Calicheamicin and DNA-cleaving

Calicheamicins, isolated from Micromonospora echinospora ssp. calichensis, combine unprecedented and extraordinary chemical and biological properties.  This includes activity in the biochemical prophage induction assay at concentrations <1 pM, high antibacterial activity, and extreme potency against various leukemia and solid neoplasms such as colon cancer and melanoma with optimal doses of 0.15-5 ug/kg. [1]

Calicheamicin-γ, as well as other enediyne antibiotics, belongs to a group of the most effective chemotherapeutic agents.  Their effectiveness is due to the unique structure and sophisticated mechanism of action by which they destroy double-stranded DNA.  The compound is a highly potent anti-tumor antibiotic that cleaves DNA with a high degree of specificity, causes sequence-selective double-strand cuts.[2]

Structural regions
Calicheamicin-γ contains two distinct structural regions. The larger of the two consists of an extended sugar residue comprising four monosaccharide units and one hexasubstituted benzene ring which are joined together through a highly unusual series of glycosidic, thioester, and hydroxylamine linkages.[3]

ADC Bio
MabPlex
Lonza
 

Researchers note that the specific calicheamicin γ–DNA-binding process depends not only on the base sequence of the double helix but also on its structure and flexibility of the compound [4]

As part of the unique mechanism of action, aryloligosaccharide deliver the molecule to its target where it tightly binds in the minor groove of double-helical DNA and displays high specificity for sequences including  5′-TCCT-3′ and 5′-TTTT-3‘ through significant hydrophobic interactions and other forces. This binding is thought to be facilitated by substantial preorganization of the oligosaccharide into a rigid, ex-tended conformation.

A significant portion of the sequence selectivity for 5′-TCCT-3′ arises from a favorable interaction between the large and polarizable iodo substituent of the hexasubstituted aromatic ring and the exocyclic amino substituents of the two guanines in the 3′-AGGA-5′ tract.[3]

Second region
The second region of calicheamicin-γ is its aglycon, a rigid, highly functionalized bicyclic core which acts as the “payload” of the molecule. The enediyne functionality of the molecule is locked within a rigid 10-membered bridged ring awaiting activation to undergo the Bergman reaction (also known as Bergman cyclization or Bergman cycloaromatization).[3]

Figure 1.0: Mechanism of Action of Calicheamicin. Calicheamicins are a group of enediyne antitumor antibiotics. Calicheamicins target DNA and cause strand scission. [1]

Also forming part of the aglycon is a trisulfide which serves as the so-called trigger. Once the molecule is in the vicinity of DNA, a series of chemical reactions unfold leading to DNA cleavage.

A nucleophile (e.g. glutathione) attacks the central sulfur atom of the trisulfide group. This causes the formation of thiolate or thiol which adds intramolecularly to the adjacent α, β-unsaturated ketone embedded within the framework of the aglycon. This reaction, converting a regional bridgehead position to a tetragonal center, causes a significant change in structural geometry which imposes a great deal of strain on the 10-membered ring.

The strain is completely relieved by the enediyne undergoing an rearrangement reaction analogous to the Bergman reaction, generating a highly reactive benzenoid diradical (1,4-didehydrobenzene).[3]

The calicheamicin diradical then abstracts hydrogen atoms from the deoxyribose (sugar) backbone of DNA, the duplex DNA, at the C-5′ position of the cytidine in 5′-TCCT-3′ and the C-4′ position of the nucleotide three base pairs removed on the 3′ side of the complementary strand.  This leads to scission or cleavage of both strands of DNA.[3]

References:
[1] Smith AL, Nicolaou KC. The enediyne antibiotics. J Med Chem. 1996 May 24;39(11):2103-17.<br>
[2] Gredicak M, Jerić I. Enediyne compounds – new promises in anticancer therapy. Acta Pharm. 2007 Jun;57(2):133-50.
[3] Nicolaou KC, Smith AL, Yue EW. Chemistry and biology of natural and designed enediynes .Proc Natl Acad Sci U S A. 1993 Jul 1;90(13):5881-8.