Cellular logic with orthogonal ribosomes

The creation and use of unnatural molecules to control cellular function is a long standing goal of the chemical community, but in general, these efforts have been directed at finding molecules to inhibit or activate a particular molecular target or function, or to elicit a particular phenotype. Here we show that multiple unnatural molecules (orthogonal ribosomes) can be used combinatorially, in a single cell, to program Boolean logic functions. These experiments show how attention to the molecular specificity of noncovalent interactions between unnatural macromolecules allows the synthesis of complex function from the "bottom-up" in living matter.     

Effect of pH on the electrochemical reduction of some heterocyclic quinones

The reduction of 1,10-phenanthroline-5,6-quinone(I), 5,8-quinolinequinone(II) and 6,7-dichloro-5,8-quinolinequinone(III) was investigated using cyclic voltammetry and coulometry at mercury electrodes and 50% dimethylsulfoxide+water solvent. Each compound is reduced to the corresponding hydroquinone in a diffusion-controlled, reversible two-electron process. The pH-dependence of the reversible potential indicated that the quinone forms were unprotonated, but the hydroquinones could be protonated at the heterocyclic nitrogen atom with pK_a = 5.3 for I and 3.5 for III. Careful analysis of the cyclic voltammetric peak shape revealed that the difference between the standard potentials for the introduction of successive electrons, E₂⁰ ? E₁⁰, was 70 ±20, >100 and 80 ± 20 mV for I–III. Investigation of the pH-dependence of E₁⁰ and E₂⁰ showed that the pK_a of the semiquinone of I was about 8.     

OptiDock: virtual HTS of combinatorial libraries by efficient sampling of binding modes in product space

Products from combinatorial libraries generally share a common core structure that can be exploited to improve the efficiency of virtual high-throughput screening (vHTS). In general, it is more efficient to find a method that scales with the total number of reagents (Sigma growth) rather with the number of products (Pi growth). The OptiDock methodology described herein entails selecting a diverse but representative subset of compounds that span the structural space encompassed by the full library. These compounds are docked individually using the FlexX program (Rarey, M.; Kramer, B.; Lengauer, T.; Klebe, G. J. Mol. Biol. 1995, 251, 470-489) to define distinct docking modes in terms of reference placements for combinatorial core atoms. Thereafter, substituents in R-cores (consisting of the core structure substituted at a single variation site) are docked, keeping the core atoms fixed at the coordinates dictated by each reference placement. Interaction energies are calculated for each docked R-core with respect to the target protein, and energies for whole compounds are calculated by finding the reference core placement for which the sum of corresponding R-core energies is most negative. The use of diverse whole compounds to define binding modes is a key advantage of the protocol over other combinatorial docking programs. As a result, OptiDock returns better-scoring conformers than does serially applied FlexX. OptiDock is also better able to find a viable docked pose for each library member than are other combinatorial approaches.     

Use of U-shaped donor-bridge-acceptor molecules to study electron tunneling through nonbonded contacts

A systematic determination of electronic coupling matrix elements in U-shaped molecules is demonstrated. The unique architecture of these systems allows for the determination of the electronic coupling through a pendant molecular moiety that resides between the donor and acceptor groups; this moiety quantifies the efficiency of electron tunneling through nonbonded contacts. Experimental electron-transfer rate constants and reaction free energies are used to calibrate a molecular-based model that describes the solvation energy. This approach makes it possible to experimentally determine electronic couplings and compare them with computational values.     

An improved synthesis of cyclopropanes from stabilized phosphonates and 1,2-dioxines

Addition of stabilized Horner-Wadsworth-Emmons (HWE) phosphonates to substituted 1,2-dioxines leads to diastereomerically pure di- and trisubstituted cyclopropanes in high yields and represents a viable alternative to ylides in the cyclopropanation reaction involving 1,2-dioxines. While yields are comparable, reaction times with these stabilized phosphonates were accelerated and the diastereoselectivity for this cyclopropanation reaction was significantly greater than for the previously reported examples employing ylides.     

Bond lengthening and through-bond interactions in p,p'-dibenzene and related molecules

The structure of p,p'-dibenzene (PDB) has been investigated by full geometry optimizations using the empirical force field (EFF) and MINDO/3 methods. While other structural parameters are in good agreement, the central bond length calculated by MINDO/3 (1.595 Å), as confirmed by an ab initio (STO-3G basis set) optimization (1.596 Å), is in striking contrast to the corresponding length calculated by EFF (1.543 Å). A detailed analysis of the electronic structure of PDB based on a quantitative perturbational molecular orbital treatment reveals that through-bond coupling of the four π systems is responsible for an elongation of the σ bond which mediates this interaction. Further studies using the EFF and MINDO/3 approaches demonstrate that extended C-C single bonds can arise even in structures with fewer than four π systems. The effect of substituents on the central bond length in PDB has been briefly investigated. (MINDO/3). A variety of other structures have been identified in which bond lengthening may result from through-bond coupling.     

KINETIC FACTORS GOVERNING SENSITIZED PHOTOOXIDATION OF EXCITABLE CELL MEMBRANES

Abstract— The kinetic factors which determine the rate at which Na⁺ channels in nerve membranes become photochemically modified were studied on giant axons from lobsters using the double sucrose gap voltage clamp technique. Axons were bathed in artificial sea water containing sensitizing dyes and illuminated from a Xe are source with light in the visible region while being repetitively step depolarized. Successive values of peak Na⁺ current and time-to-peak were monitored and rate constants for their change served as the assay for magnitude of modification. Action spectra for four sensitizers in the fluorescein series exhibited red shifts of roughly 17nm demonstrating that sensitizing species are not simply free in solution. Eosin Y diffuses to its sensitization sites with a half time of 70s indicating the existence of a major diffusion barrier which may mean that dye must penetrate to the interior of the membrane to be effective. Eosin Y is removed from sensitization sites by rinse with the same half time but shows two fractions: a faster fraction comprising 80% of sensitizing effectiveness and a slower fraction comprising 20%. The concentration dependence for Eosin Y is linear below 10 μ M and shows a progressive saturation at higher values, where the relationship is difficult to determine because of shielding. Different sensitizers vary in their ability to sensitize block of channels vs disruption of inactivation, demonstrating separate processes for the two modifications. It is suggested that both modifications proceed from single photon absorption events by individual sensitizer molecules bound or located close to the modification sites on the channels.     

Neuroprotection of Cannabidiol,Its Synthetic Derivatives and Combination Preparations against Microglia-Mediated Neuroinflammation in Neurological Disorders

The lack of effective treatment for neurological disorders has encouraged the search for novel therapeutic strategies. Remarkably, neuroinflammation provoked by the activated microglia is emerging as an important therapeutic target for neurological dysfunction in the central nervous system. In the pathological context, the hyperactivation of microglia leads to neuroinflammation through the release of neurotoxic molecules, such as reactive oxygen species, proteinases, proinflammatory cytokines and chemokines. Cannabidiol (CBD) is a major pharmacologically active phytocannabinoids derived from Cannabis sativa L. CBD has promising therapeutic effects based on mounting clinical and preclinical studies of neurological disorders, such as epilepsy, multiple sclerosis, ischemic brain injuries, neuropathic pain, schizophrenia and Alzheimer’s disease. A number of preclinical studies suggested that CBD exhibited potent inhibitory effects of neurotoxic molecules and inflammatory modulators, highlighting its remarkable therapeutic potential for the treatment of numerous neurological disorders. However, the molecular mechanisms of action underpinning CBD’s effects on neuroinflammation appear to be complex and are poorly understood. This review summarises the anti-neuroinflammatory activities of CBD against various neurological disorders with a particular focus on their main molecular mechanisms of action, which were related to the downregulation of NADPH oxidase-mediated ROS, TLR4-NFκB and IFN-β-JAK-STAT pathways. We also illustrate the pharmacological action of CBD’s derivatives focusing on their anti-neuroinflammatory and neuroprotective effects for neurological disorders. We included the studies that demonstrated synergistic enhanced anti-neuroinflammatory activity using CBD and other biomolecules. The studies that are summarised in the review shed light on the development of CBD, including its derivatives and combination preparations as novel therapeutic options for the prevention and/or treatment of neurological disorders where neuroinflammation plays an important role in the pathological components.     

Macrophage-targeting oligopeptides from Mortierella alpina

The realm of natural products of early diverging fungi such as Mortierella species is largely unexplored. Herein, the nonribosomal peptide synthetase (NRPS) MalA catalysing the biosynthesis of the surface-active biosurfactants, malpinins, has been identified and biochemically characterised. The investigation of the substrate specificity of respective adenylation (A) domains indicated a substrate-tolerant enzyme with an unusual, inactive C-terminal NRPS module. Specificity-based precursor-directed biosynthesis yielded 20 new congeners produced by a single enzyme. Moreover, MalA incorporates artificial, click-functionalised amino acids which allowed postbiosynthetic coupling to a fluorophore. The fluorescent malpinin conjugate penetrates mammalian cell membranes via an phagocytosis-mediated mechanism, suggesting Mortierella oligopeptides as carrier peptides for directed cell targeting. The current study demonstrates substrate-specificity testing as a powerful tool to identify flexible NRPS modules and highlights basal fungi as reservoir for chemically tractable compounds in pharmaceutical applications.

Specificity profiling of a nonribosomal peptide synthetase of an early diverging fungus revealed high substrate flexibility. Feeding studies with click-functionalised amino acids enabled the production of fluorescent peptides targeting macrophages.