Analogs of the Dopamine Metabolite 5,6-Dihydroxyindole Bind Directly to and Activate the Nuclear Receptor Nurr1.

The nuclear receptor-related 1 protein, Nurr1, is a transcription factor critical for the development and maintenance of dopamine-producing neurons in the substantia nigra pars compacta, a cell population that progressively loses the ability to make dopamine and degenerates in Parkinson's disease. Recently, we demonstrated that Nurr1 binds directly to and is regulated by the endogenous dopamine metabolite 5,6-dihydroxyindole (DHI). Unfortunately, DHI is an unstable compound, and thus a poor tool for studying Nurr1 function. Here, we report that 5-chloroindole, an unreactive analog of DHI, binds directly to the Nurr1 ligand binding domain with micromolar affinity and stimulates the activity of Nurr1, including the transcription of genes governing the synthesis and packaging of dopamine.

Covalent Modification and Regulation of the Nuclear Receptor Nurr1 by a Dopamine Metabolite.

Nurr1, a nuclear receptor essential for the development, maintenance, and survival of midbrain dopaminergic neurons, is a potential therapeutic target for Parkinson's disease, a neurological disorder characterized by the degeneration of these same neurons. Efforts to identify Nurr1 agonists have been hampered by the recognition that it lacks several classic regulatory elements of nuclear receptor function, including the canonical ligand-binding pocket. Here we report that the dopamine metabolite 5,6-dihydroxyindole (DHI) binds directly to and modulates the activity of Nurr1. Using biophysical assays and X-ray crystallography, we show that DHI binds to the ligand-binding domain within a non-canonical pocket, forming a covalent adduct with Cys566. In cultured cells and zebrafish, DHI stimulates Nurr1 activity, including the transcription of target genes underlying dopamine homeostasis. These findings suggest avenues for developing synthetic Nurr1 ligands to ameliorate the symptoms and progression of Parkinson's disease.

Development of 5N-Bicalutamide, a High-Affinity Reversible Covalent Antiandrogen.

Resistance to clinical antiandrogens has plagued the evolution of effective therapeutics for advanced prostate cancer. As with the first-line therapeutic bicalutamide (Casodex), resistance to newer antiandrogens (enzalutamide, ARN-509) develops quickly in patients, despite the fact that these drugs have ∼10-fold better affinity for the androgen receptor than bicalutamide. Improving affinity alone is often not sufficient to prevent resistance, and alternative strategies are needed to improve antiandrogen efficacy. Covalent and reversible covalent drugs are being used to thwart drug resistance in other contexts, and activated aryl nitriles are among the moieties being exploited for this purpose. We capitalized on the presence of an aryl nitrile in bicalutamide, and the existence of a native cysteine residue (Cys784) in the androgen receptor ligand binding pocket, to develop 5N-bicalutamide, a cysteine-reactive antiandrogen. 5N-bicalutamide exhibits a 150-fold improvement in Ki and 20-fold improvement in IC50 over the parent compound. We attribute the marked improvement in affinity and activity to the formation of a covalent adduct with Cys784, a residue that is not among the more than 160 androgen receptor point mutations associated with prostate cancer. Increasing the residence time of bound antiandrogen via formation of a covalent adduct may forestall the drug resistance seen with current clinical antiandrogens.

Disulfide-Trapping Identifies a New, Effective Chemical Probe for Activating the Nuclear Receptor Human LRH-1 (NR5A2).

Conventional efforts relying on high-throughput physical and virtual screening of large compound libraries have failed to yield high-efficiency chemical probes for many of the 48 human nuclear receptors. Here, we investigated whether disulfide-trapping, an approach new to nuclear receptors, would provide effective lead compounds targeting human liver receptor homolog 1 (hLRH-1, NR5A2). Despite the fact that hLRH-1 contains a large ligand binding pocket and binds phospholipids with high affinity, existing synthetic hLRH-1 ligands are of limited utility due to poor solubility, low efficacy or significant off-target effects. Using disulfide-trapping, we identified a lead compound that conjugates with remarkably high-efficiency to a native cysteine residue (Cys346) lining the hydrophobic cavity in the ligand binding domain of hLRH-1. Guided by computational modeling and cellular assays, the lead compound was elaborated into ligands PME8 and PME9 that bind hLRH-1 reversibly (no cysteine reactivity) and increase hLRH-1 activity in cells. When compared with the existing hLRH-1 synthetic agonist RJW100, both PME8 and PME9 showed comparable induction of the LRH-1 dependent target gene CYP24A1 in human HepG2 cells, beginning as early as 3 h after drug treatment. The induction is specific as siRNA-mediated knock-down of hLRH-1 renders both PME8 and PME9 ineffective. These data show that PME8 and PME9 are potent activators of hLRH-1 and suggest that with further development this lead series may yield useful chemical probes for manipulating LRH-1 activity in vivo.

Developing a photoreactive antagonist.

Light is an exquisite reagent for controlling the activity of biological systems, often offering improved temporal and spatial resolution over strictly genetic, biochemical, or pharmacological manipulations. This chapter describes a general approach for developing small molecules that, upon irradiation with light, may be used to rapidly inactivate targeted proteins expressed on the surfaces of cells. Highlighted is ANQX, a photoreactive AMPA receptor antagonist developed to irreversibly inactivate a subtype of glutamate-gated ion channels natively expressed on neurons.

Critical role of trkB receptors in reactive axonal sprouting and hyperexcitability after axonal injury.

Traumatic brain injury (TBI) causes many long-term neurological complications. Some of these conditions, such as posttraumatic epilepsy, are characterized by increased excitability that typically arises after a latent period lasting from months to years, suggesting that slow injury-induced processes are critical. We tested the hypothesis that trkB activation promotes delayed injury-induced hyperexcitability in part by promoting reactive axonal sprouting. We modeled penetrative TBI with transection of the Schaffer collateral pathway in knock-in mice having an introduced mutation in the trkB receptor (trkB(F616A)) that renders it susceptible to inhibition by the novel small molecule 1NMPP1. We observed that trkB activation was increased in area CA3 1 day after injury and that expression of a marker of axonal growth, GAP43, was increased 7 days after lesion. Extracellular field potentials in stratum pyramidale of area CA3 in acute slices from sham-operated and lesioned mice were normal in control saline. Abnormal bursts of population spikes were observed under conditions that were mildly proconvulsive but only in slices taken from mice lesioned 7-21 days earlier and not in slices from control mice. trkB activation, GAP43 upregulation, and hyperexcitability were diminished by systemic administration of 1NMPP1 for 7 days after the lesion. Synaptic transmission from area CA3 to area CA1 recovered 7 days after lesion in untreated mice but not in mice treated with 1NMPP1. We conclude that trkB receptor activation and reactive axonal sprouting are critical factors in injury-induced hyperexcitability and may contribute to the neurological complications of TBI.

Tuned-Affinity Bivalent Ligands for the Characterization of Opioid Receptor Heteromers.

Opioid receptors, including the mu and delta opioid receptors (MOR and DOR) are important targets for the treatment of pain. Although there is mounting evidence that these receptors form heteromers, the functional role of the MOR/DOR heteromer remains unresolved. We have designed and synthesized bivalent ligands as tools to elucidate the functional role of the MOR/DOR heteromer. Our ligands (L2 and L4) are comprised of a compound with low affinity at the DOR tethered to a compound with high affinity at the MOR, with the goal of producing ligands with "tuned affinity" at MOR/DOR heteromers compared to DOR homomers. Here we show that both L2 and L4 demonstrate enhanced affinity at MOR/DOR heteromers compared to DOR homomers, thereby providing unique pharmacological tools to dissect the role of the MOR/DOR heteromer in pain.

Bridging the gaps between synapses, circuits, and behavior.

The decade of the brain may have come and gone, but the final frontier, cracking the neuronal code, still lies ahead. Today, new technologies that allow precise spatiotemporal remote control over the activity of genetically defined populations of neurons within intact neural circuits are providing a means of obtaining a functional wiring diagram of the mammalian brain, bringing us one step closer to understanding precisely how neuronal activity codes for perception, thought, emotion, and action. These technologies and the design principles underlying them are reviewed herein.

Developing a complete pharmacology for AMPA receptors: a perspective on subtype-selective ligands.

AMPA receptors are a family of ligand-gated ion channels that play central roles in rapid neural signaling and in regulation of synaptic strength. Additionally, these receptors are implicated in a number of major psychiatric and neurological diseases. A comprehensive understanding of the roles that AMPA receptors play in the mammalian nervous system has been hampered by the dearth of ligands available to select between individual AMPA receptors subtypes. Here we provide a perspective on opportunities for developing a complete pharmacology for AMPA receptors.

AMPA receptors and synaptic plasticity: a chemist's perspective.

The ability of the mammalian brain to undergo experience-based adaptations is among its most important and fascinating properties. Such plasticity is reflected in the capacity of neuronal activity to continuously modify the neural circuitry that underlies thought, feeling and behavior. The locus of this plasticity occurs at the level of synapses, the specialized junctions where one neuron receives chemical signals from another. Synaptic connections become stronger or weaker in response to specific patterns of activity. This activity drives regulated changes in the neurotransmitter released by presynaptic neurons and in the receptors localized on postsynaptic neurons. Detailed studies of these receptors have advanced our understanding of synaptic plasticity. However, many key questions remain unresolved, and over the past decade innovative chemical approaches have emerged to tackle them. Here we review these chemical tools and their application to unraveling the molecular basis of synaptic plasticity.

TrkB signaling is required for both the induction and maintenance of tissue and nerve injury-induced persistent pain.

Activation of primary afferent nociceptors produces acute, short-lived pain, and tissue or nerve injury induces long-term enhancement of nociceptive processing, manifested as hypersensitivity to thermal and mechanical stimulation. Here we used a chemical-genetic and pharmacological approach to study the contribution of the receptor tyrosine kinase, type 2 (TrkB) to the generation and maintenance of injury-induced persistent pain. We performed the studies in wild-type mice and transgenic (TrkB(F616A)) mice that express mutant but fully functional TrkB receptors. By injecting a small molecule derivative of the protein kinase inhibitor protein phosphatase 1 (1NM-PP1), it is possible to produce highly selective inhibition of TrkB autophosphorylation in adult mice, without interfering with the activity of other protein kinases. We report that oral administration of 1NM-PP1, at doses that blocked phosphorylation of TrkB in the spinal cord, had no effect in behavioral tests of acute heat, mechanical, or chemical pain sensitivity. However, the same pretreatment with 1NM-PP1 prevented the development of tissue- or nerve injury-induced heat and mechanical hypersensitivity. Established hypersensitivity was transiently reversed by intraperitoneal injection of 1NM-PP1. Although interfering with TrkB signaling altered neither acute capsaicin nor formalin-induced pain behavior, the prolonged mechanical hypersensitivity produced by these chemical injuries was prevented by 1NM-PP1 inhibition of TrkB signaling. We conclude that TrkB signaling is not only an important contributor to the induction of heat and mechanical hypersensitivity produced by tissue or nerve injury but also to the persistence of the pain.

Mechanism and time course of cocaine-induced long-term potentiation in the ventral tegmental area.

Synaptic plasticity in the ventral tegmental area (VTA) has been implicated in the acquisition of a drug-dependent state. Even a single exposure to cocaine in naive animals is sufficient to trigger sustained changes on VTA glutamatergic synapses that resemble activity-dependent long-term potentiation (LTP) in other brain regions. However, an insight into its time course and mechanisms of action is limited. Here, we show that cocaine acts locally within the VTA to induce an LTP-like enhancement of AMPA receptor-mediated transmission that is not detectable minutes after drug exposure but is fully expressed within 3 h. This cocaine-induced LTP appears to be mediated via dopamine D(5) receptor activation of NMDA receptors and to require protein synthesis. Increased levels of high-conductance GluR1-containing AMPA receptors at synapses are evident at 3 h after cocaine exposure. Furthermore, our data suggest that cocaine-induced LTP might share the same molecular substrates for expression with activity-dependent LTP induced in the VTA by a spike-timing-dependent (STD) protocol, because we observed that STD LTP is significantly reduced or not inducible in VTA neurons previously exposed to cocaine in vivo or in vitro.

6-Azido-7-nitro-1,4-dihydroquinoxaline-2,3-dione (ANQX) forms an irreversible bond to the active site of the GluR2 AMPA receptor.

AMPA receptors mediate fast excitatory synaptic transmission and are essential for synaptic plasticity. ANQX, a photoreactive AMPA receptor antagonist, is an important biological probe used to irreversibly inactivate AMPA receptors. Here, using X-ray crystallography and mass spectroscopy, we report that ANQX forms two major products in the presence of the GluR2 AMPAR ligand-binding core (S1S2J). Upon photostimulation, ANQX reacts intramolecularly to form FQX or intermolecularly to form a covalent adduct with Glu705.

TrkB kinase is required for recovery, but not loss, of cortical responses following monocular deprivation.

Changes in visual cortical responses that are induced by monocular visual deprivation are a widely studied example of competitive, experience-dependent neural plasticity. It has been thought that the deprived-eye pathway will fail to compete against the open-eye pathway for limited amounts of brain-derived neurotrophic factor, which acts on TrkB and is needed to sustain effective synaptic connections. We tested this model by using a chemical-genetic approach in mice to inhibit TrkB kinase activity rapidly and specifically during the induction of cortical plasticity in vivo. Contrary to the model, TrkB kinase activity was not required for any of the effects of monocular deprivation. When the deprived eye was re-opened during the critical period, cortical responses to it recovered. This recovery was blocked by TrkB inhibition. These findings suggest a more conventional trophic role for TrkB signaling in the enhancement of responses or growth of new connections, rather than a role in competition.

Rapid photoinactivation of native AMPA receptors on live cells using ANQX.

AMPA (alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid) receptors, a major subtype of ionotropic glutamate receptors, mediate the majority of fast excitatory synaptic transmission in the mammalian brain. The constitutive and regulated trafficking of AMPA receptors into and out of excitatory synapses ensures rapid responses to synaptically released glutamate and provides a mechanism for synaptic plasticity. To permit the direct, quantitative, real-time measurement of native AMPA receptor trafficking in live neurons, we designed and utilized a membrane-impermeable, photoreactive AMPA receptor antagonist to rapidly and irreversibly inactivate surface receptors with ultraviolet (UV) light. The photoreactive antagonist, 6-azido-7-nitro-1,4-dihydroquinoxaline-2,3-dione (ANQX), is an aryl azide that, when irradiated with UV light, becomes a highly reactive nitrene that can covalently cross-link to and thus irreversibly antagonize bound AMPA receptors. Thus, ANQX provides a means of rapidly silencing surface-exposed AMPA receptors. Combined with a functional AMPA receptor assay, such as continuous recording of AMPA receptor-mediated ionic currents, ANQX provides a means of directly monitoring native AMPA receptor trafficking in real time.

Photoinactivation of native AMPA receptors reveals their real-time trafficking.

AMPA receptors mediate the majority of the fast excitatory transmission in the central nervous system. Much evidence suggests that the fast trafficking of AMPA receptors into and out of the postsynaptic membrane underlies changes in synaptic strength thought to be necessary for higher cognitive functions such as learning and memory. Despite the abundance of research conducted in this area, a direct, real-time functional assay that measures the trafficking of native AMPA receptors has been lacking. Toward this aim, we use a photoreactive, irreversible antagonist of AMPA receptors, ANQX, to rapidly silence surface AMPA receptors and investigate directly the trafficking of native AMPA receptors in real time. We find that the most dynamic movement of AMPA receptors occurs by lateral movement across the surface of neurons. Fast cycling of surface AMPA receptors with receptors from internal stores does occur but exclusively at extrasynaptic somatic sites. The cycling of synaptic AMPA receptors only occurs on a much longer timescale with complete exchange requiring at least 16 hr. This cycling is not dependent on protein synthesis or action potential driven network activity. These data suggest a revised model of AMPA receptor trafficking wherein a large internal store of AMPA receptors exchanges rapidly with extrasynaptic somatic AMPA receptors, and these newly inserted AMPA receptors then travel laterally along dendrites to reside stably at synapses.

A chemical-genetic approach to studying neurotrophin signaling.

Trk tyrosine kinases are receptors for members of the neurotrophin family and are crucial for growth and survival of specific populations of neurons. Yet, the functions of neurotrophin-Trk signaling in postnatal development as well as maintenance and plasticity of the adult nervous system are less clear. We report here the generation of mice harboring Trk knockin alleles that allow for pharmacological control of Trk kinase activity. Nanomolar concentrations of either 1NMPP1 or 1NaPP1, derivatives of the general kinase inhibitor PP1, inhibit NGF and BDNF signaling in TrkA(F592A) and TrkB(F616A) neurons, respectively, while no such Trk inhibition is observed in wild-type neurons. Moreover, oral administration of 1NMPP1 leads to specific inhibition of TrkA(F592A), TrkB(F616A), and TrkC(F167A) signaling in vivo. Thus, Trk knockin mice provide valuable tools for selective, rapid, and reversible inhibition of neurotrophin signaling in vitro and in vivo.

Photochemically knocking out glutamate receptors in vivo.

AMPA (alpha-amino-3-hydroxy-5-methyl-4-isooxazole) receptors, a major subtype of ionotropic glutamate receptors (iGluRs), mediate the majority of the fast communication between neurons, and the activity-dependent trafficking of AMPA receptors at synapses plays a role in mammalian learning and memory. Here we describe the design, synthesis, and evaluation of a photoreactive AMPA receptor antagonist that provides a means of "knocking out" AMPA receptors present on the surface of cells. The antagonist, 6-azido-7-nitro-1,4-dihydroquinoxaline-2,3-dione (ANQX), was designed by introducing a photoreactive azido group onto a quinoxalinedione inhibitor scaffold. Computational docking of ANQX to the AMPA receptor ligand-binding core predicted efficient binding to AMPA receptors. Glutamate-evoked currents were reversibly blocked at micromolar ANQX concentrations prior to photolysis and irreversibly blocked following photolysis. ANQX provides a means of directly evaluating the trafficking of native AMPA receptors with unparalleled spatiotemporal resolution.

Unnatural amino acid mutagenesis: a precise tool for probing protein structure and function.

The first general method for the biosynthetic incorporation of unnatural amino acids into proteins was reported in 1989. The ensuing years have seen the solid development and subsequent implementation of "unnatural amino acid mutagenesis" in a number of groundbreaking studies. Over 100 different amino acids have been incorporated into dozens of soluble and transmembrane proteins, using both cell-extract and cell-intact translation systems. The approach has provided insights into ligand-binding sites, conformational changes, and protein-protein interactions with a level of precision simply unparalleled by conventional mutagenesis. Here, the methodology is outlined, significant applications of the approach are summarized, and recent major improvements in the method are discussed. The future will likely see many more investigators utilizing this approach to manipulate proteins as it realizes its promise of becoming a tool with enormous potential.