides and esters. The free amino acids are produced and incorporated into a protein under standard conditions. This approach allows the deprotection of amino acids to be carried out in situ to avoid separate processing steps. The advantages of this approach are demonstrated by the efficient incorporation of the chemically intractable (S)‐4‐fluoroleucine, (S)‐4,5‐dehydroleucine, and (2S,3R)‐4‐chlorovaline into a protein through the direct use of their respective precursors, namely, (S)‐4‐fluoroleucine hydrazide, (S)‐4,5‐dehydroleucine hydrazide, and (2S,3R)‐4‐chlorovaline methyl ester. These results also show that the fluoro‐ and dehydroleucine and the chlorovaline are incorporated into a protein by the normal biosynthetic machinery as substitutes for leucine and isoleucine, respectively.     

Orchestrating the Biosynthesis of an Unnatural Pyrrolysine Amino Acid for Its Direct Incorporation into Proteins Inside Living Cells

We here report the construction of an E. coli expression system able to manufacture an unnatural amino acid by artificial biosynthesis. This can be orchestrated with incorporation into protein by amber stop codon suppression inside a living cell. In our case an alkyne‐bearing pyrrolysine amino acid was biosynthesized and incorporated site‐specifically allowing orthogonal double protein labeling.     

Initiation of Protein Synthesis with Non‐Canonical Amino Acids In Vivo

By transplanting identity elements into E. coli tRNA^fMet, we have engineered an orthogonal initiator tRNA (itRNA^Ty2) that is a substrate for Methanocaldococcus jannaschii TyrRS. We demonstrate that itRNA^Ty2 can initiate translation in vivo with aromatic non‐canonical amino acids (ncAAs) bearing diverse sidechains. Although the initial system suffered from low yields, deleting redundant copies of tRNA^fMet from the genome afforded an E. coli strain in which the efficiency of non‐canonical initiation equals elongation. With this improved system we produced a protein containing two distinct ncAAs at the first and second positions, an initial step towards producing completely unnatural polypeptides in vivo. This work provides a valuable tool to synthetic biology and demonstrates remarkable versatility of the E. coli translational machinery for initiation with ncAAs in vivo.     

Biphasic Enantioselective Fluorescent Recognition of Amino Acids by a Fluorophilic Probe

A fluorophilic fluorescent probe based on a perfluoroalkyl-substituted bis(binaphthyl) compound was designed and synthesized. It displayed a highly enantioselective fluorescence response toward structurally diverse amino acids in a biphasic fluorous/aqueous system with enantiomeric fluorescent enhancement ratio (ef; ΔI_D/ΔI_L) values up to 45.2 (histidine). It can be used to determine the enantiomeric compositions of amino acids and also allows the amino acid enantiomers to be visually discriminated. NMR and mass-spectroscopic investigations provided insights into the observed high enantioselectivity. This biphasic fluorescent recognition was used to determine the enantiomeric composition of the crude phenylalanine products generated by an enzyme-catalyzed asymmetric hydrolysis under various reaction conditions. The fluorous-phase-based fluorescence measurement under the biphasic conditions was able to minimize the interference of other reaction components and thus has potential in asymmetric reaction screening.     

A Facile System for Encoding Unnatural Amino Acids in Mammalian Cells

A shuttle system has been developed to genetically encode unnatural amino acids in mammalian cells using aminoacyl‐tRNA synthetases (aaRSs) evolved in E. coli. A pyrrolysyl‐tRNA synthetase (PylRS) mutant was evolved in E. coli that selectively aminoacylates a cognate nonsense suppressor tRNA with a photocaged lysine derivative. Transfer of this orthogonal tRNA–aaRS pair into mammalian cells made possible the selective incorporation of this unnatural amino acid into proteins.

     

Front Cover: Katritzky Salts for the Synthesis of Unnatural Amino Acids and Late-Stage Functionalization of Peptides (Eur. J. Org. Chem. 12/2023)

Peptide drug discovery often benefits from the large structural diversity permitted by unnatural amino acids (UAAs). Indeed, numerous approved peptide drugs include UAAs in their sequences. Therefore, innovative chemical approaches either to synthesize UAAs or to allow late-stage functionalization of peptides are emerging themes in peptide drug discovery. Thanks to the recent advances in deaminative strategies using alkylpyridiniums salts, often referred to as Katritzky salts, a variety of radical alkylation methods have been developed. In recent years the use of Katritzky salts have become popular in peptide chemistry due to their ease of preparation from a primary amine, which is a predominant functional group in amino acids. This review highlights the progress that has been made by using Katritzky salts in the synthesis of UAAs, late-stage peptide functionalization, and peptide macrocyclization.     

Influence of an Unnatural Amino Acid Side Chain on the Conformational Dynamics of Peptides

In this work, a non‐natural amino acid, H‐propargylglycine‐OH (Pra), is chosen to examine the side‐chain effect on the backbone conformation of small peptides. The conformations of two synthesized Pra‐containing tripeptides, Ac‐Pra‐Pra‐NH₂ (PPTP) and Ac‐Pra‐Ala‐NH₂ (PATP), are examined by infrared (IR) spectroscopy in combination with molecular dynamics (MD) simulations and quantum chemical computations. By analyzing the joint distributions of backbone torsional angles, several significant conformations can be identified for the two tripeptides solvated in D₂O. At room temperature, 44 % of PPTP exists in the α‐α conformation and 33 % of PATP exists in the α‐polyproline‐II conformation. Larger structural inhomogeneity is seen in both cases by MD simulations at elevated temperatures. Thus even a small side chain, such as the propargyl group can significantly alter the peptide backbone conformations. The results suggest that there is no overwhelming conformational propensity of the Pra residue in short peptides. IR spectra simulated in the amide‐I region using two different methods, reasonably reproduce the experimental IR spectra and their temperature dependence.     

Unnatural Amino Acid Synthesis Enabled by the Regioselective Cobalt(III)‐Catalyzed Intermolecular Carboamination of Alkenes

Herein, we report an unprecedented regioselective and entirely atom‐economic cobalt(III)‐catalyzed method for the non‐annulative, intermolecular carboamination of alkenes. The methodology enables the direct synthesis of unnatural amino acid derivatives and proceeds under redox‐neutral conditions with a completely regioselective C?C bond and C?N bond formation. Furthermore, this reaction exemplifies the inherently different mechanistic behavior of the Cp*Co^III catalyst and its Cp*Rh^III counterpart, especially towards β‐H‐elimination.     

基于非天然氨基酸的蛋白质生物正交标记

生物正交化学反应正日益成为在活体内对生物大分子进行特异标记的一种有效方法. 最近涌现出的一个突出的例子是将金属钯催化的碳碳偶联反应这一在有机合成领域具有里程碑意义的反应拓展到生物大分子的标记上. 在活细胞上进行生物正交反应的一个先决条件是需要将参与这类反应的正交官能团特异地引入到目标生物大分子当中. 遗传密码子拓展技术是将多种生物正交活性基团引入到蛋白质当中的一种先进的手段; 最近发展出的基于吡咯赖氨酸氨酰合成酶和tRNA的体系能够将携带有生物正交官能团的非天然氨基酸有效地引入到原核生物、真核生物, 甚至是动物体内的蛋白质上. 在这一展望中, 我们首先介绍在生物正交反应和遗传密码子拓展这两个领域内的研究前沿与进展. 接着我们将讨论将这些新发展的研究工具, 尤其是基于钯催化的生物正交反应和基于吡咯赖氨酸氨酰合成酶的遗传密码子拓展技术, 应用于标记和修饰哺乳动物细胞蛋白质上的优势和诱人前景. 生物相兼容性更好的正交反应和更为灵活的非天然氨基酸引入技术必将有力地增强和拓宽人们在活细胞环境下特异操纵蛋白质的能力.     

Lanthanide(III) Complexes with Two Hexapeptides Incorporating Unnatural Chelating Amino Acids: Secondary Structure and Stability

Unnatural metal‐chelating amino acids bearing aminodiacetate side‐chains have been introduced into two hexapeptides to obtain efficient lanthanide‐binding peptides. The synthesis of the enantiopure Fmoc‐Ada_n(tBu)₂‐OH synthons is described with overall yields of 32 and 50 % for n=2 and n=3 side‐chain carbon atoms, respectively. The two peptides AcWAda_nPGAda_nGNH₂ ( P ⁿ ) were synthesized from the protected synthons by standard solid‐phase peptide synthesis. Studies of the lanthanide complexes of the two peptides P ⁿ by luminescence titrations, mass spectrometry, circular dichroism, and solution NMR spectroscopy demonstrate that the Ada_n chain length has a dramatic effect on the complexation properties. Indeed, the flexible compound P³ forms a mononuclear complex of moderate stability (β₁₁=10^9.9), which tends to transform into a binuclear species in the presence of excess of the metal ion. Interestingly, the more compact peptide P² provides stable Ln³⁺ complexes with the exclusive formation of the mononuclear Ln P² adduct. The stability constant of Tb P² is two orders of magnitude higher (β₁₁=10^12.1) than that measured for P³ . The 800 MHz NMR spectrum of the La³⁺ complex of P² evidences a well‐defined type II β‐turn as well as a hydrophobic Trp(indole)–Pro interaction. These interactions exemplify the non‐innocent character of the peptide spacer in the complex La P² as well as the role of a peptide secondary structure in the stabilization of metal complexes.     

Biocatalytic enantioselective synthesis of N-substituted aspartic acids by aspartate ammonia lyase

The gene encoding aspartate ammonia lyase (aspB) from Bacillus sp. YM55-1 has been cloned and overexpressed, and the recombinant enzyme containing a C-terminal His(6) tag has been purified to homogeneity and subjected to kinetic characterization. Kinetic studies have shown that the His(6) tag does not affect AspB activity. The enzyme processes L-aspartic acid, but not D-aspartic acid, with a K(m) of approximately 15 mM and a k(cat) of approximately 40 s(-1). By using this recombinant enzyme in the reverse reaction, a set of four N-substituted aspartic acids were prepared by the Michael addition of hydroxylamine, hydrazine, methoxylamine, and methylamine to fumarate. Both hydroxylamine and hydrazine were found to be excellent substrates for AspB. The k(cat) values are comparable to those observed for the AspB-catalyzed addition of ammonia to fumarate ( approximately 90 s(-1)), whereas the K(m) values are only slightly higher. The products of the enzyme-catalyzed addition of hydrazine, methoxylamine, and methylamine to fumarate were isolated and characterized by NMR spectroscopy and HPLC analysis, which revealed that AspB catalyzes all the additions with excellent enantioselectivity (>97 % ee). Its broad nucleophile specificity and high catalytic activity make AspB an attractive enzyme for the enantioselective synthesis of N-substituted aspartic acids, which are interesting building blocks for peptide and pharmaceutical synthesis as well as for peptidomimetics.