Theoretical and Natural Science
- The Open Access Proceedings Series for Conferences
Theoretical and Natural Science
Vol. 3, 28 April 2023
Open
Access | Article
AlphaFold2-based structure prediction and target study of PD-L1 protein
* Author to whom correspondence should be addressed.
Abstract
PD-L1 is an immune protein in human body that can play an important role in cancer immunotherapy. By binding to antibodies, the binding activity of PD-L1 and PD-1 is blocked, which in turn inhibits cancer cells. Thus the structure of PD-L1 is very important in studying the binding of antibodies to it. However, experimental methods to solve the structures of PD- L1 and numerous complexes are expensive and consuming. Thus, it is essential to exploit computational methods to help biologists figure out the structures and the underlying mechanisms. In this paper, we explore whether AlphaFold2 is able to accurately predict the structure of PD-L1 and whether we can use AlphaFold2 to capture the binding sites of PD-L1 when binding to different antibodies. Our results show that AlphaFold2 has high confident scores and accuracy in predicting the structure of PD-L1 and the binding sites with atezolizumab and durvalumab. For the interaction between PD-L1 and the antibodies, AlphaFold2 can capture most of the hydrogen bonds as well as the salt bridges. Our work suggests that AlphaFold2 can not only be used as a tool to predict the structure of proteins, but also serves as a useful tool for antibody discovery, e.g. providing high-quality predicted structures for downstreaming docking, which brings new hope for drug discovery.
Keywords
AlphaFold2, antibody, structure, PD-L1
References
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Data Availability
The datasets used and/or analyzed during the current study will be available from the authors upon reasonable request.
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- Volume Title
- Proceedings of the 2nd International Conference on Biological Engineering and Medical Science (ICBioMed 2022), Part I
- ISBN (Print)
- 978-1-915371-25-6
- ISBN (Online)
- 978-1-915371-26-3
- Published Date
- 28 April 2023
- Series
- Theoretical and Natural Science
- ISSN (Print)
- 2753-8818
- ISSN (Online)
- 2753-8826
- DOI
- 10.54254/2753-8818/3/20220152
- Copyright
- © 2023 The Author(s)
- Open Access
- This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited