B-ring-aryl substituted luotonin A analogues with a new binding mode to the topoisomerase 1-DNA complex show enhanced cytotoxic activity.
Topoisomerase 1 inhibition is an important strategy in targeted cancer chemotherapy. The drugs currently in use acting on this enzyme belong to the family of the camptothecins, and suffer severe limitations because of their low stability, which is associated with the hydrolysis of the δ-lactone moiety in their E ring. Luotonin A is a natural camptothecin analogue that lacks this functional group and therefore shows a much-improved stability, but at the cost of a lower activity. Therefore, the development of luotonin A analogues with an increased potency is important for progress in this area. In the present paper, a small library of luotonin A analogues modified at their A and B rings was generated by cerium(IV) ammonium nitrate-catalyzed Friedländer reactions. All analogues showed an activity similar or higher than the natural luotonin A in terms of topoisomerase 1 inhibition and some compounds had an activity comparable to that of camptothecin. Furthermore, most compounds showed a better activity than luotonin A in cell cytotoxicity assays. In order to rationalize these results, the first docking studies of luotonin-topoisomerase 1-DNA ternary complexes were undertaken. Most compounds bound in a manner similar to luotonin A and to standard topoisomerase poisons such as topotecan but, interestingly, the two most promising analogues, bearing a 3,5-dimethylphenyl substituent at ring B, docked in a different orientation. This binding mode allows the hydrophobic moiety to be shielded from the aqueous environment by being buried between the deoxyribose belonging to the G(+1) guanine and Arg364 in the scissile strand and the surface of the protein and a hydrogen bond between the D-ring carbonyl and the basic amino acid. The discovery of this new binding mode and its associated higher inhibitory potency is a significant advance in the design of new topoisomerase 1 inhibitors.
Sección Departamental de Química Analítica, Facultad de Farmacia, Universidad Complutense, Madrid, Spain; BIOHET (Biologically Relevant Heterocycles) group, Facultad de Farmacia, Universidad Complutense, Madrid, Spain.
Víctor
V
González-Ruiz
Departamento de Bioquímica y Biología Molecular II, Facultad de Farmacia, Universidad Complutense, Madrid, Spain; Instituto de Investigación Sanitaria del Hospital Clínico San Carlos, Madrid, Spain.
Irene
I
Pascua
Departamento de Bioquímica y Biología Molecular II, Facultad de Farmacia, Universidad Complutense, Madrid, Spain; Instituto de Investigación Sanitaria del Hospital Clínico San Carlos, Madrid, Spain.
Tamara
T
Fernández-Marcelo
BIOHET (Biologically Relevant Heterocycles) group, Facultad de Farmacia, Universidad Complutense, Madrid, Spain; Departamento de Química Orgánica y Farmacéutica, Facultad de Farmacia, Universidad Complutense, Madrid, Spain.
Pascual
P
Ribelles
BIOHET (Biologically Relevant Heterocycles) group, Facultad de Farmacia, Universidad Complutense, Madrid, Spain; Departamento de Química Orgánica y Farmacéutica, Facultad de Farmacia, Universidad Complutense, Madrid, Spain.
Giulia
G
Bianchini
Departamento de Química Orgánica y Farmacéutica, Facultad de Farmacia, Universidad Complutense, Madrid, Spain; Department of Chemical and Biotechnology, SASTRA University, Thanjavur, India.
Vellaisamy
V
Sridharan
Departamento de Bioquímica y Biología Molecular II, Facultad de Farmacia, Universidad Complutense, Madrid, Spain; Instituto de Investigación Sanitaria del Hospital Clínico San Carlos, Madrid, Spain.
Pilar
P
Iniesta
BIOHET (Biologically Relevant Heterocycles) group, Facultad de Farmacia, Universidad Complutense, Madrid, Spain; Departamento de Química Orgánica y Farmacéutica, Facultad de Farmacia, Universidad Complutense, Madrid, Spain.
M Teresa
MT
Ramos
Sección Departamental de Química Analítica, Facultad de Farmacia, Universidad Complutense, Madrid, Spain; BIOHET (Biologically Relevant Heterocycles) group, Facultad de Farmacia, Universidad Complutense, Madrid, Spain.
Ana I
AI
Olives
Sección Departamental de Química Analítica, Facultad de Farmacia, Universidad Complutense, Madrid, Spain; BIOHET (Biologically Relevant Heterocycles) group, Facultad de Farmacia, Universidad Complutense, Madrid, Spain.
M Antonia
MA
Martín
BIOHET (Biologically Relevant Heterocycles) group, Facultad de Farmacia, Universidad Complutense, Madrid, Spain; Departamento de Química Orgánica y Farmacéutica, Facultad de Farmacia, Universidad Complutense, Madrid, Spain.
J Carlos
JC
Menéndez
D000596:Amino Acids / Q000737:chemistry; D000970:Antineoplastic Agents / Q000138:chemical synthesis / Q000737:chemistry; D002166:Camptothecin / Q000737:chemistry; D002563:Cerium / Q000737:chemistry; D002626:Chemistry, Pharmaceutical / Q000379:methods; D003460:Crystallization; D004247:DNA / Q000737:chemistry*; D004264:DNA Topoisomerases, Type I / Q000737:chemistry*; D006367:HeLa Cells; D006801:Humans; D006860:Hydrogen Bonding; D008024:Ligands; D009682:Magnetic Resonance Spectroscopy; D008968:Molecular Conformation; D009566:Nitrates / Q000737:chemistry; D011485:Protein Binding; D011758:Pyrroles / Q000737:chemistry*; D011809:Quinones / Q000737:chemistry*; D059004:Topoisomerase I Inhibitors / Q000494:pharmacology
D000596:Amino Acids; D000970:Antineoplastic Agents; D008024:Ligands; D009566:Nitrates; D011758:Pyrroles; D011809:Quinones; D059004:Topoisomerase I Inhibitors; C480761:luotonin A; D002563:Cerium; D004247:DNA; D004264:DNA Topoisomerases, Type I; C528909:TOP1 protein, human; C006568:ammonium nitrate; D002166:Camptothecin