US 6,506,906 B1 · Preparation and use of bifunctional molecules having DNA sequence binding specificity

Abstract

Small molecule polyamides that specifically bind with subnanomolar affinity to any predetermined sequence in the human genome with potential use in molecular biology and human medicine are described. Further, the designed compounds which target the minor groove of B-form double helical DNA offer a general approach for the control of gene-expression. Simple rules are disclosed which provide for rational control of the DNA-binding sequence specificity of synthetic polyamides containing N-methylpyrrole and N-methylimidazole amino acids. A series of molecular templates for polyamide design are disclosed which provide for small molecules which recognize predetermined DNA sequences with affinities and specificities comparable to sequence-specific DNA-binding proteins such as transcription factors. These design rule are applied to provide a polyamide for specific targeting of a predetermined 7 base pair sequence from a conserved HIV gene promoter at subnanomolar concentration. The pyrrole-imidazole polyamides described herein represent the only class of designed small molecules to date that can bind any predetermined sequence of double helical DNA.

Claims8

Dependent claims

A polyamide of the formula

or a pharmaceutically acceptable salt thereof, wherein:
n is 5-11;
m is 0-6;
each Y is independently selected from the group consisting of
wherein
p is 0 to 5, provided that at least one Y is not —NH-;
Z is a covalent bond or
wherein
r is 1-3;
each X is independently selected from the group consisting C and N;
each R1 is independently selected from the group consisting of H, C1-6 alkylamine, C1-6 alkyldiamine, C1-6 alkylcarboxylate, C1-6 alkyl, C1-6 alkenyl, C1-6 alkynyl and C1-6 alkyl-L;
each R2 independently selected from the group consisting of H and OH if X is C, and is not present if X is N;
R3 is selected from the group consisting of H, Cl, NO, N-acetyl, benzyl, C1-6 alkyl, C1-6 alkenyl, and C1-6 alkynyl;
and
R4 is —NR5R6 or —NH(CH2)0-6NR5R6, where R5 and R6 are independently chosen from the group consisting of H, Cl, NO, N-acetyl, benzyl, C1-6 alkyl, C1-6 alkylamine, C1-6 alkyldiamine, C1-6 alkylcarboxylate, C1-6 alkenyl, C1-6 alkyl, and C1-6 alkyl-L;
wherein L is a detectable label, and wherein at least one R1, R5, of R6 is C1-6 alkyl-L.

13 more elements

A polyamide selected from the group consisting of

ImPyPyPy-γ-PyPyPyPy-β-Dp, PyPyImPy-γ-PyPyPyPy-β-Dp, ImPyPyPy-γ-ImPyPyPy-β-Dp, PyImPyPy-γ-PyImPyPy-β-Dp, ImPyImPy-γ-PyPyPyPy-β-Dp, ImImPyPy-γ-PyPyPyPy-β-Dp, ImImImPy-γ-PyPyPyPy-β-Dp, ImImPyPy-γ-ImPyPyPy-β-Dp, ImPyPyPy-γ-ImImPyPy-β-Dp, ImImPyPy-γ-ImImPyPy-β-Dp, ImPyImPy-γ-ImPyImPy-β-Dp, ImImImPy-γ-ImPyPyPyPy-β-Dp, ImImImIm-γ-PyPyPyPy-β-Dp, Im-β-PyPy-γ-Im-β-PyPy-β-Dp, Im-β-ImIm-γ-Py-β-PyPy-β-Dp, Im-β-ImPy-γ-Im-β-ImPy-β-Dp, ImPyPyPyPy-γ-ImPyPyPyPy-β-Dp, ImImPyPyPy-γ-ImPyPyPyPy-β-Dp, ImPyImPyPy-γ-ImPyPyPyPy-β-Dp, ImImPyImIm-γ-PyPyPyPyPy-β-Dp, ImPyPyImPy-γ-ImPyPyImPy-β-Dp, ImPy-β-PyPy-γ-ImPy-β-PyPy-β-Dp, ImIm-β-ImIm-γ-PyPy-β-PyPy-β-Dp, ImPy-β-ImPy-γ-ImPy-β-ImPy-β-Dp, ImPy-β-PyPyPy-γ-ImPyPy-β-PyPy-β-Dp, ImIm-β-PyPyPy-γ-PyPyPy-β-PyPy-β-Dp, ImPy-β-ImPyPy-γ-ImPyPy-β-PyPy-β-Dp, ImIm-β-PyPyPy-γ-ImImPy-β-PyPy-β-Dp, ImPy-β-PyPyPy-γ-PyPyPy-β-ImPy-β-Dp, ImPyPyPyPyPy-γ-ImPyPyPyPyPy-β-Dp, ImPyPy-β-PyPy-γ-ImPyPy-β-PyPy-β-Dp, ImPyPyPy-β-Py-γ-Im-β-PyPyPyPy-β-Dp, ImImPyPyPyPy-γ-ImImPyPyPyPy-β-Dp, Im-β-PyPyPyPy-γ-Im-β-PyPyPyPy-β-Dp, ImPyPyPy-β-Py-γ-ImPyPyPy-β-Py-β-Dp, ImPyImPyPyPy-γ-ImPyPyPyPyPy-β-Dp, ImPyPy-β-PyPy-γ-ImPy-β-PyPyPy-β-Dp, ImPyPyPyPy-β-γ-ImPyPyPyPy-β-β-Dp, ImPy-β-ImPyPy-γ-ImPy-β-ImPyPy-β-Dp, Im-β-PyPyPyPy-γ-ImPyPyPy-β-Py-β-Dp, Im-β-ImPyPyPy-γ-ImPyPyPy-β-Py-β-Dp, ImPyPy-β-PyPyPy-β-Dp, ImImPy-β-PyPyPy-β-Dp, ImImIm-β-PyPyPy-β-Dp, ImPyPyPyPy-β-PyPyPy-β-Dp, ImPyPyPy-β-PyPyPy-β-Dp, ImPyPy-β-PyPyPyPyPy-β-Dp, ImPyPyPy-β-PyPyPy-β-Dp, ImImPyPy-β-PyPyPyPy-β-Dp, ImImImPy-β-PyPyPyPy-β-Dp, ImPyPyPy-β-ImPyPyPy-β-Dp, ImImPyPy-β-ImPyPyPy-β-Dp, ImImPyPyPy-β-PyPyPyPyPy-β-Dp, ImImImPyPy-β-PyPyPyPyPy-β-Dp, ImIm-β-PyPy-β-PyPy-β-PyPy-β-Dp, ImImPy-β-PyPyPy-β-PyPyPy-β-PyPyPy-β-Dp, PyImPy-γ-ImPyPy-β-PyPyPy-β-PyPyPy-β-Dp, PyImPy-γ-ImPyPy-β-PyPyPy-β0PyPyPy-β-Dp, ImImPy-γ-ImPyPy-β-PyPyPy-β-Dp, ImPyPy-γ-ImPyPy-G-PyPyPy-β-Dp, ImPyPyPy-γ-ImImImPy-β-PyPyPy-β-Dp, ImImPyPy-β-Dp, ImImPyPy-γ-ImImPyPy-β-PyPyPyPy-β-Dp, and ImImPyPy-γ-PyPyPyPy-β-PyPyPyPy-β-Dp, bound to a detectable label wherein Im is N-methyl-Imidazole, Py is methylpyrrole, βis β-alanine, Dp is dimethylaminopropylamide, and γ is γ-aminobutyric acid.

Dependencies are inferred from the claim text.

Preparation and use of bifunctional molecules having DNA sequence binding specificity

Life of this patent

Preparation and use of bifunctional molecules having DNA sequence binding specificity

Life of this patent

Abstract

Claims8