Photochemical Methods for Peptide Macrocyclisation

Photochemical reactions have been the subject of renewed interest over the last two decades, leading to the development of many new, diverse and powerful chemical transformations. More recently, these developments have been expanded to enable the photochemical macrocyclisation of peptides and small proteins. These constructs benefit from increased stability, structural rigidity and biological potency over their linear counterparts, providing opportunities for improved therapeutic agents. In this review, an overview of both the established and emerging methods for photochemical peptide macrocyclisation is presented, highlighting both the limitations and opportunities for further innovation in the field.     

Understanding GFP posttranslational chemistry: structures of designed variants that achieve backbone fragmentation, hydrolysis, and decarboxylation

The green fluorescent protein (GFP) creates a fluorophore out of three sequential amino acids by promoting spontaneous posttranslational modifications. Here, we use high-resolution crystallography to characterize GFP variants that not only undergo peptide backbone cyclization but additional denaturation-induced peptide backbone fragmentation, native peptide hydrolysis, and decarboxylation reactions. Our analyses indicate that architectural features that favor GFP peptide cyclization also drive peptide hydrolysis. These results are relevant for the maturation pathways of GFP homologues, such as the kindling fluorescent protein and the Kaede protein, which use backbone cleavage to red-shift the spectral properties of their chromophores. We further propose a photochemical mechanism for the decarboxylation reaction, supporting a role for the GFP protein environment in facilitating radical formation and one-electron chemistry, which may be important in activating oxygen for the oxidation step of chromophore biosynthesis. Together, our results characterize GFP posttranslational modification chemistry with implications for the energetic landscape of backbone cyclization and subsequent reactions, and for the rational design of predetermined spontaneous backbone cyclization and cleavage reactions.     

Photochemical cleavage of leader peptides

We report a photolabile linker compatible with Fmoc solid phase peptide synthesis and Cu(I)-catalyzed alkyne-azide cycloaddition that allows photochemical cleavage to afford a C-terminal peptide fragment with a native amino terminus.     

Discovery,structure, and chemical synthesis of disulfide-rich peptide toxins and their analogs

Disulfide bond-rich peptide toxins are promising scaffolds for the development of medicinal peptides because they possess a rigid 3D structure formed by multiple disulfide bonds. In this review, we discussed recent advances in the discovery, structural elucidation and chemical synthesis of disulfide-rich peptide toxins and their analogs.     

212.8 nm laser photolysis of aromatic and aliphatic amino acids and related peptides.

The comparison of the photochemical properties of three aromatic and five aliphatic amino acids and three dipeptides was carried out using 212.8 nm laser irradiation and high performance liquid chromatography. The photochemical sensitivity, photolysis quantum yield and quantum yield of peptide bond scission were determined. Two-photon absorption coefficients of solvent (liquid water) and cell windows material (fused silica) at lambda = 212.8 nm were established.     

Expedient asymmetric synthesis of all four isomers of N,N'-protected 2,3-diaminobutanoic acid

2,3-Diaminobutanoic acid (DAB) is found in several peptide antibiotics, toxins, and biologically active molecules. This paper describes the practical and highly enantioselective synthesis of all four N,N'-protected DAB stereoisomers using an asymmetric Rh(I)-phosphine-catalyzed hydrogenation of isomeric enamides as the key step. Thermal and photochemical isomerization of the enamide hydrogenation substrates coupled with catalyst-geometric isomer pairing allows targeted synthesis of single DAB isomers in maximum yield.     

Antibodies and DNA Photoproducts: Applications, Milestones and Reference Guide

Polyclonal and monoclonal antibodies recognizing the primary DNA photoproducts induced by ultraviolet radiation (UVR) have proven to be essential tools in the study of photochemical and photobiological phenomena. As specific "DNA damage binding proteins" these reagents have been used to develop a diverse array of technical procedures applied to a plethora of important problems in DNA photochemistry and the biological effects of UVR at the molecular, developmental, organism and population levels. This survey attempts to cover this science from an historical perspective and to reveal the great breadth of discovery and contribution associated with the development and application of DNA damage antibodies to the current body of science.     

N‐Heterocyclic Carbene Catalyzed Photoenolization/Diels–Alder Reaction of Acid Fluorides

The combination of light activation and N‐heterocyclic carbene (NHC) organocatalysis has enabled the use of acid fluorides as substrates in a UVA‐light‐mediated photochemical transformation previously observed only with aromatic aldehydes and ketones. Stoichiometric studies and TD‐DFT calculations support a mechanism involving the photoactivation of an ortho‐toluoyl azolium intermediate, which exhibits “ketone‐like” photochemical reactivity under UVA irradiation. Using this photo‐NHC catalysis approach, a novel photoenolization/Diels–Alder (PEDA) process was developed that leads to diverse isochroman‐1‐one derivatives.     

Transmembrane Signaling Mediated by Water in Bovine Rhodopsin

Abstract— Unhydrated air-dried films of rhodopsin from bovine rod outer segment membranes do not produce its active state, metarhodopsin II. In order to reveal requirements for its formation, we studied changes in H-bonding of water, peptide carbonyl and carboxylic acid in the photochemical reactions by means of difference Fourier transform infrared spectroscopy, under both hydrated and unhydrated conditions. A water molecule near Glull3, which undergoes H-bonding change in bathorhodopsin, remained in the unhydrated film, but with a weaker H-bonding state than in the hydrated film. The other water molecules, which shift in lumirhodopsin and metarhodopsin I as well as in bathorhodopsin of the hydrated film, were not observed in the unhydrated film. Effects of the dehydration were detected in all the C=O stretching vibrations of the peptide backbone and of Asp83 in the formation of bathorhodopsin. The C=O stretching band of Asp83 of lumirhodopsin and metarhodopsin I is intensified in the unhydrated film. We propose that structural changes at the intradiscal site in the interaction between the Schiff base and Glull3 affect water molecules, the peptide backbone, Asp83 and Glul22 in helices B and C through consecutive photochemical processes to metarhodopsin II.     

Aminium cation radical of glycylglycine and its deprotonation to aminyl radical in aqueous solution

The photochemical reaction between glycylglycine and triplet 4-carboxybenzophenone has been investigated using time-resolved chemically induced dynamic nuclear polarization (CIDNP). It is shown that the mechanism of the peptide reaction with triplet excited carboxybenzophenone is electron transfer from the amino group of the peptide, leading to the formation of an aminium cation radical that deprotonates to a neutral aminyl radical. Simulation of the CIDNP kinetics leads to an estimation of the paramagnetic relaxation time for the alpha-protons at the N-terminus at 20 to 40 mus with the best-fit value of 25 mus.     

DARK INTERACTION AND OXYGEN DEPENDENT PHOTOBINDING BETWEEN AN AROMATIC TETRAPEPTIDE AND DNA MODIFIED BY 5- METHOXYPSORALEN MONOADDUCTS

The binding of the tetrapeptide lysyl-tryptophyl-glycyl-lysine t -butyl ester to native DNA and DNA photochemically modified by 5-methoxypsoralen has been investigated by fluorescence spectroscopy. The peptide exhibits a higher affinity for the modified DNA than for the undamaged DNA. This is due to the presence of strong stacking sites in the vicinity of 5-methoxypsoralen monoadducts. Upon irradiation at 365 nm of the peptide-modified DNA complexes, a cross-linking of the peptide to the nucleic acid is observed. This photochemical addition requires the presence of oxygen and involves, in part, singlet oxygen.     

Beiträge zur Chemie der Pyrrolpigmente, 35. Mitt.: Eine regioselektive,reversible Addition an Bilatriene-abc

Using spectroscopic methods (UV-VIS,¹H-NMR) the reversible addition of donors (alcohols, amines, thiols, HCN, bisulfit and C-H acidic compounds) to bilatrienes-abc was investigated. This equilibrium is in close analogy to the addition of donors to a carbonyl group (as was deduced from thermodynamic and kinetic measurements) and is also the basis for understanding the photochemical isomerization of bilatrienes-abc in the adsorbed state. Based thereon a recipe for the isomerization of bilatrienes-abc in homogeneous phase giving high yields of the (E, Z, Z)-diastereomer is presented; in addition the (E, Z, E)-diastereomer of aetiobiliverdin-IV- was isolated and characterized for the first time. A model compound representing the intramolecular addition of a donor attached to a side chain (mimicking a peptide unit) was synthesized and studied with respect to its photochemical behaviour.

34. Mitt.:H. Falk undK. Thirring, Z. Naturforsch. im Druck.     

Synthesis of Bifunctional Azobenzene Glycoconjugates for Cysteine‐Based Photosensitive Cross‐Linking with Bioactive Peptides

Azobenzene linker molecules can be utilized to control peptide/protein function when they are ligated to appropriately spaced amino acid side chains of the peptide. This is because the photochemical E/Z isomerization of the azobenzene N?N double bond allows to switch peptide conformation between folded and unfolded. In this context, we have introduced carbohydrate‐functionalized azobenzene derivatives in order to advance the biocompatible properties of azobenzene peptide linkers. Chloroacetamide‐functionalized and O‐allylated carbohydrate derivatives were synthesized and conjugated with azobenzene to achieve new bifunctional cross‐linkers, in order to allow ligation to cysteine side chains by nucleophilic substitution or thiol‐ene reaction, respectively. The photochromic properties of the new linker glycoconjugates were determined and first ligation reactions performed.     

The cathelicidins--structure, function and evolution

The cathelicidin family of host defense peptides includes a group of cationic and usually amphipathic peptides that display a variety of activities related to host defense functions, among which the most acknowledged is a direct antimicrobial activity against various microbial pathogens. All members of this family are synthesized as precursors characterized by an N-terminal cathelin-like domain which is relatively well conserved also in evolutionary distant vertebrates. By contrast, the C-terminal region, which carries the active peptide, appears to be a focus for genetic mechanisms that have selectively generated a considerable sequence diversity. This process is particularly striking in Cetartiodactyls, where repeated gene duplication events and subsequent divergence have produced an array of distinct family members. The corresponding mature cathelicidin peptides are considerably diverse in length, amino acid sequence and structure, variously adopting alpha-helical, elongated or beta-hairpin conformations. The diverse nature of these peptides may account for distinct functions and for a diverse spectrum of activity and/or antimicrobial potency.     

Solid-phase synthesis of bicyclic dipeptide mimetics by intramolecular cyclization of alcohols, thiols, amines, and amides with N-acyliminium intermediates

A general strategy for the solid-phase synthesis of structurally diverse bicyclic dipeptide mimetics is presented. Depending on the amino acid side-chain (R(1)), peptide-derived N-acyliminium intermediates may undergo nucleophilic attack from either side-chain functional groups (-OH, -NH(2), -SH, and -CONH(2)) or the amide backbone (-CONH-) of the peptide, thus affording a range of aza-, thia-, and oxabicycloalkanes in excellent purity and diastereoselectivity. [reaction: see text]     

Properties of 2-, 3-, and 4-acetylpyridine substituted ruthenium(II) bis(bipyridine) complexes: substituent effect on the electronic structure,spectra, and photochemistry of the complex

Bis(2,2′-bipyridine) complexes of ruthenium(II) with 2-, 3-, and 4-acetylpyridine derivatives were synthesized and structurally characterized. The effect of changing the location of the pyridine's acetyl substituent was studied experimentally and theoretically to clarify the effect of substituent position on the chemical behavior and photochemical properties of the complex. The substituent position on the heterocyclic-pyridine was found to strongly affect the chemical and photochemical properties of the complex. Variation of the position of the substituent, and thus ligand modification brought by as a consequence of this variation, offers possibilities to design complexes of desired structural and photochemical properties.     

Aggregation in nanobundles and the effect of diverse environments on the solution-phase photochemistry and photophysics of -Re(CO)3L+ (L = 1,10-phenanthroline, 2,2'-bipyridine) pendants bonded to poly(4-vinylpyridine)

The UV-vis spectroscopy and photochemical properties of {(vpy-[Re(CO)3(2,2'-bpy)])m(vpy-[Re(CO)3(phen)])n(vpy)p}(CF3SO3)(m+n)}, vpy = 4-vinylpyridine, m = 131, n = 131 or m = 200, n = 150, and m + n + p = 600, were investigated in solution phase. The polymers exist in solution as aggregates of polymer strands with radii as large as approximately 10(2) nm. Given the size of the poly-vpy backbone, the aggregates must contain a large number of strands. The luminescence spectrum exhibits a strong resemblance to the emission spectrum of {(vpy-[Re(CO)3(phen)])200(vpy)400}(CF3SO3)200. The existence of Re(I) chromophores in diverse environments was shown by the intrinsic kinetics of the luminescence, the decay kinetics of the MLCT excited states observed by time resolved-absorption spectroscopy, and the quenching of the luminescence by various quenchers. Redox reactions of the MLCT excited states with the quenchers were responsible for the luminescence quenching. While static quenching resulted when Cu(II) and Fe(III) EDTA complexes were the quenchers, a dynamic quenching resulted with Fe(CN)6(4-) or 2,2',2' '-triethanolamine, TEOA. The photochemical and photophysical properties of the mixed-pendant polymers have been discussed in terms of arrays of MLCT excited states whose energies are determined by the diverse environments of the Re(I) chromophores. Conversions (with and without radiation) of the upper-energy MLCT excited states to the ground state and lower-energy MLCT excited states and the latter excited state to the ground state account for the experimental results.     

Circular logic: nonribosomal peptide-like macrocyclization with a ribosomal peptide catalyst

A protease from ribosomal peptide biosynthesis macrocyclizes diverse substrates, including those resembling nonribosomal peptide and hybrid polyketide-peptide products. The proposed mechanism is analogous to thioesterase-catalyzed chemistry, but the substrates are amide bonds rather than thioesters.     

Dendritic macromers for hydrogel formation: Tailored materials for ophthalmic,orthopedic, and biotech applications

Dendritic macromolecules are well‐defined highly branched macromolecules synthesized via a divergent or convergent approach. A salient feature of the macromolecules described herein, and a goal of our research effort, is to prepare dendritic macromolecules suitable for in vitro and in vivo use by focusing on biocompatible building blocks and biodegradable linkages. These dendritic macromolecules can be subsequently crosslinked to form hydrogels using a photochemical acrylate‐based or a chemical ligation strategy. The properties—mechanical, swelling, degradation, and so forth—of the hydrogels can be tuned by altering the composition, crosslinking chemistry, wt %, generation number and so forth. The utility and diverse applicability is demonstrated through successful use of these hydrogels in three unique applications: hydrogel adhesives for repairing corneal wounds, hydrogel scaffolds for cartilage tissue engineering, and hydrogel reaction chambers for high throughput screening of molecular recognition events. © 2007 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 383–400, 2008.