The pyrrolobenzodiazepines (PBDs) are a class of naturally occurring and synthetic DNA minor-groove binding agents. They covalently bind to the C2-amino group of guanines, and can form mono-alkylated adducts and cross-links depending on the structure of the molecule. PBDs can be extremely cytotoxic, and there are reports of IC50 values in cell lines in the high femtomolar ranges. Synthetic A-ring-linked PBD dimers have found use as payloads in antibody drug conjugates (ADCs) due to their potent cytoxicity, and a number of ADCs are now in clinical trials. The C-ring of the PBD structure has been under-exploited as a means to improve cytotoxicity, and for joining PBD units together to create novel dimers. This lack of interest in the C-ring may have been due to literature reports that related C2-linked PBD dimers are poorly DNA interactive and cytotoxic. Using our proprietary molecular dynamics (MD) protocols, we undertook a series of MD simulations to establish a rationale for the poor DNA-binding affinity of C2-linked PBD dimers. We were able to determine a number of characteristics preventing efficient DNA-interaction including (a) their shape does not follow the curvature of the DNA minor groove, (b) if a molecule is attached to DNA via one imine moiety, the other imine moiety is not oriented in an appropriate position to effect the second covalent cross-linking event, (c) if a cross-linked model is produced, significant DNA distortion is observed, suggesting that rapid repair would occur in cells, perhaps contributing to the low cytotoxicity. During this study, our models and simulations suggested that, after covalent adduct formation, C1-substituents should extend along the minor groove in an appropriate orientation to form extensive van der Waals interactions with functional groups on the minor groove floor. This was reflected in free energy of binding calculations. For example, in the case of one C2-linked dimer, calculations suggested a weak binding affinity (i.e., -42.74 kcal/mol) with the DNA sequence 5’-GCGATACTCGC-3’, whereas under identical experimental conditions, an equivalent C1-linked dimer had a much higher binding affinity (i.e., -50.42 kcal/mol). Based on these promising in silico data, a small library of C1-PBD molecules was synthesised, and biophysical results indicated that they possessed significant DNA-binding affinity. HPLC-MS experiments using DNA sequences based on the STAT3 and NF-ÊB transcription factor consensus sequences showed that some library members converted up to 60% of the DNA to covalent adducts within 3 hours. Furthermore, in preliminary experiments in cell lines such as MDA-MB231, the same molecules were highly cytotoxic with IC50 values in the nanomolar region (e.g., 36 nM after 72 hour incubation for one compound). Studies are now underway to further functionalise the C1-position of PBDs to enhance cytotoxicity, and to assess their viability as novel payloads for use in ADCs.

Citation Format: Paul J. M. Jackson, George Procopiou, Nicolas Veillard, Julia Mantaj, K Miraz Rahman, David E. Thurston. In silico design, synthesis and evaluation of a new family of C1-substituted pyrrolobenzodiazepines (PBDs). [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4779.