Structure of a Covalent DNA Minor Groove Adduct with a Pyrrolobenzodiazepine Dimer: Evidence for Sequence-Specific Interstrand Crosslinking

Abstract

The structure of the interstrand cross-linked adduct formed between a C8-C8'-linked pyrrolobenzodiazepine (PBD) dimer (DSB-120; 1,1'-(propane-1,3-diyldioxy)bis[(11aS)-7-methoxy-1,2,3,11a-t etrahydro-5H- pyrrolo[2,1-c][1,4]benzodiazepin-5-one]) and a self-complementary d(CICGATCICG)2 duplex has been determined from high-field 1D- and 2D-NMR data using a simulated annealing procedure. The refined structure supports earlier observations from solution NMR experiments and indicates that the covalently bound molecule spans six DNA base pairs in the minor groove, forming a symmetric cross-link between the spatially separated internal guanines and with active recognition of an embedded 5'-GATC bonding site. This result confirms that template-directed approaches are useful for the design of linked DNA-interactive PBD dimers with viable DNA cross-linking potential. Further, head-to-head connection of the PBD moieties results in an overall retention of 5'-GA bonding site preference for each alkylating PBD subunit. Structural analysis indicates that cross-link formation results in a localized perturbation of the DNA duplex, attributable in part to a mutual reduction in dynamic mobility or "covalent clamping" within the Gua4-Cyt7 base tract. However, ligand-induced distortion is confined to the Cyt7 and Ino8 residues on each strand. The Gua(N2)-Gua(N2) cross-link is stabilized by two directed H-bonds from the formed animal residues to N3 acceptor atoms of adenine bases on the 3'-side of each covalently modified guanine. Evidence for sequence-specific cross-linking with DSB-120 is provided by extended modeling studies which suggest that recognition of the favored d(.GATC.) motif is dominated by van der Waals steric factors, although electrostatic and H-bonded interaction terms also play a key role. This conclusion supports recent covalent footprinting studies revealing that this PBD dimer shows a selectivity for embedded base sequences of the type 5'-(pu/py)GATC(py/pu).

The XPF-ERCC1 endonuclease and homologous recombination contribute to the repair of minor groove DNA interstrand crosslinks in mammalian cells produced by the pyrrolo[2,1-c][1,4]benzodiazepine dimer SJG-136

“…Major groove crosslinking agents such as cisplatin induce a high degree of helical distortion (29). Molecular modelling of an SJG-136 crosslink in the minor groove of DNA shows very little helical distortion (30,31). Since helical distortion or changes in chromatin structure are major DNA motifs recognized by many DNA repair proteins (32,33), minor groove DNA damage and crosslinks would be less well recognized and repaired less readily.…”

From Anthramycin to Pyrrolobenzodiazepine (PBD)‐Containing Antibody–Drug Conjugates (ADCs)

“…Thus heterocyclic fragments (e.g., pyrroles, furans, imidazoles, thiophenes, indoles, benzofurans and biaryl units) have been added to this position to create PBD C8‐conjugates3a, 7, 25b, 28, 41 (e.g., GWL‐78,3a KMR‐28‐39,7 Figure 1). Similarly, two PBD units have been joined through their C8‐positions to create C8/C8′‐linked PBD dimers,10, 37a, 42 and this approach led to the design and synthesis of the C8/C8′‐linked PBD dimer SJG‐13643 (Figure 1). The C7‐position has also been used as a potential linking point for PBD dimers,8a but molecules joined in this way have significantly less DNA cross‐linking potential and cytotoxicity, as the two PBD units are not properly aligned for alkylation of guanine bases 8b.…”

SJG-136 (NSC 694501), a Novel Rationally Designed DNA Minor Groove Interstrand Cross-Linking Agent with Potent and Broad Spectrum Antitumor Activity

“…DSB-120 is a highly efficient DNA interstrand crosslinker in both naked DNA and intact cells (8,9). Nuclear magnetic resonance spectroscopy and molecular modeling studies indicate that DSB-120 spans 6 bp in the minor groove, actively recognizing and cross-linking a 5Ј-GATC sequence (10,11).…”