What is Pyrrolobenzodiazepine (PBD)?

Pyrrolobenzodiazepines (PBDs) are a class of anti-tumor antibiotics, including the naturally occurring anthramycins, siberomycins, chromanamycins, neomycins, and DC-81. They selectively bind to the 5'-purine-guanine-purine sequence DNA minor groove and form a covalent bond with the exocyclic amino group of the guanine base to exert their biological activity.

Synthetic PBD dimer, in which two PBD monomers are connected by a flexible propyldioxy bond through the phenol C8 position of the aromatic A ring, has high cytotoxicity in vitro and can efficiently produce DNA strands Cross-links between the naked DNA and the cells. Such a molecule has been shown to span 6 base pairs in the small groove of DNA, and it is covalently bound to the guanine on the opposite chain that are separated spatially in the central sequence 5'-PuGATCPy-3' (where Pu is a purine and Py is a pyrimidine). Recent studies, using HPLC/MS and short oligonucleotides with determined sequences have indicated that in addition to inter-chain cross-links, PBD dimers can also form sequence-selective intra-chain cross-link adducts and monoalkylated adducts. An important feature of the formed inter-strand cross-links is that they minimize the distortion of the characteristics of DNA, which seems to contribute to their persistence and effective biological activity in the cell.

Figure 1: Summary of structure–activity relationships (SARs) for (A) the PBD monomers, (B) the PBD dimers, and (C) the indolinobenzodiazepine analogues. Modifications that enhance activity are shown in blue, and those which reduce activity are shown in red. (Dr. Julia Mantaj, 2017)

Bind to DNA

The covalent binding of monomer and dimer PBD to DNA is achieved through a two-step process

The first step involves identifying favorable low-energy binding sites through the rapid, reversible, non-covalent association of molecules in the minor groove. If the interaction between these non-covalent molecules such as hydrogen bonding, van der Waals forces, and electrostatic contact are weak, the PBD may dissociate and re-associate at another site. This process will be repeated until a suitable low-energy site contains one or two bird guanines. The group (applicable to PBD monomer or dimer, respectively) has undergone a nucleophilic attack at position C11 of PBD.

In the second step, the PBD forms one or two covalent bonds with the guanine base and then locks the molecule in place.

The initial non-covalent bonding is a fast process, and since the rate of the covalent bonding depends on the PBD structure and DNA sequence, the covalent bonding may take 3 to 24 hours to complete.

Once covalently bound to DNA, PBD monomer and dimers mediate some cellular processes, including DNA strand breaks, inhibition of DNA processing enzymes (such as, endonuclease BamH1, RNA polymerase, and ligase), and specific transcription factors (such as, SP 1, NF-Y and NF-κB), and various signal transduction pathways (such as, p53-dependent and independent pro-apoptosis, modulation of JNK/AP-1, VEGF and SDF1α signaling).

Figure 2: structure of ADC drug m276-PBDb (Steven Seaman, 2017).

PBD-based ADC

In view of the performance of the PBD dimer as an ADC load so far, compared with many other types of loads, the structural simplicity and ease of synthesis of the PBD dimer may significantly, increase the percentage of PBD ADCs in the future.

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What is Pyrrolobenzodiazepine (PBD)?

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