Indolocarbazole Glycosides in Inactive Conformations

Abstract

Indolocarbazole glycosides related to rebeccamycin represent a promising category of antitumor agents targeting DNA and topoisomerase I. These drugs prefer to adopt a closed conformation with an intramolecular hydrogen bond between the indole NH group and the pyranose oxygen atom. Three pairs of indolocarbazole monoglycosides bearing an NH or an N-methyl indole moiety were synthesized and their biological properties investigated at the molecular and cellular level. Replacing the indole NH proton with a methyl group reduces DNA interaction and abolishes activity against DNA topoisomerase I. Surface plasmon resonance studies performed with a pair of water-soluble indolocarbazole glycosides and two hairpin oligonucleotides containing an [AT]4 or a [CG]4 sequence indicate that both the NH and the N-methyl derivative maintain a relatively high affinity for DNA (Keq = 2 - 6 x 10(5) M(-1)) but the incorporation of the methyl group restricts access to the DNA. The number of ligand binding sites (n) on the oligonucleotides is about twice as high for the NH compound compared to its N-methyl analogue. Modeling and 1H NMR studies demonstrate that addition of the N-methyl group drives a radical change in conformation in which the orientation of the aglycone relative to the beta-glucoside is reversed. The loss of the closed conformation by the N-methyl derivatives perturbs thir ability to access DNA binding sites and prevents the drug from inhibiting topoisomerase I. As a consequence, the NH compounds exhibit potent cytotoxicity against CEM leukemia cells with an IC50 value in the 1 microM range, whereas the N-methyl analogues are 10 to 100 times less cytotoxic. These studies offer circumstantial evidence supporting the importance of the closed conformation in the interaction of indolocarbazole glycosides with their molecular targets, DNA and topoisomerase I.

Novel Antitumor L‐Arabinose Derivative of Indolocarbazole with High Affinity to DNA

“…[12,13] The indolocarbazole derivatives containing two sugar residues, AT2433-A1 and AT2433-B1, showed comparable affinity to short fragments [d(AT) 4 ) m À1 , respectively. [11,15,16] However, these high values might result from the tight binding of these ligands to the terminal stacking contacts of the short hairpins. [20] Intracellular targets of AIC other than DNA might include CDKs.…”

“…Moreover, the sugar residue can enhance the binding of the conjugate to its target, as well as increases water solubility. [1,2,[6][7][8][9][10][11][12][13][14][15][16] Intercalation of indolocarbazoles alters duplex conformation, in particular by causing local extension and unwinding of DNA strands. [10][11][12][13][14][15][16] However, the DNA binding constants of currently used indolocarbazoles containing one carbohydrate substituent are relatively low (K a (2 10 5 ) m…”

Semi‐interpenetrating polymer networks from castor oil‐based polyurethane and nitrokonjac glucomannan

“…Moreover, the sugar residue can enhance the binding of the conjugate to its target, as well as increases water solubility 1. 2, 6–16…”

“…Intercalation of indolocarbazoles alters duplex conformation, in particular by causing local extension and unwinding of DNA strands 10–16. However, the DNA binding constants of currently used indolocarbazoles containing one carbohydrate substituent are relatively low ( K a ≤(2×10 5 ) M −1 ) 10.…”

RebG‐ and RebM‐Catalyzed Indolocarbazole Diversification

“…To examine the dependence of RebM on metal divalent ions, EDTA (1 mm final concentration) or divalent metal (CaCl 2 , CoCl 2 , CuCl 2 , FeCl 2 , MgCl 2 , MnCl 2 , NiSO 4 , and ZnCl 2 , 1 mm final concentration) were added to the assay. Under the conditions adopted for kinetic determinations-RebM (100 nm) was used in the assay with fixed SAM (200 mm) and variable 19 (4, 6, 10, 15, and 20 mm) or with fixed 19 (20 mm) and variable SAM (5,10,20,50, and 100 mm)-the initial (first 5 min) velocity was linear. For structural elucidation, the preparative reaction of 19 with RebM was proportionately scaled up to 10 mL (50 mm 19, 100 mm SAM, 10 mm RebM) or 4 mL for 33/34.…”