Molecular recognition. Design of new receptors for complexation and catalysis

Abstract

In recent years there has been intense activity in the design of synthetic molecules capable of enzyme-like recognition and binding of small substrates.¹ Two fundamental approaches have been taken. The first has generally involved non-directional binding forces (such as solvophobic, π-stacking and dispersion interactions) in water-soluble cyclophane frameworks.² This approach led to extremely important quantitative insights into the hydrophobic effect and the enthalpic and entropic contributions of solvent reorganization to binding.³ However, the weakly oriented nature of the binding interactions has resulted in only moderate substrate selectivity beyond the shape recognition permitted by the cavity. In nature such selectivity is a prerequisite for the chiral recognition and catalytic activity of enzymes and is achieved by hydrogen bonding and electrostatic interactions. The second major approach to artificial receptors makes use of these more directional interactions by incorporating several hydrogen bonding groups into a cleft or cavity of defined geometry.⁴ The resulting hosts form strong and selective complexes to those substrates with complementary shape and hydrogen bonding characteristics.⁵ In these cases, however, the binding free energy is solvent dependent, diminishing to zero as the polarity of the medium increases, due to the strong solvation of the hydrogen bonding sites. A central goal in contemporary molecular recognition research must be to develop receptors that effectively use directed hydrogen bonding interactions in competitive solvents. Success will probably require combining strong (possibly charged) hydrogen bonding groups with hydrophobic sites capable not only of effective apolar association with the substrate but also of protecting the polar sites from full solvation.     

Testing antimicrobials against biofilm bacteria

Standard laboratory methods are needed to assess the efficacy of antimicrobial agents that are applied to biofilm bacteria. Existing standard suspension tests and dried surface tests show much greater efficacy than antimicrobial agents applied to biofilms. The greater resistance of biofilm bacteria to antimicrobial agents can be attributed to a number of interacting factors, including reaction and diffusion processes that limit an agent's accessibility to bacteria, phenotypic changes in biofilm bacteria caused by stress, and adaptation of the bacteria. Because biofilm systems are so diverse, a variety of new biofilm tests with features that differ in important ways from existing tests will ultimately be required. For example, the biofilm test apparatus may include a pump and a continuous-flow stirred tank reactor. This report provides an overview of biofilm testing and suggests a strategy for creating standard test methods.     

On-chip dielectrophoretic recovery and detection of a lactate sensing probiotic from model human saliva

Early detection has led to increased survival for multiple cancers; however, the 5-year survival rate of oral carcinoma (OC) has remained at 40% for the last several decades. Screening for OC is routinely done via visual examinations, followed by tissue biopsy and laboratory testing. Point-of-care testing would be a more convenient and widely available alternative for at-risk individuals. Increased lactate production is a hallmark of many head-and-neck tumors, due to the Warburg Effect, where tumor cells favor glycolysis in the place of oxidative phosphorylation. To detect excess lactate, we have modified the commensal bacterium Escherichia coli Nissle 1917 to express fluorescent reporter genes in response to extracellular lactate. Administering this commensal as a mouth wash and subsequently collecting saliva for the detection of the reporter may allow for noninvasive, early detection of cancerous lesions in at-risk individuals. Furthermore, we demonstrate a new on-chip electrokinetic technique to recover these probiotic probes from model saliva fluid to improve the detection of reporter gene activation.     

Cellular delivery of peptide nucleic acids and inhibition of human telomerase.

BACKGROUND: Human telomerase has an essential RNA component and is an ideal target for developing rules correlating oligonucleotide chemistry with disruption of biological function. Similarly, peptide nucleic acids (PNAs), DNA analogs that bind complementary sequences with high affinity, are outstanding candidates for inducing phenotypic changes through hybridization. RESULTS: We identify PNAs directed to nontemplate regions of the telomerase RNA that can overcome RNA secondary structure and inhibit telomerase by intercepting the RNA component prior to holoenzyme assembly. Relative potencies of inhibition delineate putative structural domains. We describe a novel protocol for introducing PNAs into eukaryotic cells and report efficient inhibition of cellular telomerase by PNAs. CONCLUSIONS: PNAs directed to nontemplate regions are a new class of telomerase inhibitor and may contribute to the development of novel antiproliferative agents. The dependence of inhibition by nontemplate-directed PNAs on target sequence suggests that PNAs have great potential for mapping nucleic acid structure and predictably regulating biological processes. Our simple method for introducing PNAs into cells will not only be useful for probing the complex biology surrounding telomere length maintenance but can be broadly applied for controlling gene expression and functional genomics.     

Cucurbit[7]uril Inhibits Islet Amyloid Polypeptide Aggregation by Targeting N Terminus Hot Segments and Attenuates Cytotoxicity

Two “hot segments” within an islet amyloid polypeptide are responsible for its self-assembly, which in turn is linked to the decline of β-cells in type 2 diabetes (T2D). A readily available water-soluble, macrocyclic host, cucurbit[7]uril (CB[7]), effectively inhibits islet amyloid polypeptide (IAPP) aggregation through ion–dipole and hydrophobic interactions with different residues of the monomeric peptide in its random-coil conformation. A HSQC NMR study shows that CB[7] likely modulates IAPP self-assembly by interacting with and masking major residues present in the “hot segments” at the N terminus. CB[7] also prevents the formation of toxic oligomers and inhibits seed-catalyzed fibril proliferation. Importantly, CB[7] recovers rat insulinoma cells (RIN-m) from IAPP-assembly associated cytotoxicity.     

Regioselective coupling reactions of 2,4-diaminopyridine derivatives with aryl halides: the synthesis of elaborated pyridines

The development of a synthetically useful, regioselective cross-coupling of 2,4-diaminopyridines with aryl and heteroaryl halides is reported. Selectivity for coupling through either amine is controlled by a simple change in the reaction conditions. Cross-coupling through the 2-amino group predominates in the presence of a palladium catalyst, whilst the 4-amino coupled product predominates in the absence of palladium.     

Differential Harnack Estimates for Time-Dependent Heat Equations with Potentials

In this paper, we prove a differential Harnack inequality for positive solutions of time-dependent heat equations with potentials. We also prove a gradient estimate for the positive solution of the time-dependent heat equation.