Activators of cylindrical proteases as antimicrobials: identification and development of small molecule activators of ClpP protease

ClpP is a cylindrical serine protease whose ability to degrade proteins is regulated by the unfoldase ATP-dependent chaperones. ClpP on its own can only degrade small peptides. Here, we used ClpP as a target in a high-throughput screen for compounds, which activate the protease and allow it to degrade larger proteins, hence, abolishing the specificity arising from the ATP-dependent chaperones. Our screen resulted in five distinct compounds, which we designate as Activators of Self-Compartmentalizing Proteases 1 to 5 (ACP1 to 5). The compounds are found to stabilize the ClpP double-ring structure. The ACP1 chemical structure was considered to have drug-like characteristics and was further optimized to give analogs with bactericidal activity. Hence, the ACPs represent classes of compounds that can activate ClpP and that can be developed as potential novel antibiotics.     

Simplex optimization of acoustic assay for plasminogen activators

This article discusses the optimization of a newly developed method for measuring the activity of plasminogen activators using a thickness-shear-mode acoustic sensor. A variable-size simplex algorithm was used for optimization. Preliminary tests were performed to design the first simplex. A desirability function was defined to translate each performance value to a membership value of 0 to 1. If there was more than one performance variable, their membership values were translated to an aggregated membership value using another function that considers their individual influence on sensor performance. Two rounds of optimization were carried out for streptokinase followed by a single optimization for tissue-type plasminogen activator. In the last optimization, ratios of control variables were used in order to reduce the number of parameters and to formulate easily adjustable assay conditions. The results showed the usefulness of the simplex method for optimizing this type of assay, and the importance of preliminary tests and prior knowledge in providing rapid convergence using fewer experiments. The optimized plasminogen activator assay can be considered a reference method for measurement of all members of this drug class.     

WWW small molecule modeling

Computational chemistry and molecular modeling sites have proliferated on the Internet's world wide web. This paper provides present links to some of the more most useful ones for small organic molecule modeling, and offering free resources.     

WWW small molecule modeling

Computational chemistry and molecular modeling sites have proliferated on the Internet's world wide web. This paper provides present links to some of the more most useful ones for small organic molecule modeling, and offering free resources.     

Fluorous tagged small molecule microarrays

The affinity fluorous interaction between fluorous tagged small molecules and a fluoroalkyl modified glass surface was shown to facilitate the detection of protein-ligand binding interactions in the fabrication and screening of small molecule microarrays.     

Structural diversity of small molecule libraries

A novel method for assessing structural diversity is presented. Maximum common subgraph identity is used as the measure of similarity between two chemical structures. A conditional probability treatment of similarity distributions for libraries of chemical structures is used to define diversity. This evaluation method together with the evaluation of traditional physicochemical properties is used to assess a large number of chemical libraries and to understand structural differences between these.     

In-adamantane, a small inside-out molecule

The hydrocarbon in-adamantane (1), a high-energy adamantane isomer in which one methine hydrogen atom is inside the cage, is predicted by ab initio calculations to be isolable at dry ice temperature. It has 440 kJ/mol of hydrogenic strain but appears to be stable against dimerization, moisture, and air. The inverted CH bond is compressed, and the IR and NMR spectra are unusual. The symmetrical pentadecafluoro derivative (2) has an estimated half-life of 100 years at room temperature.     

固相有机合成小分子化合物库

从杂环化合物库和非杂环化合物库两方面介绍了组合化学中采用固相合成技术所构建的小分子化合物库。     

Probing small molecule binding to amyloid fibrils

Much effort has focussed in recent years on probing the interactions of small molecules with amyloid fibrils and other protein aggregates. Understanding and control of such interactions are important for the development of diagnostic and therapeutic strategies in situations where protein aggregation is associated with disease. In this perspective article we give an overview over the toolbox of biophysical methods for the study of such amyloid-small molecule interactions. We discuss in detail two recently developed techniques within this framework: linear dichroism, a promising extension of the more traditional spectroscopic techniques, and biosensing methods, where surface-bound amyloid fibrils are exposed to solutions of small molecules. Both techniques rely on the measurement of physical properties that are very directly linked to the binding of small molecules to amyloid aggregates and therefore provide an attractive route to probe these important interactions.     

Protein splicing triggered by a small molecule

The use of small molecules that turn specific proteins on or off provides a level of temporal control that is difficult to achieve using standard genetic approaches. Consequently, the development of small-molecule switches of protein function is a very active area of chemical biology, sometimes referred to as chemical genetics. Most studies in this area rely on the identification of small molecules that bind directly to the active site of a target protein, thereby acting as agonists or antagonists of function. Strategies have also been described in which the small molecule triggers a change in the secondary, tertiary, or ternary structure of the protein, in so doing changing the functional state of the molecule. Another approach to this problem would be to alter the primary structure of a target protein in response to a small-molecule trigger; a dramatic change in primary sequence would be directly coupled to function. In principle, this can be achieved by harnessing protein splicing, a posttranslational editing process that results in the precise removal of an internal domain (termed an intein) from two flanking sequences termed the N- and C-exteins. In this communication we introduce a technique that allows protein splicing to occur only in the presence of the small molecule, rapamycin. This approach is expected to be independent of the nature of the two exteins and so should provide a general vehicle for controlling protein function using small molecules.     

Strong enantioselective self-recognition of a small chiral molecule

In the present report, we have crystallized a single enantiomer and the racemate of N-3,5-dinitrobenzoyl (DNB) leucine. In both cases, the X-ray structures show clear evidence of homochiral dimerization in the solid state. Moreover, only homochiral dimers were observed in the unit cell of the racemate, a result of solid-state enantioselective complexation. The crystal structures support a chiral recognition mechanism involving two hydrogen bonds and an offset pi-pi interaction between the DNB rings.     

Computational insight into small molecule inhibition of cyclophilins

Cyclophilins (Cyp) are a family of cellular enzymes possessing peptidyl-prolyl isomerase activity, which catalyze the cis-trans interconversion of proline-containing peptide bonds. The two most abundant family members, CypA and CypB, have been identified as valid drug targets for a wide range of diseases, including HCV, HIV, and multiple cancers. However, the development of small molecule inhibitors that possess nM potency and high specificity for a particular Cyp is difficult given the complete conservation of all active site residues between the enzymes. Monte Carlo statistical sampling coupled to free energy perturbation theory (MC/FEP) calculations have been carried out to elucidate the origin of the experimentally observed nM inhibition of CypA by acylurea-based derivatives and the >200-fold in vitro selectivity between CypA and CypB from aryl 1-indanylketone-based μM inhibitors. The computed free-energies of binding were in close accord with those derived from experiments. Binding affinity values for the inhibitors were determined to be dependent upon the stabilization strength of the nonbonded interactions provided toward two catalytic residues: Arg55 and Asn102 in CypA and the analogous Arg63 and Asn110 residues in CypB. Fine-tuning of the hydrophobic interactions allowed for enhanced potency among derivatives. The aryl 1-indanylketones are predicted to differentiate between the cyclophilins by using distinct binding motifs that exploit subtle differences in the active site arrangements. Ideas for the development of new selective compounds with the potential for advancement to low-nanomolar inhibition are presented.     

Dedifferentiation of lineage-committed cells by a small molecule

Combinatorial libraries were screened for molecules that induce mouse myogenic lineage committed cells to dedifferentiate in vitro. A 2,6-disubstituted purine, reversine, was discovered that induces lineage reversal of C2C12 cells to become multipotent progenitor cells which can redifferentiate into osteoblasts and adipocytes. This and other such molecules are likely to provide new insights into the molecular mechanisms that control cellular dedifferentiation and may ultimately be useful to in vivo stem cell biology and therapy.     

Efficient synthesis of small molecule macroarrays: optimization of the macroarray synthesis platform and examination of microwave and conventional heating methods

We report a method for the efficient construction of small molecule macroarrays using microwave-assisted SPOT-synthesis. Macroarrays of 1,3-diphenylpropenones (chalcones) were synthesized rapidly and in high purity starting from robust, Wang-linker-derivatized planar supports. We have optimized the entire chalcone macroarray construction process and evaluated the efficiency and utility of microwave-assisted reactions in array synthesis. Microwave heating was found to be most beneficial for reactions that require temperatures greater than the boiling points of the solvents. These microwave-assisted conditions permitted straightforward access to macroarrays of 2,4,6-triarylpyridines derived from the original chalcone scaffold.     

Ultrasensitive small molecule fluorogenic probe for human heparanase

Heparanase (HPA) is a critical enzyme involved in the remodeling of the extracellular matrix (ECM), and its elevated expression has been linked with diseases such as various types of cancer and inflammation. The detection of heparanase enzymatic activity holds tremendous value in the study of the cellular microenvironment, and search of molecular therapeutics targeting heparanase, however, no structurally defined probes are available for the detection of heparanase activity. Here we present the development of the first ultrasensitive fluorogenic small-molecule probe for heparanase enzymatic activity via tuning the electronic effect of the substrate. The probe exhibits a 756-fold fluorescence turn-on response in the presence of human heparanase, allowing one-step detection of heparanase activity in real-time with a picomolar detection limit. The high sensitivity and robustness of the probe are exemplified in a high-throughput screening assay for heparanase inhibitors.

Heparanase, a critical enzyme involved in the remodeling of the extracellular matrix, activates a disaccharide probe HADP to give a strong fluorescence signal.     

Solid-state nanopores for ion and small molecule analysis

Solid-state nanopore in analytical chemistry has developed rapidly in the 1990s and it is proved to be a versatile new tool for bioanalytical chemistry. This review focuses on the analysis of ions and small molecules with nanopores including nanopipettes, polymer film nanopores, Si₃N₄ nanopores, graphene nanopores, MoS₂ nanopores and MOFs.