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SfN 2013—New Tools for Rational Drug Design

See Allison Curley's snapshots from the conference.

January 28, 2014. On November 12, 2013, the penultimate morning of the Neuroscience 2013 conference in San Diego, Bryan Roth of the University of North Carolina, Chapel Hill, gave a special lecture titled, “How Synthetic and Chemical Biology Will Transform Neuroscience.” In actuality, it would be a talk on how team science can transform neuroscience, prefaced Roth, emphasizing that a great number of people have been involved in the work he would discuss.

Roth played a video of a young man experiencing florid hallucinations shortly after smoking the psychotomimetic drug salvinorin A, the main ingredient in the salvia plant. A member of the mint family, salvia has been used for centuries in the spiritual practices of the Mazatec people in Mexico, but more recently, salvinorin A has become a recreational drug that is marketed and sold as a legal alternative to marijuana. Throughout his talk, Roth used salvinorin A to illustrate the approach his group has taken to improve drug discovery. The salvinorin A story “is emblematic of a large field of drug discovery that’s currently ongoing … to create drugs that engage specific signaling pathways,” he said.

Scanning the receptor-ome
The plasma membrane is home to over 1,000 different flavors of receptors. In order to identify the specific molecular targets of salvinorin A, Roth and his team screened the compound against all known drug targets (collectively termed the receptor-ome). Using robotic screening and automated analysis of competition radioligand binding assays, this approach can screen hundreds of compounds against the known drug targets at once, an approach Roth noted was the opposite of the single-compound approach typically used by drug companies.

Using this high-throughput approach, Roth and colleagues found that salvinorin A selectively activates κ-opioid G protein-coupled receptors (GPCRs; see Roth et al., 2002). GPCRs represent the largest target class and comprise 4 percent of human DNA, making them “very good molecular targets,” said Roth. Functional studies revealed that salvinorin A is a very potent and selective κ-opioid receptor (KOR) agonist, with very rapid pharmacokinetics. It is quickly converted to the inactive salvinorin B, which explains why users only hallucinate for a short period of time. Surprisingly, salvinorin A showed no action on serotonin 5HT2A receptors, the predominant target of other hallucinogens.

In addition to characterizing compounds of unknown pharmacology, this approach has broader implications for drug discovery. The salvinorin A example suggests that opioid receptor antagonists could be useful for treating psychotic disorders such as schizophrenia and implicates these receptors in the modulation of perception.

Designing drugs and receptors
Next, Roth and his team turned to how salvinorin A engages with its target, KOR. Although it took over five years and many collaborations, he said, the crystal structure of all four opioid receptors was finally reported in 2012 (Wu et al., 2012), opening up the possibility for structure-based drug design.

KOR agonists are promising analgesics, but side effects such as hallucinations limit their clinical potential. Activation of a GPCR stimulates two different downstream pathways: the G protein second messenger system and signaling through β-arrestin. Some drug-dependent behaviors are mediated by G protein signaling, while others stem from β-arrestin’s effect, Roth said. He and colleagues have developed ligands that show a preference for one pathway over the other, and the hope is that this biased signaling can be harnessed to develop drugs that have only the desired effect(s) (see SRF related news report).

Roth’s graduate student Kate White explored the functional selectivity of KOR ligands in a poster she presented the following day. Using β-arrestin 2 knockout mice (that exclusively rely on G protein signaling), White has identified behaviors that seem to rely on one pathway versus the other. She has also identified biased KOR ligands in vitro, and in-vivo experiments with these tools are underway.

Drug design is complicated by the fact that ligands often act at more than one receptor type, many times leading to toxicity and side effects, said Roth. One way to get at this multi-target problem is the Similarity ensemble approach (SEA), which can be used to predict the off-target effects of drugs. Developed by Roth in collaboration with Brian Shoichet at the University of California, San Francisco, SEA is a computer-screening tool that relates targets by ligand similarity irrespective of protein sequence or structure (Keiser et al., 2007).

However, multiple targets aren’t always problematic, Roth continued, and may actually be helpful in many cases. With so many risk alleles linked to complex diseases such as schizophrenia (see SRF related conference report), treatment will require either combinations of medications or drugs that act at multiple targets. Roth developed an automated approach to create the latter that uses machine learning algorithms and large databases of pharmacological information to create novel drug-like compounds in silico (Besnard et al., 2012). By permitting the de novo, rational design of compounds, this approach removes a major roadblock to central nervous system drug discovery, he added.

To discover how salvinorin A’s profound effects on human consciousness are achieved, Roth harnessed the “awesome power of yeast genetics” to create a new technology: Designer Receptors Exclusively Activated by Designer Drugs (DREADDs). Like a chemical version of optogenetics, DREADDs are receptors that have been engineered to respond to the otherwise inert ligand clozapine-N-oxide. By adding this small molecule to animals’ food or water, researchers can control GPCR signaling and, therefore, neural activity. Complementary to optogenetics, this chemogenetic approach allows for longer lasting and broader effects, and provides researchers with another powerful tool with which to dissect neural signaling. DREADDs have spread like wildfire through the neuroscience research community for a wide variety of applications such as stimulating receptors in the cortex and hippocampus, and silencing neurons (including the parvalbumin-expressing ones of particular interest to the schizophrenia research community (see SRF related news report; SRF news report).

Together, predicted Roth, novel structural biology technologies and the non-invasive modulation of neuronal networks will, within the next several years, allow for any drug with a beneficial or harmful effect to be screened against all known druggable targets. This in turn could pave the way for safer and more effective drugs.—Allison A. Curley.

Comments on News and Primary Papers
Comment by:  Hugo Geerts
Submitted 29 January 2014
Posted 5 February 2014

Multi-target drug discovery has typically been neglected in the world of genetics and high-throughput screening because of the difficulty of rationally defining a pharmacological profile, but it has major advantages for treating complex disorders such as schizophrenia. It is no wonder that the currently approved antipsychotics do have a rich pharmacology and substantially improve the clinical phenotype. With so many different genotypes defining individual patients, focusing on only one target is likely to have small effects that might disappear in clinical trials with larger patient populations. Even over all indications (not only CNS), more than half of the first-in-class medicines approved in the last decade have been found by using phenotypic assays and have typically multi-target pharmacology (Swinney and Anthony, 2011).

The approach presented here suggests a rational way to identify 1) a set of targets and 2) chemical structures that might serve as hits for further medical chemistry development. It might therefore alleviate the concerns of many medical chemistry departments in pharmaceutical companies.

Changing the mindset from developing the next extremely specific and potent inhibitor to pursuing multi-target pharmacology is urgently needed to break the deadlock of unsuccessful new drug development in schizophrenia.


Swinney DC, Anthony J. How were new medicines discovered? Nat Rev Drug Discov . 2011 Jul ; 10(7):507-19. Abstract

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Comments on Related News

Related News: SfN 2013—Different Roads to Dopamine Dysfunction in Schizophrenia

Comment by:  Melkaye Melka
Submitted 5 December 2013
Posted 9 December 2013

Atypical antipsychotics have been used to treat psychiatric disorders such as schizophrenia. However, the mechanisms of action of antipsychotics remain poorly understood. On the other hand, dopamine neurons form the focus of attention in the etiology and pathophysiology of schizophrenia. As noted by Michele Solis’ snapshot from the conference, the work of Grace and colleagues showed that prenatal injections of methylazoxymethanol acetate (MAM), a DNA-methylating agent, lead to hyperactive dopamine signaling (Moore et al., 2006). Focusing on the mechanisms of action, previous studies have suggested that antipsychotic drugs may cause promoter methylation of genes involved in psychosis (Dong et al., 2009). DNA methylation changes have also been associated with major psychosis (Mill et al., 2008).

In a recent in-vivo study, we have observed organ-specific (hippocampus, cerebellum, and liver) changes in DNA methylation following a therapeutic dose of a model antipsychotic drug (olanzapine) (Melka et al., 2013, in press). In particular, we noted that the dopamine signaling pathway was one of the most significant networks affected by olanzapine-induced DNA methylation changes. Specifically, the results showed that olanzapine significantly alters promoter DNA methylation of genes involved in dopamine synthesis, transport, receptors, and metabolism. These results support a dopamine hypothesis of psychosis and a role for epigenetic mechanisms in the development of psychosis, as well as its treatment with antipsychotic drugs. Given that some of the genes affected are tissue specific and affect a variety of networks, our results could also explain the delayed therapeutic response of antipsychotics as well as their patient-specific efficacy and side effects.


Dong E, Grayson DR, Guidotti A, Costa E. Antipsychotic subtypes can be characterized by differences in their ability to modify GABAergic promoter methylation: Epigenomics 2009; 1: 201-1. Abstract

Melka MG, Castellani CA, Laufer BI, Rajakumar N, O’Reilly R and Singh SM. Olanzapine induced DNA methylation changes support the dopamine hypothesis of psychosis. J Mol Psychiatry; 2013; 1:19. (In press)

Mill J, Tang T, Kaminsky Z, Khare T, Yazdanpanah S, Bouchard L, Jia P, Assadzadeh A, Flanagan J, Schumacher A, Wang SC, Petronis A. Epigenomic profiling reveals DNA-methylation changes associated with major psychosis. Am J Hum Genet . 2008 Mar ; 82(3):696-711. Abstract

Moore H, Jentsch JD, Ghajarnia M, Geyer MA, Grace AA. A neurobehavioral systems analysis of adult rats exposed to methylazoxymethanol acetate on E17: implications for the neuropathology of schizophrenia. Biol Psychiatry . 2006 Aug 1 ; 60(3):253-64. Abstract

View all comments by Melkaye Melka