Noteworthy Chemistry

April 28, 2014

Your nose makes a good sensor. Human beings have excellent olfactory systems; for example, the human nose can detect chemicals such as methyl mercaptan (MeSH) and indole at the sub–part-per-billion level. Numerous chemical sensors depend on color changes for detecting analytes with the naked eye, but very few sensors are designed for the “naked nose”.

Odor is difficult to quantify, but olfaction-based sensing can be a convenient qualitative method, especially in environments where instrumentation is not available. Y. Li, C. D. M. Filipe, and co-workers at McMaster University (Hamilton, ON) designed odor-generating biosensors based on tryptophanase (TPase), a metabolic enzyme that, together with coenzyme pyridoxal phosphate (PLP), cocatalyzes the conversion of S-methyl-L-cysteine (1) to MeSH and L-tryptophan (3) to indole (4). Pyruvate (2) is a byproduct of these reactions.

TPase and PLP cocatalyze the release of MeSH and indole

The authors first biotinylated TPase to make it available for bioconjugation with various antibodies. They then linked the biotinylated TPase to the anti–rabbit IgG (ARIgG) antibody, which selectively recognizes rabbit IgG (RIgG). (IgG is immunoglobulin G.) In the presence of 1 (or 3) and PLP, ARIgG-tethered TPase reacts with RIgG-bound magnetic beads to release olfactible quantities of MeSH (or indole).

This odor-based detection system has a fast response time: It generates 100 ppb MeSH in <5 min. Its best estimated threshold (BET) is as low as 85 nM. When the system is coupled with pyridoxal kinase, an enzyme that uses adenosine triphosphate (ATP) to synthesize PLP, the TPase-based biosensor selectively detects ATP with a BET of 0.32 µM. The sensor distinguishes ATP from similar analytes such as guanosine triphosphate, cytidine triphosphate, and uridine triphosphate. (Angew. Chem., Int. Ed. 2014, 53, 2620–2622; Xin Su)

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Here’s a new way to predict runaways in low-temperature reactions. T. Lakshminarasimhan at Biocon Bristol-Myers Squibb R&D Center (Bangalore, India) describes the use of nonisothermal reaction calorimetry coupled with kinetic modeling to estimate the temperature at which the time to maximum rate for a runaway reaction is 24 h (TMRad 24).

The reaction sequence in question is the ortho-lithiation of N-Boc-3-fluoro-4-aniline, followed by the addition of iodine. Both steps are carried out at –75 to –70 ºC. The main safety concern is the stability of the lithio intermediate, which can eliminate LiF and form a benzyne that undergoes additional decomposition reactions.

Instead of using an adiabatic calorimetric method (in which the low-temperature reaction mixture must be transferred), the author carried out the reaction in a Mettler Toledo RC1e reaction calorimeter. The lithio intermediate was gradually warmed from –67°C to 20°C. The heat and temperature data acquired in this experiment were exported to DynoChem software to fit the kinetic parameters. This procedure allowed the TMRad 24 to be calculated; in this system, it is –57.3 ºC. (Org. Process Res. Dev. 2014, 18, 315–320; Will Watson)

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Gelation is a promising method for removing mercury. The stimulus-responsive behavior of molecular gels makes them promising candidates for environmental remediation operations. Gel-based materials respond to metal ions, reductants, oxidants, and enzymes, but predicting which molecules will form gels is a challenge.

K. K. Carter, H. B. Rycenga, and A. J. McNeil* at the University of Michigan (Ann Arbor) examined a series of mercury-containing compounds to elucidate the relationship between their chemical structures and their ability to form gels. They found a complex relationship between the chemical structures and properties of these compounds, but they established that gel formation can remove >98% of Hg2+ from contaminated water.

Under the assumption that the 1-D interactions drive the growth of gel fibers, the authors used the Cambridge Structural Database to identify molecules that exhibit 1-D intermolecular interactions in the solid state, specifically Hg–arene interactions. They found a promising candidate in compound 1 and tested three derivatives of this compound (2, 3, and 4 in the figure) for their ability to form gels in mixtures of water and organic solvents.

Hg–arene gelators

The usefulness of 1 is limited because high concentrations of the gelator and an organic cosolvent are required. In addition, the gel dissolves rapidly in the presence of chloride ion. One of its derivatives (3) removes >99% of the Hg2+ from water at lower concentrations, and it is insensitive to Cl.

Gel formation appears to be more sensitive to the position and identity of the substituents than to the quinoxalinone framework. The authors examined the solubility properties of their nine compounds in MeOH and EtOH at various temperatures. They found that all the compounds undergo a solid–solid transformation in MeOH, and some do the same in EtOH. The variety of polymorphs observed and the lack of a solvent that works for all the compounds complicated comparisons among structurally similar gelators and nongelators.

The authors added Hg(OAc)2 to bottled water, tap water, and water from the Huron River. They mixed the mercury-contaminated water with MeOH solutions that contained quinoxalinone compounds and observed instantaneous gel formation. All of the gelators removed >98% of the Hg2+ from the water. Gel formation is selective for Hg2+ in the presence other metal ions. Gels do not form in water to which no Hg(OAc)2 is added. (Langmuir 2014, 30, 3522–3527; Nancy McGuire)

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Use mechanical force to run polymerization reactions. J. N. Ravnsbæk and T. M. Swager* at MIT (Cambridge, MA) used a ball mill to synthesize poly[2-methoxy-5-(2′-ethylhexyloxy)phenylenevinylene] (MEH-PPV) in the solid state via the Gilch method (strong base catalysis). They investigated the influence of several variables on the ball milling–promoted polymerization, such as milling time, milling frequency, and ball size.

The authors’ mechanochemical process rapidly produces MEH-PPV. After 10 min, the polymer plateaus at ≈40 kDa Mn in 60–67% yield. Regardless of the ball-milling time, the molecular weight distribution remains relatively constant. The authors determined that this process is a combination of constructive and destructive polymerization events; the constructive pathway dominates below a 40 kDa Mn. A threshold frequency (>15 Hz) is required for polymerization; yield increases with increasing frequency.

A minimum impact energy is required to achieve sufficient mixing for polymerization to occur. Milling balls must be ≥10 mm in diam to reach the minimum energy.

The authors also show that ball milling promotes the polymerization of a dithiocarbamate monomer with low polydispersity (1.4) and significant yields (54%) under milder base conditions. (ACS Macro Lett. 2014, 3, 305–309; LaShanda Korley)

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A small-molecule screen identifies a NER inhibitor. Nucleotide excision repair (NER) removes DNA lesions that are caused by exposure to UV light and many chemical agents, including platinum-based drugs that are used as solid-tumor anticancer treatments. Platinum compounds work by binding DNA directly; binding saturates DNA repair mechanisms, blocks essential cellular processes, and results in apoptosis and an antineoplastic effect.

Although the initial response to platinum chemotherapy is strong, NER can repair platinum-derived lesions, which leads to treatment resistance. Inhibiting NER pharmacologically is expected to make current chemotherapy more efficient and to limit toxic side effects, but DNA repair pathway inhibitors themselves are usually toxic.

F. Coin and colleagues at the University of Strasbourg (France) and Pierre and Marie Curie University (Paris) used a drug-repositioning and screening technique to identify potent, specific, nontoxic, bioavailable drug candidates that inhibit NER. They applied qualifying compounds from the Prestwick Chemical Library to a cell-based screening assay that they developed. They used UV irradiation rather than platinum drugs to form lesions on the cells.

After fixing the cells, the authors used antibodies and microscopy to identify (6-4)PP, a major UV-induced lesion. They chose a spirolactone (17-hydroxy-7α-mercapto-3-oxo-17α–pregn-4-ene-21-carboxylic acid γ-lactone acetate, 1) for its ability to induce a dramatic decrease in NER activity. Compound 1 is an aldosterone antagonist that binds mineralocorticoid receptors. It is structurally similar to budesonide, cortisone, diflorasone, and eplerenone.

In additional experiments, the authors determined that 1 specifically induces the degradation of the XPB helicase subunit of the transcription-repair factor TFIIH that is involved in NER. This degradation occurs within minutes after a drug is added and is rapidly reversible. After studying the results of other analogues structurally related to 1, the authors determined that the molecule’s ability to prevent the removal of DNA lesions is a specific function that is unrelated to its role as an aldosterone antagonist.

The authors found that 1 increases the sensitivity of different types of human cancer cells to platinum-based anticancer agents. When the platinum derivatives are combined with 1, their cytotoxicity significantly increases, demonstrating that nontoxic 1 is an adjuvant in platinum-based chemotherapy. (Chem. Biol. 2014, 21, 398–407; Abigail Druck Shudofsky)

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Nanocantilevers help measure drug efficacy. Bioavailability is a fundamental factor in pharmacology: It denotes the rate and extent to which a drug enters systematic circulation. The bioavailability of a drug, however, does not necessarily correlate to its efficacy; for example, serum proteins inhibit the activity of antibiotics by reducing their concentration via competitive binding.

Against this backdrop, it is crucial to determine the availability of free drugs in the physiological environment. J. W. Ndieyira, R. A. McKendry, and coauthors at University College London, Jomo Kenyatta University of Agriculture and Technology (Nairobi, Kenya), the University of Queensland (Brisbane, Australia), and the University of Cambridge (UK) addressed this challenge by developing surface-stress sensors with nanomechanical cantilevers for rapidly and sensitively quantifying active free drugs in human serum.

Antibiotics such as vancomycin rely on binding to bacterial cell wall precursors to inhibit bacterial growth, but serum proteins may compete with drug binding. Nanomechanical cantilevers undergo quantifiable mechanical changes when they “recognize” surface-bound receptors (antibiotic targets). The authors devised a silicon cantilever array tethered to a model bacterial cell-wall analogue on one side of its surface. The bending of the cantilever is monitored by using a photodetector.

Using vancomycin and oritavancin as model antibiotics, the authors established a mathematical model that quantitatively describes changes in the cantilevers’ surface stress when vancomycin or oritavancin reacts with receptors in the presence of various competing ligands. By measuring surface-binding constants under physiological conditions, they quantitatively demonstrated the dependence of surface binding on competing events in the solution phase.

This work provides a useful method for evaluating the efficacy of antibiotics in clinical settings and also helps elucidate a complex chemical system with multiple pathways and equilibria. The technique is practical for determining optimal doses of drugs and can be modified to comply with other therapies. (Nat. Nanotech. 2014, 9, 225–232; Xin Su)

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Use the oxygen in water to convert cyclic amines to lactams. Amides and lactams are useful building blocks in organic synthesis, but it is difficult to convert amines directly to amides by oxidizing the methylene group. J. R. Khusnutdinova, Y. Ben-David, and D. Milstein* at the Weizmann Institute of Science (Rehovot, Israel) developed a straightforward method for converting cyclic amines to lactams that uses water as the oxygen source.

On the basis of previous work on producing carboxylic acids by dehydrogenating alcohols in water, the authors used the same type of catalyst—an acridine-based pincer-type ruthenium complex—in the presence of a catalytic amount of base to effect the transformation with the simultaneous liberation of hydrogen (see figure). In a model system, with pyrrolidine (1; n = 1, R = H) as the substrate, 5 mol% of catalyst 2, and 5 mol% NaOH, pyrrolidone (3) is obtained with 91% conversion and 83% yield.

Conversion of pyrrolidine to pyrrolidone with the oxygen in water

The authors expanded the method to other heterocycles such as piperidine, morpholine, N-methylpiperazine, and indoline. They believe that the reaction proceeds by the formation of a hemiaminal, followed by dehydrogenation to the amide. When they used H218O in the reaction, 98% of the 18O was incorporated into the product. This result confirmed that water is the oxygen source.

Yields from the reaction are modest (43–85%), but this method is an atom-economic synthesis of lactams that does not require stoichiometric amounts of oxidants. (J. Am. Chem. Soc. 2014, 136, 2998–3001; José C. Barros)

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Spirolactone 1, a NER inhibitor