Studies on chemical modification of Tulipa gesneriana lectin

Modification of lysine, tyrosine, histidine, aspartic acid and glutamic acid residues did not affect the agglutinating activity of the Tulipa gesneriana lectin (TGL). Modification of two arginine residues per subunit in the lectin with either 2,3-butanedione or phenylglyoxal led to an almost complete loss of activity. An inactive lectin modified with 2,3-butanedione recovered a full activity on dialysis against Tris-HCl buffer. The presence of 0.1 M (alpha-1----6) linked mannotriose, a potent inhibitor of the lectin, protected all the arginine residues from modification and the lectin was fully active. Circular dichroism spectroscopy showed that no significant conformational change of TGL occurred following arginine modification. A treatment of the lectin solution with N-bromosuccinimide or 2-hydroxy-5-nitrobenzyl bromide, chemical reagents for tryptophan modification, caused turbidity of the solution, accompanied with complete loss of activity. The fluorescence emission spectrum of the lectin showed a characteristic tryptophan emission with a maximum centered at 336 nm. Upon addition of manno-oligosaccharides a decrease of the fluorescence intensity was observed, indicating that the environment of tryptophan residues altered. These results suggest that arginine and tryptophan residues are importantly involved in the sugar binding of TGL.     

Covalent binding of human serum albumin and ovalbumin by chloramine-T and chemical modification of the proteins

The covalent binding of ³⁵S-chloramine-T to human resum albumin (HSA) and ovalbumin is described. At pH 6.5, up to 24 chloramine-T molecules were found to be covalently bound per molecule of HSA; with ovalbumin the binding was only 5–7 molecule per protein molecule. Binding was accompanied by extensive modification of methionine, cysteine, histidine, tyrosine and lysine. Three new peaks appeared in the amino acid profiles of the modified proteins; two were identified as 1-aminoadipic acid (oxidation of lysine) and 3-chlorotyrosine. The most sites for covalent binding are lysine residues.     

Combining weak affinity chromatography, NMR spectroscopy and molecular simulations in carbohydrate-lysozyme interaction studies

By examining the interactions between the protein hen egg-white lysozyme (HEWL) and commercially available and chemically synthesized carbohydrate ligands using a combination of weak affinity chromatography (WAC), NMR spectroscopy and molecular simulations, we report on new affinity data as well as a detailed binding model for the HEWL protein. The equilibrium dissociation constants of the ligands were obtained by WAC but also by NMR spectroscopy, which agreed well. The structures of two HEWL-disaccharide complexes in solution were deduced by NMR spectroscopy using (1)H saturation transfer difference (STD) effects and transferred (1)H,(1)H-NOESY experiments, relaxation-matrix calculations, molecular docking and molecular dynamics simulations. In solution the two disaccharides β-d-Galp-(1→4)-β-D-GlcpNAc-OMe and β-D-GlcpNAc-(1→4)-β-D-GlcpNAc-OMe bind to the B and C sites of HEWL in a syn-conformation at the glycosidic linkage between the two sugar residues. Intermolecular hydrogen bonding and CH/π-interactions form the basis of the protein-ligand complexes in a way characteristic of carbohydrate-protein interactions. Molecular dynamics simulations with explicit water molecules of both the apo-form of the protein and a ligand-protein complex showed structural change compared to a crystal structure of the protein. The flexibility of HEWL as indicated by a residue-based root-mean-square deviation analysis indicated similarities overall, with some residue specific differences, inter alia, for Arg61 that is situated prior to a flexible loop. The Arg61 flexibility was notably larger in the ligand-complexed form of HEWL. N,N'-Diacetylchitobiose has previously been observed to bind to HEWL at the B and C sites in water solution based on (1)H NMR chemical shift changes in the protein whereas the disaccharide binds at either the B and C sites or the C and D sites in different crystal complexes. The present study thus highlights that protein-ligand complexes may vary notably between the solution and solid states, underscoring the importance of targeting the pertinent binding site(s) for inhibition of protein activity and the advantages of combining different techniques in a screening process.     

Porous Protein Crystals as Catalytic Vessels for Organometallic Complexes

Porous protein crystals, which are protein assemblies in the solid state, have been engineered to form catalytic vessels by the incorporation of organometallic complexes. Ruthenium complexes in cross‐linked porous hen egg white lysozyme (HEWL) crystals catalyzed the enantioselective hydrogen‐transfer reduction of acetophenone derivatives. The crystals accelerated the catalytic reaction and gave different enantiomers based on the crystal form (tetragonal or orthorhombic). This method represents a new approach for the construction of bioinorganic catalysts from protein crystals.     

Halomethyl-Triazoles for Rapid,Site-Selective Protein Modification

Post-translational modifications (PTMs) are used by organisms to control protein structure and function after protein translation, but their study is complicated and their roles are not often well understood as PTMs are difficult to introduce onto proteins selectively. Designing reagents that are both good mimics of PTMs, but also only modify select amino acid residues in proteins is challenging. Frequently, both a chemical warhead and linker are used, creating a product that is a misrepresentation of the natural modification. We have previously shown that biotin-chloromethyl-triazole is an effective reagent for cysteine modification to give S-Lys derivatives where the triazole is a good mimic of natural lysine acylation. Here, we demonstrate both how the reactivity of the alkylating reagents can be increased and how the range of triazole PTM mimics can be expanded. These new iodomethyl-triazole reagents are able to modify a cysteine residue on a histone protein with excellent selectivity in 30 min to give PTM mimics of acylated lysine side-chains. Studies on the more complicated, folded protein SCP-2L showed promising reactivity, but also suggested the halomethyl-triazoles are potent alkylators of methionine residues.     

AJICAP: Affinity Peptide Mediated Regiodivergent Functionalization of Native Antibodies

The need for atom‐precise biomolecule modification, and particularly the irreversible formation of covalent bonds to specific amino acids in proteins, has become an essential issue in the fields of pharmaceuticals and chemical biology. For example, antibody–drug conjugates (ADCs) are increasingly common entries into the clinical oncology pipeline. Herein, we report a new method of affinity peptide mediated regiodivergent functionalization (AJICAP?) that enables the synthesis of ADCs from native IgG antibodies. We succeeded in introducing thiol functional groups onto three lysine residues in IgGs using Fc affinity peptide reagents without antibody engineering. A cytotoxic molecule was then connected to the newly introduced thiol group, and both a surface plasmon resonance binding assay and in vivo xenograft mouse model results showed that the resulting ADC could selectively target and kill HER2‐positive cells. Our strategy provides a new approach for constructing complex antibody‐derived biomolecules.     

Lysine‐Targeting Covalent Inhibitors

Targeted covalent inhibitors have gained widespread attention in drug discovery as a validated method to circumvent acquired resistance in oncology. This strategy exploits small‐molecule/protein crystal structures to design tightly binding ligands with appropriately positioned electrophilic warheads. Whilst most focus has been on targeting binding‐site cysteine residues, targeting nucleophilic lysine residues can also represent a viable approach to irreversible inhibition. However, owing to the basicity of the ϵ ‐amino group in lysine, this strategy generates a number of specific challenges. Herein, we review the key principles for inhibitor design, give historical examples, and present recent developments that demonstrate the potential of lysine targeting for future drug discovery.     

Covalent modification of gaseous peptide ions with N-hydroxysuccinimide ester reagent ions

Covalent modification of primary amine groups in multiply protonated or deprotonated polypeptides in the gas phase via ion/ion reactions is demonstrated using N-hydroxysuccinimide (NHS) esters as the modifying reagents. During the ion/ion reaction, the peptide analyte ions and the NHS or sulfo-NHS based reagent form a long-lived complex, which is a prerequisite for the covalent modification chemistry to occur. Ion activation of the peptide-reagent complex results in a neutral NHS or sulfo-NHS molecule loss, which is a characteristic signature of covalent modification. As the NHS or sulfo-NHS group leaves, an amide bond is formed between a free, unprotonated, primary amine group of a lysine side chain in the peptide and the carboxyl group in the reagent. Subsequent activation of the NHS or sulfo-NHS loss product ions results in sequence informative fragment ions containing the modification. The N-terminus primary amine group does not make a significant contribution to the modification process; this behavior has also been observed in solution phase reactions. The ability to covalently modify primary amine groups in the gas phase with N-hydroxysuccinimide reagents opens up the possibility of attaching a wide range of chemical groups to gaseous peptides and proteins and also for selectively modifying other analytes containing free primary amine groups.     

Morphological evolution of inorganic crystal into zigzag and helical architectures with an exquisite association of polymer: a novel approach for morphological complexity

The morphology of potassium sulfate (K(2)SO(4)) crystals grown in a viscous polymer solution of poly(acrylic acid) (PAA) was remarkably changed from the tilted columnar assembly into zigzag and helical architectures with increasing PAA concentration. The habit modification of orthorhombic K(2)SO(4) with adsorption of PAA molecules on a specified crystal face fundamentally led to the formation of tilted unit crystals. Concurrently with the habit modification, a diffusion-limited condition controlling the assembly of tilted units was achieved in the presence of PAA molecules in the matrix. Various complex morphologies, including zigzag and helical assembly, emerged through the formation of twinned crystals with the variation of the diffusion condition. Understanding the morphogenesis observed in this report would provide a novel approach for sophisticated crystal design by using an exquisite association of organic and inorganic materials.     

Diastereospecific photocyclization of a isopropylbenzophenone derivative in crystals and the morphological changes

Reaction of crystals of 2,4,6-triisopropylbenzophenone derivative with the (S)-phenylethylamide group caused diastereospecific Norrish type II photocyclization by UV irradiation to give (R,S)-cyclobutenol as a sole product. In contrast, the solution photolysis gave an almost 1:1 mixture of (R,S)- and (S,S)-cyclobutenol. The specific diastereodifferentiation in the crystalline state is attributed to the smooth transformation with minimum molecular motion due to the very similar molecular shapes as well as the 2-fold helical arrangements between the reactant crystal and the product (R,S)-cyclobutenol crystal. UV irradiation of the bulk crystals led to cracking and breaking into small fragments. In contrast, the microcrystals maintained the single-crystalline morphology in the course of photocyclization, suggesting the single-crystal-to-single-crystal transformation.     

Lysine modification of human serum albumin and its effect on protein conformation and nalidixic acid binding

In order to investigate the involvement of lysine residues of human serum albumin (HSA) in nalidixic acid (NA) binding, various modified preparations of HSA such as 44% carbamylated (C₄₄), 83% carbamylated (C₈₃) and 85% acetylated (A₈₅) were made by treating the HSA solution with a different molar excess of potassium cyanate and acetic anhydride. The extent of modification, charge homogeneity and conformational changes of these derivatives were checked by TNBSA reaction method, polyacrylamide gel electrophoresis (PAGE) and gel filtration using Sephacryl S-200 HR column, respectively. Binding of NA to HSA and its derivatives was examined using fluorescence quenching titration method to determine the binding constant. The emergence of a single band in PAGE and single symmetrical peak in gel filtration results confirmed the charge and size homogeneity of these derivatives. Hydrodynamic properties such as Stokes radius and frictional ratio, as obtained from the analytical gel filtration results suggested molecular expansion in C₈₃ and A₈₅ HSAs while C₄₄ HSA retained the native conformation. Addition of NA to both native and modified HSA derivatives quenched the fluorescence intensity of the protein at 344 ​nm to a different extent. Whereas the values of the Stern-Volmer constant (K_SV) and bimolecular quenching rate constant (k_q) suggested, NA-HSA complex formation, binding constant (K_a) value suggested an intermediate binding affinity between NA and HSA. Furthermore, the decrease in the K_a value with the extent of modification was indicative of the involvement of lysine residues in NA-HSA interaction.     

Lysine‐directed staining of proteins for MS‐based analyses

Visualization of proteins and MS‐based analyses are elemental tasks in modern biochemistry. Nevertheless, reports about covalent protein dyes and their suitability for subsequent MS experiments remain scarce. In a recent work, we demonstrated that covalent prestaining of proteins with Uniblue A drastically speeds up proteomic workflows. The present study introduces dabsyl chloride as another truly MS‐compatible protein stain. Remarkably, although Uniblue A and dabsyl chloride employ different nucleophilic reaction mechanisms, both are highly specific for lysine residues. The predictable peptide modifications allow easy integration into state‐of‐the‐art bioinformatic workflows. Further, lysine‐directed derivatizations with hydrophobic reagents such as dabsyl chloride complement the cysteine‐directed ALiPHAT strategy for increasing the sensitivity of peptide identifications.     

A Robust Analytical Approach for the Identification of Specific Protein Carbonylation Sites: Metal-Catalyzed Oxidations of Human Serum Albumin

The formation of protein carbonyls in the metal-catalyzed oxidation of human serum albumin (HSA) is characterized using a new analytical approach that involves tagging the modification site with multiple hydrazide reagents. Protein carbonyl formation at lysine and arginine residues was catalyzed with copper and iron ions, and the resulting oxidation patterns in HSA are contrasted. A total of 18 modification sites were identified with iron-ion catalysis and 14 with copper-ion catalysis. However, with the more stringent requirement of identification with at least two tagging reagents, the number of validated modification sites drops to 10 for iron and nine for copper. Of the 14 total validated sites, there were only five in common for the two metal ions. The results illustrate the value of using multiple tagging agents and highlight the selective and specific nature of metal-catalyzed protein oxidations.     

Enzymetically Regulating the Self‐Healing of Protein Hydrogels with High Healing Efficiency

Enzyme‐mediated self‐healing of dynamic covalent bond‐driven protein hydrogels was realized by the synergy of two enzymes, glucose oxidase (GOX) and catalase (CAT). The reversible covalent attachment of glutaraldehyde to lysine residues of GOX, CAT, and bovine serum albumin (BSA) led to the formation and functionalization of the self‐healing protein hydrogel system. The enzyme‐mediated protein hydrogels exhibit excellent self‐healing properties with 100 % recovery. The self‐healing process was reversible and effective with an external glucose stimulus at room temperature.     

Arylfluorosulfate‐Based Electrophiles for Covalent Protein Labeling: A New Addition to the Arsenal

Selective covalent modification of a targeted protein is a powerful tool in chemical biology and drug discovery, with applications ranging from identification and characterization of proteins and their functions to the development of targeted covalent inhibitors. Most covalent ligands contain an affinity motif and an electrophilic warhead that reacts with a nucleophilic residue of the targeted protein. Because the electrophilic warhead is prone to react and modify off‐target nucleophiles, its reactivity should be balanced carefully to maximize target selectivity. Arylfluorosulfates have recently emerged as latent electrophiles for selective labeling of context‐specific tyrosine and lysine residues in protein pockets. Here, we review the recent but intense introduction of arylfluorosulfates into the arsenal of available warheads for selective covalent modification of proteins. We highlight the untapped potential of this functional group for use in chemical biology and drug discovery.     

Orthogonal Protein Assembly on DNA Nanostructures Using Relaxases

DNA‐binding proteins are promising reagents for the sequence‐specific modification of DNA‐based nanostructures. Here, we investigate the utility of a series of relaxase proteins—TrwC, TraI, and MobA—for nanofunctionalization. Relaxases are involved in the conjugative transfer of plasmids between bacteria, and bind to their DNA target sites via a covalent phosphotyrosine linkage. We study the binding of the relaxases to two standard DNA origami structures—rodlike six‐helix bundles and flat rectangular origami sheets. We find highly orthogonal binding of the proteins with binding yields of 40–50 % per binding site, which is comparable to other functionalization methods. The yields differ for the two origami structures and also depend on the position of the binding sites. Due to their specificity for a single‐stranded DNA target, their orthogonality, and their binding properties, relaxases are a uniquely useful addition to the toolbox available for the modification of DNA nanostructures with proteins.     

Glycation sites in neoglycoglycoconjugates from the terminal monosaccharide antigen of the O‐PS of Vibrio cholerae O1, serotype Ogawa,and BSA revealed by matrix‐assisted laser desorption–ionization tandem mass spectrometry

We present the MALDI‐TOF/TOF‐MS analyses of various hapten–bovine serum albumin (BSA) neoglycoconjugates obtained by squaric acid chemistry coupling of the spacer‐equipped, terminal monosaccharide of the O‐specific polysaccharide of Vibrio cholerae O1, serotype Ogawa, to BSA. These analyses allowed not only to calculate the molecular masses of the hapten–BSA neoglycoconjugates with different hapten–BSA ratios (4.3, 6.6 and 13.2) but, more importantly, also to localize the covalent linkages (conjugation sites) between the hapten and the carrier protein. Determination of the site of glycation was based on comparison of the MALDI‐TOF/TOF‐MS analysis of the peptides resulting from the digestion of BSA with similar data resulting from the digestion of BSA glycoconjugates, followed by sequencing by MALDI‐TOF/TOF‐MS/MS of the glycated peptides. The product‐ion scans of the protonated molecules were carried out with a MALDI‐TOF/TOF‐MS/MS tandem mass spectrometer equipped with a high‐collision energy cell. The high‐energy collision‐induced dissociation (CID) spectra afforded product ions formed by fragmentation of the carbohydrate hapten and amino acid sequences conjugated with fragments of the carbohydrate hapten. We were able to identify three conjugation sites on lysine residues (Lys235, Lys437 and Lys455). It was shown that these lysine residues are very reactive and bind lysine specific reagents. We presume that these Lys residues belong to those that are considered to be sterically more accessible on the surface of the tridimensional structure. The identification of the y‐series product ions was very useful for the sequencing of various peptides. The series of a‐ and b‐product ions confirmed the sequence of the conjugated peptides. Copyright © 2010 John Wiley & Sons, Ltd.     

Crystal and electronic structure of heteromolecular complexes of 3,6-bis(3,5-dymethylpyrazole-1-yl)-1,2,4,5-tetrazine with azoles

X-ray crystallography is used to investigate heteromolecular crystals of 3,6-bis(3,5-dimethylpyrazole-1-yl)-1,2,4,5-tetrazine with NH-donating azole derivatives. The effect is studied of the structure of azole on molecular packing in the crystal and the characteristics of covalent bonds in the molecule of 3,6-disubstituted tetrazine. The distribution of electron density critical points inside crystal cells is analyzed to identify and quantitatively describe the intermolecular interactions underlying the formation of lateral and stacking motifs.     

Synthesis and SAR study of novel peptide aldehydes as inhibitors of 20S proteasome

Based on the analysis of the crystal structure of MG101 (1) and 20S proteasomes, a new series of peptide aldehyde derivatives were designed and synthesized. Their ability to inhibit 20S proteasome was assayed. Among them, Cbz-Glu(OtBu)-Phe-Leucinal (3c), Cbz-Glu(OtBu)-Leu-Leucinal (3d), and Boc-Ser(OBzl)-Leu-Leucinal (3o) exhibited the most activity, which represented an order of magnitude enhancement compared with MG132 (2). The covalent docking protocol was used to explore the binding mode. The structure-activity relationship of the peptide aldehyde inhibitors is discussed.     

Thermodynamic Evaluation of the Interactions between Anticancer Pt(II) Complexes and Model Proteins

In this work, we have analysed the binding of the Pt(II) complexes ([PtCl(4′-phenyl-2,2′:6′,2″-terpyridine)](CF₃SO₃) (1), [PtI(4′-phenyl-2,2′:6′,2″-terpyridine)](CF₃SO₃) (2) and [PtCl(1,3-di(2-pyridyl)benzene) (3)] with selected model proteins (hen egg-white lysozyme, HEWL, and ribonuclease A, RNase A). Platinum coordination compounds are intensively studied to develop improved anticancer agents. In this regard, a critical issue is the possible role of Pt-protein interactions in their mechanisms of action. Multiple techniques such as differential scanning calorimetry (DSC), electrospray ionization mass spectrometry (ESI-MS) and UV-Vis absorbance titrations were used to enlighten the details of the binding to the different biosubstrates. On the one hand, it may be concluded that the affinity of 3 for the proteins is low. On the other hand, 1 and 2 strongly bind them, but with major binding mode differences when switching from HEWL to RNase A. Both 1 and 2 bind to HEWL with a non-specific (DSC) and non-covalent (ESI-MS) binding mode, dominated by a 1:1 binding stoichiometry (UV-Vis). ESI-MS data indicate a protein-driven chloride loss that does not convert into a covalent bond, likely due to the unfavourable complexes’ geometries and steric hindrance. This result, together with the significant changes of the absorbance profiles of the complex upon interaction, suggest an electrostatic binding mode supported by some stacking interaction of the aromatic ligand. Very differently, in the case of RNase A, slow formation of covalent adducts occurs (DSC, ESI-MS). The reactivity is higher for the iodo-compound 2, in agreement with iodine lability higher than chlorine.