Interaction Analysis of Adenovirus L5 Protein With Pancreatic Cancer Cell Surface Receptor to Analyze Its Affinity for Oncolytic Virus Therapy

This study seeks to investigate the interaction profile of the L5 protein of oncolytic adenovirus with the overexpressed surface receptors of pancreatic cancer. This is an important area of research because pancreatic cancer is one of the most fatal malignancies with a very low patient survival rate. Multiple therapies to date to improve the survival rate are reported; however, they show a comparatively low success rate. Among them, oncolytic virus therapy is a type of immunotherapy that is currently under deliberation by researchers for multiple cancer types in various clinical trials. Talimogene laherparepvec (T-VEC) is the first oncolytic virus approved by the US Food and Drug Administration (FDA) for melanoma. The oncolytic virus not only kills cancer cells but also activates the anticancer immune response. Therefore, it is preferred over others to deal with aggressive pancreatic cancer. The efficacy of therapy primarily depends on how effectively the oncolytic virus enters and infects the cancer cell. Cell surface receptors and their interactions with virus coat proteins are a crucial step for oncolytic virus entry and a pivotal determinant. The L5 proteins of the virus coat are the first to interact with host cell surface receptors. Therefore, the objective of this study is to analyze the interaction profile of the L5 protein of oncolytic adenovirus with overexpressed surface receptors of pancreatic cancer. The L5 proteins of three adenovirus serotypes HAdV2, HAdV5, and HAdV3 were utilized in this study. Overexpressed pancreatic cancer receptors include SLC2A1, MET, IL1RAP, NPR3, GABRP, SLC6A6, and TMPRSS4. The protein structures of viral and cancer cell protein were docked using the High Ambiguity Driven protein–protein DOCKing (HADDOCK) server. The binding affinity and interaction profile of viral proteins against all the receptors were analyzed. Results suggest that the HAdV3 L5 protein shows better interaction as compared to HAdV2 and HAdV5 by elucidating high binding affinity with 4 receptors (NPR3, GABRP, SLC6A6, and TMPRSS4). The current study proposed that HAdV5 or HAdV2 virus pseudotyped with the L5 protein of HAdV3 can be able to effectively infect pancreatic cancer cells. Moreover, the current study surmises that the affinity maturation of HAdV3 L5 can enhance virus attachment with all the receptors of cancer cells.

Figure (S1) Molecular Dynamic (MD) simulation plots of GABRP receptor: (a) Plot represent pressure equilibration step NPT (b) Potential Energy plot. Represents the steady decrease in potential energy. Native protein reached its minimized state on 2000 ps. (c) Plot represents density equilibration step NPT (d) Plot of temperature equilibration step NVT on 300k temperature (e) RMSD plot shows protein backbone energy minimization by 50ns MD simulation (f) Radius of gyration plot. The compactness of protein stabilizes around 3.7 to 3.9 Rg(nm) from time steps 18000ps to 50000ps.    Table S1. (a) The cartoon representation of HAdV2 L5 protein red color ribbon show active residues and green color represent passive residue predicted by CPORT. (b) The cartoon representation active and passive residues of HAdV3 L5 protein. (c) The cartoon representation active and passive residues of HAdV5 L5 protein predicted by CPORT. Figure (S5) CPORT active and passive residues representation of pancreatic cancer receptors. The list of active residues for all seven receptors is provided in Table S2. (a) The cartoon representation of SLC2A1 red color ribbon show active residues and green color represent passive residue predicted by CPORT. (b) The cartoon representation active and passive residues of MET receptor. (c) The cartoon representation active and passive residues of IL1RAP receptor predicted by CPORT. (d) The cartoon representation active and passive residues of NPR3 receptor predicted by CPORT. (e) The cartoon representation active and passive residues of GABRP receptor predicted by CPORT. (f) The cartoon representation active and passive residues of SLC6A6 receptor predicted by CPORT. (g) The cartoon representation active and passive residues of TMPRSS4 receptor predicted by CPORT.  Table S3. (a) The cartoon representation of CAR, red color ribbon show active residues and green color represent passive residue predicted by CPORT. (b) The cartoon representation active and passive residues of DSG2. (c)The representation of CD46 active and passive residues. (d) The cartoon representation active and passive residues of CR1 sushi domain 1 and 2 (PDB id: 2MCZ) predicted by CPORT. (e) The cartoon representation active and passive residues of CR1 sushi domain 15, 16, and 17 (PDB id: 5FO9) predicted by CPORT.  115,116,120,177,178,179,183,184,185,300,302,304,305,356,357,358,359,360,361,362,363,424,425,427,428,429 2 MET Chain A: 40,98,137,140,162,391,394,395,396,397,398,399,401,402,403,404,405,408,415,523,524,525,526,528,540,543,549,552,554,555,586,607,740 Chain B: 104,141,385,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,416,526,527,541,543,544,553,554,555,556,587,700,703 3 IL1RAP
Figure (S12) Protein-protein interaction complex of HAdV2 L5 protein with SLC6A6 receptor: HADDOCK run generate 9 clusters, superimposed structures of all clusters and plots of HADDOCK scores, Cluster size, RMSD, Van der Waals energy, Electrostatic energy, Desolvation energy, Restraints violation energy, Buried Surface Area, and Z-Score are given above. The cluster 1 is the best possible interaction complex for SLC6A6 and HAdV2 with HADDOCK score of -115.8 +/-6.9 and lowest Z-score of -1.6 selected for the further analysis.
Figure (S13) Protein-protein interaction complex of HAdV2 L5 protein with TMPRSS4 receptor: HADDOCK run generate 8 clusters, superimposed structures of all clusters and plots of HADDOCK scores, Cluster size, RMSD, Van der Waals energy, Electrostatic energy, Desolvation energy, Restraints violation energy, Buried Surface Area, and Z-Score are given above. The cluster 8 is the best possible interaction complex for TMPRSS4 and HAdV2 L5 protein with HADDOCK score of 139.9 +/-9.5 and Z-score of -1.9 selected for the further analysis.
Figure (S14) Protein-protein interaction complex of HAdV2 L5 protein with CAR receptor: HAD-DOCK run generate 3 clusters, superimposed structures of all clusters and plots of HADDOCK scores, Cluster size, RMSD, Van der Waals energy, Electrostatic energy, Desolvation energy, Restraints violation energy, Buried Surface Area, and Z-Score are given above. The cluster 3 is the best possible interaction complex for CAR and HAdV2 L5 protein with HADDOCK score of -57.2 +/-11.9 and Z-score of -1.0 selected for the further analysis.
Figure (S15) Protein-protein interaction complex of HAdV2 L5 protein with DSG2 receptor: HAD-DOCK run generate 5 clusters, superimposed structures of all clusters and plots of HADDOCK scores, Cluster size, RMSD, Van der Waals energy, Electrostatic energy, Desolvation energy, Restraints violation energy, Buried Surface Area, and Z-Score are given above. The cluster 5 is the best possible interaction complex for DSG2 and HAdV2 L5 protein with HADDOCK score of -66.5 +/-11.8 and Z-score of -1.1 selected for the further analysis.                HADDOCK run generate 8 clusters, superimposed structures of all clusters and plots of HADDOCK scores, Cluster size, RMSD, Van der Waals energy, Electrostatic energy, Desolvation energy, Restraints violation energy, Buried Surface Area, and Z-Score are given above. The cluster 1 is the top interaction complex with HADDOCK score of -76.9 +/-2.7 and Z-score of -1.5 selected for the further analysis.
Figure (S32) Protein-protein interaction complex of HAdV5 L5 protein with TMPRSS4 receptor: HADDOCK run generate 3 clusters, superimposed structures of all clusters and plots of HADDOCK scores, Cluster size, RMSD, Van der Waals energy, Electrostatic energy, Desolvation energy, Restraints violation energy, Buried Surface Area, and Z-Score are given above. The cluster 1 is the top interaction complex with HADDOCK score of 88.5 +/-0.9 and Z-score of -1.0 selected for the further analysis.
Figure (S33) Protein-protein interaction complex of HAdV5 L5 protein with CAR receptor: HAD-DOCK run generate 17 clusters, superimposed structures of top 10 clusters and plots of HADDOCK scores, Cluster size, RMSD, Van der Waals energy, Electrostatic energy, Desolvation energy, Restraints violation energy, Buried Surface Area, and Z-Score are given above. The cluster 2 is the best possible interaction complex for CAR and HAdV5 L5 protein with HADDOCK score of -66.9 +/-2.3 and Z-score of -1.6 selected for the further analysis.
Figure (S34) Protein-protein interaction complex of HAdV5 L5 protein with DSG2 receptor: HAD-DOCK run generate 9 clusters, superimposed structures of all clusters and plots of HADDOCK scores, Cluster size, RMSD, Van der Waals energy, Electrostatic energy, Desolvation energy, Restraints violation energy, Buried Surface Area, and Z-Score are given above. The cluster 2 is the best possible interaction complex for DSG2 and HAdV5 L5 protein with HADDOCK score of -76.2 +/-1.3 and Z-score of -2.2 selected for the further analysis.
Figure (S35) Protein-protein interaction complex of HAdV5 L5 protein with CR1 receptor sushi domain 1 and 2: HADDOCK run generate 10 clusters, superimposed structures of all clusters and plots of HADDOCK scores, Cluster size, RMSD, Van der Waals energy, Electrostatic energy, Desolvation energy, Restraints violation energy, Buried Surface Area, and Z-Score are given above. The cluster 3 is the best possible interaction complex for CR1 and HAdV5 L5 protein with HADDOCK score of -86.1 +/-8.3 and Z-score of -1.8 selected for the further analysis.