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.     

Long‐Range Chemical Ligation from N→N Acyl Migrations in Tryptophan Peptides via Cyclic Transition States of 10‐ to 18‐Members

Chemical ligations to form native peptides from N→N acyl migrations in Trp‐containing peptides via 10‐ to 18‐membered cyclic transition states are described. In this study, a statistical, predictive model that uses an extensive synthetic and computational approach to rationalize the chemical ligation is reported. N→N acyl migrations that form longer native peptides without the use of Cys/Ser/Tyr residues or an auxiliary group at the ligation site were achieved. The feasibility of these traceless chemical ligations is supported by the N?C bond distance in N‐acyl isopeptides. The intramolecular nature of the chemical ligations is justified by using competitive experiments and theoretical calculations.     

Semisynthesis of Biologically Active Glycoforms of the Human Cytokine Interleukin 6

Human interleukin 6 (IL‐6) is a potent cytokine with immunomodulatory properties. As the influence of N‐glycosylation on the in vivo activities of IL‐6 could not be elucidated so far, a semisynthesis of homogeneous glycoforms of IL‐6 was established by sequential native chemical ligation. The four cysteines of IL‐6 are convenient for ligations and require only the short synthetic glycopeptide 43–48. The Cys‐peptide 49–183 could be obtained recombinantly by cleavage of a SUMO tag. The fragment 1–42 was accessible by the simultaneous cleavage of two inteins, leading to the 1–42 thioester with the native N‐terminus. Ligation and refolding studies showed that the inherently labile Asp? Pro bond 139–140 was detrimental for the sequential C‐ to N‐terminal ligation. A reversed ligation sequence using glycopeptide hydrazides gave full‐length IL‐6 glycoproteins, which showed full bioactivity after efficient refolding and purification.     

Copper‐Mediated Selenazolidine Deprotection Enables One‐Pot Chemical Synthesis of Challenging Proteins

While chemical protein synthesis has granted access to challenging proteins, the synthesis of longer proteins is often limited by low abundance or non‐strategic placement of cysteine residues, which are essential for native chemical ligations, as well as multiple purification and isolation steps. We describe the one‐pot total synthesis of human thiosulfate:glutathione sulfurtransferase (TSTD1). WT‐TSTD1 was synthesized in a C‐to‐N synthetic approach involving multiple NCL reactions, Cu^II‐mediated deprotection of selenazolidine (Sez), and chemoselective deselenization. The seleno‐analog Se‐TSTD1, in which the active site Cys is replaced with selenocysteine, was also synthesized with a kinetically controlled ligation with an N‐to‐C synthetic approach. The catalytic activity of the two proteins indicated that Se‐TSTD1 possessed only four‐fold lower activity than WT‐TSTD1, thus suggesting that selenoproteins can have physiologically comparable sulfutransferase activity to their cysteine counterparts.     

Cysteine/Penicillamine Ligation Independent of Terminal Steric Demands for Chemical Protein Synthesis

The chemical ligation of two unprotected peptides to generate a natural peptidic linkage specifically at the C‐ and N‐termini is a desirable goal in chemical protein synthesis but is challenging because it demands high reactivity and selectivity (chemo‐, regio‐, and stereoselectivity). We report an operationally simple and highly effective chemical peptide ligation involving the ligation of peptides with C‐terminal salicylaldehyde esters to peptides with N‐terminal cysteine/penicillamine. The notable features of this method include its tolerance of steric hinderance from the side groups on either ligating terminus, thereby allowing flexible disconnection at sites that are otherwise difficult to functionalize. In addition, this method can be expanded to selective desulfurization and one‐pot ligation‐desulfurization reactions. The effectiveness of this method was demonstrated by the synthesis of VISTA (216‐311), PD‐1 (192‐288) and Eglin C.     

Three new phosphoric triamides with a [C(O)NH]P(O)[N(C)(C)]2 skeleton: a database analysis of C—N—C and P—N—C bond angles

In N,N,N′,N′‐tetraethyl‐N′′‐(4‐fluorobenzoyl)phosphoric triamide, C₁₅H₂₅FN₃O₂P, (I), and N‐(2,6‐difluorobenzoyl)‐N′,N′′‐bis(4‐methylpiperidin‐1‐yl)phosphoric triamide, C₁₉H₂₈F₂N₃O₂P, (II), the C—N—C angle at each tertiary N atom is significantly smaller than the two P—N—C angles. For the other new structure, N,N′‐dicyclohexyl‐N′′‐(2‐fluorobenzoyl)‐N,N′‐dimethylphosphoric triamide, C₂₁H₃₃FN₃O₂P, (III), one C—N—C angle [117.08 (12)°] has a greater value than the related P—N—C angle [115.59 (9)°] at the same N atom. Furthermore, for most of the analogous structures with a [C(=O)NH]P(=O)[N(C)(C)]₂ skeleton deposited in the Cambridge Structural Database [CSD; Allen (2002). Acta Cryst. B 58 , 380–388], the C—N—C angle is significantly smaller than the two P—N—C angles; exceptions were found for four structures with the N‐methylcyclohexylamide substituent, similar to (III), one structure with the seven‐membered cyclic amide azepan‐1‐yl substituent and one structure with an N‐methylbenzylamide substituent. The asymmetric units of (I), (II) and (III) contain one molecule, and in the crystal structures, adjacent molecules are linked via pairs of N—H...O=P hydrogen bonds to form dimers.     

Computational Insights into the Charge Relaying Properties of β‐Turn Peptides in Protein Charge Transfers

Density functional theory calculations suggest that β‐turn peptide segments can act as a novel dual‐relay elements to facilitate long‐range charge hopping transport in proteins, with the N terminus relaying electron hopping transfer and the C terminus relaying hole hopping migration. The electron‐ or hole‐binding ability of such a β‐turn is subject to the conformations of oligopeptides and lengths of its linking strands. On the one hand, strand extension at the C‐terminal end of a β‐turn considerably enhances the electron‐binding of the β‐turn N terminus, due to its unique electropositivity in the macro‐dipole, but does not enhance hole‐forming of the β‐turn C terminus because of competition from other sites within the β‐strand. On the other hand, strand extension at the N terminal end of the β‐turn greatly enhances hole‐binding of the β‐turn C terminus, due to its distinct electronegativity in the macro‐dipole, but does not considerably enhance electron‐binding ability of the N terminus because of the shared responsibility of other sites in the β‐strand. Thus, in the β‐hairpin structures, electron‐ or hole‐binding abilities of both termini of the β‐turn motif degenerate compared with those of the two hook structures, due to the decreased macro‐dipole polarity caused by the extending the two terminal strands. In general, the high polarity of a macro‐dipole always plays a principal role in determining charge‐relay properties through modifying the components and energies of the highest occupied and lowest unoccupied molecular orbitals of the β‐turn motif, whereas local dipoles with low polarity only play a cooperative assisting role. Further exploration is needed to identify other factors that influence relay properties in these protein motifs.     

Acetato(N‐phenylpyridine‐2‐carboxamidato‐κ2N,N)(N‐phenylpyridine‐2‐carboxamide‐κ2N1,O)copper(II)

The title complex, [Cu(C₁₂H₉N₂O)(C₂H₃O₂)(C₁₂H₁₀N₂O)], is a neutral Cu^II complex with a primary N₃O₂ coordination sphere. The Cu centre coordinates to both a deprotonated and a neutral molecule of N‐phenylpyridine‐2‐carboxamide and also to an acetate anion. The coordination around the metal centre is asymmetric, the deprotonated ligand providing two N donor atoms [Cu—N = 1.995 (2) and 2.013 (2) Å] and the neutral ligand providing one N and one O donor atom to the coordination environment [Cu—N = 2.042 (2) Å and Cu—O = 2.2557 (19) Å], the fifth donor being an O atom of the acetate ion [Cu—O = 1.9534 (19) Å]. The remaining O atom from the acetate ion can be considered as a weak donor atom [Cu—O = 2.789 (2) Å], conferring to the Cu complex an asymmetric octahedral geometry. The crystal structure is stabilized by intermolecular N—H...O, C—H...O and C—H...π interactions.     

2J(P,C) and 3J(P,C) Coupling Constants in Some New Phosphoramidates. Crystal Structures of CF3C(O)N(H)P(O)[N(CH3)(CH2C6H5)]2 and 4‐NO2‐C6H4N(H)P(O)[4‐CH3‐NC5H9]2

Some new phosphoramidates were synthesized and characterized by ¹H, ¹³C, ³¹P NMR, IR spectroscopy and elemental analysis. The structures of CF₃C(O)N(H)P(O)[N(CH₃)(CH₂C₆H₅)]₂ ( 1 ) and 4‐NO₂‐C₆H₄N(H)P(O)[4‐CH₃‐NC₅H₉]₂ ( 6 ) were confirmed by X‐ray single crystal determination. Compound 1 forms a centrosymmetric dimer and compound 6 forms a polymeric zigzag chain, both via ‐N‐H…O=P‐ intermolecular hydrogen bonds. Also, weak C‐H…F and C‐H…O hydrogen bonds were observed in compounds 1 and 6 , respectively. ¹³C NMR spectra were used for study of ²J(P,C) and ³J(P,C) coupling constants that were showed in the molecules containing N(C₂H₅)₂ and N(C₂H₅)(CH₂C₆H₅) moieties, ²J(P,C)>³J(P,C). A contrast result was obtained for the compounds involving a five‐membered ring aliphatic amine group, NC₄H₈. ²J(P,C) for N(C₂H₅)₂ moiety and in NC₄H₈ are nearly the same, but ³J(P, C) values are larger than those in molecules with a pyrrolidinyl ring. This comparison was done for compounds with six and seven‐membered ring amine groups. In compounds with formula XP(O)[N(CH₂R)(CH₂C₆H₅)]₂, ²J(P,CH₂)_benzylic>²J(P,CH₂)_aliphatic, in an agreement with our previous study.     

Chemical Synthesis of Proteins with Non‐Strategically Placed Cysteines Using Selenazolidine and Selective Deselenization

Although native chemical ligation has enabled the synthesis of hundreds of proteins, not all proteins are accessible through typical ligation conditions. The challenging protein, 125‐residue human phosphohistidine phosphatase 1 (PHPT1), has three cysteines near the C‐terminus, which are not strategically placed for ligation. Herein, we report the first sequential native chemical ligation/deselenization reaction. PHPT1 was prepared from three unprotected peptide segments using two ligation reactions at cysteine and alanine junctions. Selenazolidine was utilized as a masked precursor for N‐terminal selenocysteine in the middle segment, and, following ligation, deselenization provided the native alanine residue. This approach was used to synthesize both the wild‐type PHPT1 and an analogue in which the active‐site histidine was substituted with the unnatural and isosteric amino acid β‐thienyl‐l ‐alanine. The activity of both proteins was studied and compared, providing insights into the enzyme active site.     

Efficient Chemical Protein Synthesis using Fmoc‐Masked N‐Terminal Cysteine in Peptide Thioester Segments

We report an operationally simple method to facilitate chemical protein synthesis by fully convergent and one‐pot native chemical ligations utilizing the fluorenylmethyloxycarbonyl (Fmoc) moiety as an N‐masking group of the N‐terminal cysteine of the middle peptide thioester segment(s). The Fmoc group is stable to the harsh oxidative conditions frequently used to generate peptide thioesters from peptide hydrazide or o‐aminoanilide. The ready availability of Fmoc‐Cys(Trt)‐OH, which is routinely used in Fmoc solid‐phase peptide synthesis, where the Fmoc group is pre‐installed on cysteine residue, minimizes additional steps required for the temporary protection of the N‐terminal cysteinyl peptides. The Fmoc group is readily removed after ligation by short exposure (<7 min) to 20 % piperidine at pH 11 in aqueous conditions at room temperature. Subsequent native chemical ligation reactions can be performed in presence of piperidine in the same solution at pH 7.     

1,N6‐Etheno‐2′‐deoxytubercidin hemihydrate

The title compound [systematic name: 7‐(2‐deoxy‐β‐d ‐erythro‐pentofuranosyl)‐7H‐imidazo[1,2‐c]pyrrolo[2,3‐d]pyrimidine hemihydrate], 2C₁₃H₁₄N₄O₃·H₂O or (I)·0.5H₂O, shows two similar conformations in the asymmetric unit. These two conformers are connected through one water molecule by hydrogen bonds. The N‐glycosylic bonds of both conformers show an almost identical anti conformation with χ = −107.7 (2)° for conformer (I‐1) and −107.0 (2)° for conformer (I‐2). The sugar moiety adopts an unusual N‐type (C3′‐endo) sugar pucker for 2′‐deoxyribonucleosides, with P = 36.8 (2)° and τ_m = 40.6 (1)° for conformer (I‐1), and P = 34.5 (2)° and τ_m = 41.4 (1)° for conformer (I‐2). Both conformers and the solvent molecule participate in the formation of a three‐dimensional pattern with a `chain'‐like arrangement of the conformers. The structure is stabilized by intermolecular O—H...O and O—H...N hydrogen bonds, together with weak C—H...O contacts.     

Zinc(II)‐N2O2 ligation complex‐based DNA/protein binder and cleaver having enhanced cytotoxic and phosphatase activity

The alkyne arms containing zinc(II) N₂O₂ ligation complexes ( 1 ) and ( 2 ) were prepared from 2,2′‐{cyclohexane‐1,2‐diylbis[nitrilo(E)methylylidene]}bis[5‐(prop‐2‐yn‐1‐yloxy)phenol] (L¹) and 2,2′‐{1,2‐phenylenebis[nitrilo(E)methylylidene]}bis[5‐(prop‐2‐yn‐1‐yloxy)phenol] (L²) and characterized by analytical and various spectral techniques. The molecular geometry of 1 and 2 was optimized by Density Functional Theory (DFT) at B3LYP/6‐311G(d,p) level and compared with literature. The complexes are stable in solution, and their solution structure was assessed using NMR and ESI‐MS spectroscopy. Topological analysis of the electron density and nature of the bonding in the complexes has been determined by using Bader's AIM method. The interaction and binding modes of calf thymus DNA (CT‐DNA) with complexes ( 1 and 2 ) were investigated by using absorption and emission spectral and viscometric studies. The nuclease activity investigated through gel electrophoresis reveals that 1 and 2 exhibits a significant DNA cleavage activity via a hydrolytic pathway and is further confirmed by an experiment performed in the presence of T4 ligase. The protein binding ability of 1 and 2 with bovine serum albumin (BSA) protein evaluated show good protein binding propensity. In‐vitro cytotoxicity of the complexes has shown significant activity against human brain tumor (U87 MG) and breast carcinoma (BT20) cancer cell lines. The comet assay has been used to determine the extent of DNA fragmentation in cancer cells. The phosphatase activity investigated through kinetic measurements establishes that the zinc complexes possess significant hydrolytic efficiency and follow the order 2  >  1 . The DFT calculations have also been carried out to support the proposed mechanistic pathway of catalytic activity.     

Total Chemical Synthesis of the Enzyme Sortase AΔN59 with Full Catalytic Activity

The enzyme sortase A is a ligase which catalyzes transpeptidation reactions. 1 , 2 Surface proteins, including virulence factors, that have a C terminal recognition sequence are attached to Gly₅ on the peptidoglycan of bacterial cell walls by sortase A. 1 The enzyme is an important anti‐virulence and anti‐infective drug target for resistant strains of Gram‐positive bacteria. 2 In addition, because sortase A enables the splicing of polypeptide chains, the transpeptidation reaction catalyzed by sortase A is a potentially valuable tool for protein science. 3 Here we describe the total chemical synthesis of enzymatically active sortase A. The target 148 residue polypeptide chain of sortase A_ΔN59 was synthesized by the convergent chemical ligation of four unprotected synthetic peptide segments. The folded protein molecule was isolated by size‐exclusion chromatography and had full enzymatic activity in a transpeptidation assay. Total synthesis of sortase A will enable more sophisticated engineering of this important enzyme molecule.     

The first phosphoramide–mercury(II) complex with a Cl2Hg–OP[N(C)(C)]3 segment

Mercury(II) exhibits a strong preference for linear coordination which has been attributed to relativistic effects splitting the 6p orbitals and promoting sp hybridization. If the two ligands attached to the mercury(II) ion are weak donors, the metal ion can act as a good Lewis acid and expand its coordination number. Moreover, mercury has a special affinity for softer bases, such as S and N atoms, and has much less affinity for hard bases, such as those including an O atom. The asymmetric unit of dichlorido[tris(piperidin‐1‐yl)phosphane oxide‐κO]mercury(II)–dichloridomercury(II) (2/1), [HgCl₂{(C₅H₁₀N)₃PO}]₂·[HgCl₂], is composed of one HgCl₂{(C₅H₁₀N)₃PO} complex and one half of a discrete HgCl₂ entity located on an inversion centre. The coordination environment around the Hg^II centre in the complex component is a distorted T‐shape. Bond‐valence‐sum calculations confirm the three‐coordination mode of the Hg^II atom of the complex molecule. The noncovalent nature of the Hg…Cl and Hg…O interactions in the structure are discussed.     

Syntheses and Spectroscopic Study of Some New N‐4‐Fluorobenzoyl Phosphoric Triamides; Crystal Structures of 4‐F‐C6H4C(O)N(H)P(O)R2, R = NH‐C(CH3)3, NH‐CH2C6H5, N(CH3)(CH2C6H5)

Some new N‐4‐Fluorobenzoyl phosphoric triamides with formula 4‐F‐C₆H₄C(O)N(H)P(O)X₂, X = NH‐C(CH₃)₃ ( 1 ), NH‐CH₂‐CH=CH₂ ( 2 ), NH‐CH₂C₆H₅ ( 3 ), N(CH₃)(C₆H₅) ( 4 ), NH‐CH(CH₃)(C₆H₅) ( 5 ) were synthesized and characterized by ¹H, ¹³C, ³¹P NMR, IR and Mass spectroscopy and elemental analysis. The structures of compounds 1 , 3 and 4 were investigated by X‐ray crystallography. The P=O and C=O bonds in these compounds are anti. Compounds 1 and 3 form one dimensional polymeric chain produced by intra‐ and intermolecular ‐P=O···H‐N‐ hydrogen bonds. Compound 4 forms only a centrosymmetric dimer in the crystalline lattice via two equal ‐P=O···H‐N‐ hydrogen bonds. ¹H and ¹³C NMR spectra show two series of signals for the two amine groups in compound 1 . This is also observed for the two α‐methylbenzylamine groups in 5 due to the presence of chiral carbon atom in molecule. ¹³C NMR spectrum of compound 4 shows that ²J(P,C_aliphatic) coupling constant for CH₂ group is greater than for CH₃ in agreement with our previous study. Mass spectra of compounds 1 ‐ 3 (containing 4‐F‐C₆H₄C(O)N(H)P(O) moiety) indicate the fragments of amidophosphoric acid and 4‐F‐C₆H₄CN⁺ that formed in a pseudo McLafferty rearrangement pathway. Also, the fragments of aliphatic amines have high intensity in mass spectra.     

An unusual chain cadmium(II) coordination polymer: catena‐poly[[(2,2′‐bipyridyl‐κ2N,N′)cadmium(II)]‐di‐μ‐chlorido‐[(2,2′‐bipyridyl‐κ2N,N′)cadmium(II)]‐di‐μ‐thiocyanato‐κ2N:S;κ2S:N]

The title complex, [CdCl(NCS)(C₁₀H₈N₂)]_n, represents an unusual Cd^II coordination polymer constructed by two types of anionic bridges and 2,2′‐bipyridyl (bipy) terminal ligands. These two types of bridges are arranged around inversion centers. The distorted octahedral coordination of the Cd^II center is provided by two chloride ions, one N‐ and one S‐donor atom from two thiocyanate ions, and a pair of N atoms from the chelating bipy ligand. Interestingly, adjacent Cd^II ions are interconnected alternately by paired chloride [Cd...Cd = 3.916 (1) Å] and thiocyanate bridges [Cd...Cd = 5.936 (1) Å] to generate an infinite one‐dimensional coordination chain. Furthermore, weak interchain C—H...S interactions between the bipy components and thiocyanate ions lead to the formation of a layered supramolecular structure.     

Zinkkomplexe des N,N,S‐Liganden 2‐Mercaptobenzyl‐bis‐(2‐pyridylmethyl)amin

Zinc Complexes of the N,N,S‐Ligand 2‐Mercaptobenzyl‐bis‐(2‐pyridylmethyl)amine An improved synthesis of the title ligand MBPA–H has made its complex chemistry accessible. With diethyl zinc it forms the reactive ethyl complex (MBPA)Zn–C₂H₅ ( 1 ) whose reaction with phenol leads to (MBPA)Zn–OC₆H₅ ( 2 ). With zinc nitrate the labile compound (MBPA)Zn–ONO₂ ( 3 ) is formed which in turn is converted with thiophenolate into (MBPA)Zn–SC₆H₅ ( 4 ). Structure determinations of 2 and 3 have confirmed severely deformed trigonal‐bipyramidal coordinations of the zinc atom whose ligation patterns correspond to those in some hydrolytic zinc enzymes.     

Chemical Synthesis of Interleukin‐2 and Disulfide Stabilizing Analogues

Chemical protein synthesis allows the construction of well‐defined structural variations and facilitates the development of deeper understanding of protein structure–function relationships and new protein engineering strategies. Herein, we report the chemical synthesis of interleukin‐2 (IL‐2) variants on a multimilligram scale and the formation of non‐natural disulfide mimetics that improve stability against reduction. The synthesis was accomplished by convergent KAHA ligations; the acidic conditions of KAHA ligation proved to be valuable for the solubilization of the hydrophobic segments of IL‐2. The bioactivity of the synthetic IL‐2 and its analogues were shown to be equipotent to recombinant IL‐2 and exhibit improved stability against reducing agents.     

Solid‐Phase Total Synthesis of Yaku'amide B Enabled by Traceless Staudinger Ligation

We report a solid‐phase strategy for total synthesis of the peptidic natural product yaku'amide B ( 1 ), which exhibits antiproliferative activity against various cancer cells. Its linear tridecapeptide sequence bears four β,β‐dialkylated α,β‐dehydroamino acid residues and is capped with an N‐terminal acyl group (NTA) and a C‐terminal amine (CTA). To realize the Fmoc‐based solid‐phase synthesis of this complex structure, we developed new methods for enamide formation, enamide deprotection, and C‐terminal modification. First, traceless Staudinger ligation enabled enamide formation between sterically encumbered alkenyl azides and newly designed phosphinophenol esters. Second, application of Eu(OTf)₃ led to chemoselective removal of the enamide Boc groups without detaching the resin linker. Finally, resin‐cleavage and C‐terminus modification were simultaneously achieved with an ester–amide exchange reaction using CTA and AlMe₃ to deliver 1 in 9.1 % overall yield (24 steps from the resin).