The use of molecular dynamics simulations to evaluate the DNA sequence-selectivity of G-A cross-linking PBD-duocarmycin dimers

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• 作者：Paul J.M. Jackson ; Khondaker M. Rahman ; David E. Thurston
• 关键词：DNA cross-linking ; Pyrrolobenzodiazepine ; Duocarmycin ; PBD&ndash ; CPI dimer ; Molecular dynamics ; PBD ; CPI ; CBI ; Seco-amino CI
• 刊名：Bioorganic & Medicinal Chemistry Letters
• 出版年：2017
• 出版时间：1 January 2017
• 年：2017
• 卷：27
• 期：1
• 页码：102-108
• 全文大小：1161 K
• 卷排序：27

文摘

The pyrrolobenzodiazepine (PBD) and duocarmycin families are DNA-interactive agents that covalently bond to guanine (G) and adenine (A) bases, respectively, and that have been joined together to create synthetic dimers capable of cross-linking G–G, A–A, and G–A bases. Three G–A alkylating dimers have been reported in publications to date, with defined DNA-binding sites proposed for two of them. In this study we have used molecular dynamics simulations to elucidate preferred DNA-binding sites for the three published molecular types. For the PBD–CPI dimer UTA-6026 (1), our simulations correctly predicted its favoured binding site (i.e., 5′-C(G)AATTA-3′) as identified by DNA cleavage studies. However, for the PBD–CI molecule (‘Compound 11’, 3), we were unable to reconcile the results of our simulations with the reported preferred cross-linking sequence (5′-ATTTTCC(G)-3′). We found that the molecule is too short to span the five base pairs between the A and G bases as claimed, but should target instead a sequence such as 5′-ATTTC(G)-3′ with two less base pairs between the reacting G and A residues. Our simulation results for this hybrid dimer are also in accord with the very low interstrand cross-linking and in vitro cytotoxicity activities reported for it. Although a preferred cross-linking sequence was not reported for the third hybrid dimer (‘27eS’, 2), our simulations predict that it should span two base pairs between covalently reacting G and A bases (e.g., 5′-GTAT(A)-3′).