A Brief Guide to Preparing a Peptide–Drug Conjugate

Peptide–drug conjugates (PDCs) have recently emerged as interesting hybrid constructs not only for targeted therapy, but also for the early diagnosis of different pathologies. In most cases, the crucial step in the PDC synthesis is the final conjugation step, where a specific drug is bound to a particular peptide-/peptidomimetic-targeting unit. Thus, this concept paper aims to give a short guide to determining the finest conjugation reaction, by considering in particular the reaction conditions, the stability of the linker and the major pros and cons of each reaction. Based on the recent PDCs reported in literature, the most common and efficient conjugation methods will be systematically presented and compared, generating a short guide to consult while planning the synthesis of a novel peptide–drug conjugate.     

Preparation of Mesoporous V–Ce–Ti–O for the Selective Oxidation of Methanol to Dimethoxymethane

Mesoporous V–Ce–Ti–O oxides were synthesized through the combination of sol–gel and hydrothermal methods and were characterized by different techniques. N₂ adsorption showed that the mesoporous oxides with 0–20 wt.% V₂O₅ possessed the surface areas of about 160 m² g^?1 with narrow pore size distribution centered around 4–5 nm. Vanadium species were highly dispersed in the samples, as confirmed by the wide angle XRD and Raman spectroscopy. The surface acidity of the materials was determined by the microcalorimetric adsorption of NH₃. Temperature programmed reduction and O₂ chemisorption were used to probe the redox property of the materials. It was found that the mesoporous V–Ce–Ti–O possessed bifunctional characters of acidic and redox properties that catalyzed the oxidation of methanol to dimethoxymethane (DMM). These bifunctional characters were further enhanced by the addition of V₂O₅ and SO₄ ^2? onto V–Ce–Ti–O simultaneously. Such supported catalysts exhibited excellent performance for the selective oxidation of methanol to DMM. Specifically, 72% conversion of methanol with 85% selectivity to DMM was achieved at 423 K over a SO₄ ^2?–V₂O₅/V–Ce–Ti–O catalyst.     

Recent Chemical Approaches for Site-Specific Conjugation of Native Antibodies: Technologies toward Next-Generation Antibody–Drug Conjugates

Antibody–drug conjugates (ADCs), which consist of three components, antibody, linker, and payload, can function as “magic bullets”. These conjugates offer the ability to target drug delivery to specific cells, based on cell-specific recognition and the binding of an antigen by a monoclonal antibody (mAb). In particular, by delivering a cytotoxic payload to cancer cells, ADCs are expected to provide a breakthrough in oncology treatments by providing a way to increase efficacy and decrease toxicity, in comparison with traditional chemotherapeutic treatments. The development of ADC therapeutics has dramatically progressed in the past decade and two ADCs have been approved and used as anticancer drugs in the clinic. However, several critical issues regarding the performance of ADCs are still being discussed and investigated. Indeed, in the past few years, several groups have reported that, changing the number and position of the drug payloads in the ADCs, affects the pharmacokinetics, drug release rates, and biological activity. The use of conventional heterogeneous conjugation methods for ADC preparation results in the drug/antibody ratio and connecting position of the payload having stochastic distributions. Therefore, it is important to investigate how these potential problems can be circumvented through site-specific conjugation. Herein, various site-specific chemical conjugation strategies with native mAbs that are currently used for the production of ADCs, including residue-selective labeling for generating ADCs, disulfide rebridging, and affinity-peptide-mediated site-specific chemical conjugation technologies, are reviewed and described.     

Protein Domain Specific Covalent Inhibition of Human DNA Polymerase β

DNA polymerase β (Pol β) is a frequently overexpressed and/or mutated bifunctional repair enzyme. Pol β possesses polymerase and lyase active sites, that are employed in two steps of base excision repair. Pol β is an attractive therapeutic target for which there is a need for inhibitors. Two mechanistically inspired covalent inhibitors ( 1 , IC₅₀=21.0 μM; 9 , IC₅₀=18.7 μM) that modify lysine residues in different Pol β active sites are characterized. Despite modifying lysine residues in different active sites, 1 and 9 inactivate the polymerase and lyase activities of Pol β. Fluorescence anisotropy experiments indicate that they do so by preventing DNA binding. Inhibitors 1 and 9 provide the basis for a general approach to preparing domain selective inhibitors of bifunctional polymerases. Such molecules could prove to be useful tools for studying the role of wild type and mutant forms of Pol β and other polymerases in DNA repair.     

Dihydroartemisinin–Bile Acid Hybridization as an Effective Approach to Enhance Dihydroartemisinin Anticancer Activity

A series of hybrid compounds based on natural products—bile acids and dihydroartemisinin—were prepared by different synthetic methodologies and investigated for their in vitro biological activity against HL-60 leukemia and HepG2 hepatocellular carcinoma cell lines. Most of these hybrids presented significantly improved antiproliferative activities with respect to dihydroartemisinin and the parent bile acid. The two most potent hybrids of the series exhibited a 10.5- and 15.4-fold increase in cytotoxic activity respect to dihydroartemisinin alone in HL-60 and HepG2 cells, respectively. Strong evidence that an ursodeoxycholic acid hybrid induced apoptosis was obtained by flow cytometric analysis and western blot analysis.     

The Application of an Emerging Technique for Protein–Protein Interaction Interface Mapping: The Combination of Photo-Initiated Cross-Linking Protein Nanoprobes with Mass Spectrometry

Protein–protein interaction was investigated using a protein nanoprobe capable of photo-initiated cross-linking in combination with high-resolution and tandem mass spectrometry. This emerging experimental approach introduces photo-analogs of amino acids within a protein sequence during its recombinant expression, preserves native protein structure and is suitable for mapping the contact between two proteins. The contact surface regions involved in the well-characterized interaction between two molecules of human 14-3-3ζ regulatory protein were used as a model. The employed photo-initiated cross-linking techniques extend the number of residues shown to be within interaction distance in the contact surface of the 14-3-3ζ dimer (Gln8–Met78). The results of this study are in agreement with our previously published data from molecular dynamic calculations based on high-resolution chemical cross-linking data and Hydrogen/Deuterium exchange mass spectrometry. The observed contact is also in accord with the 14-3-3ζ X-ray crystal structure (PDB 3dhr). The results of the present work are relevant to the structural biology of transient interaction in the 14-3-3ζ protein, and demonstrate the ability of the chosen methodology (the combination of photo-initiated cross-linking protein nanoprobes and mass spectrometry analysis) to map the protein-protein interface or regions with a flexible structure.     

A Metabolomic Approach to Identifying Chemical Mediators of Mammal–Plant Interactions

Different folivorous marsupials select their food from different subgenera of Eucalyptus, but the choices cannot be explained by known antifeedants, such as formylated phloroglucinol compounds or tannins, or by nutritional quality. Eucalypts contain a wide variety of plant secondary metabolites so it is difficult to use traditional methods to identify the chemicals that determine food selection. Therefore, we used a metabolomic approach in which we employed ¹H nuclear magnetic resonance spectroscopy to compare chemical structures of representatives from the two subgenera and to identify chemicals that consistently differ between them. We found that dichloromethane extracts of leaves from most species in the subgenus Eucalyptus differ from those in Symphyomyrtus by the presence of free flavanones, having no substitution in Ring B. Although flavanoids are known to deter feeding by certain insects, their effects on marsupials have not been established and must be tested with controlled feeding studies.     

A New Approach to the Synthesis of Mg–Al Layered Hydroxides

Theoretical Foundations of Chemical Engineering - Mg–Al layered hydroxides with the composition Mg4Al2(OH)12CO3?3H2O are synthesized by mixing crystalline magnesium and aluminum...     

Selective Oxidation of Methanol to Green Oxygenates – Feasibility Study of Fixed-Bed and Membrane Reactors

A feasibility study of a conventional fixed-bed reactor and a packed-bed membrane reactor (PBMR) in distributor configuration is carried out for the selective oxidation of methanol to the oxygenates dimethoxymethane and methyl formate on a VO_x/TiO₂ catalyst. Kinetic experiments provided the reaction network and a reliable kinetic model of six main reactions involved. The PBMR offers significant advantages and potential for the formation of both target products due to an effective kinetic coupling of the oxidative dehydrogenation of methanol and the consecutive reaction steps to dimethoxymethane and methyl formate in a broad range of operation conditions.     

Selective Oxidation of Cyclohexane to Cyclohexanone Catalyzed by Phenanthroline–CuCl2 Complex

A highly efficient oxidation of cyclohexane to cyclohexanone is accomplished over phenanthroline–CuCl₂ catalyst in relatively mild conditions. This study realized nearly 100% selectivity for cyclohexanone at 24.4% conversion of cyclohexane. The reaction has been studied by various parameters like performance of copper(II) salts, effect of solvents, influence of bases, the ratio of o-phenanthroline: CuCl₂, and reaction time. In order to further study this reaction system, the possible mechanism was proposed.     

Selective Oxidation of Propane to Acrolein over Ce-Doped Ag–Mo–P–O Catalysts: Influence of Ce Promoter

The selective oxidation of propane to acrolein was performed on Ce-doped Ag_0.3Mo_0.5P_0.3O _x catalysts. The maximal acrolein yield of 4.4% with 28.7% acrolein selectivity was obtained on Ce_0.1Ag_0.3Mo_0.5P_0.3O _y catalyst. The apparent activation energy of Ag_0.3Mo_0.5P_0.3O _x catalysts decreased with the addition of Ce. The addition of Ce facilitated the C-H activation of propane and enhanced conversion of intermediate propene to acrolein. The reducibility and the concentration of Mo⁵⁺ improved as the Ce content increased and was closely related to acrolein selectivity and propane conversion. The role of Ce in these catalysts was proposed: there was formation of the redox cycle Ce³⁺ + Mo⁶⁺ Ce⁴⁺ + Mo⁵⁺ in Ce-doped Ag_0.3Mo_0.5P_0.3O _x catalysts, leading to the modification of properties and catalytic performance of these catalysts.     

Efficient Site-Specific Antibody–Drug Conjugation by Engineering a Nature-Derived Recognition Tag for Microbial Transglutaminase

Microbial transglutaminase (mTG) has recently emerged as a powerful tool for antibody engineering. In nature, it catalyzes the formation of amide bonds between glutamine side chains and primary amines. Being applied to numerous research fields from material sciences to medicine, mTG enables efficient site-specific conjugation of molecular architectures that possess suitable recognition motifs. In monoclonal antibodies, the lack of native transamidation sites is bypassed by incorporating specific peptide recognition sequences. Herein, we report a rapid and efficient mTG-catalyzed bioconjugation that relies on a novel recognition motif derived from its native substrate Streptomyces papain inhibitor (SPI_P). Improved reaction kinetics compared to commonly applied sequences were demonstrated for model peptides and for biotinylation of Her2-targeting antibody trastuzumab variants. Moreover, an antibody–drug conjugate assembled from trastuzumab that was C-terminally tagged with the novel recognition sequence revealed a higher payload-antibody ratio than the reference antibody.     

Targeted Nanoswitchable Inhibitors of Protein–Protein Interactions Involved in Apoptosis

Progress in drug delivery is hampered by a lack of efficient strategies to target drugs with high specificity and precise spatiotemporal regulation. The remote control of nanoparticles and drugs with light allows regulation of their action site and dosage. Peptide-based drugs are highly specific, non-immunogenic, and can be designed to cross the plasma membrane. In order to combine target specificity and remote control of drug action, here we describe a versatile strategy based on a generalized template to design nanoswitchable peptides that modulate protein–protein interactions upon light activation. This approach is demonstrated to promote photomodulation of two important targets involved in apoptosis (the interactions Bcl-xL–Bak and MDM2–p53), but can be also applied to a large pool of therapeutically relevant protein–protein interactions mediated by α-helical motifs. The template can be adjusted using readily available information about hot spots (residues contributing most to the binding energy) at the protein–protein interface of interest.     

Selective Hydrogenolysis of Glycerol to 1, 2 Propanediol Over Cu–ZnO Catalysts

A series of Cu–ZnO catalysts with varying Cu to Zn weight ratio are prepared by co-precipitation method. The catalysts were characterized by surface area, XRD, TPR and N₂O chemisorption to measure Cu metal area. These catalysts were evaluated for hydrogenolysis of glycerol. The catalyst with Cu to Zn ratio of 50:50 is highly active under relatively low H₂ pressure. The catalysts are highly selective towards 1,2 propanediol (>93%). The glycerol conversion depends upon the bifunctional nature of catalyst where it requires both acidic sites and metal surface. The presence of sufficient amount with small particle size of ZnO and Cu are required for high conversion of glycerol and selectivity to 1,2 propanediol. Different reaction parameters are studied in order to optimize the reaction conditions.     

Selective Delivery of Doxorubicin to EGFR+ Cancer Cells by Cetuximab–DNA Conjugates

Doxorubicin is a hydrophobic anticancer drug that has poor selectivity, due to the lack of active targeting capability. Here, learning lessons from the success of antibody–drug conjugates, we have designed a new doxorubicin delivery system without conjugating doxorubicin to antibody directly. In this setup, cetuximab, an antibody that targets the epidermal growth factor receptor (EGFR) in cancer cells, was conjugated to a single-stranded DNA with a carefully designed sequence in a site-selective manner by using the DNA-templated protein conjugation (DTPC) method. The DNA duplex in the conjugates serves as a carrier of doxorubicin through noncovalent intercalation, and cetuximab functions as the targeting agent; this could drastically decrease systemic toxicity and potentially avoid under- or overdosing. The size of conjugates loaded with doxorubicin was about 8.77 or 16.61 nm when characterized by dynamic light scattering and atomic force microscopy, respectively. In vitro cytotoxicity and selective cancer cell killing was investigated against two EGFR⁺ cell lines (KB and MDA-MB-231) and one EGFR⁻ cell line (NIH-3T3). Cytotoxicity and flow cytometry data showed that doxorubicin loaded in cetuximab–DNA conjugates was more potent in terms of cell cytotoxicity than free doxorubicin in EGFR-overexpressed cell lines, thus suggesting that the conjugates were more selectively and easily taken up into cells, followed by rapid release of doxorubicin from the system into the cytoplasm from endosomes.     

Covalent Linkage of an R-ω-Transaminase to a d-Amino Acid Oxidase through Protein Splicing to Enhance Enzymatic Catalysis of Transamination

R-ω-Transaminases (RTAs) catalyse the conversion of R-configured amines [e.g., (R)-1-phenylethylamine] into the corresponding ketones (e.g., acetophenone), by transferring an amino group from an amino donor [e.g., (R)-1-phenylethylamine] onto an amino acceptor (e.g., pyruvate), resulting in a co-product (e.g., d -alanine). d -Alanine can be deaminated back to pyruvate by d -amino acid oxidase (DAAOs). Here, through in vivo subunit splicing, the N terminus of an RTA subunit (RTA^S) was specifically ligated to the C terminus of a DAAO subunit (DAAO^S) through native peptide bonds (RTA&DAAO). RTA^S is in close proximity to DAAO^S, at a molecular-scale distance. Thus the transfer of pyruvate and d -alanine between RTA and DAAO can be directional and efficient. Pyruvate→d -alanine→pyruvate cycles are efficiently formed, thus promoting the forward transamination reaction. In a different, in vitro noncovalent approach, based on coiled-coil association, the RTA^S N terminus was specifically associated with the DAAO^S C terminus (RTA#DAAO). In addition, the two mixed individual enzymes (RTA+DAAO) were also studied. RTA&DAAO has a shorter distance between the paired subunits (RTA^S–DAAO^S) than RTA#DAAO, and the number of the paired subunits is higher than in the case of RTA#DAAO, whereas RTA+DAAO cannot form the paired subunits. RTA&DAAO exhibited a transamination catalysis efficiency higher than that of RTA#DAAO and much higher than that of RTA+DAAO.     

Prediction of Protein–Protein Interaction with Pairwise Kernel Support Vector Machine

Protein–protein interactions (PPIs) play a key role in many cellular processes. Unfortunately, the experimental methods currently used to identify PPIs are both time-consuming and expensive. These obstacles could be overcome by developing computational approaches to predict PPIs. Here, we report two methods of amino acids feature extraction: (i) distance frequency with PCA reducing the dimension (DFPCA) and (ii) amino acid index distribution (AAID) representing the protein sequences. In order to obtain the most robust and reliable results for PPI prediction, pairwise kernel function and support vector machines (SVM) were employed to avoid the concatenation order of two feature vectors generated with two proteins. The highest prediction accuracies of AAID and DFPCA were 94% and 93.96%, respectively, using the 10 CV test, and the results of pairwise radial basis kernel function are considerably improved over those based on radial basis kernel function. Overall, the PPI prediction tool, termed PPI-PKSVM, which is freely available at http://159.226.118.31/PPI/index.html, promises to become useful in such areas as bio-analysis and drug development.     

Selective oxidation of methyl mandelate to methyl phenyl glyoxylate using liquid–liquid–liquid phase transfer catalysis

The conversion of the traditional liquid–liquid (L–L) phase transfer catalysis (PTC) into liquid–liquid–liquid (L–L–L) PTC offers several advantages. L–L–L PTC is a novel strategy which offers catalyst recovery, waste reduction including better selectivity and improving profitability. The middle catalyst-rich phase formed between the other two phases is the locale of main reaction and it intensifies the rates of reaction by order of magnitude. In the current work, oxidation of methyl mandelate to methyl phenyl glyoxylate has been studied by using L–L–L PTC with tetra-butyl ammonium bromide as a catalyst at 45 °C. It leads to 100% selectivity towards methyl phenyl glyoxylate within very short reaction time. The method offers several advantages including catalyst separation and reusability. The effects of different parameters were studied in detail. A mathematical model is developed and validated with the observed reaction data.     

Selective Oxidation of Isobutane and Isobutene to Methacrolein over Te–Mo Mixed Oxide Catalysts

A series of Te–Mo–O catalysts were prepared by decomposing (NH₄)₄TeMo₆O₂₂ · 2H₂O telluromolybdate under different conditions and tested for the oxidation of isobutane and isobutene. Characterization results (XRD, FTIR, TG, TPR, XPS, and BET) showed that their structure and properties depend on calcination conditions. Catalytic tests showed that molybdenum may be the key element for the activation of isobutane, whereas the selective oxidation of isobutene to methacrolein (MAL) might proceed mainly on the surface of the TeMo-containing crystalline phase. Thus, relatively high selectivities and yields of MAL and methacrylic acid (MAA) can be obtained over these specially designed catalysts.     

Selective Hydrocracking of Fischer–Tropsch Waxes to High-quality Diesel Fuel Over Pt-promoted Polyoxocation-pillared Montmorillonites

Polyoxocation ([AlO₄Al₁₂(OH)₂₄(H₂O)₁₂]⁷⁺ and [Zr₄(OH)₁₄(H₂O)₁₀]²⁺)-pillared montmorillonites were prepared by ion exchange, and they were used as solid acid catalysts, in comparison to some other solid acids, for the selective hydrocracking of Fischer–Tropsch waxes to diesel-ranged hydrocarbons. XRD patterns and elemental analyses proved that the polyoxocations were successfully introduced into the interlayer region of the montmorillonites. N₂ adsorption–desorption measurement indicated that polyoxocation-pillared montmorillonites have large BET surface areas (>230 m² g^?1), high thermal stability (>673 K), and large pores (comparing to those in zeolites). FT-IR spectra of chemisorbed pyridine indicated that polyoxocation-pillared montmorillonites possess both Lewis and Bronsted acid sites on the solid surface. Temperature-programmed desorption of ammonia indicated that the acidity strength of the polyoxocation-pillared montmorillonites was weaker than those of H–ZSM-5, H–Y, WO₃/ZrO₂, and Al₂O₃–SiO₂. In the hydrocracking of Fischer–Tropsch (F–T) waxes, the acidity strength of the solid acids in bifunctional catalysts greatly influences the product composition. Pt-promoted H–Y afforded a high yield of gasoline-ranged hydrocarbons (>90%) while Pt-promoted H–ZSM-5 afforded a larger amount of gas products due to its strong solid acid sites. On the other hand, among various catalysts, Pt-modified polyoxocation-pillared montmorillonites afforded the highest yield of diesel-ranged hydrocarbons (>70%) due to the appropriately weak acid strength, high thermal stability, large BET surface area, and large pore size. Pt is necessary for the hydrocracking of F–T waxes because it enables hydrogenation/dehydrogenation. However, a high Pt loading on the catalyst produces more light hydrocarbons due to the stimulation of hydrogenolysis. High hydrogen pressure improved the selectivity for diesel-ranged hydrocarbons but decreased the conversion of F–T waxes due to the suppression of alkane dehydrogenation. The hydrocracking of F–T waxes at a low temperature with a large amount of catalyst for longer reaction time increased the yield of diesel-ranged hydrocarbons.