A new method is changing the way we think about molecule design, bringing us closer to the possibility of using large language models (LLMs) to streamline the creation of new medicines and materials. Imagine asking, in plain language, for a molecule with specific properties, and receiving a comprehensive plan on how to synthesize it. This futuristic vision is now within reach, thanks to a collaboration between researchers from MIT and the MIT-IBM Watson AI Lab.

A New era in molecular discovery

Traditionally, discovering the right molecules for medicines and materials has been a slow and resource-intensive process. It often involves the use of vast computational power and months of painstaking work to explore the nearly infinite pool of potential molecular candidates. However, this new method, blending LLMs with other machine-learning models known as graph-based models, offers a promising solution to speed up this process.

These researchers have developed an innovative system that augments an LLM with graph-based AI models, designed specifically to handle molecular structures. The approach allows users to input natural language queries specifying the desired molecular properties, and in return, the system provides not only a molecular design but also a step-by-step synthesis plan.

LLMs and graph models

LLMs like ChatGPT have revolutionized the way we interact with text, but they face challenges when it comes to molecular design. Molecules are graph structures—composed of atoms and bonds—which makes them fundamentally different from text. LLMs typically process text as a sequence of words, but molecules do not follow a linear structure. This discrepancy has made it difficult for LLMs to understand and predict molecular configurations in the same way they handle sentences.

To bridge this gap, MIT’s researchers created Llamole—a system that uses LLMs to interpret user queries and then switches between different graph-based AI modules to generate molecular structures, explain their rationale, and devise a synthesis strategy. The system combines the power of text, graphs, and synthesis steps into a unified workflow.

As a result, this multimodal approach drastically improves performance. Llamole was able to generate molecules that were far better at meeting user specifications and more likely to have a viable synthesis plan, increasing the success rate from 5 percent to 35 percent.

Llamole’s success lies in its unique ability to seamlessly combine language processing with graph-based molecular modeling. For example, if a user requests a molecule with specific traits—such as one that can penetrate the blood-brain barrier and inhibit HIV—the LLM interprets the plain-language request and switches to a graph module to generate the appropriate molecular structure.

This switch occurs through the use of a new type of trigger token, allowing the LLM to activate specific modules as needed. The process unfolds in stages: the LLM first predicts the molecular structure, then uses a graph neural network to encode the structure, and finally, a retrosynthetic module predicts the necessary steps to synthesize the molecule. The seamless flow between these stages ensures that the LLM maintains an understanding of what each module does, further enhancing its predictive accuracy.

“The beauty of this is that everything the LLM generates before activating a particular module gets fed into that module itself. The module is learning to operate in a way that is consistent with what came before,” says Michael Sun, an MIT graduate student and co-author of the study.

Simplicity meets precision

One of the most striking aspects of this new method is its ability to generate simpler, more cost-effective molecular structures. In tests, Llamole outperformed other LLM-based methods and achieved a notable 35 percent success rate in retrosynthetic planning, up from a mere 5 percent with traditional approaches. “On their own, LLMs struggle to figure out how to synthesize molecules because it requires a lot of multistep planning. Our method can generate better molecular structures that are also easier to synthesize,” says Gang Liu, the study’s lead author.

By designing molecules with simpler structures and more accessible building blocks, Llamole could significantly reduce the time and cost involved in developing new compounds.

The road ahead

Though Llamole’s current capabilities are impressive, there is still work to be done. The researchers built two custom datasets to train Llamole, but these datasets focus on only 10 molecular properties. Moving forward, they hope to expand Llamole’s capabilities to design molecules based on a broader range of properties and improve the system’s retrosynthetic planning success rate.

In the long run, the team envisions Llamole serving as a foundation for broader applications beyond molecular design. “Llamole demonstrates the feasibility of using large language models as an interface to complex data beyond textual description, and we anticipate them to be a foundation that interacts with other AI algorithms to solve any graph problems,” says Jie Chen, a senior researcher at MIT-IBM Watson AI Lab.

With further refinements, Llamole could revolutionize fields from pharmaceuticals to material science, offering a glimpse into the future of AI-driven innovation in molecular discovery.

The University of the Free State (UFS) and the Free State Department of Health are not just introducing new technology, but embarking on a journey that will revolutionize surgery and patient care in the region. This is the message delivered by MaQueen Letsoha-Mathae, Premier of the Free State, during the official launch of the Versius Surgical Robotic System on 11 March 2025 at the UFS Faculty of Health Sciences. The Free State is now the first region in Southern Africa to implement this technology, having successfully completed nine robotic-assisted surgeries at Universitas Academic Hospital within the last month.

The successful procedures, which took place between 24 February and 6 March, included complex surgeries such as radical prostatectomies and cholecystectomies, demonstrating the Versius system’s potential to improve patient outcomes. Prof Freddie Claassen, Academic Head of the Department of Urology at UFS and Universitas Hospital, was among the first surgeons from the university to be trained on the system and use it in operations.

A Significant Milestone

“This moment marks a significant milestone not only for our beloved Free State, but for the entire health-care landscape in Southern Africa. We are not merely launching a new technology; we are embarking on a journey that will transform the future of surgery and patient care in our province and beyond,” said Letsoha-Mathae.

She emphasized that the introduction of the Versius Surgical Robotic System aligns with the Free State’s vision to become a hub of healthcare innovation and excellence in Southern Africa. “With this groundbreaking system, we are not only enhancing surgical precision, but also significantly improving patient outcomes,” Letsoha-Mathae added.

The Versius Surgical Robotic System is known for its versatility and adaptability, seamlessly integrating into any operating room. It can be used in high-specialty procedures, including thoracic, colorectal, general and upper gastrointestinal, hernia, gynaecology, and urology surgeries.

Prof Hester C. Klopper, Vice-Chancellor and Principal of UFS, reflected on the role of the university in shaping the future of healthcare. “This moment is not just a technological milestone, but a symbol of what we can achieve as an institution when we unite academic excellence, visionary leadership, and a commitment to community impact with partners in the private sector and government,” she said.

She stressed that the launch reaffirms UFS’s ongoing dedication to academic excellence, technological innovation, and societal impact, while addressing some of the most pressing healthcare challenges both regionally and globally. “Versius is an investment in the well-being of our communities and an essential step towards bridging the healthcare gap in our region,” said Prof Klopper.

Enhancing Surgical Precision

Prof Vasu Reddy, Deputy Vice-Chancellor of Research and Internationalisation at UFS, explained the significant benefits of robotic-assisted surgeries. “Robots such as the Versius system are tools that enhance the senses and skills of surgeons during delicate operations. Unlike traditional surgery, which requires large incisions, robotic surgery enables doctors to perform operations with smaller cuts, reduced pain, and less scarring,” he said.

Robotic surgery improves surgical outcomes by allowing for greater precision, accuracy, and reduced chances of complications. “The robots do not tire, they do not lose focus, and they can handle repetitive tasks with ease, making the entire process safer for patients,” Prof Reddy continued. He further highlighted the role of AI and robotics in healthcare, emphasizing that human innovation and machine precision together can elevate the standard of care.

According to Premier Letsoha-Mathae, the Versius Surgical Robotic System represents a significant leap towards enhancing healthcare delivery in Southern Africa. “The benefits of Versius are profound: patients will experience quicker recoveries and an earlier return to work, ultimately leading to a healthier, more productive society,” she said.

The system’s modular and scalable design ensures that it can be integrated into operating rooms with minimal infrastructure changes, making it accessible across both private and state healthcare sectors. This adaptability promises to expand access to robotic-assisted surgery, helping to bridge the gap in healthcare delivery.

Through the collaboration between the Department of Health and UFS, the launch of the Versius Surgical Robotic System is a testament to the shared commitment to addressing regional and global healthcare challenges. It also underscores the importance of continuing innovation and academic excellence in advancing healthcare technology and patient care.

A new study by researchers at the Rajiv Gandhi Centre for Biotechnology (RGCB), Kerala, India, has revealed a crucial connection between mRNA processing and oxidative stress response, shedding light on a condition that plays a pivotal role in the development of various diseases, including cancer, cardiovascular disorders, neurological diseases, and diabetes, as well as aging. The research emphasizes the critical impact of oxidative stress, particularly in the heart, which contributes to several health conditions such as hypertension, heart failure, hypoxia, ischemia-reperfusion injury, atherosclerosis, and hypertrophy (excessive development of an organ or tissue).

The team of scientists at RGCB, led by Dr. Rakesh S. Laishram (Scientist), Dr. Feba Shaji, and Dr. Jamshaid Ali, discovered that during oxidative stress, when reactive oxidative species exceed the cell’s capacity to neutralize them, the production of antioxidant proteins is boosted. This is achieved by enhancing the fidelity of RNA processing, a mechanism that helps cells combat oxidative stress. The study, published in Redox Biology journal, uncovers this novel pathway in gene expression.

In the gene expression process, DNA is transcribed into RNA, which is then translated into proteins responsible for carrying out various cellular functions. Manipulations in these pathways—whether through DNA, RNA, or proteins—can alter gene expression depending on the cellular state. RNA processing, a key pathway controlling gene expression, involves the cleavage of RNA. Interestingly, this cleavage is not always precise, with multiple potential cleavage sites, a phenomenon known as cleavage heterogeneity.

“Controlling oxidative stress is crucial for maintaining cellular health and preventing human diseases. One key way cells regulate oxidative stress is by controlling gene expression through alterations in DNA, RNA, or proteins,” says Dr. Laishram, highlighting the importance of this research in understanding how cells respond to oxidative stress through imprecisions in RNA processing. “This underscores the therapeutic potential of targeting cleavage precision in RNA to mitigate oxidative stress and its associated pathologies.”

Dr. Chandrabhas Narayana, Director of RGCB, described it a significant contribution to understanding how antioxidants influence the pathogenesis and development of diseases.

While previous research had not fully elucidated the mechanism, regulation, or biological implications of cleavage imprecision, this study challenges the common perception that such imprecision is merely error-prone. Dr. Shaji and her team discovered that cleavage imprecision is tightly regulated, playing a critical role in controlling gene expression in response to oxidative stress. Key oxidative stress response genes, such as NQO1, HMOX1, PRDX1, and CAT, show higher heterogeneity compared to genes involved in non-stress responses. Furthermore, the number of cleavage sites on these RNA molecules is reduced, enabling cells to better respond to oxidative stresses.

The RGCB researchers have now shown that this heterogeneity is driven by a fidelity cleavage complex that cleaves RNA at a primary site during oxidative stress. This study marks the first example of the biological significance of cleavage imprecision, which regulates gene expression in the cellular oxidative stress response. The findings offer a novel mechanism of antioxidant response, distinct from other oxidative stress pathways, with far-reaching implications for understanding the pathogenesis of diseases such as cancer, cardiovascular conditions, inflammation, neurodegeneration, aging, and diabetes.

This breakthrough could pave the way for new therapeutic approaches targeting oxidative stress, offering hope for the treatment of a wide range of diseases where antioxidant responses are vital.