Small Molecules probes

Chattopadhaya and co-workers [162] recently reported another approach used to avoid some of the drawbacks associated with the use of FPs. The authors described a small molecule-based procedure that makes use of the unique reactivity between the cysteine residue at the N-terminus of a target protein and cell-permeable, thioester-based small molecule probes resulting in site-specific, covalent tagging of proteins. 

Chattopadhaya S, Srinivasan R, Yeo DSY et al (2009) Site-specific covalent labeling of proteins inside live cells using small molecule probes. Bioorg Med Chem 17 981-989... 

Nonideal interactions can be also be characterized using small-molecule probes.7 Ideally, these probes should elute at Vu. Cation-exchange interactions can be detected by excessive retention of arginine or lysine.8 Ion-exclusion effects can be characterized by early elution of citrate or glutamic acid. Hydrophobic interactions can be detected by late elution of phenylethyl alcohol or benzyl alcohol.8... 

Strausberg RL, Schreiber SL. (2003) From knowing to controlling A path from genomics to drugs using small molecule probes. Science 300 294-295. 

Arya P, Barkley A, Randall KD, Automated High-Throughput Synthesis of Artificial Glycopeptides. Small-Molecule Probes for Chemical Glycobiology, J. Comb. Chem., 4(3) 193-8, 2002. 

The choice of assay type in a drug discovery campaign is complicated. Are you seeking an agonist, an antagonist, or a selective modulator What tools (cell lines, recombinant proteins, small molecule probes, etc.) are at your disposal How many compounds do you want to profile What are your cost and time constraints Each of these issues can modify your determination of the optimal assay for your particular project. 

Here, we cover several examples that included stereoselective diversity-oriented synthesis approaches. The examples covered in this section are indicative of the growing interest in this area and of the need for developing novel approaches leading to fast access to obtaining natural product-like compounds to be used as small-molecule probes. 

Alkaloid Natural Product-inspired Small-molecule Probes for XIAP... 

Small-molecule probes of other endocytic trafficking pathways... 

Parallel to the efforts of identifying substrate proteins for a particular enzyme, the activity-based small molecule probes pioneered by Cravatt and coworkers can facilitate the identification of the biological functions of an enzyme that catalyzes protein post-translational modifications (145). The major advantage of this type of probes is that potentially they can detect enzymes that are in the active states, and thus can provide snapshots of enzymes that are in the active states at different development stages or different types of cells. Among enzymes that catalyze PTM, so far probes have been developed for studying proteases (145, 146), kinases (147), pTyr phosphatases (148), and protein Arg deiminases (149). 

Several of the most useful small-molecule probes are complex natural products isolated from marine, fungal, or plant sources. As natural products have built-in biologic properties efforts in the synthesis of compound libraries increasingly use natural product scaffolds as a starting material because they promise higher hit rates in biologic screens (23). 

Glansdorp EG, Thomas GL, Lee JK, Dutton JM, Salmond GP, Welch M, Spring DR. Synthesis and stability of small molecule probes for Pseudomonas aeruginosa quorum sensing modulation. Org. Biomol. Chem. 2004 2 3329-3336. 

As a result of the experimental woik simmarized in this review the value of the gas chromatographic method for studying polymers seems to be well established. Surface and bulk properties of polymers can be measured both from a thermodynamic and kinetic point of view. Because of its simplicity and precision it should become the method of choice for the study of thermoch namic interactions of small molecule probes or solutes in systems where the prfymer is flie m or phase. Further advances in the kinetic theory of the GC process (wld provide even more reliable data about time dependent processes such as diffu on, adsorption, complex fcwmar-tion and possibly even chemical reaction. 

M. Fernandez-Suarez, H. Baruah, L. Martinez-Hernandez, K.T. Xie, J.M. Baskin, C.R. Bertozzi, A.Y. Ting, Redirecting lipoic acid ligase for cell surface protein labeling with small-molecule probes. Nat. Biotechnol. 25, 1483-1487 (2007)... 

These small molecule probes of DNA (ds and ss) and RNA do not identify organisms, but indicate probable viability because the genome is intact. When cells in suspension or on a slide are stained and examined under a UV-epi-illuminated microscope or in a flow cytometer, with or without cell sorting, then viability can be estimated with fairly high precision and accuracy. This and related topics are developed in Ref. and in portions of the molecular probes pages (www.probes.com), which the reader may find particularly useful. 

Fielding, L., Fletcher, D., Rutherford, S., Kaur, J., Mestres, J. Exploring the active site of human factor Xa protein by NMR screening of small molecule probes. Org. Biomol. Chem. 2003, 1, 4235-4241. 

Discovering Small Molecule Probes for Biological Mechanisms... 

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