Immunoinformatics Approach to Design a Chimeric CD70-Peptide Vaccine against Renal Cell Carcinoma

Abstract

Renal cell carcinoma (RCC) accounts for the majority of cancer-related deaths worldwide. Overexpression of CD70 has been linked to advanced stages of RCC. Therefore, this study aims to develop a multiepitope vaccine targeting the overexpressed CD70 using immunoinformatics techniques. In this investigation, in silico multiepitope vaccines were constructed by linking specific CD70 protein epitopes for helper T lymphocytes and CD8⁺ T lymphocytes. To enhance immunogenicity, sequences of cell-penetrating peptide (CPP), penetratin (pAntp), along with the entire sequence of tumor necrosis factor-α (TNF-α), were attached to the N-terminal and C-terminal of the CD70 epitopes. Computational assessments were performed on these chimeric vaccines for antigenicity, allergenicity, peptide toxicity, population coverage, and physicochemical properties. Furthermore, refined 3D constructs were subjected to a range of analyses, encompassing structural B-cell epitope prediction and molecular docking. The chosen vaccine construct underwent diverse assessments such as molecular dynamics simulation, immune response simulation, and in silico cloning. All vaccines comprised antigenic, nontoxic, and nonallergenic epitopes, ensuring extensive global population coverage. The vaccine constructs demonstrated favorable physicochemical characteristics. The binding affinity of chimeric vaccines to the TNF receptor remained relatively stable, influenced by the alignment of vaccine components. Molecular docking and dynamics analyses predicted stable interactions between CD70-CPP-TNF and the TNF receptor, indicating potential efficacy. In silico codon optimization and cloning of the vaccine nucleic acid sequence were accomplished using the pET28a plasmid. Furthermore, this vaccine displayed the capacity to modulate humoral and cellular immune responses. Overall, the results suggest therapeutic potential for the chimeric CD70-CPP-TNF vaccine against RCC. However, validation through in vitro and in vivo experiments is necessary. This trial is registered with NCT04696731 and NCT04046445.

Figure 1

Population coverage analysis. Prediction of the population coverage for six potential human vaccine candidates with MHC Class I and II alleles around the world.

Figure 2

The outcomes from diverse structure validation tools affirmed the reliability and precision of the CD70^(epitopes)−CPP-TNF^{(Whole sequence)} (Homo sapiens) vaccine construct. (a) The 3D model of the CD70^(epitopes)−CPP-TNF^{(Whole sequence)} (Homo sapiens) vaccine construct was developed. (b) The ProSA-web z-score plot displayed a Z-score = −7.62. (c) The Ramachadran plot exhibited 89.5% of residues in the most favored regions. (d) The ERRAT overall quality factor exceeded 86%. (e) Postrefinement, the verify 3D indicated a score of 70.42% for the model.

Figure 3

The iMOD server's normal mode analysis of the human CD70-CPP-TNF-TNF receptor complex with normal mode analysis (NMA) outputted the following plots. (a) The docked complex of the CD70-CPP-TNF-TNF receptor complex. Stability of the protein–protein complex was investigated through. (b) B-factor values, (c) deformability, (d) eigenvalue, (e) covariance map (red, white, and blue colors correspond to correlated, uncorrelated and anticorrelated motions), and (f) elastic network. The darker gray colors correspond to stiffer spring.

Figure 4

Based on the 100 ns MD simulations of the CD70-CPP-TNF–TNF receptor complex, the figure shows the: (a) root-mean-square deviation (RMSD) plot of vaccine. (b) RMSD plot of receptor. (c) Root-mean-square fluctuation (RMSF) plot of the ligand (blue line) and receptor (pink line). (d) Hydrogen bonds. (e) The radius of Gyration (Rg) plot of ligand. (f) The Rg plot of receptor. (g) Solvent accessible surface area (SASA) of the vaccine construct (red line), TNF receptor (blue line), and vaccine-TNF receptor complex (black line). (h) Interaction energy plot over the simulation timescale.

Figure 5

In silico cloning of human CD70-CPP-TNF vaccine construct into pET28A (+) vector. The red region denotes the 1233 bp cloned vaccine nucleic acid sequence.

Figure 6

In silico simulation of immune response using CD70-CPP-TNF vaccine as an antigen after subsequent three injections. (a) Immunoglobulins and antigen levels, (b) B-cell population per state, (c) B-cell population, (d) T helper cell population per state, (e) T helper cell population, (f) T cytotoxic cell population per state, and (g) production of cytokines.