Design, synthesis, and analysis of minor groove binder pyrrolepolyamide-2'-deoxyguanosine hybrids

Abstract

Pyrrolepolyamide-2'-deoxyguanosine hybrids (Hybrid 2 and Hybrid 3) incorporating the 3-aminopropionyl or 3-aminopropyl linker were designed and synthesized on the basis of previously reported results of a pyrrolepolyamide-adenosine hybrid (Hybrid 1). Evaluation of the DNA binding sequence selectivity of pyrrolepolyamide-2'-deoxyguanosine hybrids was performed by CD spectral and T(m) analyses. It was shown that Hybrid 3 possessed greater binding specificity than distamycin A, Hybrid 1 and Hybrid 2.

Figure 1

Structures of Distamycin A, Netropsin, Hybrid 1, Hybrid 2, and Hybrid 3.

Scheme 1

Reaction conditions (i) CL₃CCOCL, Et₂O, rt, 1 hour. (ii) HNO₃, Ac₂O, −10°C ∼ rt, 1 hour. (iii) NaOMe, MeOH, rt, 15 minutes. (iv) 1. H₂, 10% Pd/C, AcOEt, rt, 12 hours; 2. (Boc)₂O, Et₂O, rt, 2 hours. (v) 1. 1 M NaOH, H₂O/MeOH, 60°C, 1 ~ 2 hours; 2. 10% HCL aq. (vi) 1. H₂, 10% Pd/C, AcOEt, rt, 12 hours; 2. 6, EDCI, DMAP, DMF, rt, 3 hours. (vii) 1. AcCL, MeOH, 0°C, 30 minutes. 2. 6, EDCI, DMAP, DMF, rt, 3 hours. (viii) 1. AcCL, MeOH, 0°C, 30 minutes; 2. HCOOH, CDI, THF, −40°C, 30 minutes. (ix) ethyl β-alanine, EDCI, DMAP, DMF, rt, 3 hours.

Scheme 2

Reaction conditions (i) 3-(Fmoc-amino)propionyl chloride (prepared from N-Fmoc-β-alanine and SOCL₂), THF/Pyridine, rt, 72 hours. (ii) 10, EDCI, DMAP, DMF, rt, 24 hours. (iii) 0.2 M TEAF, THF, rt, 30 minutes.

Figure 2

CD spectra for the DNA duplexs with ligand (Hybrid 2, Hybrid 3, Dst, or compound 11) at several [Iigand]/[duplex] ratios in buffer consisting of 10 mM sodium phosphate, 10 mM NaCL, and 0.1 mM Na₂EDTA at pH 7.0 and 20°C: 3.0 mL of duplex solution (5.8 μM) titrated ligand (Hybrid 2, Hybrid 3, and Dst: 0–14.5 μM) and 3.0 mL of duplex solution (4 μM) titrated ligand (compound 11: 0–12 μM). *DNA duplexs: DNA 1  = d-(5′-CGCAAATTGGC-3′)-d-(3′-GCGTTTAACCG-5′), DNA 2  = d-(5′-CGCAGACTGGC-3′)-d-(3′-GCGTCTGACCG-5′), DNA 3  = d-(5′-GCACGACTACG-3′)-d-(3′-CGTGCTGATGC-5′), DNA 1 contains the high affinity binding site (5′-AAATT-3′) of Dst.

Scheme 3

Reaction conditions (i) sodium phenoxide, 1,4-dioxane, rt, 1.5 hours. (ii) 1. Propane-1,3-diamine (1.1 eq.), rt, 3.5 hours; 2. pyridinium hydrochloride. (iii) 17, DCC, HOBT, DIEA, DMF, rt, 24 hours. (v) 1. AcCL, MeOH, 0°C, 30 minutes; 2. HCOOH, CDI, THF, −40°C, 1 hour.

Scheme 4

Reaction conditions (i) 1. piperidine, DMF, rt, 20 minutes. 2. 19, Et₃N, DMF, 60°C 12 hours. (ii) 0.5 M DBU, pyridine, rt, 12 hours. (iii) 0.05 M NaOMe, MeOH/pyridine, rt, 2 hours.