Nova Patents
EP0699208A1

Novel peptide nucleic acids

Abstract

This record has no abstract on file.

Term

Term ended

Projected expiry passed 25 April 2014, 12.4 years ago.

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2 claims: 1 independent, 1 dependent

  1. 1
    Claims of equivalent WO 9425477 A2 WHAT IS CLAIMED IS:1. A compound having the formula: L1 L2 Ln wherein: n is at least 2, each of Lx-Ln is independently selected from the group consisting of hydrogen, hydroxy, (C1-C4) alkanoyl, naturally occurring nucleobases, non-naturally occurring nucleobases, aromatic moieties, DNA intercalators, nucleobase-binding groups, heterocyclic moieties, and reporter ligands, at least one of L1-Ln being a naturally occurring nucleobase, a non-naturally occurring nucleobase, a DNA intercalator, or a nucleobase-binding group;each of C1-^1 is (CR6R7)y where R6 is hydrogen and R7 is selected from the group consisting of the side chains of naturally occurring alpha amino acids, or R6 and R7 are independently selected from the group consisting of hydrogen, (C2-C6) alkyl, aryl, aralkyl, heteroaryl, hydroxy, (Cx- C6) alkoxy, (C^Cg) alkylthio, NR3R4 and SR5, where R3 and R4 are as defined above, and R5 is hydrogen, (C^Cg) alkyl, hydroxy-, alkoxy-, or alkylthio- substituted (C^Cg) alkyl, or R6 and R7 taken together complete an alicyclic or heterocyclic system;each of O~-On is (CR6R7)Z where R6 and R7 are as defined above;each of y and z is zero or an integer from 1 to 10, the sum y + z being greater than 2 but not more than 10;each of G'-G"'1 is -NR3C0- , -NR3CS-, -NR3S0- or - NR3S02-, in either orientation, where R3 is as defined above;each of A1-An and B1-Bn are selected such that: (a) A is a group of formula (Ila) , (lib) or (lie) , and B is N or R3N+, provided that at least one A is a group of formula (lie) ;or (b) A is a group of formula (lid) and B is CH;or (c) A is a group of formula (Ila) or (lib) and B is N or R3N+, provided at least one of y or z is not 1 or 2;:ila) (lib) (He) (lid) where X is 0, S, Se, NR3, CH2 or C(CH3)2;Y is a single bond, 0, S or NR4;each of p and q is zero or an integer from 1 to 5, the sum p+q being not more than 10;each of r and s is zero or an integer from 1 to 5, , the sum r+s being not more than 10;each R1 and R2 is independently selected from the group consisting of hydrogen, (C1-C4) alkyl which may be hydroxy- or alkoxy- or alkylthio- substituted, hydroxy, alkoxy, alkylthio, amino and halogen;and each R3 and R4 is independently selected from the group consisting of hydrogen, (C1-C4) alkyl, hydrox or alkoxy- or alkylthio-substituted (C^ C^ ) alkyl, hydroxy, alkoxy, alkylthio and amino;Q is -C02H, -CONR'R", -S03H or -S02NR'R'' or an activated derivative of -C02H or -S03H;and I is -NHR'"R"" or -NR' " C(0)R" " , where R' , R" , R' ' ' and R' ' ' ' are independently selected from the group consisting of hydrogen, alkyl, amino protecting groups, reporter ligands, intercalators, chelators, peptides, proteins, carbohydrates, lipids, steroids, oligonucleotides and soluble and non-soluble polymers. The compound of claim 1 having the formula: wherein: each L is independently selected from the group consisting of hydrogen, phenyl, heterocyclic moieties, naturally occurring nucleobases, and non-naturally occurring nucleobases;each R7' is independently selected from the group consisting of hydrogen and the side chains of naturally occurring alpha amino acids;n is an integer from 1 to 60, each k, 1, and m is, independently, zero or an integer from 1 to 5;each p is zero or 1;Rh is OH, NH2 or -NHLysNH2 ;and R1 is H or COCH, The compound of claim 1 having the formula: wherein : each L is independently selected from the group consisting of hydrogen, phenyl, heterocyclic moieties, naturally occurring nucleobases, and non-naturally occurring nucleobases;each R7' is independently selected from the group consisting of hydrogen and the side chains of naturally occurring alpha amino acids;n is an integer from 1 to 60, each k, 1, and m is, independently, zero or an integer from 1 to 5;each p is zero or 1;Rh is OH, NH2 or -NHLysNH2;and R- is H or COCH3. 4. A compound having one of the following formulas : wherein: L is selected from the group consisting of hydrogen, hydroxy, (C1-C4) alkanoyl, naturally occurring nucleobases, non-naturally occurring nucleobases, aromatic moieties, DNA intercalators, nucleobase-binding groups, and heterocyclic moieties, reporter ligands, wherein amino groups are, optionally, protected by amino protecting groups;each C is (CR6R7)y where R6 is hydrogen and R7 is selected from the group consisting of the side chains of naturally occurring alpha amino acids, or R6 and R7 are independently selected from the group consisting of hydrogen, (C2-C6) alkyl, aryl, aralkyl, heteroaryl, hydroxy, (Cx- C6) alkoxy, alkylthio, NR3R4 and SR5, where R3 and R4 are as defined above, and R5 is hydrogen, alkyl, hydroxy-, alkoxy-, or alkylthio- substituted alkyl, or R6 and R7 taken together complete an alicyclic or heterocyclic system;each D is (CR6R7)Z where R6 and R7 are as defined above;each of y and z is zero or an integer from 1 to 10, the sum y + z being greater than 2 but not more than 10;A and B are selected such that : (a) A is a group of formula (lie) and B is N or R3N+;or (b) A is a group of formula (lid) and B is CH;or (c) A is a group of formula (Ila) or (lib) and B is N or R3N+, provided at least one of y or z is not 1 or 2;(Ha) (lib) (He) (lid) where X is O, S, Se, NR3, CH2 or C(CH3)2;Y is a single bond, 0, S or NR4;each of p and q is zero or an integer from 1 to 5, the sum p+q being not more than 10;each of r and s is zero or an integer from 1 to 5, the sum r+s being not more than 10;each R1 and R2 is independently selected from the group consisting of hydrogen, (C1-C4) alkyl which may be hydroxy- or alkoxy- or alkylthio- substituted, hydroxy, alkoxy, alkylthio, amino and halogen;and each R3 and R4 is independently selected from the group consisting of hydrogen, (C1-C4) alkyl, hydrox or alkoxy- or alkylthio-substituted (C1-C4) alkyl, hydroxy, alkoxy, alkylthio and amino;each E is COOH, CSOH, SOOH, S02OH or an activated or protected derivative thereof;and each F is NHR3 or NPgR3, where R3 is as defined above, and Pg is an amino protecting group. 5. The compound of claim 4 having the formula: , wherein: each L is independently selected from the group consisting of hydrogen, phenyl, heterocyclic moieties, naturally occurring nucleobases, and non-naturally occurring nucleobases;each R7' is independently selected from the group consisting of hydrogen and the side chains of naturally occurring alpha amino acids;and each k, 1, and m is, independently, zero or an integer from 1 to 5. The compound of claim 4 having the formula H wherein: each L is independently selected from the group consisting of hydrogen, phenyl, heterocyclic moieties, naturally occurring nucleobases, and non-naturally occurring nucleobases;each R7' is independently selected from the group consisting of hydrogen and the side chains of naturally occurring alpha amino acids;and each k, 1, and m is, independently, zero or an integer from 1 to 5. 7. A process for preparing a compound according to claim 1, comprising the steps of: A) providing a polymer substrate, said polymer being funetionalized with a chemical group capable of forming an anchoring linkage with an amino acid;B) coupling said polymer with a first amino acid through said anchoring linkage, said first amino acid having formula (IV) : L (IV) wherein : L is selected from the group consisting of naturally occurring nucleobases, non-naturally occurring nucleobases, aromatic moieties, DNA intercalators, nucleobase-binding groups, heterocyclic moieties, and reporter ligands, wherein amino groups are, optionally, protected by amino protecting groups;each C is (CR6R7)y where R6 is hydrogen and R7 is selected from the group consisting of the side chains of naturally occurring alpha amino acids, or R6 and R7 are independently selected from the group consisting of hydrogen, (C2-C6) alkyl, aryl, aralkyl, heteroaryl, hydroxy, (Ci- Cg) alkoxy, (Ci-Cg) alkylthio, NR3R4 and SR5, where R3 and R4 are as defined above, and R5 is hydrogen, (Ci-Cg) alkyl, hydroxy-, alkoxy-, or alkylthio- substituted (Cι-C6) alkyl, or R6 and R7 taken together complete an alicyclic or heterocyclic system;each D is (CR5R7)Z where R6 and R7 are as defined above;each of y and z is zero or an integer from 1 to 10, the sum y + z being greater than 2 but not more than 10;A and B are selected such that : (a) A is a group of formula (lie) and B is N or R3N+;or (b) A is a group of formula (lid) and B is CH;or (c) A is a group of formula (Ila) or (lib) and B is N or R3N+, provided at least one of y or z is not 1 or 2;(Ha) (lib) ( lie) ( lid) where : X is 0, S, Se, NR3, CH2 or C(CH3)2;Y is a single bond, 0, S or NR4;each of p and q is zero or an integer from 1 to 5, the sum p+q being not more than 10;each of r and s is zero or an integer from 1 to 5, the sum r+s being not more than 10;each R1 and R2 is independently selected from the group consisting of hydrogen, (C1-C4) alkyl which may be hydroxy- or alkoxy- or alkylthio- substituted, hydroxy, alkoxy, alkylthio, amino and halogen;and each R3 and R4 is independently selected from the group consisting of hydrogen, (Ci-C4) alkyl, hydrox or alkoxy- or alkylthio-substituted (Ci-C4) alkyl, hydroxy, alkoxy, alkylthio and amino;each E is COOH, CSOH, SOOH, S02OH or an activated or protected derivative thereof;and each F is NHR3 or NPgR3, where R3 is as defined above, and Pg is an amino protecting group;C) removing said amino protecting group from said coupled first amino acid to generate a free amino group;and D) reacting said free amino group with a second amino acid having formula (IV) to form a peptide chain. 8. The process of claim 7 further comprising the steps of : E) removing said amino protecting group from said second amino acid to generate a terminal free amino group on said peptide chain;and F) reacting said free amino group on said peptide chain with a further amino acid having formula (IV) to lengthen said peptide chain. 9. The process of claim 8 wherein steps E and F are performed a plurality of times. 10. The process of claim 8 further comprising removing at least one protecting group remaining on the amino acid moieties of the peptide chain. 11. The process of claim 7 further comprising cleaving said anchoring linkage without substantially degrading said peptide chain. 12. The process of claim 7 wherein the polymer substrate contains polystyrene, polyacrylamide, silica, a composite material, cotton, or a derivative thereof. 13. The process of claim 8 wherein the chemical group capable of forming said anchoring linkage is chloro-, bromo- and iodo-substituted alkyl, amino-substituted alkyl, amino and aryl-substituted alkyl, amino- and alkylaryl- substituted alkyl, hydroxy-substituted alkyl, or a derivative thereof having a spacer group that can be cleaved substantially without degradation of said polypeptide. 14. The process of claim 13 wherein chloro-substi- tuted alkyl is chloromethyl, amino-substituted alkyl is aminomethyl, amino- and alkyl-substituted aryl is a- aminobenzyl, amino- and alkylaryl-substituted alkyl is selected from the group consisting of Q!-amino-3- and α-amino- 4-methylbenzyl, and hydroxy-substituted alkyl is hydroxymethyl . 15. The process of claim 13 wherein: the chemical group is derived from an amino-containing moiety selected from amino-substituted alkyl, amino- and aryl substituted alkyl, and amino- and alkylaryl-substituted alkyl;and the chemical group includes a spacer group derived from the group consisting of 4- (haloalkyl) aryl-lower alkanoic acids, Boc-aminoacyl-4- (oxymethyl) aryl-lower alkanoic acids, N-Boc-p-acylbenzhydrylamines, N-Boc-4'- (lower alkyl) -p- acylbenzhydrylamines, N-Boc-4'- (lower alkoxy) -p- acylbenzhydrylamines, and 4-hydroxymethylphenoxy-lower alkanoic acids. 16. A process for sequence-specific recognition of a double-stranded polynucleotide, comprising contacting said polynucleotide with a compound that is different from natural RNA and that binds to one strand of the polynucleotide, thereby displacing the other strand, said being the compound of claim 1. 17. A process for modulating the expression of a gene in an organism, comprising administering to said organism a compound according to claim 1 that specifically binds to DNA or RNA deriving from said gene, said compound being the compound of claim 1. 18. The process of claim 17 wherein said modulation includes inhibiting transcription of said gene. 19. The process of claim 17 wherein said modulation includes inhibiting replication of said gene.