Upregulation of p53 through induction of MDM2 degradation: Anthraquinone analogs.

In a previous study, a novel anthraquinone analog BW-AQ-101 was identified as a potent inducer of MDM2 degradation, leading to upregulation of p53 and apoptosis in cell culture studies. In animal models of acute lymphocytic leukemia, treatment with BW-AQ-101 led to complete disease remission. In this study, we systematically investigated the effect of substitution patterns of the core anthraquinone scaffold. Through cytotoxicity evaluation in two leukemia cell lines, the structure-activity relationship of thirty-two analogs has been examined. Several analogs with comparable or improved potency over BW-AQ-101 have been identified. Western-blot assays verified the effect of the potent compounds on the MDM2-p53 axis. The study also suggests new chemical space for further optimization work.

Biphasic actions of SecA inhibitors on Prl/Sec suppressors: Possible physiological roles of SecA-only channels.

SecA is an essential component in the bacterial Sec-dependent protein translocation process. We previously showed that in addition to the ubiquitous, high-affinity SecYEG-SecDF·YajC protein translocation channel, there is a low-affinity SecA-only channel that elicits ion channel activity and promotes protein translocation. The SecA-only channels are less efficient, and like Prl suppressors, lack signal peptide specificity; they function in the absence of signal peptides. The presence of SecYEG-SecDF·YajC alters the sensitivity of ATPase inhibitor Rose Bengal. In this study, we found that the suppressor membranes are much more resistant to inhibition by Rose Bengal. Similar results have been found for a SecA-specific inhibitor. Moreover, biphasic responses of inhibition of ion current and protein translocation activities were observed for many PrlA/SecY and PrlG/SecE suppressor membranes, with a low IC50 value similar to that of the SecA-only channels and a very high IC50. However, the suppressor strains are as sensitive to the inhibitor as the parental strain, suggesting that SecA-only channels have some essential physiological function(s) in the cells that are inhibited by the specific SecA inhibitor.

Using Chemical Probes to Assess the Feasibility of Targeting SecA for Developing Antimicrobial Agents against Gram-Negative Bacteria.

With the widespread emergence of drug resistance, there is an urgent need to search for new antimicrobials, especially those against Gram-negative bacteria. Along this line, the identification of viable targets is a critical first step. The protein translocase SecA is commonly believed to be an excellent target for the development of broad-spectrum antimicrobials. In recent years, we developed three structural classes of SecA inhibitors that have proven to be very effective against Gram-positive bacteria. However, we have not achieved the same level of success against Gram-negative bacteria, despite the potent inhibition of SecA in enzyme assays by the same inhibitors. In this study, we use representative inhibitors as chemical probes to gain an understanding as to why these inhibitors were not effective against Gram-negative bacteria. The results validate our initial postulation that the major difference in effectiveness against Gram-positive and Gram-negative bacteria is in the additional permeability barrier posed by the outer membrane of Gram-negative bacteria. We also found that the expression of efflux pumps, which are responsible for multidrug resistance (MDR), have no effect on the effectiveness of these SecA inhibitors. Identification of an inhibitor-resistant mutant and complementation tests of the plasmids containing secA in a secAts mutant showed that a single secA-azi-9 mutation increased the resistance, providing genetic evidence that SecA is indeed the target of these inhibitors in bacteria. Such results strongly suggest SecA as an excellent target for developing effective antimicrobials against Gram-negative bacteria with the intrinsic ability to overcome MDR. A key future research direction should be the optimization of membrane permeability.

A metal-free turn-on fluorescent probe for the fast and sensitive detection of inorganic azides.

Sodium azide is toxic and widely used in agricultural, commercial products, and research laboratories. Thus it is of a significant environmental concern and there is a need for the development of a rapid detection method. A fluorogenic dibenzylcyclooctyne derivative (Fl-DIBO) is herein described as a fluorescent probe for the rapid detection of inorganic azide via Strain-Promoted Azide-Alkyne Cycloaddition (SPAAC). Fl-DIBO was found to be highly selective toward NaN3 in comparison to other common anions with good sensitivity and detection limit of 10µM.

Design, Synthesis and Evaluation of Triazole-Pyrimidine Analogues as SecA Inhibitors.

SecA, a key component of the bacterial Sec-dependent secretion pathway, is an attractive target for the development of new antimicrobial agents. Through a combination of virtual screening and experimental exploration of the surrounding chemical space, we identified a hit bistriazole SecA inhibitor, SCA-21, and studied a series of analogues by systematic dissections of the core scaffold. Evaluation of these analogues allowed us to establish an initial structure-activity relationship in SecA inhibition. The best compounds in this group are potent inhibitors of SecA-dependent protein-conducting channel activity and protein translocation activity at low- to sub-micromolar concentrations. They also have minimal inhibitory concentration (MIC) values against various strains of bacteria that correlate well with the SecA and protein translocation inhibition data. These compounds are effective against methicillin-resistant Staphylococcus aureus strains with various levels of efflux pump activity, indicating the capacity of SecA inhibitors to null the effect of multidrug resistance. Results from studies of drug-affinity-responsive target stability and protein pull-down assays are consistent with SecA as a target for these compounds.

Click with a boronic acid handle: a neighboring group-assisted click reaction that allows ready secondary functionalization.

The feasibility of a neighboring boronic acid-facilitated facile condensation of an aldehyde is described. This reaction is bio-orthogonal, complete at room temperature within minutes, and suitable for bioconjugation chemistry. The boronic acid group serves the dual purpose of catalyzing the condensation reaction and being a handle for secondary functionalization.

Post-synthesis DNA modifications using a trans-cyclooctene click handle.

Post-synthesis DNA modification is a very useful method for DNA functionalization. This is achieved by using a modified NTP, which has a handle for further modifications, replacing the corresponding natural NTP in polymerase-catalyzed DNA synthesis. Subsequently, the handle can be used for further functionalization after PCR, preferably through a very fast reaction. Herein we describe polymerase-mediated incorporation of trans-cyclooctene modified thymidine triphosphate (TCO-TTP). Subsequently, the trans-cyclooctene group was reacted with a tetrazine tethered to other functional groups through a very fast click reaction. The utility of this DNA functionalization method was demonstrated with the incorporation of a boronic acid group and a fluorophore. The same approach was also successfully used in modifying a known aptamer for fluorescent labelling applications.

A click-and-release approach to CO prodrugs.

Carbon monoxide belongs to the family of signaling molecules and has been shown to possess therapeutic effects. Similar to NO, safe delivery of CO is a key issue in developing CO-based therapeutics. Herein we report a "click and release" CO-prodrug approach, which allows the release of CO under physiological conditions without the need for light irradiation. The system releases CO in a triggered and controllable manner and possesses the potential of tunable release rates.

Redox-based selective fluorometric detection of homocysteine.

Plasma homocysteine (Hcy) is an important risk factor for various diseases. A novel redox-sensitive fluorescent probe is developed for the selective detection of Hcy. A linear calibration curve has been obtained in buffer and plasma for the quantitative determination of Hcy in such media.

3,6-Substituted-1,2,4,5-tetrazines: tuning reaction rates for staged labeling applications.

Cycloaddition reactions involving tetrazines have proven to be powerful bioorthogonal tools for various applications. Conceivably, sequential and selective labeling using tetrazine-based reactions can be achieved by tuning the reaction rate. By varying the substituents on tetrazines, cycloaddition rate variations of over 200 fold have been achieved with the same dienophile. Upon coupling with different dienophiles, such as norbornene, the reaction rate difference can be over 14,000 fold. These substituted tetrazines can be very useful for selective labeling under different conditions.

2,6-dansyl azide as a fluorescent probe for hydrogen sulfide.

A second-generation sulfonyl azide-based fluorescent probe, 2,6-DNS-Az, has been developed for the quantitative detection of H2S in aqueous media such as phosphate buffer and bovine serum. Compare to the first-generation 1,5-DNS-Az probe, this probe shows both high sensitivity in phosphate buffer without the need for addition of surfactant and selectivity for sulfide over other anions and biomolecules, and thus can be used as a useful tool for detection of H2S in the biological system.

An unexpected copper catalyzed 'reduction' of an arylazide to amine through the formation of a nitrene intermediate.

Azido nitrobenzoxadiazole (NBD) was observed to undergo a 'reduction' reaction in the absence of an obvious reducing agent, leading to amine formation. In the presence of an excess amount of DMSO, a sulfoxide conjugate was also formed. The ratio of these two products was both temperature- and solvent-dependent, with the addition of water significantly enhancing the ratio of the 'reduction' product. Two intermediates of the azido-NBD reaction in DMSO were trapped and characterized by low-temperature EPR spectroscopy. One was an organic free radical (S=1/2) and another was a triplet nitrene (S=1) species. A mechanism was proposed based on the characterized free radical and triplet intermediates.

Arylboronic acid chemistry under electrospray conditions.

Boronic acids are important in the organic and biological arenas. Thus, their identification and characterization are important. ESI-MS is a well-known tool for such uses. Herein we report a systematic analysis of the chemical behavior of arylboronic acids under ESI-MS conditions. Such information will be very critical to understanding the gas-phase chemistry of boronic acids in an ESI mass spectrometer ion source in general and the MS analysis of boronic acids and their macromolecular conjugates in particular.

Rapid and specific post-synthesis modification of DNA through a biocompatible condensation of 1,2-aminothiols with 2-cyanobenzothiazole.

Post-synthesis modification of DNA is an important way of functionalizing DNA molecules. Herein, we describe a method that first enzymatically incorporates a cyanobenzothiazole (CBT)-modified thymidine. The side-chain handle CBT can undergo a rapid and site-specific cyclization reaction with 1,2-aminothiols to afford DNA functionalization in aqueous solution. Another key advantage of this method is the formation of a single stereo/regioisomer in the process, which allows for precise control of DNA modification to yield a single component for aptamer selection work and other applications.

A fluorescent probe for rapid aqueous fluoride detection and cell imaging.

A stable and highly selective fluorescent probe has been designed and synthesized for the rapid detection of fluoride ions (F(-)) in aqueous solution and living cells. The design was based on the high reactivity of F(-) toward a silyl group.

A Novel Base-Promoted Cyclization: Synthesis of Substituted Benzo[b]furans.

A new base-promoted cyclization for the synthesis of substituted benzo[b]furans is described. This method is simple and inexpensive and gives good yields.

Clicking 1,2,4,5-tetrazine and cyclooctynes with tunable reaction rates.

Substituted tetrazines have been found to undergo facile inverse electron demand Diels-Alder reactions with "tunable" reaction rates.

Design, synthesis, and polymerase-catalyzed incorporation of click-modified boronic acid-TTP analogues.

DNA molecules are known to be important materials in sensing, aptamer selection, nanocomputing, and construction of unique architectures. The incorporation of modified nucleobases affords unique DNA properties for applications in areas that would otherwise be difficult or not possible. Earlier, we demonstrated that the boronic acid moiety can be introduced into DNA through polymerase-catalyzed reactions. In order to study whether such incorporation by polymerase is a general phenomenon, we designed and synthesized four boronic acid-modified thymidine triphosphate (TTP) analogues. The synthesis of certain analogues was through the use of a single dialkyne tether for both the Sonogashira coupling with thymidine and the later Cu-mediated [3+2] cycloaddition for linking the boronic acid moiety. This approach is much more efficient than the previously described method, and paves the way for the preparation of a large number of boronic acid-modified TTPs with a diverse set of structural features. All analogues showed very good stability under polymerase chain reaction (PCR) conditions and were recognized as a substrate by DNA polymerase, and thus incorporated into DNA.

Facile derivatization of azide ions using click chemistry for their sensitive detection with LC-MS.

By employing a click reaction, a novel method was developed for the sensitive detection of inorganic azides at as low as 21 ppb.