Extended Reality Helps Drug Designers Realize Bold Visions

Drug designers can interact with their creations by using 3D modeling tools that integrate virtual and augmented reality

If a picture is worth 1,000 words, a 3D model of a new drug candidate is worth far more. After all, such a model can help the drug candidate’s designers make sense of their voluminous data—which typically represents a sizable investment. When this data is “seen,” it can generate a return on investment by improving decision-making processes. For example, it can reveal imperfections in a drug’s design and prompt revisions that can prevent costly clinical failures.

A 3D model can be especially useful if it is produced with extended reality (XR) technology, suggests Nanome, an XR software company. XR, which encapsulates artificial reality (AR) and virtual reality (VR), enables drug designers to actually walk around and manipulate the molecules they create.

Two people using Nanome's virtual and augmented reality software
Nanome, a virtual and augmented reality software company, offers an immersive real-time collaboration platform that allows users to build and reach inside molecular models.

“Spatial computing technologies can enable scientists everywhere to have more of a real human interaction with a structure,” says Sam Hessenauer, Nanome’s co-founder and CTO. “With our XR platform, users can see and manipulate molecules in real time using voice or keyboard commands. They can wire the molecule to simulation and informatics tools to map the data onto structures and collaborate on design ideas.”

Accommodating plug-ins

Nanome offers more than a dozen out-of-the-box plug-ins that let users see chemical interactions. For example, last year, in 2023, Nanome introduced the CyroEM plug-in for the Nanome XR platform to help scientists view and manipulate cryogenic electron microscopy. According to Hessenauer, it lets users “visualize many of the newer innovations around the atomic coordinates of larger biological systems, like those involving multiple proteins, and enhance human understanding of their structural biology.”

“The fact that you can have plug-ins is super-powerful in and of itself,” adds Keita Funakawa, Nanome’s co-founder and COO. Users can develop their own plug-ins, such as custom database, real-time atom scoring, docking algorithm, or molecular simulation plug-ins. Indeed, users can incorporate their own proprietary tools into the Nanome XR platform.

Introducing MARA

Near the end of the year, Nanome introduced MARA, a molecular analysis and reasoning assistant for AI-assisted scientific informatics. It is built around large language models to augment scientific reasoning, perform advanced multistep informatics tasks, and dynamically handle intermediary data schemas.

MARA reflects a plug-and-play approach that may encompass users’ own back-end computational tools. Hessenauer expects that this approach will help scientists address more advanced data science challenges.

MARA democratizes molecular design. “Every chemist, scientist, or biologist in the organization can leverage internal expertise that typically has been limited to a handful of people,” Hessenauer says. “Language models are great micro-reasoning engines. They can amplify the capabilities of automation, and when we direct that toward informatics, scientists can ask more hypothesis-oriented questions of a computer system that orchestrates workflows, data retrieval, and calculations.”

Helping pharma innovate

Nanome’s technology is applicable to many specialties within biologics development and chemical engineering. Initially, the company is focusing on enterprise pharmaceutical companies to help them leverage their existing data and tools infrastructure. “They’re ripe for innovation,” Hessenauer observes.

Nanome’s XR platform is already being used by top-tier biopharma organizations. Novartis, for example, uses Nanome to help scientists work together virtually, across sites and disciplines. By stepping into the VR world to design or analyze a 3D molecule, biologists, chemists, and managers have the same frame of reference. “With VR,” Funakawa says, “they can get on the same page much quicker and make critical decisions much faster.”

During the pandemic, researchers at Oak Ridge National Laboratory combined VR and neutron crystallography to design accurate, highly detailed, models of the SARS-CoV-2 main protease, and then to test novel compounds against it.

Designing a better way

Social activities—notably rugby matches and film festivals at University of California, San Diego—brought Nanome’s four co-founders together. (Besides Hessenaur and Funakawa, Nanome’s co-founders are Steven McCloskey and Edgardo Leija, the company’s CEO and CXO, respectively.)

“We were learning chemistry and engineering from textbooks and blackboards,” Funakawa recalls, “but we had video games with graphics that were way better.” The desire to explore, analyze, and design molecular systems in a video game–like environment provided a core vision that transformed the four from friends to entrepreneurs.

“Steve bought the first Oculus Kickstarter [developer model] that came out,” Hessenauer notes. Tinkering commenced. Gradually, the entrepreneurs’ video game–inspired vision led to product iterations that merited inclusion in the National Science Foundation’s Innovation Corps (I-Corps), a program in which the scientific method is used to build viable businesses.

Each product iteration was succeeded by interviews with multiple scientists to identify strengths and weaknesses for the next iteration. “We encountered a lot of different scientists,” Funakawa says. “One was trying to visualize X-ray crystallography in three dimensions, using a mouse and computer screen. That pain point illustrated the need for the platform the team was developing. Things snowballed from there.”

Having Novartis literally across the street helped, too. “We started our collaboration with them in 2017,” Funakawa says. “That was a pivotal point for our company because we met biweekly and got in-depth feedback.”

In those days, the challenges revolved around constraints imposed by the hardware of the times. Virtual reality headsets weren’t available off the shelf, and VR software lacked external sensors, robust graphics cards, and high-end desktop computers. “Now, all that’s in the headset,” Funakawa points out.

Preparing for what’s next

Today, one of the key hurdles is simply to overcome the wait-and-see mindset that is common when introducing new technology into regulated industries. While some scientists and executives instinctively see the advantages of XR-enabled drug design, others are more hesitant. “It’s like when iPhones first came out and organizations had to determine how to integrate them into their operations,” Hessenauer says.

There’s also a bit of training required in terms of how to function in a virtual environment. “Nonetheless, in every pharmaceutical company we interact with, someone owns a headset and generally knows the technology,” Hessenauer remarks. “So, it’s getting easier.”

As XR becomes more mainstream, there’s also a tendency to delay adoption in favor of the next big hardware advancement. Nanome encourages scientific teams to achieve proof of concept with existing headsets rather than risk falling behind the technology curve, and to plan a broader rollout with the next iteration of headset.

Another challenge is price. “High-quality scientific XR technology is expensive to develop,” Funakawa notes, “Biopharmaceutical companies may easily underestimate the expense of deploying such systems.” He adds, however, that this expense seems less daunting when it is seen as an investment that offers a substantial return: “For the tech-forward-thinking folks we’ve talked to, it’s a no-brainer.”

As Nanome matures, it is building a platform around XR to enable scientists not just to walk around a 3D model, but to access analytics and workflows in new ways. “We’re passionate about realizing a cohesive vision and building the next, ultimate interface,” Funakawa declares.