Small-angle X-ray scattering and structural modeling of full-length: cellobiohydrolase I from Trichoderma harzianum

Cellobiohydrolases hydrolyze cellulose releasing cellobiose units. They are very important for a number of biotechnological applications, such as, for example, production of cellulosic ethanol and cotton fiber processing. The Trichoderma cellobiohydrolase I (CBH1 or Cel7A) is an industrially important exocellulase. It exhibits a typical two domain architecture, with a small C-terminal cellulose-binding domain and a large N-terminal catalytic core domain, connected by an O-glycosylated linker peptide. The mechanism by which the linker mediates the concerted action of the two domains remains a conundrum. Here, we probe the protein shape and domain organization of the CBH1 of Trichoderma harzianum (ThCel7A) by small angle X-ray scattering (SAXS) and structural modeling. Our SAXS data shows that ThCel7A linker is partially-extended in solution. Structural modeling suggests that this linker conformation is stabilized by inter- and intra-molecular interactions involving the linker peptide and its O-glycosylations.     

Improved Methodology for the Synthesis of a Cathepsin B Cleavable Dipeptide Linker,Widely Used in Antibody-Drug Conjugate Research

Antibody-drug conjugates (ADCs) represent an emerging class of biopharmaceutical agents that deliver highly potent anticancer agents (payloads) selectively to tumors or components associated with the tumor microenvironment. The linker, responsible for the connection between the antibody and payload, is a crucial component of ADCs. In certain examples the linker is composed of a cleavable short peptide which imparts an additional aspect of selectivity. Especially prevalent is the cathepsin B cleavable Mc-Val-Cit-PABOH linker utilized in many pre-clinical ADC candidates, as well as the FDA approved ADC ADCETRIS^® (brentuximab vedotin). An alternative route for the synthesis of the cathepsin B cleavable Mc-Val-Cit-PABOH linker is reported herein that involved six steps from l-Citrulline and proceeded with a 50% overall yield. In this modified route, the spacer (a para-aminobenzyl alcohol moiety) was incorporated via HATU coupling followed by dipeptide formation. Importantly, this route avoided undesirable epimerization and proceeded with improved overall yield. Utilizing this methodology, a drug-linker construct incorporating a potent small-molecule inhibitor of tubulin polymerization (referred to as KGP05), was synthesized as a representative example.     

Simple formylacetal (CH2) as a novel linker for saccharide synthesis on soluble-polymer support

Described herein is a new formylacetal (CH₂) linker for immobilization of small molecules onto a soluble-polymer support, poly(ethylene glycol) ω-monomethyl ether (MPEG), and its application to saccharide synthesis. This small linker allows immobilization of a hindered hydroxy group such as the 4-hydroxy group of glucose onto MPEG. The linker is stable under several reaction conditions including glycosylation. Removal of this support was found to be achieved through cleavage of the CH₂ linker either by a Lewis acid (TMSI or Ce(OTf)_x) or a Brønsted acid (trifluoroacetic acid) in moderate to good yields. In combination with solid acid catalyst, simpler operations became possible during the working-up and purification processes.     

Versatile solid-phase synthesis of secondary amines from alcohols. Development of an N-Boc-(o-nitrobenzene)sulfonamide linker

The development of a versatile amine releasing linker based on the modified o-nitrobenzene sulfonamide protective group is described. This new N-Boc-o-nitrobenzenesulfonamide (Boc-ONBS) linker enables the elaboration on resin of primary and secondary amines by sequential substitution of the sulfonamide moiety using the Mitsunobu reaction. A 16-member array of secondary and Boc protected primary amines was then prepared using this linker.     

Efficient synthesis of antisense phosphorothioate oligonucleotides using a universal solid support

It is demonstrated that solid support containing a novel universal linker could be efficiently used to synthesize both phosphorothioate oligodeoxyribonucleotides and second-generation 2′-O-methoxyethyloligoribonucleotides with high yield and quality as judged by ion-pair-liquid chromatography-electrospray mass spectroscopy, ³¹P NMR and reversed phase HPLC. Analysis of oligonucleotides shows quality being superior to that produced with standard succinyl-linker solid supports, without contamination of materials resulting from linker or support backbone decomposition.     

Preparation and sorption studies of polyester microsphere copolymers containing β-Cyclodextrin

Polyester copolymer sorbent materials that incorporate β-Cyclodextrin (β-CD) were prepared using water-in-oil (w/o) micro-emulsion conditions at variable β-CD: cross linker mole ratios; where the cross linker units were sebacoyl chloride (SCl) and terephthaloyl chloride (TCl). The copolymers were characterized using TGA, nitrogen adsorption, and NMR/IR spectroscopy. The dye-based sorption properties of the copolymers with p-nitrophenol (PNP) in aqueous solution were evaluated at pH 4.6 and 295 K using UV-Vis spectrophotometry. The uptake of PNP varied from 0.221 to 0.352 mmol/g, according to the nature of the cross linker and the copolymer mole ratio. The sorption capacity of SCl-based copolymers exceed that for TCl-based copolymers, and correlate with the relative swelling properties and hydrated surface areas of the sorbent frameworks. ¹H NMR spectroscopy of copolymers with low levels of linker content (i.e. SCl or TCl) indicate dual sorption sites for PNP (i.e. β-CD inclusion sites and non-inclusion (interstitial) linker domains). The existence of dual sorption sites is similarly concluded for copolymers containing higher levels of cross linker. Inclusion complexes are firstly formed between PNP and the β-CD inclusion sites of the copolymer; thereafter, PNP is adsorbed onto the linker domains of the copolymer sorbent framework.     

Intercalating nucleic acids (INAs) containing insertions of 6H-indolo[2,3-b]quinoxaline

6H-Indolo[2,3-b]quinoxaline was studied as a covalently bound heteroaromatic intercalator. Six monomers were synthesized and incorporated into DNA oligonucleotides. Through a study of linker length dependence it was concluded that the linker between the oligo and the intercalator must consist of at least five C atoms in order to stabilize a DNA duplex. An intercalator with a 2′-deoxy-d-riboside linker to the oligo could also stabilize a DNA/RNA duplex, while (S)-4-(6-methylindolo[2,3-b]quinoxalin-3-ylmethoxy)-butane-1,2-diol was able to stabilize both DNA/DNA, DNA/RNA and a DNA/LNA duplex. Mismatch studies revealed a huge sensitivity to the C-C mismatch at the 5′-site of the intercalator.     

Synthesis of pyridinium N-chloramines for antibacterial applications

To develop more efficacious antibacterial agents, a new type of cationic N-chloramines that contain a pyridinium moiety and a N-chloramine moiety covalently linked via an alkyl chain were prepared and characterized. Preliminary assays indicated that 1) the compound with a propylidene linker exhibited higher antibacterial activity than the quaternary ammonium counterpart; 2) the chain length of the alkyl linker had major effects on their biocidal properties. Our results may inspire exploration of more pyridinium N-chloramines for antibacterial applications.     

Molecular Umbrella as a Nanocarrier for Antifungals

A molecular umbrella composed of two O-sulfated cholic acid residues was applied for the construction of conjugates with cispentacin, containing a “trimethyl lock” (TML) or o-dithiobenzylcarbamoyl moiety as a cleavable linker. Three out of five conjugates demonstrated antifungal in vitro activity against C. albicans and C. glabrata but not against C. krusei, with MIC₉₀ values in the 0.22–0.99 mM range and were not hemolytic. Antifungal activity of the most active conjugate 24c, containing the TML–pimelate linker, was comparable to that of intact cispentacin. A structural analogue of 24c, containing the Nap-NH₂ fluorescent probe, was accumulated in Candida cells, and TML-containing conjugates were cleaved in cell-free extract of C. albicans cells. These results suggest that a molecular umbrella can be successfully applied as a nanocarrier for the construction of cleavable antifungal conjugates.     

A Sub-Micromolar MraYAA Inhibitor with an Aminoribosyl Uridine Structure and a (S,S)-Tartaric Diamide: Synthesis,Biological Evaluation and Molecular Modeling

New inhibitors of the bacterial tranferase MraY are described. Their structure is based on an aminoribosyl uridine scaffold, which is known to be important for the biological activity of natural MraY inhibitors. A decyl alkyl chain was introduced onto this scaffold through various linkers. The synthesized compounds were tested against the MraY_AA transferase activity, and the most active compound with an original (S,S)-tartaric diamide linker inhibits MraY activity with an IC₅₀ equal to 0.37 µM. Their antibacterial activity was also evaluated on a panel of Gram-positive and Gram-negative strains; however, the compounds showed no antibacterial activity. Docking and molecular dynamics studies revealed that this new linker established two stabilizing key interactions with N190 and H325, as observed for the highly potent inhibitors carbacaprazamycin, muraymycin D2 and tunicamycin.     

Synthesis of C-11 linked active ester derivatives of vitamin D3 and their conjugations to 42-residue helix-loop-helix peptides

Derivatives of vitamin D₃ carrying an 8-carbon linker at C-11 terminating in an active ester were synthesized from commercial vitamin D₃ using a disassembly-reassembly strategy. Vitamin D₃ was cleaved at the C6-C7 double bond and the ‘upper’ fragment was converted, via a series of reactions, to derivatives substituted at C-11 with an 8-carbon linker terminating in an ethyl ester. Reassembly with modified ‘lower’ fragments using Horner-Wittig olefination followed by linker ester hydrolysis and re-esterification with p-nitrophenol gave C-11 substituted p-nitrophenyl esters. These vitamin D derivatives were conjugated to 42-amino acid helix-loop-helix peptides by reaction of their p-nitrophenyl esters with lysyl side-chain amino groups on the peptides. The vitamin D—peptide conjugates, being potential specific binder candidates for vitamin D-binding protein, were characterized by mass spectroscopy and CD measurements.     

Tetracationic compounds based on 1,4-diazabicyclo[2.2.2]octane: antibacterial activity and reactions with N-containing nucleophiles

Antibacterial activity of tetracationic compounds based on 1,4-diazabicyclo[2.2.2]octane (DABCO) bis-quaternary salts with dodecyl substituents bound by linker groups containing four carbon atoms was studied. All the compounds exhibited activity against the test-strains under study. The gram-positive culture S. aureus was found to be the most sensitive to the influence of compounds in question. The highest activity against S. aureus was exhibited by the compounds containing a but-2-yne or a butane linker; their efficiency exceeded that of the reference compound, antibiotic Ciprofloxacin. For the gram-negative culture P. aeruginosa, the highest activity was exhibited by the compound containing a but-2-yne linker. The compounds with a but-2-yne or a butane linker are stable in the presence of nitrogen-containing nucleophiles, which makes them promising for further studies.     

Tricine as a convenient scaffold for the synthesis of C-terminally branched collagen-model peptides

A novel and convenient method for the synthesis of C-terminally branched collagen-model peptides has been achieved using tricine (N-[tris(hydroxymethyl)methyl]glycine) as a branching scaffold and 1,2-diaminoethane or 1,4-diaminobutane as a linker. The peptide sequence was incorporated directly onto the linker and scaffold during solid-phase synthesis without additional manipulations. The resulting branched triple-helical peptides exhibited comparable thermal stabilities to the parent, unbranched sequence, and served as substrates for matrix metalloproteinase-1 (MMP-1). The tricine-based branch reported herein represents the simplest synthetic scaffold for the convenient synthesis of covalently linked homomeric collagen-model triple-helical peptides.     

Distigmasterol-Modified Acylglycerols as New Structured Lipids—Synthesis,Identification and Cytotoxicity

Plant sterols, also referred as phytosterols, have been known as bioactive compounds which have cholesterol-lowering properties in human blood. It has been established that a diet rich in plant sterols or their esters alleviates cardiovascular diseases (CVD), and also may inhibit breast, colon and lung carcinogenesis. Phytosterols, in their free and esterified forms, are prone to thermo-oxidative degradation, where time and temperature affect the level of degradation. Looking for new derivatives of phytosterols with high thermo-oxidative stability for application in foods, our idea was to obtain novel structured acylglycerols in which two fatty acid parts are replaced by stigmasterol residues. In this work, asymmetric (1,2- and 2,3-) distigmasterol-modified acylglycerols (dStigMAs) were synthesized by the covalent attachment of stigmasterol residues to sn-1 and sn-2 or sn-2 and sn-3 positions of 3-palmitoyl-sn-glycerol or 1-oleoyl-sn-glycerol, respectively, using a succinate or carbonate linker. The chemical structures of the synthesized compounds were identified by NMR, HR-MS, and IR data. Moreover, the cytotoxicity of the obtained compounds was determined. The dStigMAs possessing a carbonate linker showed potent cytotoxicity to cells isolated from the small intestine and colon epithelium and liver, whereas the opposite results were obtained for compounds containing a succinate linker.     

Enantiomerically pure chiral pyridino-crown ethers: synthesis and enantioselectivity toward the enantiomers of α-(1-naphthyl)ethylammonium perchlorate

Seven new enantiomerically pure chiral pyridino-crown ethers (S,S)-4–(R,R)-10 were prepared. Three of them [(S,S)-4, (S,S)-7 and (R,R)-10] contain one, and two of them [(S,S)-5 and (S,S)-8] contain two linker chains with a terminal double bond. These linker chains were connected to the carbon atom at position 9 (opposite the pyridine moiety) of the macrocycle. The terminal double bond of the linker makes it possible to attach these ligands to silica gel to obtain chiral stationary phases (CSPs). The enantioselectivity of the new ligands toward the enantiomers of α-(1-naphthyl)ethylammonium perchlorate (NEA) was also determined by a titration ¹H NMR method.     

New chiral bis(diphenylphospholane) ligands: design, synthesis, and application to catalytic enantioselective aldol reaction to ketones

New chiral bidentate diphenylphospholanes were designed targeting a catalytic enantioselective aldol reaction to ketones. Ligands 5l and 5m having cis-2-butenyl and cyclopropyl groups at the linker part, respectively, were identified as effective chiral ligands for a CuF-catalyzed enantioselective aldol reaction to ketones. Catalysts prepared from CuF·3PPh₃·2EtOH and these ligands produced ketone aldol products with up to 66% ee, which is promising particularly for this extremely difficult and important catalytic enantioselective carbon-carbon bond forming reaction. The enantioselectivity was strongly dependent on the linker structure. Construction of a deep chiral pocket around the copper metal with stable bidentate chelation is the key to meaningful enantioinduction.     

Effect of Trichoderma reesei Proteinases on the Affinity of an Inorganic-Binding Peptide

An inorganic-binding peptide sequence with high affinity to silica-containing materials was fused to a glycoside hydrolase GH26 mannanase, ManA, from the extremely thermophilic bacterium Dictyoglomus thermophilum. The resulting recombinant enzyme produced in Escherichia coli, ManA-Linker, displayed high binding affinity towards synthetic zeolite while retaining its catalytic activity at 80 °C. ManA-Linker was able to bind to the zeolite at different pH levels, indicating a true pH-independent binding. However, complete degradation of the peptide linker was observed when the recombinant ManA-Linker was exposed to the supernatant from the filamentous fungus Trichoderma reesei. This degradation was caused by extracellular proteinases produced by T. reesei during its growth phase. Several derivatives of ManA-Linker were designed and expressed in E. coli. All the derivatives carrying a single sequence of the linker were still susceptible to T. reesei proteinase degradation. Complete substitution of the linker sequence by (GGGGS)₁₆ resulted in a proteinase-resistant ManA derivative, ManA-Linker-(GGGGS)₁₆, which was able to bind to zeolite in a pH-dependent manner.     

Enhanced two-photon absorption of novel four-branched chromophore via vibronic coupling

A novel four-branched chromophore TOZ-4 with starburst linker was synthesized and showed two-photon absorption cross-section (δ) as large as 5254 GM, which was principally resulted from vibronic coupling enhancement.     

From a Well-Defined Organozinc Precursor to Diverse Luminescent Coordination Polymers Based on Zn(II)-Quinolinate Building Units Interconnected by Mixed Ligand Systems

Introduction of photoactive building blocks into mixed-ligand coordination polymers appears to be a promising way to produce new advanced luminescent materials. However, rational design and self-assembly of the multi-component supramolecular systems is challenging from both a conceptual and synthetic perspective. Here, we report exploratory studies that investigate the potential of [Zn(q)₂]₂[tBuZn(OH)]₂ complex (q = deprotonated 8-hydroxyquinoline) as an organozinc precursor as well as a mixed-ligand synthetic strategy for the preparation of new luminescent coordination polymers (CPs). As a result we present three new 2D mixed-ligand Zn(II)-quinolinate coordination polymers which are based on various zinc quinolinate secondary building units interconnected by two different organic linker types, i.e., deprotonated 4,4′-oxybisbenzoic acid (H₂obc) as a flexible dicarboxylate linker and/or selected bipyridines (bipy). Remarkably, using the title organozinc precursors in a combination with H₂obc and 4,4′-bipyridine, a novel molecular zinc quinolinate building unit, [Zn₄(q)₆(bipy)₂(obc)₂], was obtained which self-assembled into a chain-type hydrogen-bonded network. The application of the organometallic precursor allowed for its direct reaction with the selected ligands at ambient temperature, avoiding the use of both solvothermal conditions and additional base reagents. In turn, the reaction involving Zn(NO₃)₂, as a classical inorganic precursor, in a combination with H₂obc and bipy led to a novel 1D coordination polymer [Zn₂(q)₂(NO₃)₂(bipy)]. While the presence of H₂obc was essential for the formation of this coordination polymer, this ditopic linker was not incorporated into the isolated product, which indicates its templating behavior. The reported compounds were characterized by single-crystal and powder X-ray diffraction, elemental analysis as well as UV-Vis and photoluminescence spectroscopy.