Detection of a metallo-beta-lactamase (IMP-1) by fluorescent probes having dansyl and thiol groups

A fluorescent probe for the detection of a metallo-beta-lactamase (IMP-1), N-[2-(5-dimethylaminonaphthalen-1-ylsulfonylamino)ethyl]-3- mercaptopropionamide (Dansyl-C2SH), 1, was designed based on combining the inhibitory function of mercaptocarboxylate and a fluorophore. The binding of 1 to IMP-1 was investigated by fluorescence spectroscopy. Compound 1 can act as fluorescent probe for detecting IMP-1 selectively.     

Adsorption and separation of poly-aromatic hydrocarbons by a hydrogen-bonded coordination polymer

A residual-host prepared by thermal removal of naphthalene (NA) from the inclusion compound [Ni(SCN)(2)(isonicotinic acid)(2)]·(NA)(0.5) was found to function as an adsorbent for aromatic molecules and exhibit method-dependent selectivity.     

Molecular understanding of the adhesive interactions between silica surface and epoxy resin: Effects of interfacial water

The molecular mechanism of the adhesion between silica surface and epoxy resin under atmospheric conditions is investigated by periodic density-functional-theory (DFT) calculations. Slab models of the adhesion interface were built by integrating a fragment of epoxy resin and hydroxylated (0 0 1) surface of α-cristobalite in the presence of adsorbed water molecules. Effects of adsorbed water on the adhesion interaction are evaluated on the basis of geometry-optimized structures, adhesion energies, and forces. Calculated results demonstrate that adsorbed water molecules significantly reduce both the adhesion energies and forces of the silica surface–epoxy resin interface. The reduction of adhesion properties can be associated with structural deformation of water molecules confined in the tight space between the adhesive and adherend as well as structural flexibility of the hydrogen-bonding network in the interfacial region during detachment of the epoxy resin from the hydrophilic silica surface. © 2018 Wiley Periodicals, Inc.     

A convenient stereoselective synthesis of β-lactams from β-hydroxy-α-thioalkylesters prepared from Michael/aldol tandem reaction or stereoselective addition of thiols to the Baylis-Hillman adducts

A convenient stereoselective synthesis of β-lactams from thio-Michael/aldol tandem adduct is described. syn-Selective tandem reaction followed by amidation and intramolecular S_N2 reaction provided β-lactams in diastereomerically pure form. The tandem reaction with aliphatic aldehydes, on the other hand, afforded a mixture of diastereomers of corresponding tandem adducts in about 3:1 ratio so that the conversion to β-lactams afforded a diastereomeric mixture. As an alternative approach to prepare the tandem adducts, the stereoselective Michael addition of aliphatic thiols to Baylis-Hillman adduct was developed. The stereoselectivity was sensitive to the protective group at the hydroxyl group and TBS protection brought the most successful syn-selective formation of the tandem adducts. The procedure could be applied to the ketone derivatives of the Baylis-Hillman adduct but no selectivity was observed for the nitrile-Baylis-Hillman adducts. A similar conversion of the adduct provided desired β-lactams stereoselectively.     

Application of plug–plug technique to ACE experiments for discovery of peptides binding to a larger target protein: A model study of calmodulin‐binding fragments selected from a digested mixture of reduced BSA

To discover peptide ligands that bind to a target protein with a higher molecular mass, a concise screening methodology has been established, by applying a “plug–plug” technique to ACE experiments. Exploratory experiments using three mixed peptides, mastoparan‐X, β‐endorphin, and oxytocin, as candidates for calmodulin‐binding ligands, revealed that the technique not only reduces the consumption of the protein sample, but also increases the flexibility of the experimental conditions, by allowing the use of MS detection in the ACE experiments. With the plug–plug technique, the ACE–MS screening methodology successfully selected calmodulin‐binding peptides from a random library with diverse constituents, such as protease digests of BSA. Three peptides with K_d values between 8–147 μM for calmodulin were obtained from a Glu‐C endoprotease digest of reduced BSA, although the digest showed more than 70 peaks in its ACE–MS electropherogram. The method established here will be quite useful for the screening of peptide ligands, which have only low affinities due to their flexible chain structures but could potentially provide primary information for designing inhibitors against the target protein.     

Efficient on-column conversion of IgG1 trisulfide linkages to native disulfides in tandem with Protein A affinity chromatography

Protein trisulfide linkages are generated by the post-translational insertion of a sulfur atom into a disulfide bond. Molecular heterogeneity was detected in a recombinant IgG₁ monoclonal antibody (mAb) and attributed to the presence of a protein trisulfide moiety. The predominant site of trisulfide modification was the bond between the heavy and light chains. The trisulfide was eliminated during purification of the IgG₁ mAb via a cysteine wash step incorporated into Protein A affinity column chromatography. Analysis of the cysteine-treated mAb by electrophoresis and peptide mapping indicated that the trisulfide linkages were efficiently converted to intact disulfide bonds (13% trisulfide decreased consistently to 1% or less) without disulfide scrambling or an increase in free sulfhydryls. The on-column trisulfide conversion caused no change in protein folding detectable by hydrogen/deuterium exchange or differential scanning calorimetry. Consistent with this, binding of the mAb to its antigen in vitro was insensitive to the presence of the trisulfide modification and to its removal by the on-column cysteine treatment. Similar, high efficiency trisulfide conversion was achieved for a second IgG₁ mAb using the column wash strategy (at least 7% trisulfide decreased to 1% or less). Therefore, trisulfide/disulfide heterogeneity can be eliminated from IgG₁ molecules via a convenient and inexpensive procedure compatible with routine Protein A affinity capture.     

Ring system-based chemical graph generation for de novo molecular design

Generating chemical graphs in silico by combining building blocks is important and fundamental in virtual combinatorial chemistry. A premise in this area is that generated structures should be irredundant as well as exhaustive. In this study, we develop structure generation algorithms regarding combining ring systems as well as atom fragments. The proposed algorithms consist of three parts. First, chemical structures are generated through a canonical construction path. During structure generation, ring systems can be treated as reduced graphs having fewer vertices than those in the original ones. Second, diversified structures are generated by a simple rule-based generation algorithm. Third, the number of structures to be generated can be estimated with adequate accuracy without actual exhaustive generation. The proposed algorithms were implemented in structure generator Molgilla. As a practical application, Molgilla generated chemical structures mimicking rosiglitazone in terms of a two dimensional pharmacophore pattern. The strength of the algorithms lies in simplicity and flexibility. Therefore, they may be applied to various computer programs regarding structure generation by combining building blocks.     

Coordination framework hosts consisting of 4-pyridyl-substituted carboxylic acid (PCA) dimers and 1D chains of Ni2+ and SCN-: a rational structural extension toward coordination framework hosts with large rectangular cavities

For the expansion of a rectangular cavity (RC) defined by two isonicotinic acid (isoH) dimers as bridging ligands and two SCN bridges, we conducted a structural extension based on the elongation of the bridging ligands by the replacement of isoH with longer 4-pyridyl-substituted carboxylic acid (PCA). For this purpose, the following three PCAs have been employed: trans-3-(4-pyridyl)propenoic acid (acrylH), 4-(4-pyridyl)benzoic acid (pybenH), and trans-3-(4-(4-pyridyl)phenyl)propenoic acid (pppeH). Self-assembly of Ni2+, SCN-, and each of four PCAs involving isoH, acrylH, pybenH, and pppeH in the presence of an aromatic guest gave four inclusion compounds formulated as [Ni(SCN)2(isoH)2].1/2(benz[a]anthracene) (1), [Ni(SCN)2(acrylH)2].1/2(benz[a]anthracene) (2), [Ni(SCN)2(pybenH)2].(pyrene) (3), and [Ni(SCN)2(pppeH)2](3/)(2).(benz[a]anthracene) (4). X-ray crystal structural determination of 1-4 revealed that the proposed structural extension was successful. Their crystal structures are layered structures of two-dimensional (2D) grid-type coordination frameworks (2D host layers) framed with bridging ligands of the corresponding PCA dimers and 1D chains consisting of Ni2+ ions and mu(1,3)-SCN- ions. The lengths of the PCA dimers are 12.269(5) A (isoH dimer), 16.890(4) A (acrylH dimer), 20.89(2) A (pybenH dimer), 25.387(3) A (pppeH dimer A), and 25.527(4) A (pppeH dimer B). Each 2D host layer has RCs defined by the two corresponding PCA dimers and the two SCN bridges. The dimensions of RCs are expanded in proportion to the increase in the lengths of the PCA dimers: 29.52 x 5.60-7.20 A2 (4) > 24.95 x 5.46-7.38 A2 (3) > 20.88 x 5.49-7.25 A2 (2) > 16.41 x 5.53-7.43 A2 (1). These expansions reflect the number of aromatic guests that can be included in RCs. RC of 1 include only one molecule of benz[a]anthracene, whereas RCs of 3 or 4 includes two molecules of pyrene or benz[a]anthracene, respectively. Comparison of the lengths between the PCA dimers and 4,4'-bipyridine-type ligands demonstrated that a design strategy-the preparation of a bridging ligand through self-assembly of two PCAs-is both efficient and particularly suitable for the preparation of very long bridging ligands.