Scientists at Johns Hopkins School of Medicine set out to systematically map protein-DNA interactions across the human genome using a combination of bioinformatics and a protein-microarray strategy. Their exploration of the protein-DNA interactome identified over 17,000 interactions between 460 DNA sequences predicted to regulate transcription and 4191 proteins of varied functional classes. As well as finding known transcription factors (TFs), the work uncovered a large number of previously uncharacterised TFs. Of the unconventional DNA-binding proteins, over 300 exhibited sequence-specific DNA-binding.

One example of the sequence-specific DNA binders identified was ERK2 (MAP kinase-1), a serine/threonine kinase involved in cellular signalling. The Johns Hopkins team found that ERK2 is a transcriptional repressor of interferon-γ inducible genes and that this function is independent of its catalytic kinase activity. Whilst ERK2 has been extensively studied because of its importance in regulation of cellular proliferation, this unexpected additional role of ERK2 adds another level of complexity. Knowledge of the transcriptional repressor function may shed new light on knock-out experiments with ERK2.

The study, published in the journal Cell, examined only a fraction of the human proteome, raising the possibility that there may be thousands of proteins that also function as transcription factors. Certainly something else to consider in drug discovery when your enzyme inhibitor doesn’t do the same as the knockout!

Neurotrophins – a family of proteins essential for the development, survival and function of neurons – exert their actions through two classes of receptor, Trk tyrosine kinase receptors and p75NTR. There has been considerable interest in using neurotrophins such as nerve growth factor (NGF) for the treatment of neuronal damage as well as for conditions such as stress and depression, but the use of NGF itself has been limited by poor CNS penetration and side effects such as hyperalgesia. This has led to a search for stable small molecules with neurotrophic activity and specificity for TrkA or TrkB receptors although, so far, none of the mimetics can fully reproduce the effects of NGF in animals.

Writing in the journal Chemistry & Biology, researchers at Emory University School of Medicine have now shown that the tricyclic antidepressant, amitriptyline, which had been thought to act predominantly by blocking serotonin and noradrenaline transporters, interacts directly with the extracellular domain of both TrkA and TrkB receptors. Amitriptyline induced TrkA and TrkB homo- and heterodimerization and activation in mouse brain, but heterodimerization was found not to be required for Trk receptor activation. Truncation of the amitriptyline binding motif on TrkA, but not the corresponding region on TrkB, abolished the receptor homo- and heterodimerization. Amitriptyline, but not other tricyclic antidepressants or selective serotonin reuptake inhibitors, promoted TrkA autophosphorylation in primary neurons and induced neurite outgrowth in PC12 cells. In mice, amitriptyline was further shown to suppress neuronal apoptosis caused by the neuroexitotoxin, kainic acid, in a TrkA-dependent manner. Inhibition of TrkA, but not TrkB, abolished the neuroprotective effect of amitriptyline without affecting its antidepressant activity.

Amitriptyline was found to bind to a motif in the first leucine-rich motif of the extracellular domain of the TrkA receptor with a Kd of 3 µM, which approximates to the brain concentration achieved when used to treat depression or neuropathic pain. Although significantly lower than the affinity of NGF for TrkA, it suggests that amitriptyline affinity for TrkA might be sufficient to explain at least some of its biological activity.

Schistosomiasis is caused by infection with one of several species of parasitic worms and, although not usually fatal, is considered to be the second only to malaria in terms of human impact. Infection with the parasite typically occurs when wading, swimming or washing in water containing fresh water snails, the intermediate host for the parasite.

Although many countries are working to eradicate the disease by drug treatment, snail control, education and improved sanitation, the disease remains endemic in more than 70 countries and is estimated to affect around 200 million people worldwide. Schistosomiasis is readily treated with praziquantel but, despite being the mainstay of treatment for several decades, the mechanism of action of praziquantel is still debated. Writing in the journal PLoS Neglected Tropical Diseases, researchers at University of Minnesota Medical School have now shown how praziquantel kills a species of free-living flatworm that is often used as a model organism. These worms have remarkable regenerative properties and are able to reform a complete body from even a small fragment. Praziquantel was found to cause aberrant regeneration, producing two-headed organisms with duplicated, integrated central nervous systems and organs. The team further showed that voltage-operated calcium channel (VOCC) β subunits are important for the activity of praziquantel, supporting an earlier hypothesis about its mechanism of action.

The authors hope that elucidation of the mechanism of praziquantel toxicity – albeit in a free-living flatworm species – will help in the rational design of new antischistosomal drugs.

The immunomodulator, FTY720 (fingolimod) is currently undergoing phase III clinical trials for the treatment of relapsing-remitting multiple sclerosis. FTY720 is a prodrug that, once phosphorylated to FTY720-P, is believed to act primarily by targeting sphingosine-1-phosphate (S1P) receptors on lymphocytes and endothelial cells. This leads to retention of lymphocytes in lymph nodes that, in turn, prevents attacks on myelin sheaths.

Although FTY720-P is a potent agonist of several S1P receptors, its beneficial effects in multiple sclerosis are believed to be mediated primarily through the S1P1 receptor. Because specific knockout of the S1P1 receptor on haematopoietic cells in mice and treatment with FTY720 show similar effects on lymphocyte recirculation, the efficacy of FTY720-P has been attributed to ‘functional antagonism’ leading to complete internalisation and desensitisation of receptors. However, writing in the journal Nature Chemical Biology, scientists at Novartis now provide evidence that, despite internalisation, signalling by S1P1 receptors bound to FTY720-P persists for hours. Although calcium signalling – which depends on cell surface localisation of the receptor – was inhibited by treatment with FTY720, other signalling pathways remained activated. In both stably transfected and primary cell lines, persistent activation of S1P1 receptors by FTY720 led to prolonged inhibition of adenylate cyclase and increased ERK phosphorylation. Similar effects were not observed with the endogenous agonist, S1P, and by exploring analogues of FTY-720, the length of the aliphatic side chain was found to be crucially important for persistent signalling and receptor internalisation.

Shortening the lipophilic side chain by one methylene group decreased the effect and shortening by two methylene groups abolished the effect completely, despite all three compounds having similar intrinsic potencies. The ability of the S1P1 antagonist, WN146 – which does not itself induce lymphocyte sequestration – to inhibit prolonged S1P1 signalling caused by treatment with FTY720-P suggests that direct agonism rather than functional antagonism may be the predominant mechanism of action of FTY720-P.

As well as being used as a spice to add flavour and colour to a variety of dishes, turmeric has long been valued in parts of Asia for its medicinal properties. Although turmeric has been used for centuries as an antiseptic and has been claimed to be effective in a wide range of conditions including autoimmune diseases, heart disease, Alzheimer’s disease and cancer, it is only recently that scientists have begun to explore its properties in detail.

Curcumin, a molecule with a broad spectrum of antioxidant and anti-inflammatory properties, has been identified as the main active ingredient of turmeric and scientists at the University of Michigan have now described how curcumin acts in the body. Instead of interacting directly with numerous unrelated membrane proteins, the team found that curcumin regulates the action of membrane proteins indirectly by changing the physical properties of the bilayer.

Writing in the Journal of the American Chemical Society, the researchers describe in detail how curcumin inserts deep into the membrane in a transbilayer orientation, anchored by hydrogen bonds to the phosphate groups of lipids. The insertion into the membrane is similar to that seen with cholesterol and, like cholesterol, curcumin induces segmental ordering in the membrane. Using a combination of solid-state NMR and differential scanning calorimetry experiments, the team showed that curcumin has a strong effect on membrane structure even at low concentrations. The team plan to use similar experiments to explore the action of other drugs, such as capsaicin, which also interact with membranes.

Bacterial resistance – often arising as a result of over, or inappropriate, use of antibiotics – is a major obstacle to the treatment of many bacterial infections. Recently, interference with quorum sensing has emerged as a strategy for the development of new antibiotics which minimises the evolution of drug-resistant strains. Quorum sensing is a process used by bacteria to coordinate gene expression according to local population densities. The bacteria secrete signalling molecules, known as autoinducers, and have receptors that specifically recognize the signalling molecules released by other bacteria of the same or different species. Bacterial cell density and concentration of autoinducers control factors such as expression of virulence factors, pathogenicity and biofilm formation.

Writing in the journal Nature Chemical Biology, researchers from Albert Einstein College of Medicine of Yeshiva University have recently described the effectiveness of 5′-methylthioadenosine/S-adenosylhomocysteine nucleosidase (MTAN) inhibitors against Vibrio cholera and Escherichia coli O157:H7. MTAN plays a key role in the synthesis of autoinducers essential for bacterial quorum sensing and the absence of the nucleosidase in mammals suggests that it is likely to be an attractive target for antimicrobial drug design. Three transition state analogue inhibitors of MTAN were found to be highly potent at blocking quorum sensing, bacterial virulence and biofilm formation. Importantly, the effect persisted for several generations.

See also this earlier article on quorum sensing.

Peroxisome proliferator-activated receptors (PPARs) are nuclear receptors that play essential roles in the regulation of cellular differentiation, development and metabolism. Since the introduction of the thiazolidinedione class of PPAR-γ activators in the late 1990s to treat type 2 diabetes, the use of PPAR-γ ligands to treat other conditions, including cancer, has been investigated. Researchers at the Mayo Clinic discovered that human anaplastic thyroid tumour cells treated with the PPAR-γ activator, RS5444, express a protein known as p21 that inhibits cell replication and suppresses tumour growth, but the underlying mechanism was not understood.

The group has now shown that activation of PPAR-γ with RS5444 (also known as CS-7017) turns on the RhoB tumor suppressor gene, which in turn induces p21 expression, thereby shutting down the cell cycle and blocking tumour growth. The researchers say that it is unusual for a cancer drug to be able to cause re-expression of a suppressed gene in this way, and hope that other cancers in which RhoB is deactivated, such as head and neck, brain, and lung cancers, might respond to RS5444 or to similar drugs. RS5444 is undergoing phase I/II clinical trials (in combination with paclitaxel) in patients with anaplastic thyroid cancer and phase II trials (in combination with carboplatin/paclitaxel) in patients with metastatic non-small cell lung cancer.

A new study describes a high affinity interaction between siramesine and phosphatidic acid, a component of cell membranes that also acts as a signalling molecule. Siramesine is a sigma receptor agonist, selective for the σ2 subtype, which was originally under development for the treatment of anxiety but failed to show efficacy in clinical trials.

Siramesine was subsequently shown to kill cancer cells by destabilising their lysosomes. Vincristine, a microtubule destabilising antimitotic drug, which is used in various chemotherapy regimens, greatly sensitised cancer cells to the cytotoxic effects of siramesine.

The new study suggests that it may be possible to design small molecules to specifically scavenge phospholipids involved in the signalling cascades controlling cell survival.

It has been estimated that as many as 50 million people worldwide suffer from schizophrenia and many of these will be treated with antipsychotic medicines. The so-called typical antipsychotics have been available since the mid-1950s and a number of newer agents, the atypical antipsychotics, have been introduced since 1990. Increased dopaminergic activity is thought to be a contributory factor in schizophrenia and all of the antipsychotic medicines interact with the dopamine D2 receptor although they have different affinities and modulate the receptor in different ways.

A new study has shown that, regardless of their effect on G-protein coupled signalling via the D2 receptor, antipsychotic drugs potently antagonize the dopamine-mediated interaction of the D2 receptor with β-arrestin-2.

Arrestins are proteins that were initially found to regulate signal transduction by silencing GPCRs, although they have recently been shown to directly activate signalling pathways. The new results suggest that selective targeting of the interaction of D2 with β-arrestin-2 may provide a new opportunity for the development of antipsychotic medicines. More generally, targeting β-arrestin signalling pathways may open opportunities in other therapeutic areas.