Designing improved p53 peptide therapeutic using computer simulations

Dr. Atanu Maity and Asha Rani Choudhury’s joint interview with Bio Patrika hosting “Vigyan Patrika”, a series of author interviews. Atanu and Asha are joint-first authors on the recent research paper “Effect of Stapling on the Thermodynamics of Protein-Peptide Binding”, published in J. Chem. Inf. Model. (2021). In this interview, they talk about this work and its relevance in the context of the therapeutics development.

Dr. Atanu Maity is a postdoctoral fellow at the Department of Chemistry in IIT Bombay working with Prof. Rajarshi Chakrabarti. He is from Tamluk, a small town in West Bengal. He completed B.Sc. in Chemistry from Tamralipta Mahavidyalaya in 2009. He did M.Sc. from Vidyasagar University in 2011 with a specialization in physical chemistry. After that, he joined the Division of Bioinformatics of Bose Institute, Kolkata to pursue a Ph.D. in computational biochemistry. His doctoral work was focused on the dynamics of different proteins of the Bcl-2 family involved in the intrinsic pathway of apoptosis. After his Ph.D. he moved to IIT Bombay in 2018 to join the institute postdoctoral program. In his postdoc, he is addressing different problems from physical chemistry and biological science using molecular dynamics simulation.

Asha Rani Choudhury is currently a Ph.D. student at the Department of Chemistry in IIT Bombay under the supervision of Prof. Rajarshi Chakrabarti enrolled in the year of July 2018. Prior to this, she obtained her Master degree in chemistry in 2017 securing 1st position in university level from the Department of Chemistry, Berhampur University, Odisha and Bachelor’s degree in chemistry in 2015 from Vikram deb autonomous college, Jeypore under Berhampur university, Odisha. Her research work focuses on elucidating the conformational dynamics of protein by using protein stapling procedure and its thermodynamical effect on protein-protein interaction. She is also looking forward to work in the area of free energy calculation by different enhanced sampling method and study the kinetics of protein-peptide binding. Besides her research work, she also loves running, cycling, playing chess and badminton.

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How would you explain your paper’s key results to the non-scientific community?

Different physiological processes, taking place inside our body are complex interactions between biomolecules like protein, nucleic acid, etc at the molecular level. Any undesirable change in these interactions can lead to a situation that is known as disease. Designing medicine or therapeutic against disease is finding molecules that can interfere with this modified interaction and restore normalcy. To increase the effectiveness of these therapeutics, it is possible to design and propose modifications using computational approaches. In the present work, one such modification has been tested using computer simulations.

The interaction between two important proteins most commonly associated with cancer, mdm2 and p53, is known to serve as the guardian of the cell. Whenever there is a threat of damage to cells from stresses, different survival machinery in our body are awakened which can act upon to repair the damage. One can think of these machinery as a team of multiple players where the players are biomolecules mostly proteins. One such team is led by the protein p53 which is known for its tumor suppression activities. In response to stress, it arrests the growth of the cell and decides whether to repair the damage or to remove it. Interestingly when there is no such stress, p53 prefers to stay with its best friend mdm2, another important player in the current work.

Schemiatic

In case of the infamous disease cancer, the infected cells adopt a strategy to fool us by increasing the number of mdm2 so that most of the p53 are engaged and are unavailable for its tumor suppression function which otherwise can successfully remove/repair the infected cells.

To get rid of this, scientists have used a precise and smaller version of p53 (p53 peptide) as a therapeutic which can bind with mdm2 stronger than p53 and set the latter free for its function ensuring a healthy cell cycle. However, due to the flexible nature, the peptide lacks specificity and often fails to replace p53.

In the present work, using computer simulation we have modeled the binding of mdm2 with the p53 peptide along with p53 peptide with two modifications that reduce the flexibility of the peptide. Two specific amino acids of the p53 peptide have been replaced with hydrocarbon chains (popularly known as the stapling agent) and joined together to introduce restraint along the peptide helical axis. These rigidifications have been shown to improve the binding with mdm2 compared to wild-type p53-mdm2 binding. Detailed analyses of different binding energy components have shown significant improvement in the entropy of binding and the extent of improvement depends on the nature of the stapling agent.

A stapled peptide that can bind to RBD to mimic the binding of ACE-2 with higher affinity can be a potential candidate for therapeutic against SARS-Cov2.

What are the possible consequences of these findings for your research area?

The possible consequences of this work are two-way. The binding of the predicted stapled peptide can be studied in-vitro and in-vivo. On the other hand, the design strategy used here can be applied to find peptide therapeutics to target protein-protein interactions involved in other diseases. For example, the association of SARS-Cov2 with the host cell is initiated by the binding of Receptor Binding Domain (RBD) of SARS-Cov2 with Angiotensin-Converting Enzyme-2 (ACE-2) of human cell. A stapled peptide that can bind to RBD to mimic the binding of ACE-2 with higher affinity can be a potential candidate for therapeutic against SARS-Cov2.

What was the exciting moment (eureka moment) during your research?

Dr. Atanu Maity: The introduction of stapling agent to cross-link the side chain of amino acids of p53 reduces the conformational flexibility of the p53 peptide in an aqueous solution and its impact has been reflected in the entropy of binding. This rigidification of the peptide conformation makes us curious to ask the question, whether this can prevent denaturation? To check that, the wild type and the two stapled peptides were subjected to thermal (simulated at 330K) and chemical (simulated in the presence of 8M urea) denaturation. The wild-type peptide unfolds both at a high temperature and in the presence of urea. Interestingly, in the presence of an aliphatic stapling agent, the peptide retains its secondary structure completely at 330K and undergoes partial unfolding in the presence of urea. On the other hand, the enhanced restraints imposed by the aromatic stapling agent are able enough to endure both thermal and chemical denaturation.

Thus, the entropically favorable rigidification of the peptide by the stapling agent can successfully prevent their thermal and chemical denaturation as well. That was quite exciting!!

Asha Rani Choudhury: The p53 peptide is anchored to the mdm2 binding pocket with the help of three residues phenylalanine(F3), tryptophan(W7), and leucine(L10). Proper orientation of these residues is crucial for the binding process. A comparison of this orientation in the free peptide and the mdm2-bound peptide gives an idea about the reorganization required for the complexation process. For wild-type p53 peptide, a significant reorientation is required for complexation which is reflected in the high entropic penalty of binding. An introduction of stapling agent reduces the extent of reorientation required for complexation and the entropic penalty.

The correlation between the anchoring residue orientation in free peptide and the entropy of binding is really exciting.

What do you hope to do next?

As a continuation of the current work, we would like to use the mechanistic insights gained from this study in designing stapled peptide therapeutics to prevent SARS-Cov2 RBD and human ACE-2 binding. As our future goal, we would like to understand complex biological processes from the perspective of biomolecular dynamics. Using different tools of computational microscopy, we intend to find interesting mechanistic insights into these processes which can contribute to answer some of the unanswered questions and help to improve therapeutic strategies.

Where do you seek scientific inspiration?

Dr. Atanu Maity: The wonders of nature and the quest of understanding it, have been my constant source of inspiration. I seek inspiration from fascinating inventions and discoveries of all kinds. The survival of Deinococcus radiodurans in outer space for three years and the AlphaFold intending to solve Levinthal’s paradox amaze me equally and inspire me.

Asha Rani Choudhury: Recent commendable advances in computational chemistry and therapeutic drug designing by using different computational approaches fascinate me to challenge myself in this area and I would be very much happy if I can contribute to society in terms of designing new therapeutic strategies. Moreover, the joy of discovering new things and challenges that we come across during research keep me motivated.

How do you intend to help Indian science improve?

Dr. Atanu Maity: I think the improvement of Indian science depends on a large number of factors starting from the effort of the individual researcher to the proper allocation of resources/funds for research. As a senior researcher, I would like to focus on being part of rigorous research on interesting scientific problems and provide a proper learning platform and thorough guidance to my junior colleagues. In addition to that, I would like to be involved in improving science communication to a general audience to increase awareness about scientific research. Finally, I would put effort to improve the computational facilities at an institutional level and build more regional and national computational facilities.

Asha Rani Choudhury: Although research in India is continuously evolving, there are some elements that need to be taken care of such as computational resources, funding and motivating young researchers, etc. Furthermore,networking among different international and national institutes by organizing various conferences, webinars, workshops, and collaborations between experimental and computational laboratories will improve the overall research in India.

Reference

Maity A., Choudhury A. R. and Chakrabarti R., Effect of Stapling on the Thermodynamics of Protein-Peptide Binding. J. Chem. Inf. Model. 2021, 61, 1989−2000.

Email: atanuchem48@gmail.com, ashachoudhury95@gmail.com, rajarshi.chakrabarti@gmail.com

Lab: https://rajarshichakrabarti.wixsite.com/rajarshichakrabarti

Edited by: Anjali Mahilkar

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