A Boron Delivery Antibody (BDA) with Boronated Specific Residues: New Perspectives in Boron Neutron Capture Therapy from an In Silico Investigation

Abstract

Boron Neutron Capture Therapy (BNCT) is a tumor cell-selective radiotherapy based on a nuclear reaction that occurs when the isotope boron-10 (¹⁰B) is radiated by low-energy thermal neutrons or epithermal neutrons, triggering a nuclear fission response and enabling a selective administration of irradiation to cells. Hence, we need to create novel delivery agents containing ¹⁰B with high tumor selectivity, but also exhibiting low intrinsic toxicity, fast clearance from normal tissue and blood, and no pharmaceutical effects. In the past, boronated monoclonal antibodies have been proposed using large boron-containing molecules or dendrimers, but with no investigations in relation to maintaining antibody specificity and structural and functional features. This work aims at improving the potential of monoclonal antibodies applied to BNCT therapy, identifying in silico the best native residues suitable to be substituted with a boronated one, carefully evaluating the effect of boronation on the 3D structure of the monoclonal antibody and on its binding affinity. A boronated monoclonal antibody was thus generated for specific ¹⁰B delivery. In this context, we have developed a case study of Boron Delivery Antibody Identification Pipeline, which has been tested on cetuximab. Cetuximab is an epidermal growth factor receptor (EGFR) inhibitor used in the treatment of metastatic colorectal cancer, metastatic non-small cell lung cancer, and head and neck cancer.

Keywords: 4-borono-L-phenylalanine; Boron Delivery Antibody strategy; Boron Neutron Capture Therapy; docking; molecular dynamics.

Figure 1

The BDA pipeline.

Figure 2

Chemical structures of the best boronated compounds identified and their fragments.

Figure 3

Evaluation of distance and orientation of each fragment with respect to the native residue by a Python script. Left: schematic representation of the different angles in which a docking pose can be located with respect to the reference residue; the residue vector (CG to CZ) and the ligand vector (C5 to B) serve as references for the calculation of the angle between them. Right: concrete example of the angle calculation between the Tyr residue and the p-toluene boronic acid ligand pose.

Figure 4

Cetuximab Fab: spheres indicate the location of Tyr (yellow), Trp (green), Phe (red), and His (blue) residues that were mutated into Gly and Ala. The contact area with the receptor, enclosed by a box, was not considered in this study.

Figure 5

Best fragment poses for Phe mutation. (a) Docking pose number 2 for p-toluene boronic acid fragment probe in comparison with the native residue chain B Phe128, mutated to Gly; (b) Docking pose number 1 for phenylboronic acid fragment probe in comparison with the native residue chain B Phe128, mutated to Ala.

Figure 6

Best fragment poses for Tyr mutation. (a) Docking pose numbers 3, 4, and 7 for p-toluene boronic acid fragment probe in comparison with the native residues chain A Tyr173 and 140, mutated to Gly; (b) Docking pose numbers 4, 5, 7, 9, and 20 for phenylboronic acid fragment probe in comparison with the native residues chain A Tyr173 and 140, mutated to Ala; (c) Docking pose number 10 for phenylboronic acid fragment probe in comparison with the native residues chain A Tyr192 and 186, mutated to Ala; (d) Docking pose numbers 11 and 16 for phenylboronic acid fragment probe in comparison with the native residue chain B Tyr200, mutated to Ala; (e) Docking pose numbers 11 and 14 for p-toluene boronic acid fragment probe in comparison with the native residue chain B Tyr200.

Figure 7

Fragment probe pose in comparison with the native residue—the case of Trp. Docking pose number 8 for p-toluene boronic acid fragment probe in comparison with the native residue chain B Tyr109, mutated to Gly.

Figure 8

Comparison of protein structures: 3D superimposition of representative structures obtained from cluster analysis shows structural similarity among wild type and boronated proteins, especially in the EGFR interaction region.