Computational Chemistry Software Empowers Students to Dive into Research Innovation – Everywhere
Chemistry and chemical biology professor uses industry experience to create research opportunities for students
Informed by industry
As virtual reality and artificial intelligence (AI) become more and more of a presence in the world, Stevens is providing students and faculty many opportunities to keep themselves competitive with the latest technologies. One example of this is the work of Sunil Paliwal, teaching associate professor in the Department of Chemistry and Chemical Biology (CCB), based on his 15 years of working in the pharmaceutical industry at Schering-Plough Research Institute (later Merck). Today, Paliwal is bringing molecular modeling software into his classrooms, allowing for students to understand drug development in a new and industry-relevant way.
When Paliwal first started working in industry, technology was such that if his group came up with ten compounds that they thought might work for their needs, the team had to synthesize all ten compounds. However, likely not all of the compounds would work for the system, and a lot of the team’s work would be for nothing.
“Making compounds costs money; it generates waste,” explained Paliwal. “I used to think if there was a computer software that could tell you if [the compound] is good, it would expedite efficiency and discovery.” Additionally, this would reduce the costs for the organization, and create less chemical waste.
As time went on, a variety of such software was created. There are databases such as Scifinder, which allows for checking for compound synthesis and novelty, and the ChemOffice suite, which has molecule-drawing options such as ChemDraw for drawing compounds and assessing their physical properties. These tools have been widely adopted by the pharmaceutical industry. “When I worked in industry, I used them a lot,” said Paliwal. Additionally there are now software companies such as Schödinger, which has a suite of tools for pharmaceutical development, including the Maestro modeling program.
“When I came to Stevens, after some time, I realized that these molecular modeling programs are now available [for teaching],” said Paliwal. “I knew the value of this, and I strongly suggested [to Stevens] that we obtain and implement the license.”
‘I knew the value’
Paliwal wanted to integrate these tools into his research and teaching. Said Paliwal, “Given significant advancement and inclusion of computational tools including machine learning and AI in the drug discovery in the last several years, I wanted to teach these essential computational tools to the students to provide valuable modern research experience.”
This software is useful for the students in multiple ways. For one, they are powerful learning tools that allow the students to better understand the process of synthesizing molecules. Additionally, however, these tools are used in industry; and gaining familiarity with the tools themselves is a benefit.
Paliwal first introduced the software into undergraduate chemistry lab courses. “Initially this was helpful during the [Covid-19] pandemic,” said Paliwal. The software can be downloaded by students and used even when they are at home. “It gave students hands-on experience while we were waiting for labs to reopen.”
However, Paliwal soon realized that the implications could go far beyond pandemic shutdowns and enhance the research experience for more students. In the fall of 2022, he introduced an 800-level course to provide drug discovery research experience to the group of master’s students. “The course enables students to experience collaborating and problem-solving culture while learning and applying important computational tools,” said Paliwal.
The pandemic provided Palwal and his students with the perfect test subject. Paxlovid, the Covid-19 medicine developed by Pfizer, is a combination of two compounds, one of which has been extensively studied by the scientific community and one that is a Covid-era innovation. The biochemistry of these compounds is all public — one can look up the chemical composition online through refutable sites such as PubMed. “That gave us a really good starting point,” said Paliwal. “We wanted to develop a better medicine based on this Pfizer Covid compound. We basically want to make a better analog of this.”
In this course, students use artificial intelligence programs for designing novel drug molecules and their synthesis. Paliwal’s course walks students through how he would approach this process when he was in industry. Students go through a patent search and learn to read the patent for a compound. They then model their found compound in modeling software. Based on this model, students can design new ligands and use the various software elements to determine if that ligand would work for their goal for the compound. They then can use software to check if this compound is novel.
“Students used these tools to design novel molecules and their synthesis for the treatment of COVID-19,” explained Paliwal. “At the end of the course, students obtained valuable skills desired in the pharma and biotech industrial sector, and also academia.”
Successful from the start
This spring, the master’s students are taking a follow-up course to synthesize the compound they created in the previous semester. Paliwal also expanded involvement in the class to undergraduates taking their senior research course. Graduate students and undergraduates work together, learning how to use this technology in a team setting that mimics the way that science is performed in the real world. These students create a community which allows its members to learn from each other.
Paliwal already sees the course as a success. Of the four master’s students who took the course, three were invited to give poster presentations at a variety of prestigious conferences: Merck’s Emerging Talent Symposium in 2022 in New Jersey, the New Jersey Academic Drug Discovery Consortium on Infectious Diseases in 2022, and the American Chemical Society Meeting in Indianapolis in 2023.
“These meeting presentations provided visibility to our students, The Department of Chemistry and Chemical Biology, and the Institute,” said Paliwal. “Students had opportunities to network with other students, faculty, and potential employers at these meetings. These efforts are critically important to enhance the quality of our graduate education and therefore attract high-quality students.”
But it is not only graduate students who have also had a chance to share their exciting work with the public. Jenna Booth ’23 is a Stevens undergraduate who, along with her team, presented her research at the Independent Colleges and Universities of New Jersey (ICUNJ) undergraduate research symposium in 2023. Booth said that she was “grateful” to have had the opportunities that Paliwal’s collaborative course offered her. “I was able to talk about the work we are doing using Schrödingercomputational modeling to develop novel analogs to the Pfizer COVID drug. I even had the chance to meet and talk to individuals working in drug development and vaccine distribution at Pfizer and Johnson & Johnson about our research and progress,” said Booth. “Receiving the third place award out of the 35 undergraduate individuals presenting was the icing on the cake!”
Kenny Wong, Teaching Associate Professor of Biology and Associate Chair of Graduate Studies in CCB, collaborated with Paliwal to create the course and also agrees that it has already been a success. “Dr. Paliwal has a reputation as a nurturing educator,” said Wong. “Big science is a team sport, and he created an inclusive and engaging course that brought out the best in our students. I am very happy with the outcome that supported our student success."
Paliwal already has ideas for how to improve the course in the future, including by adding new software. By combining his industry expertise with the latest technology, Paliwal is allowing students additional opportunities for research experience and helping them to be prepared for the workforce. Paliwal’s hard work is another advancement that makes Stevens a leader in technology with a purpose.