The pharmacology of a traditional African psychedelic plant medicine called ibogaine has led to the development of two new drug candidates for the potential treatment of addiction and depression. Taking inspiration from ibogaine’s impact on the serotonin transporter (SERT), which is also the target of SSRI antidepressants such as fluoxetine, scientists from University of California, San Francisco (UCSF), Yale, and Duke universities virtually screened 200 million molecular structures to find those that blocked SERT in the same way as did ibogaine. Their newly reported studies showed that at very low doses, the two new lead compounds blunted symptoms of both disorders in mice.
“Some people swear by ibogaine for treating addiction, but it isn’t a very good drug. It has bad side effects, and it’s not approved for use in the U.S.,” said Brian Shoichet, PhD, professor in the UCSF School of Pharmacy. “Our compounds mimic just one of ibogaine’s many pharmacological effects, and still replicate its most desirable effects on behavior, at least in mice.” Shoichet is co-senior author of the team’s published paper in Cell, titled “Structure-based discovery of conformationally selective inhibitors of the serotonin transporter.” In their report the authors stated, “In mouse behavioral assays, both compounds had anxiolytic- and antidepressant-like activity, with potencies up to 200-fold better than fluoxetine (Prozac), and one substantially reversed morphine withdrawal effects.”
The serotonin transporter (SERT, SLC6A4) is the target of drugs including antidepressants and psychostimulants, and competitive inhibitors selective for SERT are widely used therapeutically to treat clinical depression, the authors noted. Examples include fluoxetine, citalopram, and paroxetine. Cocaine is a less selective competitive inhibitor for SERT, which also blocks the closely related transporters for norepinephrine and dopamine (NET and DAT). “In addition, ibogaine and its metabolite noribogaine, are alkaloids that non-competitively inhibit SERT and DAT, but are much less selective, with an affinity for many receptors and channels,” the team continued.
Ibogaine is found in the roots of the iboga plant, which is native to central Africa, and has been used for millennia during shamanistic rituals. In the 19th and 20th centuries doctors in Europe and the U.S. experimented with its use in treating a variety of ailments, but the drug never gained widespread acceptance and was ultimately made illegal in many countries.
Part of the problem, Shoichet explained, is that ibogaine interferes with many aspects of human biology. “Ibogaine binds to hERG, which can cause heart arrhythmias, and from a scientific standpoint, it’s a ‘dirty’ drug, binding to lots of targets beyond SERT,” Shoichet said.
SERT adopts three conformations: outward-open, occluded, and inward-open, the team continued. All known inhibitors, except ibogaine, target the outward-open state. Unlike other SERT inhibitors, Ibogaine has unusual antidepressant and substance-withdrawal effects, and stabilizes the inward-open conformation of SERT. However, the investigators continued, “ibogaine’s promiscuity and cardiotoxicity limit the understanding of inward-open state ligands. “Before this experiment, we didn’t even know if the benefits of ibogaine came from its binding to SERT,” Shoichet noted.
For their studies reported in Cell, the researchers used Shoichet’s computational docking approach to identify small molecules that interacted with the inward-open state of SERT. Docking involves systematically testing virtual chemical structures for binding with a protein, enabling scientists to identify new drug leads without having to synthesize them in the lab. “We used the cryo-EM structure of SERT complexed with ibogaine in an inward-open conformation7 (PDB: 6DZZ) to computationally dock a library of over 200 million make-on-demand molecules,” the investigators explained. “From the docking against SERT, a diverse set of high-ranking compounds, physically complementing the inward-open state of SERT and topologically unrelated to previously known inhibitors, were prioritized for synthesis and biochemical testing.” The collective studies to demonstrate the potential real world utility of the compounds, involved dozens of scientists from the laboratories of Shoichet, Allan Basbaum, PhD, and Aashish Manglik, MD, PhD, (UCSF); Gary Rudnick, PhD, (Yale); and Bill Wetsel, PhD, (Duke).
Shoichet, who has used docking on brain receptors to identify drugs to treat depression and pain, became interested in SERT and ibogaine after Rudnick, an expert on SERT at Yale, spent a sabbatical in his lab. Singh picked up the project in 2018, hoping to turn the buzz around ibogaine into a better understanding of SERT.
For the Shoichet lab this was the first docking experiment on a transporter—a protein that moves molecules into and out of cells—rather than on a receptor. One round of docking whittled the virtual library from 200 million to just 49 molecules, 36 of which could be synthesized. Rudnick’s lab tested them and found that 13 inhibited SERT.
The team then held virtual-reality-guided “docking parties,” to help Singh prioritize five molecules for optimization. The two most potent SERT inhibitors were shared with Basbaum and Wetsel’s teams for rigorous testing on animal models of addiction, depression, and anxiety. “All of a sudden, they popped—that’s when these drugs looked a lot more potent than even paroxetine [Paxil],” Shoichet said. “The compounds were also selective for SERT, with little meaningful activity against well-known off-targets such as NET, DAT, and the serotonergic GPCRs, in contrast to the broad promiscuity of ibogaine,” the team wrote. “All of these compounds represent new chemotypes, topologically unrelated to known SERT inhibitors in the IUPHAR or ChEMBL databases.”
Manglik, an expert with cryo-electron microscopy (cryo-EM), confirmed that one of the two drugs, dubbed “8090,” fit into SERT at the atomic level in a way that closely resembled Singh and Shoichet’s computational predictions. The drugs inhibited SERT in a similar way to ibogaine, but unlike the psychedelic, their effect was potent and selective, with no spillover impacts on a panel of hundreds of other receptors and transporters. The authors noted, “In mouse behavioral assays, both compounds had anxiolytic- and antidepressant-like activity, with potencies up to 200-fold better than fluoxetine (Prozac), and one substantially reversed morphine withdrawal effects.”
“This is really the way science should be done,” Basbaum said. “We took a group with expertise in disparate fields and came up with something that might really make a difference … With this sort of potency, we hope to have a better therapeutic window without side effects. Dropping the dose almost 200-fold could make a big difference for patients. And as the authors noted, “As observed against other flexible targets, the new chemotypes conferred new in vitro activities that likely contributed to the unusually high efficacy of the new SERT inhibitors in animal models of depressive-like responses … the selectivity of the new SERT inhibitors versus off-targets like NET, DAT, and serotonergic GPCRs, and for a particular SERT conformational state, may make them useful as tool molecules to probe transporter function and therapeutic translation.”
“This kind of project begins with visualizing what kinds of molecules will fit into a protein, docking the library, optimizing, and then relying on a team to show the molecules work,” said Isha Singh, PhD, a co-first author of the paper who did the work as a postdoc in Shoichet’s lab. “Now we know there’s a lot of untapped therapeutic potential in targeting SERT.”
Shoichet has submitted the structures of both new molecules to Sigma Aldrich, aiming to make them available for further testing by other scientists, while he continues to hunt for more precise molecules. “ … we are making them openly available via the Millipore-Sigma probe collection,” the investigators noted in their paper.” With millions of patients continuing to suffer from depression or addiction, new prospective therapies are needed.
