Chemical Synthesis of the 20 kDa Heme Protein Nitrophorin 4 by α‐Ketoacid‐Hydroxylamine (KAHA) Ligation

The chemical synthesis of the 184‐residue ferric heme‐binding protein nitrophorin 4 was accomplished by sequential couplings of five unprotected peptide segments using α‐ketoacid‐hydroxylamine (KAHA) ligation reactions. The fully assembled protein was folded to its native structure and coordinated to the ferric heme b cofactor. The synthetic holoprotein, despite four homoserine residues at the ligation sites, showed identical properties to the wild‐type protein in nitric oxide binding and nitrite dismutase reactivity. This work establishes the KAHA ligation as a valuable and viable approach for the chemical synthesis of proteins up to 20 kDa and demonstrates that it is well‐suited for the preparation of hydrophobic protein targets.     

A Threonine‐Forming Oxazetidine Amino Acid for the Chemical Synthesis of Proteins through KAHA Ligation

α‐Ketoacid‐hydroxylamine (KAHA) ligation allows the coupling of unprotected peptide segments through the chemoselective formation of an amide bond. Currently, the most widely used variant employs a 5‐membered cyclic hydroxylamine that forms a homoserine ester as the primary ligation product. In order to directly form amide‐linked threonine residues at the ligation site, we prepared a new 4‐membered cyclic hydroxylamine building block. This monomer was applied to the synthesis of wild‐type ubiquitin‐conjugating enzyme UbcH5a (146 residues) and Titin protein domain TI I27 (89 residues). Both the resulting UbcH5a and the variant with two homoserine residues showed identical activity to a recombinant variant in a ubiquitination assay.     

Tris­[2‐(benzoyl­amino)­ethyl]­amine

Tris­[2‐(benzoyl­amino)­ethyl]­amine [alternatively, N,N′,N′′‐(nitrilo­tri­ethyl)­tri­benz­amide], C₂₇H₃₀N₄O₃, adopts a folded structure, forming a symmetrical cavity with an average depth of 7.3 Å and width ranging from 4.1–4.4 Å. The folded structure is a result of one intramolecular N—H?O hydrogen bond. A linear chain motif along the c axis best describes the extended intermolecular N—H?O hydrogen bonding.     

Polycyclic N‐Heterocyclic Compounds. 56 Reaction of N‐(5,6‐Dihydro[1]benzoxepino[5,4‐d]pyrimidin‐4‐yl)amidine or Its Amide Oxime Derivatives with Hydroxylamine Hyrdochloride

The reactions of N‐(5,6‐dihydro[1]benzoxepino[5,4‐ d]pyrimidin‐4‐yl)amidines or its amide oxime derivatives with hydroxylamine hydrochloride gave abnormal cyclization products via a ring cleavage of pyrimidine component accompanied with a ring closure of [1,2,4]oxadiazole.     

Synthesis of Enantiomerically Pure Isoxazolidine Monomers for the Preparation of β3‐Oligopeptides by Iterative α‐Keto Acid?Hydroxylamine (KAHA) Ligations

A versatile method for the synthesis of enantiomerically pure isoxazolidine monomers for the synthesis of β³‐oligopeptides via α‐keto acid? hydroxylamine (KAHA) ligation is presented. This one‐pot synthetic method utilizes in situ generated nitrones bearing gulose‐derived chiral auxiliaries for the asymmetric 1,3‐dipolar cycloaddition with methyl 2‐methoxyacrylate. The resulting enantiomerically pure isoxazolidine monomers bearing diverse side chains (proteinogenic and non‐proteinogenic) can be synthesized in either configuration (like‐ and unlike‐configured). The scalable and enantioselective synthesis of the isoxazolidine monomers enables the use of the synthesis of β³‐oligopeptides via iterative α‐keto acid? hydroxylamine (KAHA) ligation.     

Stereospecific control of peptide gas‐phase ion chemistry with cis and trans cyclo ornithine residues

We report non‐chiral amino acid residues cis‐ and trans‐1,4‐diaminocyclohexane‐1‐carboxylic acid (cyclo‐ornithine, cO) that exhibit unprecedented stereospecific control of backbone dissociations of singly charged peptide cations and hydrogen‐rich cation radicals produced by electron‐transfer dissociation. Upon collision‐induced dissociation (CID) in the slow heating regime, peptide cations containing trans‐cO residues undergo facile backbone cleavages of amide bonds C‐terminal to trans‐cO. By contrast, peptides with cis‐cO residues undergo dissociations at several amide bonds along the peptide ion backbone. Diastereoisomeric cO‐containing peptides thus provide remarkably distinct tandem mass spectra. The stereospecific effect in CID of the trans‐cO residue is explained by syn‐facially directed proton transfer from the 4‐ammonium group at cO to the C‐terminal amide followed by neighboring group participation in the cleavage of the CO―NH bond, analogous to the aspartic acid and ornithine effects. Backbone dissociations of diastereoisomeric cO‐containing peptide ions generate distinct [b_n]⁺‐type fragment ions that were characterized by CID‐MS³ spectra. Stereospecific control is also reported for electron‐transfer dissociation of cis‐ and trans‐cO containing doubly charged peptide ions. The stereospecific effect upon electron transfer is related to the different conformations of doubly charged peptide ions that affect the electron attachment sites and ensuing N―C_α bond dissociations.     

Nitroxide‐mediated controlled radical polymerizations of styrene derivatives

Several (protected) amine and alcohol functionalized styrene monomers were synthesized via readily accessible synthetic routes. The controlled radical copolymerization of these functionalized styrene monomers with styrene was performed using two alkoxyamines, namely N‐(2‐methylpropyl)‐N‐(1‐diethylphosphono‐2,2‐dimethylpropyl)‐O‐(2‐carboxylprop‐2‐yl) hydroxylamine (MAMA‐SG1) and N‐tert‐butyl‐N‐(2‐methyl‐1‐phenylpropyl)‐O‐(1‐phenylethyl)hydroxylamine. The copolymers obtained showed low polydispersities, controlled molecular weights, and a random topology. The thermal properties of the polymers were determined with differential scanning calorimetry. All polymers were amorphous and showed glass transition temperatures between 40 and 111 °C. Deprotection of the copolymers afforded amine or alcohol pendant polystyrenes which were readily functionalized with isocyanates. © 2011 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2012     

Intramolecular cyclization assistance for fast degradation of ornithine‐based poly(ester amide)s

Inspired by the spontaneous cyclization of ornithine in peptides, polyesters containing protected ornithine (Orn) side chains along the backbone were synthesized and shown to degrade rapidly upon deprotection through intramolecular cyclization. A new ornithine‐based poly(ester amide) PEA 1 and a lysine‐based control PEA 2, both bearing the light‐sensitive protecting group o‐nitrobenzyl alcohol (ONB), were synthesized. Tert‐butyl carbamate (Boc)‐protected versions 1‐Boc and 2‐Boc were also synthesized for proof of concept. GPC confirmed that 1‐Boc degrades over 40 times faster than 2‐Boc following deprotection into the designed intramolecular cyclization products. Finally, TEM visualization of particles made from 1 encapsulating iron oxide nanoparticles reveals complete disruption of nanoparticles and release of payload within a day upon UV irradiation. © 2013 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2013 , 51, 3783–3790     

Polycyclic N‐heterocyclic compounds. Part 66: Synthesis of N‐[2‐([1,2,4]oxadiazol‐5‐yl)cyclopenten‐1‐yl]formamide oximes and their evaluation as inhibitors of platelet aggregation

N‐[2‐([1,2,4]Oxadiazol‐5‐yl)cyclopenten‐1‐yl]formamide oximes were synthesized by fusion of (6,7‐dihydro‐5H‐cyclopenta[1,2‐d]pyrimidin‐4‐yl)amidines and/or their amide oximes with hydroxylamine hydrochloride through a subsequent rearrangement reaction. Assay of the products for anti‐platelet aggregation activity revealed that certain of them showed promising inhibitory effect on arachidonic acid‐induced platelet aggregation. J. Heterocyclic Chem., (2011).     

Photoprotected Peptide α‐Ketoacids and Hydroxylamines for Iterative and One‐Pot KAHA Ligations: Synthesis of NEDD8

The convergent synthesis of proteins by multiple ligations requires segments protected at the N‐ and/or C‐terminus with masking groups that are orthogonal to the acid‐ and base‐labile protecting groups used in Fmoc‐SPPS. They must be stable to solid‐phase peptide synthesis, HPLC purification, and ligation conditions and easily removed in the presence of unprotected side chains. In this report, we document photolabile protecting groups for both α‐ketoacids and hydroxylamines, the key functional groups employed in the α‐ketoacid–hydroxylamine (KAHA) ligation. The novel photoprotected α‐ketoacid is easily installed onto numerous different C‐terminal peptide α‐ketoacids and removed by UV light under aqueous conditions. These advances were applied to the one‐pot synthesis of NEDD8, an important modifier protein, by three different convergent routes. These new protecting groups provide greater flexibility on the order of fragment assembly and reduce the number of reaction and purification steps needed for protein synthesis with the KAHA ligation.     

Design,Synthesis, EPR‐Studies and Conformational Bias of Novel Spin‐Labeled DCC‐Analogues for the Highly Regioselective Labeling of Aliphatic and Aromatic Carboxylic Acids

Novel types of spin‐labeled N,N′‐dicyclohexylcarbodiimides (DCC) are reported that bear a 2,2,6,6‐tetramethylpiperidinyloxyl (TEMPO) residue on one side and different aromatic and aliphatic cyclohexyl analogues on the other side of the diimide core. These readily available novel reagents add efficiently to aliphatic and aromatic carboxylic acids, forming two possible spin‐labeled amide derivatives with different radical distances of the resulting amide. The addition of aromatic DCC analogues proceeds with excellent selectivity, giving amides where the carboxylic acid is exclusively connected to the aromatic residue, while little or no selectivity was observed for the aliphatic congeners. The usefulness of these adducts in structural studies was demonstrated by EPR (electron paramagnetic resonance) measurements of biradical adducts of biphenyl‐4,4′‐dicarboxylic acids. These analyses also reveal high degrees of conformational bias for aromatic DCC derivatives, which further underlines the powerfulness of these novel reagents. This observation was further corroborated by quantum chemical calculations, giving a detailed understanding of the structural dynamics, while detailed information on the solid state structure of all novel reagents was obtained by X‐ray structure analyses.     

Polycyclic N‐Heterocyclic Compounds. Part 84: Reaction of N‐(pyrido[3′,2′:4,5]thieno[3,2‐d]pyrimidin‐4‐yl)amidines or N‐(pyrido[2′,3′:4,5]furo[3,2‐d]pyrimidin‐4‐yl)amidines with Hydroxylamine Hydrochloride

The reactions of nine N‐(pyrido[3′,2′:4,5]thieno[3,2‐d]pyrimidin‐4‐yl)amidines ( 3 ) with hydroxylamine hydrochloride produced new cyclization products. These were formed via ring cleavage of the pyrimidine component followed by a 1,2,4‐oxadiazole‐forming ring closure to give N‐[2‐([1,2,4]oxadiazol‐5‐yl)thieno[2,3‐b]pyridin‐3‐yl]formamide oximes ( 11 ). Reaction of six N‐(pyrido[2′,3′:4,5]furo[3,2‐d]pyrimidin‐4‐yl)amidines ( 12 ) with hydroxylamine hydrochloride gave similar results. Effects of the newly synthesized compounds on pentosidine formation were also evaluated.     

Facile backbone (1H, 15N, 13Ca,and 13C′) assignment of 13C/15N‐labeled proteins using orthogonal projection planes of HNN and HN(C)N experiments and its automation

Recently, we introduced an efficient high‐throughput protocol for backbone assignment of small folded proteins based on two‐dimensional (2D) projections of HN(C)N suite of experiments and its automation [Borkar et al., J. Biomol. NMR 2011, 50(3), 285–297]. This strategy provides complete sequence‐specific assignment of backbone (¹H, ¹⁵N, ¹³C^α, and ¹³C′) resonances in less than a day; thus, it has great implications for high‐throughput structural proteomics. However, in cases when such small folded protein exhibits substantial amide ¹H shift degeneracy (typically seen in alpha‐helical proteins), the strategy may fail or lead to ambiguities. Another limitation is with respect to the identification of checkpoints from the variants of 2D‐hncNH spectrum. For example, a protein with many GG, GA, AA, SS, TS, TT, and TS types of dipeptide stretches along its sequence, thus the identification of NH cross‐peak corresponding to second G, A, S, or T becomes difficult. In this backdrop, we present here two improvements to enhance the utility of the proposed high‐throughput AUTOmatic Backbone Assignment protocol: (i) use of 2D‐hNnH spectrum and its variants that display additional ¹H–¹⁵N correlations and thus help to resolve ambiguities arising because of amide ¹H shift degeneracy and (ii) optimization of the τ_CN delay in the 2D‐hncNH experiment that, when properly adjusted, is observed to help remove ambiguities in the identification of the checkpoints. These improvements have also been incorporated in the automation program AUTOmatic Backbone Assignment. Finally, the performance of the strategy and the automation has been demonstrated using the chicken SH3 domain protein. Copyright © 2012 John Wiley & Sons, Ltd.     

新颖的双胰岛素取代钴(III)卟啉的制备和表征

A novel insulin-disubstituted Co(Ⅲ)protoporphyrin IX,CoPI,where I is insulin and CoP is Co(Ⅲ)protopor-phyrin IX,was prepared by covalently coupling the propionate groups on the porphyrin ring to the ε-amino groupsof B29-Lys on insulin via amide linkages.The FTIR spectra in the amide I region(1600—1700 cm~(-1))and circulardichroism study show that CoPI has a conformation similar to the insulin at pH 6.9,whereas it exhibits significantconformational changes in structure as compared with the insulin self at pH 8.2.The pH absorption titration indi-cates that the alkaline conditions(pH≥8.0)are required for the formation of complexes between the free CoP andthe insulin.The thermodynamic and kinetic data reveal that free CoP is bound to either the zinc-insulin or free insu-lin with a dissociation constant of(2.0±0.3)×10~(-5)or(2.2±0.3)×10~(-5)mol/L.     

Polycyclic N‐heterocyclic compounds,part 67: Reaction of 6,7‐substituted N‐(quinazolin‐4‐yl)amidine derivatives with hydroxylamine hydrochloride: Formation of in vitro inhibitors of pentosidine

Reactions of N‐(quinazolin‐4‐yl)amidines and their amide oximes with hydroxylamine hydrochloride gave cyclization products that were formed by an initial ring cleavage of the pyrimidine component followed by a ring closure formation of 1,2,4‐oxadiazole to give N‐[2‐([1,2,4]oxadiazol‐5‐yl)phenyl]formamide oximes. All isolated products were evaluated for in vitro inhibitory activity on the formation of pentosidine, which is one of representative advanced glycation end products. Some products exhibited significant inhibitory activity against pentosidine formation. J. Heterocyclic Chem., (2011).     

Potassium Acyltrifluoroborate (KAT) Ligations are Orthogonal to Thiol‐Michael and SPAAC Reactions: Covalent Dual Immobilization of Proteins onto Synthetic PEG Hydrogels

The covalent immobilization of peptides, proteins, and other biomolecules to hydrogels provides a biologically mimicking environment for cell and tissue growth. Bioorthogonal chemical reactions can serve as a tool for this, but the paucity of such reactions and mutual incompatibilities limits the number of distinct molecules that can be introduced. We now report that the potassium acyltrifluoroborate (KAT ) amide‐forming ligation is orthogonal to both thiol‐Michael and strain promoted azide alkyne cycloadditions (SPAAC ) and the requisite functional groups – KAT s and hydroxylamines – are stable and compatible to hydrogel formation, protein modification, and post‐assembly immobilization of biomolecules onto hydrogels. In combination these ligations enables stepwise covalent protein immobilization of multiple BSA ‐derivatives onto the hydrogel scaffold regardless of the order of addition.     

A silaproline‐containing dipeptide

The silaproline‐containing dipeptide N‐(3,3‐di­methyl‐1‐pivaloyl‐1‐aza‐3‐sila‐5‐cyclo­pentyl­carbonyl)‐l ‐alanine iso­propyl­amide, C₁₇H₃₃N₃O₃Si, has two independent molecules in the asymmetric unit and each adopts a β‐II folded conformation, where the amide on the terminal C interacts intramolecularly with the pivaloyl O atom. The five‐membered silaproline ring is C^β‐puckered, an infrequent conformation for the homol­ogous proline ring.     

Folding‐Induced Folding: The Assembly of Aromatic Amide and 1,2,3‐Triazole Hybrid Helices

Folding‐induced folding for the construction of artificial hybrid helices from two different kinds of aromatic sequences is described. Linear compounds 1 a , 1 b , and 2 , containing one aromatic amide trimer or pentamer and one or two aromatic 1,2,3‐triazole tetramers, have been designed and synthesized. The trimeric and pentameric amide segments are driven by intramolecluar N?H???F hydrogen bonding to adopt a folded or helical conformation, whereas the triazole segment is intrinsically disordered. In organic solvents of low polarity, the amide foldamer segment induces the attached triazole segment(s) to fold through intramolecular stacking, leading to the formation of hybrid helices. The helical conformation of these hybrid sequences has been confirmed by ¹H and ¹⁹F NMR spectroscopy, UV/Vis spectroscopy, circular dichroism (CD) experiments, and theoretical calculations. It was found that the amide pentamer exhibits a stronger ability to induce the folding of the attached triazole segment(s) compared with that of the shorter trimer. Enantiomers (R)‐ 3 and (S)‐ 3 , which contain an R‐ or S‐(1‐naphthyl)ethylamino group at the end of a tetraamide segment, have also been synthesized. CD experiments showed that introduction of a chiral group caused the whole framework to produce a strong helicity bias. Density‐functional‐theory calculations on (S)‐ 3 suggested that this compound exists as a right‐handed (P) helix.     

Engineering SpyCatcher Variants with Proteolytic Sites for Less‐Trace Ligation

The SpyTag/SpyCatcher reaction is a powerful tool for bioconjugation, but it leaves a complex of considerable size after ligation. To facilitate removal of the catalytic fragment, proteolytic recognition sites (such as DDDDK, AVLQ, and WELQ) were directly engineered into the first or second loop of SpyCatcher at locations after the reactive lysine to give a set of cleavable SpyCatcher variants. Among them, SpyCatcher^DDDDK exhibits excellent reactivity with SpyTag and could still be cleaved proteolytically by enterokinase after ligation. Notably, SpyCatcher^DDDDK is disordered in solution and forms an ordered complex upon reaction with SpyTag with a second order rate constant of 99.2 ± 0.1 M^–1·s^–1, which is comparable to, if not faster than, most click reactions. The results demonstrate the high sequence plasticity of SpyCatcher and suggest that covalent bond formation may confer robustness on the folded structure against extensive mutation. These variants add to the expanding toolbox of genetically‐encoded peptide‐protein chemistry with diverse features.