Cellular Targets Of Small Molecules Research Articles

Identifying Biomolecular Targets of the Anticancer Vitamin-E-δ-Tocotrienol Using a Computational Approach: Virtual Target Screening

In recent years, evidence has mounted that a particular form of vitamin E (its δ-tocotrienol variant) may have cellular functions beyond that of an antioxidant, a role commonly ascribed to the tocotrienol class of compounds. In particular, numerous studies of δ-tocotrienol’s effect on cancer cells have identified it as a potent anticancer and antitumor agent. However, this important revelation of potential therapeutic use poses a series of new challenges, with arguably the most important being the elucidation of the precise mechanism of action responsible for the anticancer activity of δ-tocotrienol. As an initial step to address this question, we have used a computational tool, Virtual Target Screening (a molecular docking-based tool that identifies potential binding partners for small molecules), to identify potential biomolecular targets of δ-tocotrienol. Then, to gain a consensus as to the type of biomolecular entity that could be a target for δ-tocotrienol, we utilized PharmMapper and PASS (a ligand-based chemoinformatic approach), and ProBiS (a tool that analyses binding site similarities across known proteins). The results of our multipronged computational consensus-seeking approach showed that such a strategy can identify potential cellular targets of small molecules. This is evidenced by our identification of estrogen receptor-beta, a protein that has been previously shown to bind δ-tocotrienol, which elicited a cellular response. This study supports the use of such a computational approach as an initial step in target identification to avoid time-consuming, costly large-scale experimental screening, greatly reducing the experimental work to just one or a few candidate proteins.

Target Identification of Kinase Inhibitor Alisertib (MLN8237) by Using DNA-Programmed Affinity Labeling.

Accurate identification of the molecular targets of bioactive small molecules is a highly important yet challenging task in biomedical research. Previously, a method named DPAL (DNA-programmed affinity labeling) for labeling and identifying the cellular targets of small molecules and nucleic acids was developed. Herein, DPAL is applied for the target identification of Alisertib (MLN8237), which is a highly specific aurora kinase A (AKA) inhibitor and a drug candidate being tested in clinical trials for cancer treatment. Apart from the well-established target of AKA, several potential new targets of MLN8237 were identified. Among them, p38 mitogen-activated protein kinase (p38) and laminin receptor (LAMR) were validated to be implicated in the anticancer activities of MLN8237. Interestingly, these new targets were not identified with non-DNA-based affinity probes. This work may facilitate an understanding of the molecular basis of the efficacy and side effects of MLN8237 as a clinical drug candidate. On the other hand, this work has also demonstrated that the method of DPAL could be a useful tool for target identification of bioactive small molecules.

Target identification of biologically active small molecules via in situ methods

The identification of potential cellular targets of small molecules is important in biomedical research and drug discovery, but has been challenging due to a lack of proteome-based methods that enable direct investigation of small molecule-protein interaction in live cells. This review summarizes some of the recent advances in target identification of bioactive molecules (including drugs and natural products) using in situ methods for cell-based proteome profiling of potential on and off targets.

The Quest for Medicines, a Grand Challenge in the Twenty-First Century

The Quest for Medicines, a Grand Challenge in the Twenty-First Century

Small-Molecule Reagents for Cellular Pull-Down Experiments

Affinity purification of interacting proteins from cellular extracts is a powerful technique for identifying the cellular targets of small molecules. Affinity matrix-based small-molecule reagents are usually prepared by conjugating small molecules of interest to a solid support such as agarose. This protocol describes an efficient and robust method to immobilize small molecules containing a primary alcohol, a common functional group in small molecules, especially in small molecules prepared using diversity-oriented synthesis. This method comprises one element of a systematic approach to the target identification problem in chemical biology.

Surface‐Plasmon‐Resonance‐Based Chemical Proteomics: Efficient Specific Extraction and Semiquantitative Identification of Cyclic Nucleotide‐Binding Proteins from Cellular Lysates by Using a Combination of Surface Plasmon Resonance, Sequential Elution and Liquid Chromatography–Tandem Mass Spectrometry

Chemical proteomics is a powerful methodology for identifying the cellular targets of small molecules, however, it is biased towards abundant proteins. Therefore, quantitative strategies are needed to distinguish between specific and nonspecific interactions. Here, we explore the potential of the combination of surface plasmon resonance (SPR) coupled to liquid chromatography-tandem mass spectrometry (LC-MS/MS) as an alternative approach in chemical proteomics. We coupled cGMP molecules to the SPR chip, and monitored the binding and dissociation of proteins from a human lysate by using sequential elution steps and SPR. The eluted proteins were subsequently identified by LC-MS/MS. Our approach enabled the efficient and selective extraction of low-abundant cyclic-nucleotide-binding proteins such as cGMP-dependent protein kinase, and a quantitative assessment of the less- and nonspecific competitive binding proteins. The data show that SPR-based chemical proteomics is a promising alternative for the efficient specific extraction and quantitative identification of small-molecule-binding proteins from complex mixtures.

An shRNA barcode screen provides insight into cancer cell vulnerability to MDM2 inhibitors

The identification of the cellular targets of small molecules with anticancer activity is crucial to their further development as drug candidates. Here, we present the application of a large-scale RNA interference-based short hairpin RNA (shRNA) barcode screen to gain insight in the mechanism of action of nutlin-3 (1). Nutlin-3 is a small-molecule inhibitor of MDM2, which can activate the p53 pathway. Nutlin-3 shows strong antitumor effects in mice, with surprisingly few side effects on normal tissues. Aside from p53, we here identify 53BP1 as a critical mediator of nutlin-3-induced cytotoxicity. 53BP1 is part of a signaling network induced by DNA damage that is frequently activated in cancer but not in healthy tissues. Our results suggest that nutlin-3's tumor specificity may result from its ability to turn a cancer cell-specific property (activated DNA damage signaling) into a weakness that can be exploited therapeutically.

A Genome-Wide Overexpression Screen in Yeast for Small-Molecule Target Identification

We describe a multicopy gene suppression screen of drug sensitivity in Saccharomyces cerevisiae that facilitates the identification of cellular targets of small molecules. An array of yeast transformants harboring a multicopy yeast genomic library was screened for resistance to growth inhibitors. Comparison of array growth patterns for several such inhibitors allowed the differentiation of general and molecule-specific genetic suppressors. Specific resistance to phenylaminopyrimidine (1), an inhibitor identified from a kinase-directed library, was associated with the overexpression of Pkc1 and a subset of downstream kinases. Components of two other pathways (pheromone response/filamentous growth and Pho85 kinase) that genetically interact with the PKC1 MAPK signaling cascade were also identified. Consistent with the suppression screen, inhibitor 1 bound to Pkc1 in yeast cell lysate and inhibited its activity in vitro. These results demonstrate the utility of this approach for the rapid deconvolution of small-molecule targets.

A quantitative analysis and chemical approach for the reduction of nonspecific binding proteins on affinity resins.

Tubulin and actin often bind nonspecifically to affinity chromatography resins, complicating research toward identifying the cellular targets of small molecules. Reduction of nonspecific binding proteins is important for the success of such biochemical approaches. To develop strategies to circumvent this problem, we quantitatively investigated the binding of tubulin and actin to a series of affinity resins bearing 15 variant ligands on 3 commercially available polymer supports. Nonspecific protein binding was proportional to the hydrophobicity of the affinity resins and could be quantitatively correlated to the CLOGP values of the ligands, which are a measure of compound hydrophobicity. When compounds had CLOGP values greater than 1.5, (amount of tubulin) = 0.73 x CLOGP - 1.1 (n = 7, r = 0.97), and (amount of actin) = 0.42 x CLOGP - 0.79 (n = 7, r = 0.99). On the basis of these studies, we designed a novel hydrophilic poly(ethylene glycol) (PEG) spacer (26) for the conjugation of ligands to chromatography resins. As predicted by our binding algorithm, introduction of this spacer reduced the amount of nonspecific protein binding in proportion to the number of ethylene glycol units.