NYSTAR was happy to see that you recently were featured as one of NVIDIA Corporation's "Success Stories". What does this mean for you?
We are very proud that NVIDIA chose to feature our group and to help sponsor our research through a generous donation. Using 3D stereo to get "inside" a protein molecule and look at the binding site is a mind-blowing experience.
Why did you pick computational biology and structure-based design as your focus of interest?
Using computation to better understand how drugs interact with their targets has always interested to me. Simulations complement experimental approaches and reveal novel aspects about the biological systems being studied.
Describe an average day for you at Stony Brook.
There are no average days for a new assistant professor.
Please describe your top three scientific accomplishments.
In no particular order would be the fact that: (1) I have published a number of papers that I feel have advanced the field of computational chemistry. (2) I have been fortunate enough to have received a number of awards as an undergraduate, graduate, and as a new faculty member. (3) I am now running my own independent research group here at Stony Brook.
Why do you feel this research is or will become useful?
The real impact is on human health. Computation has already played a major role in development of drugs to treat various diseases; HIV/AIDS is probably the most notable example in which structure-based design played a critical role in development of several drugs. As computational methods continue to be improved new and more powerful medicines can be developed. Basic research is very important.
What's going on right now in your research laboratory that you'd most like to share?
The fact that I have a dedicated research group consisting of postdoctoral fellow Bentley Strockbine, graduate students Sudipto Mukherjee, Noel Carrascal, and undergraduates Ricky Chachra and Amee Patel all working to advance the field of structure-based drug design.
Where do you see your research going as you continue on in your career?
To continue to strike a balance between development, validation, and application of computational methods for drug design. Our group will continue to forge close collaborations with experimentalist.
Who are your key research and development partners?
The group continues to receive incredible support from many people, departments, and institutions including: The Department of Applied Mathematics at Stony Brook, the Institute for Chemical Biology and Drug Discovery at Stony Brook, the Computational Science Center at Brookhaven National Laboratory, NVIDIA Corporation, and of course the NYSTAR Watson Investigator Program.
What challenges do you and your team encounter in research and development?
The largest challenge by far is to carve out time everyday for conducting research instead of getting bogged down with other obligations.
You were awarded a Watson grant on the basis of your work using computational drug discovery of small molecules to treat HIV. How has the Watson award money impacted your research?
The award has been important on many levels. Most practically, the funding has allowed me to support very talented researchers, obtain preliminary data, and build the infrastructure necessary for a fully functional computational research lab.
The Watson Program is designed to help early career researchers in the life sciences who demonstrate a willingness and ability to develop research into economic development opportunities in the State. What challenges have you faced in identifying commercial opportunities for your research?
Ultimately our research is focused on drug discovery and design which of course can have great commercial potential. With that being said, drug discovery is very difficult, can take many years, and cost millions of dollars. Nevertheless we feel that our group is posed to make real contributions.
Did you like science as a child?
Absolutely. I was an amateur astronomer and loved collecting bugs.
As a child, what did you dream of becoming?
Astronaut or a rock star.
Why did you become a scientist?
To learn more about the physical world around me.
What do you like to do in your free time?
Spend time with family. We love to go to the Met and the Natural History Museum. New York has so much to offer.
How do you keep up with the daily progress made in the field of computational biology and structure-based design?
Read the literature, attend meetings, and most important talk with colleagues.
What changes do you anticipate seeing in your chosen field of research during the next 20 years?
Advances in computing will allow the study of larger and larger systems and lead to a greater understanding of complex biological phenomena. Computational structure-based design will continue to become more and more important and this will have great impact on the development of new "targeted" therapeutics for disease.
What advice would you give someone interested in learning more about or considering a career in computational biology and structure-based design?
Get involved early and start by reading the literature. Review articles are always a good place to start. Since the field is ultimately very interdisciplinary be open to learning about different research areas and techniques.
Could you please name some of your most recent publications?
1. Rizzo, R. C.; Toba, S.; Kuntz, I. D. A Molecular Basis for the Selectivity of Thiadiazole Urea Inhibitors with Stromelysin-1 and Gelatinase-A from Generalized Born Molecular Dynamics Simulations. J. Med. Chem., 2004, 47, 3065-3074
2. Rizzo, R. C.; Aynechi, T.; Case, D. A.; Kuntz, I. D. Estimation of Absolute Free Energies of Hydration Using Continuum Methods: Accuracy of Partial Charge Models and Optimization of Nonpolar Contributions. J. Chem. Theory Comput., 2006, 2, 128-139
3. Hornak, V.; Okur, A.; Rizzo, R. C.; Simmerling, C. HIV-1 Protease Flaps Spontaneously Open and Reclose in Molecular Dynamics Simulations. Proc. Natl. Acad. Sci. U.S.A., 2006, 103, 915-920
4. Hornak, V.; Okur, A.; Rizzo, R. C.; Simmerling, C. HIV-1 Protease Flaps Spontaneously Close to the Correct Structure in Simulations Following Manual Placement of an Inhibitor into the Open State. J. Am. Chem. Soc., 2006, 128, 2812-2813
What keeps you up at night?
Thinking about experiments and data analysis, how to over come day-to-day challenges, and how best to accomplish our overall lab goals.
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Accomplishments
