conjugation of a podoplanin-specific single-chain fragment variable (scfv) to granzyme b for designing a potential therapeutic against malignant tumors: an in-silico experiment

Introduction: monoclonal antibodies (mabs) and antibody-drug conjugates (adcs) have changed the face of cancer treatment methods drastically. herein, i attempted to conjugate a podoplanin (pdpn)-single-chain fragment variable (scfv) to granzyme b (grb) to design an antibody conjugate (named lpmab-2-(g4s)3-grb) using in-silico techniques.materials and methods: the 3d models of the pdpn­-specific scfv (lpmab-2), lpmab-2-(g4s)3-grb, and pdpn were predicted by galaxyweb, assessed through ramachandran plot analysis, and refined by 3drefine. the physicochemical properties, solubility value, and tm of lpmab-2-(g4s)3-grb were estimated/predicted and compared with lpmab-2 and grb. finally, the binding capacity of lpmab-2-(g4s)3-grb to pdpn was compared with that of lpmab-2 through docking and affinity prediction alongside identifying the residues that participate in the binding through 2d interaction plots using the ligplot+ software.results: the 3d models were predicted to be of high quality and refined successfully. the solubility and tm of lpmab-2 were predicted to decrease and increase following its conjugation with grb, respectively, whereas its estimated half-life was not affected. the docking results indicated that lpmab-2-(g4s)3-grb targets pdpn in the same orientation as that of lpmab-2 and with the exact same residues as indicated by their 2d plots. moreover, the affinity of lpmab-2-(g4s)3-grb to pdpn was predicted to be similar to that of the single scfv.conclusion: the conjugation of lpmab-2 to grb does not affect its binding capacity or characteristics in a major negative fashion. in-silico techniques could be utilized for antibody engineering, and future studies could focus on the assessment of lpmab-2-(g4s)3-grb in vitro and in vivo.