Identifying the molecular targets for the beneficial or detrimental effects of small-molecule drugs is an important and currently unmet challenge. We have developed a method, drug affinity responsive target stability (DARTS), which takes advantage of a reduction in the protease susceptibility of the target protein upon drug binding. DARTS is universally applicable because it requires no modification of the drug and is independent of the mechanism of drug action. We demonstrate use of DARTS to identify known small-molecule-protein interactions and to reveal the eukaryotic translation initiation machinery as a molecular target for the longevity-enhancing plant natural product resveratrol. We envisage that DARTS will also be useful in global mapping of protein-metabolite interaction networks and in label-free screening of unlimited varieties of compounds for development as molecular imaging agents.aging ͉ label-free ͉ proteomics ͉ small molecules

Metabolism and ageing are intimately linked. Compared to ad libitum feeding, dietary restriction (DR) or calorie restriction (CR) consistently extends lifespan and delays age-related diseases in evolutionarily diverse organisms1,2. Similar conditions of nutrient limitation and genetic or pharmacological perturbations of nutrient or energy metabolism also have longevity benefits3,4. Recently, several metabolites have been identified that modulate ageing5,6 with largely undefined molecular mechanisms. Here we show that the tricarboxylic acid (TCA) cycle intermediate α-ketoglutarate (α-KG) extends the lifespan of adult C. elegans. ATP synthase subunit beta is identified as a novel binding protein of α-KG using a small-molecule target identification strategy called DARTS (drug affinity responsive target stability)7. The ATP synthase, also known as Complex V of the mitochondrial electron transport chain (ETC), is the main cellular energy-generating machinery and is highly conserved throughout evolution8,9. Although complete loss of mitochondrial function is detrimental, partial suppression of the ETC has been shown to extend C. elegans lifespan10–13. We show that α-KG inhibits ATP synthase and, similar to ATP synthase knockdown, inhibition by α-KG leads to reduced ATP content, decreased oxygen consumption, and increased autophagy in both C. elegans and mammalian cells. We provide evidence that the lifespan increase by α-KG requires ATP synthase subunit beta and is dependent on the target of rapamycin (TOR) downstream. Endogenous α-KG levels are increased upon starvation and α-KG does not extend the lifespan of DR animals, indicating that α-KG is a key metabolite that mediates longevity by DR. Our analyses uncover new molecular links between a common metabolite, a universal cellular energy generator, and DR in the regulation of organismal lifespan, thus suggesting new strategies for the prevention and treatment of ageing and age-related diseases.

By searching for molecules that assist MyoD in converting fibroblasts to muscle cells, we have found that p300 and CBP, two related molecules that act as transcriptional adapters, coactivate the myogenic basic-helixloop-helix (bHLH) proteins. Coactivation by p300 involves novel physical interactions between p300 and the amino-terminal activation domain of MyoD. In particular, disruption of the FYD domain, a group of three amino acids conserved in the activation domains of other myogenic bHLH proteins, drastically diminishes the transactivation potential of MyoD and abolishes both p300-mediated coactivation and the physical interaction between MyoD and p300. Two domains of p300, at its amino and carboxy terminals, independently function to both mediate coactivation and physically interact with MyoD. A truncated segment of p300, unable to bind MyoD, acts as a dominant negative mutation and abrogates both myogenic conversion and transactivation by MyoD, suggesting that endogenous p300 is a required coactivator for MyoD function. The p300 dominant negative peptide forms multimers with intact p300. p300 and CBP serve as coactivators of another class of transcriptional activators critical for myogenesis, myocyte enhancer factor 2 (MEF2). In fact, transactivation mediated by the MEF2C protein is potentiated by the two coactivators, and this phenomenon is associated with the ability of p300 to interact with the MADS domain of MEF2C. Our results suggest that p300 and CBP may positively influence myogenesis by reinforcing the transcriptional autoregulatory loop established between the myogenic bHLH and the MEF2 factors.The myogenic basic helix-loop-helix (bHLH) proteins can confer the myogenic phenotype to otherwise committed cell types (15,30,45,62,77,82) and are essential for the proper development of skeletal muscles (11,13,38,60,65,68,69,88). They activate muscle gene transcription by pairing with ubiquitously expressed E proteins (17, 46) via the HLH domain and interact with the E box, a specific DNA sequence (CANNTG) (58,59), that functions as an operative binding site in a large number of transcription regulatory regions. Interaction with the E-box DNA by the heterodimeric complex is mediated by the basic regions of the myogenic bHLH and E proteins (14, 23) and is necessary but not sufficient for transcriptional activation (9, 79). This indicates that besides DNA binding, additional steps are required to activate transcription. E-box sites are expected in the genome at random approximately every 256 bp, but myogenic bHLH factors solely transactivate muscle-specific genes. Tissue-specific gene activation by the myogenic bHLH proteins is achieved through at least two mechanisms. First, not all E boxes are equivalent (10). The particular two nucleotides flanking each side of an E box have been shown to repress activation of an immunoglobulin enhancer in muscle cells by a myogenic bHLH protein (80), and E-box activity depends upon its context even in muscle genes (39,86). Second, two amino acids, alanine 114 and threon...

Menin is a tumor suppressor protein whose loss or inactivation causes multiple endocrine neoplasia type 1 (MEN1), a hereditary autosomal dominant tumor syndrome characterized by tumorigenesis in multiple endocrine organs1. Menin interacts with a multitude of proteins and involves in a variety of cellular processes2–6. Menin binds the Jun family transcription factor JunD and inhibits its transcriptional activity7,8. Several MEN1 missense mutations disrupted the menin-JunD interaction suggestive of a correlation between menin’s tumor suppressor function and its interaction with JunD and suppression of JunD activated transcription8,9. Menin also interacts with mixed lineage leukemia protein 1 MLL1, a histone H3 lysine 4 (H3K4) methyltransferase, and functions as an oncogenic cofactor to upregulate gene (including HOX genes) transcription and promote MLL1 fusion protein (MFP)-induced leukemogenesis10–12. A recent report on menin tethering MLL1 to chromatin binding factor LEDGF indicates menin as a molecular adaptor to coordinate the functions of multiple proteins13. Despite the importance of menin, it still remains poorly understood how menin could interact with many distinct partners and control multiple functions. Here we present the crystal structures of menin, free and in complexes with MLL1 or JunD, or an MLL1-LEDGF heterodimer. These structures show that menin contains a deep pocket that binds short peptides of MLL1 or JunD in the same manner, but oppositely regulates transcription. The menin-JunD interaction blocks JNK kinase-meidated JunD phosphorylation, a crucial event for JunD activation.Moreover, menin functions as a scaffold molecule to promote gene transcription by binding MLL1 through the peptide-pocket yet interacting with LEDGF at a distinct surface.

Using an in vitro binding-site selection assay, we have demonstrated that c-Myc-Max complexes bind not only to canonical CACGTG or CATGTG motifs that are flanked by variable sequences but also to noncanonical sites that consist of an internal CG or TG dinucleotide in the context of particular variations in the CA--TG consensus. None of the selected sites contain an internal TA dinucleotide, suggesting that Myc proteins necessarily bind asymmetrically in the context of a CAT half-site. The noncanonical sites can all be bound by proteins of the Myc-Max family but not necessarily by the related CACGTG-and CATGTG-binding proteins USF and TFE3. Substitution of an arginine that is conserved in these proteins into MyoD (MyoD-R) changes its binding specificity so that it recognizes CACITG instead of the MyoD cognate sequence (CAGCTG).However, like USF and TFE3, MyoD-R does not bind to all of the noncanonical c-Myc-Max sites. Although this R substitution changes the internal dinucleotide specificity of MyoD, it does not significantly alter its wild-type binding sequence preferences at positions outside of the CA--TG motif, suggesting that it does not dramatically change other important amino acid-DNA contacts; this observation has important implications for models of basic-helix-loop-helix protein-DNA binding.Members of the Myc family of proteins (c-, N-, and L-Myc) have been implicated in oncogenesis, in progression through the cell cycle (39), and in induction of apoptosis (25, 45); however, the direct targets of their activity remain unknown. Myc proteins are members (21) of the basic helix-loop-helix (bHLH) protein family (42), in which the HLH domain is responsible for dimerization (42, 43) and the adjacent basic region mediates sequence-specific DNA binding (20, 56). They belong to a bHLH protein subgroup (bHLH-LZ proteins) in which a leucine zipper motif (37) that is located immediately C terminal to the HLH domain seems to participate in the dimerization process (7,26,31,40

Drug affinity responsive target stability (DARTS) is a general methodology for identifying and studying protein‐ligand interactions. The technique is based on the principle that when a small molecule compound binds to a protein, the interaction stabilizes the target protein's structure such that it becomes resistant to proteases. DARTS is particularly useful for the initial identification of the protein targets of small molecules, but can also be used to validate potential protein‐ligand interactions predicted or identified by other means and to estimate the affinity of interactions. The approach is simple and advantageous because it can be performed using crude cell lysates and other complex protein mixtures (without requiring purified proteins), and it uses native, unmodified small molecules. The protocols in this unit describe the general approach for performing DARTS experiments, which can be easily modified and scaled to fit project‐specific criteria. Curr. Protoc. Chem. Biol. 3:163‐180 © 2011 by John Wiley & Sons, Inc.

SUMMARY The replicative machinery encounters many impediments, some of which can be overcome by lesion bypass or replication restart pathways, leaving repair for a later time. However, interstrand crosslinks (ICLs), which preclude DNA unwinding, are considered absolute blocks to replication. Current models suggest that fork collisions, either from one or both sides of an ICL, initiate repair processes required for resumption of replication. To test these proposals, we developed a single molecule technique for visualizing encounters of replication forks with ICLs, as they occur in living cells. Surprisingly, the most frequent patterns were consistent with replication traverse of an ICL, without lesion repair. The traverse frequency was strongly reduced by inactivation of the translocase and DNA binding activities of the FANCM/MHF complex. The results indicate that translocase-based mechanisms enable DNA synthesis to continue past ICLs, and that these lesions are not always absolute blocks to replication.

Small-molecule target identification is a vital and daunting task for the chemical biology community as well as for researchers interested in applying the power of chemical genetics to impact biology and medicine. To overcome this “target ID” bottleneck, new technologies are being developed that analyze protein–drug interactions, such as drug affinity responsive target stability (DARTS), which aims to discover the direct binding targets (and off targets) of small molecules on a proteome scale without requiring chemical modification of the compound. Here, we review the DARTS method, discuss why it works, and provide new perspectives for future development in this area.