7DQ8 image
Deposition Date 2020-12-22
Release Date 2021-12-29
Last Version Date 2024-07-10
Entry Detail
PDB ID:
7DQ8
Keywords:
Title:
Crystal structure of actinomycin D-echinomycin-d(ACGCGCT/AGCTCGT) complex
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
2.40 Å
R-Value Free:
0.28
R-Value Work:
0.26
R-Value Observed:
0.26
Space Group:
P 41 21 2
Macromolecular Entities
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(P*AP*GP*CP*TP*CP*GP*T)-3')
Chain IDs:A
Chain Length:7
Number of Molecules:1
Biological Source:synthetic construct
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(P*AP*CP*GP*CP*GP*CP*T)-3')
Chain IDs:B
Chain Length:7
Number of Molecules:1
Biological Source:synthetic construct
Polymer Type:polypeptide(L)
Molecule:Actinomycin D
Chain IDs:D (auth: C)
Chain Length:11
Number of Molecules:1
Biological Source:Streptomyces sp.
Polymer Type:polypeptide(L)
Molecule:Echinomycin
Chain IDs:C (auth: D)
Chain Length:8
Number of Molecules:1
Biological Source:Streptomyces sp.
Peptide-like Molecules
PRD_000001
PRD_000491
Primary Citation
Synergistic binding of actinomycin D and echinomycin to DNA mismatch sites and their combined anti-tumour effects.
Nucleic Acids Res. ? ? ? (2023)
PMID: 36919604 DOI: 10.1093/nar/gkad156

Abstact

Combination cancer chemotherapy is one of the most useful treatment methods to achieve a synergistic effect and reduce the toxicity of dosing with a single drug. Here, we use a combination of two well-established anticancer DNA intercalators, actinomycin D (ActD) and echinomycin (Echi), to screen their binding capabilities with DNA duplexes containing different mismatches embedded within Watson-Crick base-pairs. We have found that combining ActD and Echi preferentially stabilised thymine-related T:T mismatches. The enhanced stability of the DNA duplex-drug complexes is mainly due to the cooperative binding of the two drugs to the mismatch duplex, with many stacking interactions between the two different drug molecules. Since the repair of thymine-related mismatches is less efficient in mismatch repair (MMR)-deficient cancer cells, we have also demonstrated that the combination of ActD and Echi exhibits enhanced synergistic effects against MMR-deficient HCT116 cells and synergy is maintained in a MMR-related MLH1 gene knockdown in SW620 cells. We further accessed the clinical potential of the two-drug combination approach with a xenograft mouse model of a colorectal MMR-deficient cancer, which has resulted in a significant synergistic anti-tumour effect. The current study provides a novel approach for the development of combination chemotherapy for the treatment of cancers related to DNA-mismatches.

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