Pyrrolobenzodiazepines (PBDs) Do Not Bind to DNA G-Quadruplexes

Abstract

The pyrrolo[2,1-c][1,4] benzodiazepines (PBDs) are a family of sequence-selective, minor-groove binding DNA-interactive agents that covalently attach to guanine residues. A recent publication in this journal (Raju et al, PloS One, 2012, 7, 4, e35920) reported that two PBD molecules were observed to bind with high affinity to the telomeric quadruplex of Tetrahymena glaucoma based on Electrospray Ionisation Mass Spectrometry (ESI-MS), Circular Dichroism, UV-Visible and Fluorescence spectroscopy data. This was a surprising result given the close 3-dimensional shape match between the structure of all PBD molecules and the minor groove of duplex DNA, and the completely different 3-dimensional structure of quadruplex DNA. Therefore, we evaluated the interaction of eight PBD molecules of diverse structure with a range of parallel, antiparallel and mixed DNA quadruplexes using DNA Thermal Denaturation, Circular Dichroism and Molecular Dynamics Simulations. Those PBD molecules without large C8-substitutents had an insignificant affinity for the eight quadruplex types, although those with large π-system-containing C8-substituents (as with the compounds evaluated by Raju and co-workers) were found to interact to some extent. Our molecular dynamics simulations support the likelihood that molecules of this type, including those examined by Raju and co-workers, interact with quadruplex DNA through their C8-substituents rather than the PBD moiety itself. It is important for the literature to be clear on this matter, as the mechanism of action of these agents will be under close scrutiny in the near future due to the growing number of PBD-based agents entering the clinic as both single-agents and as components of antibody-drug conjugates (ADCs).

Synthesis and Biological Evaluation of a Novel C8-Pyrrolobenzodiazepine (PBD) Adenosine Conjugate. A Study on the Role of the PBD Ring in the Biological Activity of PBD-Conjugates

“…This is the case of PBD rings linked to aminopyrene [26], chalcone [27] or ciprofloxacin [23] motifs. A previously synthesized C8-linked PBD-aminopyrene conjugate was found to bind to G-quadruplex sequences, with the aminopyrene fragment driving the interactions with G-quadruplex DNA [28]. Indeed, the planar, electron-rich framework of pyrene allowed for ideal contacts with G-quadruplex structures resulting in the PBD ring portion of the conjugate not being able to bind to its DNA minor groove target [28].…”

Potential drugs used in the antibody–drug conjugate (ADC) architecture for cancer therapy

“…PBD molecules represent a significant class of sequence‐specific DNA‐alkylating agents which covalently bind to the C2‐amino groups of a guanine residue in the minor groove of double‐stranded DNAs (Antonow & Thurston, ; Cipolla, Araujo, Airoldi, & Bini, ; Gerratana, ; Hartley, ; Kamal, Reddy, Devaiah, Shankaraiah, & Reddy, ; Mantaj, Jackson, Karu, Rahman, & Thurston, ). PBDs are unable to bind to single‐stranded DNA (or RNA), representing extremely selective in the requirement of a minor groove structure for covalent binding to duplex or hairpin DNA (Rahman, Corcoran, Bui, Jackson, & Thurston, ; Rahman et al, ). In addition, they were demonstrated to have a kinetic preference for a three‐base‐pair recognition sequence, 59‐Py–G–Py‐39 (in which Py = pyrimidine and G = reacting guanine) (Rahman, Vassoler, James, & Thurston, ).…”

An Update on the Synthesis of Pyrrolo[1,4]benzodiazepines

“…The publications [15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35], cover the period 2010 to the middle of 2015, and refer solely to biological studies of PBDs. Three publications [36,37,38] are devoted to spectroscopic studies on PBDs whereas one publication deals with computational studies of PBDs [39] and another with the isolation of natural PBDs [40].…”