Art by Malia Kuo.
Have you ever wondered how scientists synthesize drugs? Everything, from the Advil you take to alleviate a headache to the Vitamin C gummies you eat to strengthen your immune system, needs to undergo rigorous scientific testing and scrutiny to ensure that it is safe for human consumption. The process of efficiently finding and synthesizing drugs is especially challenging for those treating specific medical maladies since the drug’s functional mechanism must be investigated. Drugs often function by targeting specific receptors in our bodies and either block the effects of the receptor’s typical function (antagonism) or activate the receptor to create a response (agonism).
The Challenge of Synthesizing Drugs
When synthesizing new drugs, researchers have a lot of metrics to satisfy and a lot of factors to consider. First, the specificity and favorability of the drug to the drug target: are the pieces of the receptor and drug compatible, and is there a possibility for off-target binding? Second, the size of the drug: will its molecular weight hinder its ability to get where it needs to be in the body? Third, the molecular kinetics of the drug: how many of the bonds are rotatable, and how stable and likely is the conformation it takes on to bind the receptor? It’s no secret that designing a drug that is specific, effective, and safe is no easy task: it’s why the research and development process, not to mention the process of clinical trials and safety testing, is so long and arduous.
But recently, in a collaboration between the Ellman Lab at Yale University, the Irwin and Shoichet Labs at the University of California San Francisco, the Wetsel Lab at Duke University, the Skiniotis Lab at Stanford University, and the Roth Lab at the University of North Carolina, researchers have been able to use a novel virtual screening technique to streamline the beginning stages of drug discovery by finding promising molecules that bind potently and selectively to the 5-HT2A receptor. This receptor is a serotonin receptor involved in producing both the negative (hallucinations, delusions) and positive effects (alleviation of anxiety, depression) of the psychedelic drug lysergic acid diethylamide (LSD) and its affiliates in the brain.
The virtual screening process started with a broad analysis of the commonalities between the chemical structures of a variety of FDA-approved drugs. Researchers found that the most often-observed structures included the six-membered nitrogen heterocycles piperidine and pyridine. Thus, they began looking into using a virtual library technique to create a tetrahydropyridine (THP) drug, a much less investigated subclass of the kinds of structural molecules described above. This structure also produces some obstacles for synthesis, which made it an interesting candidate for virtual screening and analysis of molecular docking and binding.
Creating a Database of THP Molecules
Using the THP structure as a foundation, the researchers created a database of 75 million THP molecules. The contents of this database were limited to synthetic chemistry techniques available to the Ellman Lab using three different types of starting materials: an amine, enal/enone, and alkyne. The researchers also implemented a molecular weight limit of 350 grams per mole to increase the likelihood that the compounds would have effective delivery in animals. They also considered a cationic property of the molecule that would help the molecule competitively bind to G-coupled protein receptors such as the 5-HT2A receptor, as well as eliminate chiral starting materials that would have resulted in mixtures of THPs with different three-dimensional structures, for a simplified single-conformation output.
Narrowing Down the Search
These 75 million THP molecules were then pared down using computational molecular binding techniques. Since the structure of the 5-HT2A receptor was unknown, the researchers composed one thousand models of the receptor bound to LSD in the hopes of analyzing the dynamics of the binding and finding a competitive molecule. Using this refined structure of the 5-HT2A receptor, the binding of the 75 million THP molecules was evaluated, and thirty molecules were selected as most likely to bind to the receptor. From the thirty molecules, seventeen molecules were able to be synthesized using commercially available materials. Four of these molecules were identified to bind to 5HT2A receptors, and two of these molecules exceeded preset binding thresholds in testing. Based upon the initial THPs that bound to the receptor, the team then designed, synthesized, and tested numerous additional analogs to obtain compounds that were potent and selective 5-HT2A receptor agonists.
“While you can dock to predict binding, at this stage, you cannot predict if a compound is going to be an agonist or an antagonist. Virtual screening is just a foot in the door; afterwards, you really need chemistry for synthesizing a lot of compounds, testing a lot of compounds, critical analysis of data, and many iterations,” said Jonathan Ellman, principal investigator of the Ellman Lab.
The 5-HT2A receptor can undergo two different pathways once activated. The first is the beta arrestin pathway, which has been linked to undesired psychedelic effects, and the second is the G-protein mediated pathway. “Our molecules are more biased towards the G-protein mediated pathway, and we didn’t see the psychedelic effects,” James Kweon, one of the lead researchers from the Ellman group, explained. While it’s very hard to predict just by looking at a chemical structure which signaling pathway will be favored, the molecules synthesized by the Ellman Lab are able to bias the receptor towards the G-protein mediated pathway rather than the beta arrestin pathway, which can then separate the psychedelic function of the receptor from the antidepressant function.
Looking Into the Future
The next steps for the Ellman Lab and their collaborators include using the same virtual screening approach to find more complex molecules to selectively target a new receptor: this time, a pain receptor that is targeted by opioid drugs such as morphine. They hope to separate the harsh respiratory distress associated with opioid use by synthesizing a molecule with great functional selectivity that can separate these negative effects from the pain-relieving positive effects.
“We’re basically trying to demonstrate that virtual screening really can be used as a tool for even more complex molecules,” Kweon said.
The kinds of molecules they’re synthesizing have a three-dimensional component which opens up more complex levels of docking analysis and will show that the technique of virtual screening is capable of taking on complex problems and solutions. Given its efficacy in successfully finding possible drug molecules fast, it’s likely this virtual screening technique will become increasingly important for the discovery of new drugs.