Identifying Ortholog Selective Fragment Molecules for Bacterial Glutaredoxins by NMR and Affinity Enhancement by Modification with an Acrylamide Warhead

Illustrated here is the development of a new class of antibiotic lead molecules targeted at Pseudomonas aeruginosa glutaredoxin (PaGRX). This lead was produced to (a) circumvent efflux-mediated resistance mechanisms via covalent inhibition while (b) taking advantage of species selectivity to target a fundamental metabolic pathway. This work involved four components: a novel workflow for generating protein specific fragment hits via independent nuclear magnetic resonance (NMR) measurements, NMR-based modeling of the target protein structure, NMR guided docking of hits, and synthetic modification of the fragment hit with a vinyl cysteine trap moiety, i.e., acrylamide warhead, to generate the chimeric lead. Reactivity of the top warhead-fragment lead suggests that the ortholog selectivity observed for a fragment hit can translate into a substantial kinetic advantage in the mature warhead lead, which bodes well for future work to identify potent, species specific drug molecules targeted against proteins heretofore deemed undruggable.

pH-Controlled Chiral Packing and Self-Assembly of a Coumarin Tetrapeptide

A coumarin-tetrapeptide conjugate, EFEK(DAC)-NH₂ (1), is reported to undergo a pH-dependent interconversion between nanotubes and nanoribbons. An examination of zeta potential measurements, circular dichroism (CD) spectra, and microscopy imaging (transmission electron microscopy and atomic force microscopy) identified three different self-assembly regimes based on pH: (1) pH 2-5, positively charged, left-handed helical nanotubes; (2) pH 6-8, negatively charged, right-handed helical nanoribbons; and (3) pH ≥ 9.0, a monomeric/disassembled peptide. The nanotubes exhibited uniform diameters of 41 ± 5 nm and wall thicknesses of 4.8 ± 0.8 nm, whereas the nanoribbons existed as either flat or twisted sheets ranging in width from 11 to 60 nm with heights of 8 ± 1 nm. The UV-vis and CD spectra of the most common antiparallel, β-sheet conformation of 1-dimer were simulated at the B3LYP/def2svpd level of theory in implicit water. These studies indicated that the transition from nanotubes to nanoribbons was coupled to an M → P helical inversion of the coumarin packing orientation, respectively, within the nanostructures. The assembly process was driven by β-sheet aggregation and π-π interactions, leading to the formation of nanoribbons, which progressively wound into helical ribbons and laterally grew into smooth nanotubes as the pH decreased.

Threading carbon nanotubes through a self-assembled nanotube

Achieving the co-assembly of more than one component represents an important challenge in the drive to create functional self-assembled nanomaterials. Multicomponent nanomaterials comprised of several discrete, spatially sorted domains of components with high degrees of internal order are particularly important for applications such as optoelectronics. In this work, single-walled carbon nanotubes (SWNTs) were threaded through the inner channel of nanotubes formed by the bolaamphiphilic self-assembly of a naphthalenediimide-lysine (NDI-Bola) monomer. The self-assembly process was driven by electrostatic interactions, as indicated by ζ-potential measurements, and cation-π interactions between the surface of the SWNT and the positively charged, NDI-Bola nanotube interior. To increase the threading efficiency, the NDI-Bola nanotubes were fragmented into shortened segments with lengths of <100 nm via sonication-induced shear, prior to co-assembly with the SWNTs. The threading process created an initial composite nanostructure in which the SWNTs were threaded by multiple, shortened segments of the NDI-Bola nanotube that progressively re-elongated along the SWNT surface into a continuous radial coating around the SWNT. The resultant composite structure displayed NDI-Bola wall thicknesses twice that of the parent nanotube, reflecting a bilayer wall structure, as compared to the monolayer structure of the parent NDI-Bola nanotube. As a final, co-axial outer layer, poly(p-phenyleneethynylene) (PPE-SO3Na, M W = 5.76 × 104, PDI - 1.11) was wrapped around the SWNT/NDI-Bola composite resulting in a three-component (SWNT/NDI-Bola/PPE-SO3Na) composite nanostructure.

Polyelectrolyte-micelle coacervates: intrapolymer-dominant vs. interpolymer-dominant association, solute uptake and rheological properties

The effects of polyelectrolyte charge density, polyelectrolyte-to-surfactant ratio, and micelle species on coacervation were studied by turbidity, dynamic light scattering, and zeta potential measurements to examine the coacervation of the weak polyelectrolyte branched polyethylenimine (BPEI) and oppositely charged sodium dodecyl sulfate (SDS) micelles as well as BPEI and mixed micelles composed of SDS and poly(ethylene glycol) 4-nonylphenyl 3-sulfopropyl ether potassium salt (PENS). The results of dynamic light scattering and zeta potential measurements are discussed in terms of pH and BPEI-to-surfactant ratio. An intrapolymer-dominant to interpolymer-dominant association model for the BPEI-micelle coacervates was proposed based on the variation of size and zeta potential of coacervate particles by their BPEI-to-surfactant ratio. The partition coefficient of solutes into BPEI-micelle coacervates was determined using UV-vis measurements as a function of pH, BPEI-to-surfactant ratio, and mixed micelle composition. Both the hydrophobicity of solutes and micelles, as well as the association mode of coacervates, impact the solute uptake efficiency. Dynamic rheological measurements on the coacervates suggest that the rheological properties of the complex coacervates are impacted by the association mode of the coacervates as well as the charge density on BPEI chains during coacervation.

Strategy for the Co-Assembly of Co-Axial Nanotube-Polymer Hybrids

Nanostructured materials having multiple, discrete domains of sorted components are particularly important to create efficient optoelectronics. The construction of multicomponent nanostructures from self-assembled components is exceptionally challenging due to the propensity of noncovalent materials to undergo structural reorganization in the presence of excipient polymers. This work demonstrates that polymer-nanotube composites comprised of a self-assembled nanotube wrapped with two conjugated polymers could be assembled using a layer-by-layer approach. The polymer-nanotube nanostructures arrange polymer layers coaxially on the nanotube surface. Femtosecond transient absorption (TA) studies indicated that the polymer-nanotube composites undergo photoinduced charge separation upon excitation of the NDI chromophore within the nanotube.

Cuprizone Intoxication Induces Cell Intrinsic Alterations in Oligodendrocyte Metabolism Independent of Copper Chelation

Cuprizone intoxication is a common animal model used to test myelin regenerative therapies for the treatment of diseases such as multiple sclerosis. Mice fed this copper chelator develop reversible, region-specific oligodendrocyte loss and demyelination. While the cellular changes influencing the demyelinating process have been explored in this model, there is no consensus about the biochemical mechanisms of toxicity in oligodendrocytes and about whether this damage arises from the chelation of copper in vivo. Here we have identified an oligodendroglial cell line that displays sensitivity to cuprizone toxicity and performed global metabolomic profiling to determine biochemical pathways altered by this treatment. We link these changes with alterations in brain metabolism in mice fed cuprizone for 2 and 6 weeks. We find that cuprizone induces widespread changes in one-carbon and amino acid metabolism as well as alterations in small molecules that are important for energy generation. We used mass spectrometry to examine chemical interactions that are important for copper chelation and toxicity. Our results indicate that cuprizone induces global perturbations in cellular metabolism that may be independent of its copper chelating ability and potentially related to its interactions with pyridoxal 5'-phosphate, a coenzyme essential for amino acid metabolism.

Controlling the length of self-assembled nanotubes by sonication followed by polymer wrapping

In this work, we report that sonication, followed by polymer-wrapping, is an effective strategy to reduce the length of self-assembled nanotubes and suspend their propensity to self-heal into their elongated precursors.

Core substituted naphthalene diimide – metallo bisterpyridine supramolecular polymers: synthesis, photophysics and morphology

A series of metallo Ru(ii), Fe(ii), Co(ii) bisterpyridine polymers were prepared with core-substituted naphthalene diimide (NDI) groups inserted between two 4′-phenyl-2,2:6′,2′′-terpyridine (phtpy) groups.

Photoinduced electron-transfer within osmium(II) and ruthenium(II) bis-terpyridine donor acceptor dyads

The synthesis and photophysical characterization of two different series of electron donor-acceptor dyads containing Ru(II) and Os(II) bis-terpyridines (M(tpy)(2)(2+)) were prepared and studied in order to compare the oft-studied Ru(tpy)(2)(2+) chromophore with the less studied Os(tpy)(2)(2+) chromophore. The first series of dyads incorporates a benzoquinone (BQ) group as the electron acceptor, whereas the second contains a substituted pyromellitimide (PI) group as the electron acceptor. Steady-state emission experiments indicated efficient quenching of the 3MLCT emission of the electronically excited Os(II)-BQ complexes (7-8) compared to both model complexes (3-4) and the Os(II)-PI complex 10. Femtosecond pump-probe absorption experiments on 7-8 yielded ultrafast electron transfer rate constants (kET) of approximately 2.0 x 10(11) s(-1) (7) and 1.3 x 10(10) s(-1) (8) that were in good agreement with the low emission quantum yield results. Charge-recombination (kCR) in these complexes was also quite rapid, with rate constants of approximately 6.7 x 10(10) s(-1) (7) and 1.2 x 10(10) s(-1) (8). The analogous Ru(II) complexes underwent charge separation with rate constants of 7.6 x 10(10) s(-1) (5) and approximately 2.3 x 10(10) s(-1) (6), while charge recombination in these complexes occurred with rate constants of approximately 2.1 x 10(10) s(-1) (5) and approximately 5.3 x 10(10) s(-1) (6). Electron transfer in the pyromellitimide-containing complexes occurred only for Os(II)-PI (10), which exhibited significantly slower electron transfer (approximately 4.3 x 10(6) s(-1)) and charge recombination (approximately 7.7 x 10(6) s(-1)) rate constants. The nearly thermoneutral free energy of electron transfer and short excited state lifetime in the case of Ru(II)-PI (9) presumably prevents electron transfer in this compound.

Ultrafast Spectroscopy of Free-Base N-Confused Tetraphenylporphyrins

The photophysical characterization of the two tautomers (1e and 1i) of 5,10,15,20-tetraphenyl N-confused free-base porphyrin, as well as the tautomer-locked 2-methyl 5,10,15,20-tetraphenyl N-confused free-base porphyrin, was carried out using a combination of steady state and time-resolved optical techniques. N-Confused porphyrins, alternatively called 2-aza-21-carba-porphyrins or inverted porphyrins, are of great interest for their potential as building blocks in assemblies designed for artificial photosynthesis, and understanding their excited-state properties is paramount to future studies in multicomponent arrays. Femtosecond resolved transient absorption experiments reveal spectra that are similar to those of tetraphenylporphyrin (H2TPP) with either Soret or Q-band excitation, with an extinction coefficient for the major absorbing band of 1e that was about a factor of 5 larger than that of H2TPP. The lifetime of the S1 state was determined at a variety of absorption wavelengths for each compound and was found to be consistent with time-resolved fluorescence experiments. These experiments reveal that the externally protonated tautomer (1e) is longer lived (tau = 1.84 ns) than the internally protonated form (1i, tau = 1.47 ns) by approximately 369 ps and that the N-methyl N-confused porphyrin was shorter lived than the tautomeric forms by approximately 317 ps (DMAc) and approximately 396 ps (benzene). Steady-state fluorescence experiments on tautomers 1e and 1i and the N-methyl analogues corroborate these results, with fluorescence quantum yields (Phi(Fl)) of 0.046 (1e, DMAc) and 0.023 (1i, benzene), and 0.025 (DMAc) and 0.018 (benzene) for the N-methyl N-confused porphyrin. The lifetime and quantum yield data was interpreted in terms of structural changes that influence the rate of internal conversion. The absorption and transient absorption spectra of these porphyrins were also examined in the context of DFT calculations at the B3LYP/6-31G(d)//B3LYP/3-21G(d) level of theory and compared to the spectra/electronic structure of H2TPP and tetraphenyl chlorin.

Photophysical Properties of a Series of Free-Base Corroles

Four free-base corroles with electron-donating or electron-withdrawing groups on the para or 2 through 6-positons of the meso phenyl rings were prepared via either Paolesse or Gross conditions and investigated for their absorption and emission properties. The triaryl corroles 5,10,15-triphenylcorrole, 5,10,15-tris(pentafluorophenyl)corrole, 5,10,15-tris(p-nitrophenyl)corrole, and 5,10,15-tris(p-methoxyphenyl)corrole were examined. Absorption, steady-state, and time-resolved fluorescence measurements were performed on all compounds in both nonpolar (dichloromethane) and polar (dimethylacetamide) solvents. The experimental evidence points to hydrogen bonding with an internal N-H group as the most likely factor in the solvent-dependent photophysical behavior of these corroles, that is also highly dependent upon substitution.

Synthesis and Spectroscopy of a Series of Substituted N-Confused Tetraphenylporphyrins

A series of N-confused tetraphenylporphyrins (H(2)NCTPPs) with substituents on either the para- or the 3,5-positions of the meso phenyl rings were prepared using Lindsey conditions. Both electron-withdrawing and electron-donating groups were chosen in order to probe the effects of peripheral substitution on the properties of the macrocycles. The series includes 5,10,15,20-tetra-(4-R-phenyl) N-confused porphyrins (where R = bromo (1), iodo (2), cyano (3), methoxy (4), 2',5'-dimethoxyphenyl (5), or ethynyl (6)) and 5,10,15,20-(3,5-di-tert-butylphenyl) N-confused porphyrin (7). Absorption and steady-state fluorescence measurements were carried out, and quantum yields were measured for all compounds in both dichloromethane (CH(2)Cl(2)) and dimethylacetamide (DMAc).

One-Step Synthesis and Characterization of Difunctionalized N-Confused Tetraphenylporphyrins

Three disubstituted N-confused porphyrins (2-4) were prepared in ca. 4% yield using a one-pot synthesis. These porphyrins bear 3,5-di-tert-butylphenyl groups substituted at the C(5) and C(20) meso positions and para-substituted (Br, NO(2), ethynyl) phenyl groups at the C(10) and C(15) meso positions. The specific orientation of the aryl rings around the macrocycle in porphyrin 2 was definitively determined using a combination of 1D ((1)H and (13)C) and 2D (gHMQC and gHMBC) NMR spectroscopy. The absorption spectra of 2-4 in CH(2)Cl(2) and dimethylacetamide are similar to those of N-confused tetraphenylporphyrin in the same solvents but have Soret and Q-bands that are shifted to lower energies. Steady-state fluorescence measurements revealed Q(x)(0,0) and Q(x)(0,1) bands similar in energy to the unsubstituted NCPs 1i and 1e. The fluorescence quantum yield results for two of these NCPs (2, 4) are atypical of porphyrin behavior and are being further investigated by time-resolved spectroscopy.

Efficient synthesis of porphyrin-containing, benzoquinone-terminated, rigid polyphenylene dendrimers

A series of rigid polyphenylene, free-base porphyrin-containing dendrimers terminated with either dimethoxybenzene or benzoquinone end-groups were prepared by a combined divergent and convergent synthesis. Unlike previous routes for preparing polyphenylene dendrimers that are incompatible with end-groups bearing certain functional moieties, the synthetic methodology chosen for this work enables incorporation of functional groups on the dendrimer end-groups during preparation of the dendrimer wedges and during synthesis of the final dendrimer. The basic strategy utilized a convergent preparation of dendrimer wedges using Suzuki coupling conditions, which were then either attached to a porphyrin core in a divergent coupling step or cyclized to form the porphyrin dendrimer in a convergent step. The latter approach was found to be more general and resulted in higher yields and more readily separated products. Steady-state absorption measurements for these dendrimers showed Soret and Q-band absorptions typical of free-base porphyrins. Preliminary steady-state fluorescence measurements of these dendrimers indicate quenching of the S1 state of the free-base porphyrin in all benzoquinone-containing dendrimers that is attributed to efficient electron-transfer from the excited porphyrin to the benzoquinone end-groups. The amount of fluorescence quenching was in good agreement with the number of benzoquinone groups at the dendrimer periphery and the distance between the porphyrin and benzoquinone groups as calculated by semiempirical (AM1) molecular orbital calculations.

Photoinduced electron transfer within porphyrin-containing poly(amide) dendrimers

The synthesis and photophysical characterization of a series of free base porphyrin-containing polyamide dendrimers terminated with anthraquinone groups (FbP-Ga-AQ(n)(), a = 1-3, n = 12, 36, 108) are described. Substantial quenching (58-75%) of the porphyrin fluorescence of FbP-Ga-AQ(n)() is observed when compared to the analogous ethyl-terminated dendrimers (FbP-Ga-Et(n)()) in steady-state fluorescence experiments and is attributed to intramolecular electron transfer. Time-resolved fluorescence experiments were fit to 2-3 exponentials, indicating multiple orientations for electron transfer, consistent with the flexible nature of these dendrimers.

Structural Characterization of Quinoxaline Homopolymers and Quinoxaline/Ether Sulfone Copolymers by Matrix-Assisted Laser Desorption Ionization Mass Spectrometry

Polyphenylquinoxalines (PPQs) are prepared from self-polymerizable quinoxaline monomers that carry fluorine, hydroxyaryl (ArOH), and phenyl substituents. In basic media, these monomers self-polymerize via a series of nucleophilic aromatic substitution reactions (SNAr), in which aromatic enolates (ArO- nucleophiles) attack the electrophilic carbons bearing F leaving groups to effect fluoride displacement. Polyphenylquinoxaline/polyether-sulfone (PPQ/PES) copolymers are synthesized similarly by combining self-polymerizable quinoxaline monomers with a 1:1 molar mixture of 4,4'-dichlorodiphenyl sulfone and bisphenol A. The MALDI mass spectra of the polymers reveal that the major products up to approximately 15,000 Da molecular mass are homo- or copolymeric macrocycles. Linear byproducts are also observed, arising from nucleophilic ring opening of already formed macrocycles. Oligomers containing at least one PPQ unit readily protonate upon MALDI, whereas PES homopolymers require alkali metal ion addition to become detectable. Molecular orbital calculations point out that the nucleophilic and electrophilic reactivities of the PPQ monomer and the PPQ growing chains generated during propagation are comparable, allowing for continued condensations via SN-Ar, until cyclization terminates this process. The calculations also predict a significantly lower electrophilic reactivity for carbons substituted by chlorine instead of fluorine, justifying the discrimination against incorporation of PES units observed for the copolymers. The computationally optimized structures of PPQ and PPQ/PES macrocycles show a diverse array of cavity sizes and geometries which depend on the size of the macrocycle, the sequence of the repeat units, and the position of the substituents in the quinoxaline ring; quinoxaline pendants (phenyl groups) are found to favor helical arrangements in the prepared macrocycles.

Photochemical generation and matrix-isolation detection of dimethylvinylidene

We report the spectroscopic characterization of dimethylvinylidene, (CH3)2C=C:, generated within an argon matrix at 14 K from a bisperoxyester precursor. The carbene was identified by comparison of the experimental IR spectrum with vibrational frequencies computed at the B3LYP/6-31G(d) level. Chemical trapping of the carbene within a 9% CO/Ar matrix to form dimethylpropadienone supports this analysis. Additional products produced during photolysis were identified by comparison to the appropriate computed vibrational frequencies. The potential energy surface of dimethylvinylidene and its intramolecular rearrangement products, 2-butyne and methylcyclopropene, were also investigated computationally at the B3LYP/6-31G(d) level. A spin-state analysis of this carbene using a variety of computational methods (CCSD(T), B3LYP, MP2) indicates the singlet state is more stable than the triplet by approximately 45 kcal mol-1. We anticipate the bisperoxyester precursor used here will be a convenient and general way for initiating future studies of alkylvinylidenes under matrix-isolation conditions.

Aryl Oxalate Derivatives as Convenient Precursors for Generation of Aryloxyl Radicals

The use of aryloxy oxalyl chlorides (AOCs), aryloxy oxalyl tert-butyl peroxides (AOBs), and diaryl oxalates (DAOs) for unimolecular generation of phenoxyl-based radicals under solution and rigid matrix conditions is described. AOCs are usable for photochemical generation of phenoxyl radicals, but are only conveniently stable as precursors when 2,6-di-tert-butylated derivatives are used. AOBs may be used as thermal precursors to aryloxyl radicals, since they typically decompose within 2-3 h at 60-85 degrees C to give phenols. (1)H-NMR solution kinetic studies find that DeltaH() = 31 kcal/mol, and DeltaS() = +3.4 cal/mol-K for decomposition of phenoxyoxalyl tert-butyl peroxide, consistent with substantial concertedness in peroxide bond cleavage. AOBs and the more stable DAOs are also convenient photochemical phenoxyl radical precursors. AOBs yield phenoxyl radicals more readily by photolysis than do corresponding DAOs, but the DAOs have fewer side reactions that can quench the product phenoxyl radicals.