Duocarmycin SA Shortened, Simplified, and Extended Agents:  A Systematic Examination of the Role of the DNA Binding Subunit

Abstract

The examination of shortened, simplified, and extended analogs of duocarmycin SA is described and constitutes a detailed study of the role of linked DNA binding subunit. In addition to enhancing the DNA binding affinity and selectivity through minor groove noncovalent contacts, the studies in conjunction with those of the accompanying article illustrate that an extended rigid N2 amide substituent is required for catalysis of the DNA alkylation reaction. This activation for DNA alkylation is independent of pH, and we propose it results from a binding-induced conformational change in the agents which increases their inherent reactivity. The ground state destabilization of the substrate results from a twist in the linking amide that disrupts the vinylogous amide stabilization of the alkylation subunit and activates the agent for nucleophilic addition. This leads to preferential activation of the agents for DNA alkylation within the narrower, deeper AT-rich minor groove sites where the inherent twist in the linking amide and helical rise of the bound conformation is greatest. Thus, shape-selective recognition (preferential AT-rich noncovalent binding) and shape-dependent catalysis (induced twist in linking N2 amide) combine to restrict SN2 alkylation to accessible adenine N3 nucleophilic sites within the preferred binding sites. Additional ramifications of this DNA binding-induced conformational change on the reversibility of the DNA alkylation reaction are discussed. The results of the study illustrate the importance of the C5‘ methoxy group and the C6 methyl ester of duocarmycin SA, and a previously unrecognized role for these substituents is proposed.

Synthesis and evaluation of duocarmycin SA analogs incorporating the methyl 1,2,8,8a-tetrahydrocyclopropa[c]imidazolo[4,5-e]indol-4-one-6-carboxylate (CImI) alkylation subunit

“…4 The study of the natural products, 5-8 their synthetic unnatural enantiomers, 9 and key analogs 10 has defined structural features that control their DNA alkylation selectivity, 4,10 efficiency, rate, reversibility, 11 and catalysis, 12 providing a detailed understanding of the relationships between structure, reactivity, and biological activity. 13 Central to these studies have been modifications in the DNA alkylation subunit of the natural products and the establishment of the impact that the deep-seated changes have on their functional reactivity and biological properties.…”

Structural Features of the (+)‐Yatakemycin/d(GACTAATTGAC)‐(GTCAATTAGTC) Complex – Quantum Mechanical Calculation of NMR Parameters as a Tool for the Characterization of Ligand/DNA Interactions

“…(+)-Yatakemycin [1][2][3][4] (1), isolated from the culture broth of Streptomyces sp. TP-A0356, [5] is the newest and most potent member of a class of natural antitumor compounds [1][2][3][4] that includes CC-1065 (3), and duocarmycins A (DA, 4) and SA (DSA, 2) shown in Scheme 1.…”

“…TP-A0356, [5] is the newest and most potent member of a class of natural antitumor compounds [1][2][3][4] that includes CC-1065 (3), and duocarmycins A (DA, 4) and SA (DSA, 2) shown in Scheme 1. [6] [a] Dipartimento di Scienze Farmaceutiche, Università degli studi These natural products derive their biological activities [1,7,8] from specific alkylation of AT-rich regions of DNA.…”

“…[31] For instance, DSA, presenting a larger χ1 value in the bound conformation than the other two analogues, shows a higher reaction efficiency than (+)-DA and (+)-DSI (Scheme 1). [24] Subsequent studies on sandwiched analogues such as (+)-and (-)-CDPI-DSA-CDPI [1][2][3][4][32][33] have made great contributions to understanding of the shape-dependent catalysis, because these compounds show faster alkylation rates. The steric bulk of the sandwiched analogues in fact forces such a compound into greater perturbation from the free planar conformation to allow penetration into the minor groove.…”

“…(+)-Yatakemycin, like the preceding sandwiched derivatives, [4,32,33] shows improved alkylating properties, [1] displaying faster alkylation rate and higher alkylation selectivity, and consequently more potent cytotoxic activity than preceding analogues (Table 1).…”