مقالات پذیرفته شده در هفتمین کنگره بین المللی زیست پزشکی
Site-directed mutagenesis for the affinity improvement of the anti-PD-1 antibody by in silico modeling
Site-directed mutagenesis for the affinity improvement of the anti-PD-1 antibody by in silico modeling
Mahsa Mirzaei,1,*Mohammad Mehdi Heidari,2Mehri Khatami,3
1. Department of Biology, Yazd University, Yazd, Iran. 2. Department of Biology, Yazd University, Yazd, Iran. 3. Department of Biology, Yazd University, Yazd, Iran.
Introduction: Cancer is a serious problem affecting the health of all human societies and the second leading cause of death worldwide. Monoclonal antibody-based immunotherapy is a type of targeted drug therapy for the treatment of cancer. Some monoclonal antibodies (mAbs) target immune checkpoint molecules for the treatment of several types of cancers. Programmable cell death 1 (PD-1) is an immune checkpoint protein that is expressed on activated T-cells, B cells, dendritic cells, natural killer cells, macrophages and monocytes. This protein plays a vital role in modulating immune responses. PD-1 ligand, PD-L1, is expressed on the surface of tumor cells to escape the antitumor immune response. Inhibition of the interaction between PD-1 and PD-L1 by mAbs has many therapeutic benefits and has led to a major advance in cancer treatment. Pembrolizumab is an anti-PD-1 mAb that was approved by the Food and Drug Administration (FDA) for 16 types of cancers. Complementary determining regions (CDRs) are regions in mAbs that bind to the antigen (Ag). The type of amino acids at the site of Ag and CDR interaction is important. Site-directed mutagenesis is one of the methods which is used to increase the affinity of mAbs. The conversion of neutral or negatively charged amino acids to positive amino acids in CDRs, especially CDR3, is one way to improve the affinity of mAbs. The purpose of this study was to optimize the affinity of the pembrolizumab using bioinformatics tools.
Methods: In this study, the structure of PD-1 in complex with pembrolizumab (wild-type anti-PD-1 Ab) was extracted from PDB server with 5ggs PDB code. SabDab server was applied to determine the sequences of CDRs. Then, PyMOL software was utilized for the investigation of interactions between anti-PD-1 Ab and PD-1 Ag. SWISS-MODEL server was used for modeling the three-dimensional structure of wild-type anti-PD-1 Ab, PD-1 Ag and mutated anti-PD-1 Abs. Moreover, we utilized the HADDOCK server and PyMOL software for the investigation of interactions between Abs and PD-1 Ag, and also for the identification of high-affinity mutated Abs.
Results: HADDOCK results showed that some of the mutations such as the replacement of arginine (R) with tyrosine (Y) at position 101 in CDR3 improved the binding affinity. The more negative HADDOCK score indicates the better affinity of the Ab. Moreover, the output files from the HADDOCK were investigated by PyMOL software. According to the results of the PyMOL software, the bonds length between Y101 in CDR3 and T76 in PD-1 Ag were changed by replacing R at position 101 (in R101, the number of bonds increased and the bonds length decreased).
Conclusion: mAbs have recently become one of the major methods for the treatment of cancer. Strategies for optimization of therapeutic mAbs can be applied to improve the affinity and function of mAbs. This study indicates that site-directed mutagenesis can improve the affinity of mAbs.