Characterization of C-alkyl amidines as bioavailable covalent reversible inhibitors of human DDAH-1

C‐Alkyl amidine analogues of asymmetric N^ω,N^ω‐dimethyl‐L ‐arginine are dual‐targeted inhibitors of both human DDAH‐1 and nitric oxide (NO) synthase, and provide a promising scaffold for the development of therapeutics to control NO overproduction in a variety of pathologies including septic shock and some cancers. Using a two‐part click‐chemistry‐mediated activity probe, a homologated series of C‐alkyl amidines were ranked for their ability to inhibit DDAH‐1 within cultured HEK 293T cells. N⁵‐(1‐Iminopentyl)‐L ‐ornithine was determined to be the most potent compound in vitro (K_d=7 μM ) as well as in cultured cells, and the binding conformation and covalent reversible mode of inhibition was investigated by comparison of interactions made with DDAH‐1 and a catalytically inactive C274S variant, as gauged by X‐ray crystallography and isothermal titration calorimetry. By interrupting the ability of the inhibitor to form a covalent bond, the contribution of this interaction could be estimated. These results suggest that further stabilization of the covalent adduct is a promising strategy for lead optimization in the design of effective reagents to block NO synthesis.     

Synthesis and Analysis of Specific Covalent Inhibitors of endo‐Xyloglucanases

A series of N‐bromoacetylglycosylamines and bromoketone C‐glycosides were synthesised from complex xyloglucan oligosaccharide (XyGO) scaffolds as specific active‐site affinity labels for endo‐xyloglucanases. Compounds based on XXXG (Xyl₃Glc₄) and XLLG (Xyl₃Glc₄Gal₂) oligosaccharides exhibited strikingly higher affinities and higher rates of irreversible inhibition than known cellobiosyl and new lactosyl disaccharide congeners when tested with endo‐xyloglucanases from two distinct glycoside hydrolase (GH) families. Intact‐protein mass spectrometry indicated that inactivation with XyGO derivatives generally resulted in a 1:1 labelling stoichiometry. Together, these results indicate that XyGO‐based affinity reagents have significant potential as inhibitors and proteomic reagents for the identification and analysis of diverse xyloglucan‐active enzymes in nature, to facilitate industrial enzyme applications.     

Multiparameter Kinetic Analysis for Covalent Fragment Optimization by Using Quantitative Irreversible Tethering (qIT)

Chemical probes that covalently modify cysteine residues in a protein-specific manner are valuable tools for biological investigations. Covalent fragments are increasingly implemented as probe starting points, but the complex relationship between fragment structure and binding kinetics makes covalent fragment optimization uniquely challenging. We describe a new technique in covalent probe discovery that enables data-driven optimization of covalent fragment potency and selectivity. This platform extends beyond the existing repertoire of methods for identifying covalent fragment hits by facilitating rapid multiparameter kinetic analysis of covalent structure–activity relationships through the simultaneous determination of K_i, k_inact and intrinsic reactivity. By applying this approach to develop novel probes against electrophile-sensitive kinases, we showcase the utility of the platform in hit identification and highlight how multiparameter kinetic analysis enabled a successful fragment-merging strategy.     

Trifunctional Saxitoxin Conjugates for Covalent Labeling of Voltage-Gated Sodium Channels**

Voltage-gated sodium ion channels (Na_Vs) are integral membrane protein complexes responsible for electrical signal conduction in excitable cells. Methods that enable selective labeling of Na_Vs hold potential value for understanding how channel regulation and post-translational modification are influenced during development and in response to diseases and disorders of the nervous system. We have developed chemical reagents patterned after (+)-saxitoxin (STX) – a potent and reversible inhibitor of multiple Na_V isoforms – and affixed with a reactive electrophile and either a biotin cofactor, fluorophore, or ‘click’ functional group for labeling wild-type channels. Our studies reveal enigmatic structural effects of the probes on the potency and efficiency of covalent protein modification. Among the compounds analyzed, a STX-maleimide-coumarin derivative is most effective at irreversibly blocking Na⁺ conductance when applied to recombinant Na_Vs and endogenous channels expressed in hippocampal neurons. Mechanistic analysis supports the conclusion that high-affinity toxin binding is a prerequisite for covalent protein modification. Results from these studies are guiding the development of next-generation tool compounds for selective modification of Na_Vs expressed in the plasma membranes of cells.     

Covalent Inhibition of the Lymphoid Tyrosine Phosphatase

Covalent inhibitors of lymphoid tyrosine phosphatase (LYP) were identified from a screen of the NIH Molecular Libraries Small Molecules Repository (MLSMR). Both of the two lead compounds identified have phosphotyrosine‐mimetic benzoic acid moieties as well as electrophilic acrylonitrile groups. Inhibition kinetics of both compounds are consistent with covalent modification of the enzyme, with nanomolar K_I and reciprocal millisecond k_inact values, representing the best efficiency ratios (k_inact/K_I) among currently reported covalent LYP inhibitors. Covalent inhibitors can provide longer efficacy and better selectivity than more conventional noncovalent inhibitors, and these lead compounds are an important step toward the development of protein tyrosine phosphatase (PTP)‐targeted covalent therapeutic compounds.     

Covalent Inhibition of New Delhi Metallo‐β‐Lactamase‐1 (NDM‐1) by Cefaclor

Covalent irreversible inhibitors can successfully treat antibiotic‐resistant infections by targeting serine β‐lactamases. However, this strategy is useless for New Delhi metallo‐β‐lactamase (NDM), which uses a non‐covalent catalytic mechanism and lacks an active‐site serine. Here, NDM‐1 was irreversibly inactivated by three β‐lactam substrates: cephalothin, moxalactam, and cefaclor, albeit at supratherapeutic doses (e.g., cefaclor K_I=2.3±0.1 mM ; k_inact=0.024±0.001 min^?1). Inactivation by cephalothin and moxalactam was mediated through Cys208. Inactivation by cefaclor proceeded through multiple pathways, in part mediated by Lys211. Use of a cefaclor metabolite enabled mass spectrometric identification of a +346.0735 Da covalent adduct on Lys211, and an inactivation mechanism is proposed. Lys211 was identified as a promising “handhold” for developing covalent NDM‐1 inhibitors and serves as a conceptual example for creating covalent inhibitors for enzymes with non‐covalent mechanisms.     

De Novo Design,Synthesis and Evaluation of Benzylpiperazine Derivatives as Highly Selective Binders of Mcl‐1

Considerable efforts have been made to the development of small‐molecule inhibitors of antiapoptotic B‐cell lymphoma 2 (Bcl‐2) family proteins (such as Bcl‐2, Bcl‐x_L, and Mcl‐1) as a new class of anticancer therapies. Unlike general inhibitors of the entire family, selective inhibitors of each member protein can hopefully reduce the adverse side effects in chemotherapy treatments of cancers overexpressing different Bcl‐2 family proteins. In this study, we designed four series of benzylpiperazine derivatives as plausible Bcl‐2 inhibitors based on the outcomes of a computational algorithm. A total of 81 compounds were synthesized, and their binding affinities to Bcl‐2, Bcl‐x_L, and Mcl‐1 measured. Encouragingly, 22 compounds exhibited binding affinities in the micromolar range (K_i<20 μM ) to at least one target protein. Moreover, some compounds were observed to be highly selective binders to Mcl‐1 with no detectable binding to Bcl‐2 or Bcl‐x_L, among which the most potent one has a K_i value of 0.18 μM for Mcl‐1. Binding modes of four selected compounds to Mcl‐1 and Bcl‐x_L were derived through molecular docking and molecular dynamics simulations. It seems that the binding affinity and selectivity of these compounds can be reasonably interpreted with these models. Our study demonstrated the possibility for obtaining selective Mcl‐1 inhibitors with relatively simple chemical scaffolds. The active compounds identified by us could be used as lead compounds for developing even more potent selective Mcl‐1 inhibitors with potential pharmaceutical applications.     

Synthesis of pyridinium polysiloxane for antibacterial coating in supercritical carbon dioxide

Antibacterial polysiloxane with pyridinium pendants was synthesized through hydrosilylation reaction of trimethylsiloxane terminated (45% methylhydrosiloxane)–dimethylsiloxane random copolymer and 4‐vinylpyridine and subsequent N‐alkylation of pyridine ring with 1‐bromohexane. The pyridinium polysiloxane was coated on cotton and formed a 35 nm layer via a novel method of deposition in supercritical carbon dioxide (scCO₂) for biocidal application. The coated fabrics provided effective antibacterial activities against both Staphylococcus aureus and Escherichia coli compared with uncoated ones that did not exhibit noticeable biocidal activities. The pyridinium polysiloxane coating layer on cotton was stable toward storage in air and washing cycles. The scCO₂ deposition technique uses ecologically responsible CO₂ as solvent and is hypothesized to work on both reactive and nonreactive surfaces due to without the use of covalent tethering groups. © 2014 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2015 , 132, 41723.     

A DNA‐Encoded Library of Chemical Compounds Based on Common Scaffolding Structures Reveals the Impact of Ligand Geometry on Protein Recognition

A DNA‐encoded chemical library (DECL) with 1.2 million compounds was synthesized by combinatorial reaction of seven central scaffolds with two sets of 343×492 building blocks. Library screening by affinity capture revealed that for some target proteins, the chemical nature of building blocks dominated the selection results, whereas for other proteins, the central scaffold also crucially contributed to ligand affinity. Molecules based on a 3,5‐bis(aminomethyl)benzoic acid core structure were found to bind human serum albumin with a K_d value of 6 nm , while compounds with the same substituents on an equidistant but flexible l ‐lysine scaffold showed 140‐fold lower affinity. A 18 nm tankyrase‐1 binder featured l ‐lysine as linking moiety, while molecules based on d ‐Lysine or (2S,4S)‐amino‐l ‐proline showed no detectable binding to the target. This work suggests that central scaffolds which predispose the orientation of chemical building blocks toward the protein target may enhance the screening productivity of encoded libraries.     

A Tailor‐Made “Tag–Receptor” Affinity Pair for the Purification of Fusion Proteins

A novel affinity “tag–receptor” pair was developed as a generic platform for the purification of fusion proteins. The hexapeptide RKRKRK was selected as the affinity tag and fused to green fluorescent protein (GFP). The DNA fragments were designed, cloned in Pet‐21c expression vector and expressed in E. coli host as soluble protein. A solid‐phase combinatorial library based on the Ugi reaction was synthesized: 64 affinity ligands displaying complementary functionalities towards the designed tag. The library was screened by affinity chromatography in a 96‐well format for binding to the RKRKRK‐tagged GFP protein. Lead ligand A7C1 was selected for the purification of RKRKRK fusion proteins. The affinity pair RKRKRK‐tagged GFP with A7C1 emerged as a promising solution (K_a of 2.45×10⁵ M ^?1). The specificity of the ligand towards the tag was observed experimentally and theoretically through automated docking and molecular dynamics simulations.     

Towards the design of non-amyloidogenic proteins

Glucose oxidase was immobilized onto poly(2-hydroxyethyl methacrylate) (pHEMA) membranes by two methods: by covalent bonding through epichlorohydrin and by entrapment between pHEMA membranes. The highest immobilization efficiency was found to be 17.4% and 93.7% for the covalent bonding and entrapment, respectively. The K_m values were 5.9 mmol dm^?3, 8.8 mmol dm^?3 and 12.4 mmol dm^?3 for free, bound and entrapped enzyme, respectively. The V_max values were 0.071 mmol dm^?3 min^?1, 0.067 mmol dm^?3 min^?1 and 0.056 mmol dm^?3 min^?1 for free, bound and entrapped enzyme. When the medium was saturated with oxygen, K_m was not significantly altered but V_max was. The optimum pH values for the free, covalently-bound and entrapped enzyme were determined to be 5, 6, and 7, respectively. The optimum temperature was 30°C for free or covalently-bound enzyme but 35°C for entrapped enzyme. The deactivation constant for bound enzyme was determined as 1.7 × 10^?4 min^?1 and 6.9 × 10^?4 min^?1 for the entrapped enzyme.     

Probing the Peptidylglycine α‐Hydroxylating Monooxygenase Active Site with Novel 4‐Phenyl‐3‐butenoic Acid Based Inhibitors

Specific inhibition of the copper‐containing peptidylglycine α‐hydroxylating monooxygenase (PHM), which catalyzes the post‐translational modification of peptides involved in carcinogenesis and tumor progression, constitutes a new approach for combating cancer. We carried out a structure–activity study of new compounds derived from a well‐known PHM substrate analogue, the olefinic compound 4‐phenyl‐3‐butenoic acid (PBA). We designed, synthesized, and tested various PBA derivatives both in vitro and in silico. We show that it is possible to increase PBA affinity for PHM by appropriate functionalization of its aromatic nucleus. Compound 2 d , for example, bears a meta‐benzyloxy substituent, and exhibits better inhibition features (K_i=3.9 μM , k_inact/K_i=427 M ^?1 s^?1) than the parent PBA (K_i=19 μM , k_inact/K_i=82 M ^?1 s^?1). Docking calculations also suggest two different binding modes for PBA derivatives; these results will aid in the development of further PHM inhibitors with improved features.     

Study on the dyeing properties of hemicyanine dyes. II. Cationic dyeable polyester

The absorption spectra of two hemicyanine fluorescent dyes, namely, trans‐4‐[p‐(N,N‐di(2‐hydroxyethyl))‐amino‐styryl]‐N‐ethyl pyridinium bromide (DHEASPBr‐C₂) and trans‐4‐[p‐(N,N‐di(2‐hydroxyethyl))‐amino‐styryl]‐N‐octyl pyridinium bromide (DHEASPBr‐C₈), were studied at various levels of pH and high temperatures, and were then employed to dye cationic dyeable polyester. Their dyeing properties, fluorescent reflectance and colorimetric properties were explored. The novel fluorescent dyes existed in two forms of monocation and dication in solutions at low pH and high temperature. Overall, the influence of pH on colour depth and the maximum reflectance of dyed cationic dyeable polyester was extremely small. The adsorption mechanism of DHEASPBr‐C₂ and DHEASPBr‐C₈ on cationic dyeable polyester fibres was in good accord with the Langmuir type. Compared with DHEASPBr‐C₂, DHEASPBr‐C₈ exhibited comparatively faster adsorption rate, higher affinity and dye uptake, while its fluorescence shown by cationic dyeable polyester was slightly weak.     

Tuning a Protein‐Labeling Reaction to Achieve Highly Site Selective Lysine Conjugation

Activated esters are widely used to label proteins at lysine side chains and N termini. These reagents are useful for labeling virtually any protein, but robust reactivity toward primary amines generally precludes site‐selective modification. In a unique case, fluorophenyl esters are shown to preferentially label human kappa antibodies at a single lysine (Lys188) within the light‐chain constant domain. Neighboring residues His189 and Asp151 contribute to the accelerated rate of labeling at Lys188 relative to the ≈40 other lysine sites. Enriched Lys188 labeling can be enhanced from 50–70 % to >95 % by any of these approaches: lowering reaction temperature, applying flow chemistry, or mutagenesis of specific residues in the surrounding protein environment. Our results demonstrated that activated esters with fluoro‐substituted aromatic leaving groups, including a fluoronaphthyl ester, can be generally useful reagents for site‐selective lysine labeling of antibodies and other immunoglobulin‐type proteins.     

Postsynthetic Covalent Modification in Covalent Organic Frameworks

The modification of covalent organic frameworks (COFs) based on postsynthetic covalent linkages is discussed in this review. In this strategy, the COF is preparedas scaffold and then assembled with functional groups with preservation of structural skeleton. Recent studies indicate that a number of COFs, such as COF-5 and 3D-OH-COOF, are controllable to postsynthetic modification. Furthermore, covalentmodifications including triazole, ester, amide, sulfide, o-carbamate, ether, and oxime are suitable for postsynthetic functionalization. The rapid development of postsynthetic modification demonstrates that this approach will provide a general platform to create COFs as robust functional porous materials for wide applications.     

Development of a High-Affinity Antibody-Binding Peptide for Site-Specific Modification

Immunoglobulin G (IgG)-binding peptides such as 15-IgBP are convenient tools for the site-specific modification of antibodies and the preparation of homogeneous antibody–drug conjugates. A peptide such as 15-IgBP can be selectively crosslinked to the fragment crystallizable region of human IgG in an affinity-dependent manner via the ϵ-amino group of Lys8. Previously, we found that the peptide 15-Lys8Leu has a high affinity (K_d=8.19 nM) due to the presence of the γ-dimethyl group in Leu8. The primary amino group required for the crosslinking to the antibodies has, however, been lost. Here, we report the design and synthesis of a novel unnatural amino acid, 4-(2-aminoethylcarbamoyl)leucine (Aecl), which possesses both the γ-dimethyl fragment and a primary amino group. A peptide containing Aecl8 (15-Lys8Aecl) was synthesized and showed a binding affinity ten times higher (K_d=24.3 nM) than that of 15-IgBP (K_d=267 nM). Fluorescein isothiocyanate (FITC)-labeled 15-Lys8Aecl with an N-hydroxy succinimide ester at the side chain of Aecl8 (FITC-15-Lys8Aecl(OSu)) successfully labeled an antibody (trastuzumab, Herceptin^®) with the fluorophore. This peptide scaffold has both strong binding affinity and crosslinking capability, and could be a useful tool for the selective chemical modification of antibodies with molecules of interest such as drugs.     

Improving the toughness of epoxy with a reactive tetrablock copolymer containing maleic anhydride

Reactive block copolymers (BCPs) provide a unique means for toughening epoxy thermosets because covalent linkages provide opportunities for greater improvement in the fracture toughness (K_IC). In this study, a tailored reactive tetrablock copolymer, poly[styrene‐alt‐(maleic anhydride)]‐block‐polystyrene‐block‐poly(n‐butyl acrylate)‐block‐polystyrene, was incorporated into a diglycidyl ether of bisphenol A based epoxy resin. The results demonstrate the advantage of reactive BCP in finely tuning and controlling the structure of epoxy blends, even with 95 wt % epoxy‐immiscible triblocks. The size of the dispersed phase was efficiently reduced to submicrometer level. The mechanical properties, such as K_IC, of these cured blends were investigated. The addition of 10 wt % reactive BCP into the epoxy resins led to considerable improvements in the toughness, imparting nearly a 70% increase in K_IC. The designed reactive tetrablock copolymer opened good prospects because of its potential novel applications in toughening modification of engineering polymer composites. © 2015 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2016 , 132, 42826.     

Reactivity Analysis of New Multivalent Electrophilic Probes for Affinity Labeling of Carbohydrate Binding Proteins

We have designed and synthesized six different multivalent electrophiles as carbohydrate affinity labeling probes. Evaluation of the reactivity of the electrophiles against peanut agglutinin (PNA) and Ricinus communis agglutinin (RCA) showed that p- and m-aryl sulfonyl fluoride are effective protein reactive groups that label carbohydrate binding lectins in a ligand-dependent fashion at a nanomolar probe concentration. Analysis of the selectivity of affinity labeling in the presence of excess BSA as a nonspecific protein indicated that m-arylsulfonyl fluoride is a more selective protein-reactive group, albeit with attenuated reactivity. Further analysis showed that the labeling efficiency of the multivalent electrophilic probes can be improved by employing reaction conditions involving 25 °C instead of typically employed 4 °C. Both isomers of arylsulfonyl fluoride groups together represent promising affinity labels for target identification studies that could serve as more efficient alternatives to photoreactive groups.     

Epoxy‐derived pHEMA membrane for use bioactive macromolecules immobilization: Covalently bound urease in a continuous model system

Poly(2‐hydroxyethylmethacrylate) (pHEMA) membranes were prepared by UV‐initiated photopolymerization of HEMA in the presence of an initiator (α‐α′‐azobisisobutyronitrile, AIBN). The epoxy group, i.e., epichlorohydrin, was incorporated covalently, and the urease was immobilized onto pHEMA membranes by covalent bonding through the epoxy group. The retained activity of the immobilized enzyme was found to be 27%. The K_m values were 18 and 34 mM for the free and the immobilized enzymes, respectively, and the V_max values were found to be 59.7 and 16.2 U mg⁻¹ for the free and the immobilized enzyme. The optimum pHs was 7.2 for both forms, and the optimum temperature for the free and the immobilized enzymes were determined to be 45 and 50°C, respectively. The immobilized urease was characterized in a continuous system and during urea degradation the operational stability rate constant for the immobilized enzyme was found to be 5.83 × 10⁻⁵ min⁻¹. © 2000 John Wiley & Sons, Inc. J Appl Polym Sci 77: 2000–2008, 2000     

Synthesis of S‐Adenosyl‐L‐homocysteine Capture Compounds for Selective Photoinduced Isolation of Methyltransferases

Understanding the interplay of different cellular proteins and their substrates is of major interest in the postgenomic era. For this purpose, selective isolation and identification of proteins from complex biological samples is necessary and targeted isolation of enzyme families is a challenging task. Over the last years, methods like activity‐based protein profiling (ABPP) and capture compound mass spectrometry (CCMS) have been developed to reduce the complexity of the proteome by means of protein function in contrast to standard approaches, which utilize differences in physical properties for protein separation. To isolate and identify the subproteome consisting of S‐adenosyl‐L ‐methionine (SAM or AdoMet)‐dependent methyltransferases (methylome), we developed and synthesized trifunctional capture compounds containing the chemically stable cofactor product S‐adenosyl‐L ‐homocysteine (SAH or AdoHcy) as selectivity function. SAH analogues with amino linkers at the N6 or C8 positions were synthesized and attached to scaffolds containing different photocrosslinking groups for covalent protein modification and biotin for affinity isolation. The utility of these SAH capture compounds for selective photoinduced protein isolation is demonstrated for various methyltransferases (MTases) acting on DNA, RNA and proteins as well as with Escherichia coli cell lysate. In addition, they can be used to determine dissociation constants for MTase–cofactor complexes.