# Patent

## Title
DNA minor groove binding compounds

## Abstract

There is provided an oligopeptide compound comprising: (a) at least one nitrogen-containing basic group attached to at least one end of the oligopeptide; and (b) two or more heterocyclic monomers, at least one of which is substituted in the heterocyclic part by a branched, cyclic or part cyclic C3-5 alkyl group, or a pharmaceutically acceptable salt or solvate thereof; which compound, salt or solvate binds to the minor groove of DNA.

## Background
FIELD OF THE INVENTION
This invention relates to synthetic compounds that have affinity for nucleic acids, and in particular to compounds that bind to the minor groove of DNA.
BACKGROUND AND PRIOR ART
Because of its fundamental role in molecular biological processes, DNA represents an important target for drug action. Compounds that can recognize defined sequences of DNA have a wide variety of potential uses, such as the modulation of gene expression.
The outer surface of double-helical DNA has two channels, namely the major and minor grooves. Both of these grooves contain chemical information by way of arrangements of hydrogen-bond donors and acceptors, electrostatic charges, dipoles, hydrophobic regions and so on.
The major groove contains approximately twice the information content of the minor groove in terms of the number of potential hydrogen-bonding contacts. In view of this, the major groove is the preferred recognition site for cellular proteins such as control proteins, promoters and repressors.
In contrast, the minor groove is normally (with a few exceptions) relatively unoccupied. The vulnerability of the minor groove makes it a particularly useful target for compounds that bind to DNA. Indeed, perhaps for this very reason, the minor groove is the binding site for certain naturally occurring antibiotics (such as netropsin and distamycin).
Netropsin and distamycin are oligopeptides based on pyrrole amino acid monomers. These compounds both bind to DNA with dissociation constants in the order of 10−5 M. They also show a preference for AT-rich regions of DNA. Although they have intrinsic biological activity, netropsin and distamycin also have many limitations including toxicity, moderate affinity and limited selectivity. A number of workers have therefore prepared synthetic analogues of netropsin and distamycin, with a view to overcoming these disadvantages. Many of these compounds are reviewed by Sondhi et al. (Curr. Med. Chem. 4, 313 (1997)), Reddy et al. (Pharmacology & Therapeutics 84, 1 (1999)), Wemmer (Biopolymers 52, 197 (2001)) and Dervan (Bioorg. Med. Chem. 9, 2215 (2001)).
Compounds designed to bind to DNA regions containing GC base pairs are described in, for example: Anti-Cancer Drug Design 5, 3 (1990); Proc. Natl. Acad. Sci. USA 89, 7586 (1992); Biochemistry 32, 4237 (1993); Science 266, 647 (1994); Anti-Cancer Drug Design 10, 155 (1995); Bioorg. Med. Chem. 8, 985 (2000); and Mol. Biol. 34, 357 (2000). Various other netropsin and distamycin analogues are described in: J. Am. Chem. Soc. 114(15), 5911 (1992); Biochemistry 31, 8349 (1992); Bioconjugate Chem. 5, 475 (1994); Biochem. Biophys. Res. Commun. 222, 764 (1996); J. Med. Chem. 43, 3257 (2000); and Tetrahedron 56, 5225 (2000). Further, the use of certain netropsin and distamycin analogues as antimicrobial, antiviral and/or antitumor agents is described in Molecular Pharmacology 54, 280 (1998), Bioorg. Med. Chem. Lett. 6(18), 2169 (1996), J. Med. Chem. 45, 805 (2002), Bioorg. Med. Chem. Lett. 12, 2007 (2002), international patent applications WO 97/28123, WO 98/21202, WO 01/74898 and WO 02/00650, as well as in U.S. Pat. Nos. 4,912,199, 5,273,991, 5,637,621, 5,698,674 and 5,753,629. Methods of synthesizing analogues of netropsin and distamycin are described in U.S. Pat. No. 6,090,947.
Cellular uptake of distamycin analogues is described in Bioorg. Med. Chem. Lett. 11, 769 (2001).
None of the above-mentioned documents describe oligopeptide analogues of netropsin or distamycin, which analogues comprise at least two heterocyclic monomers, at least one of which is substituted in the heterocyclic part by a branched, cyclic or part cyclic C3-5 alkyl group. Surprisingly, we have found that compounds of this type bind with a high affinity and specificity to the minor groove of DNA.
DESCRIPTION OF THE INVENTION
According to the invention there is provided oligopeptide compounds comprising:

    (a) at least one nitrogen-containing basic group attached to at least one end of the oligopeptide; and
    (b) two or more heterocyclic monomers, at least one of which is substituted in the heterocyclic part by a branched, cyclic or part cyclic C3-5 alkyl group,
    or a pharmaceutically acceptable salt or solvate thereof;
    which compounds, salts or solvates bind to the minor groove of DNA,
    and which compounds are referred to hereinafter as “the compounds of the invention”.


When used herein, the term “oligopeptide” includes organometallic and, particularly, organic compounds that contain at least one amide (e.g. —C(O)NH—) group that links different parts of the molecule. Preferred oligopeptide compounds are those of low molecular weight (e.g. below 2000, such as below 1500 and, particularly, below 1000 g mol−1). Preferred oligopeptide compounds also include those that comprise heterocyclic amino acids (i.e. heterocyclic groups that possess both carboxylic acid and amine functionalities) that are coupled to each other via linkages that include at least one amide bond (e.g. a direct amide bond or a linkage formed by reaction of two heterocyclic amino acids with a compound that possesses two carboxylic acid groups, two amine groups or one acid and one amine group). Suitable compounds possessing two carboxylic acid groups, two amine groups or one acid and one amine group are known to those skilled in the art, for example the “linkers” disclosed in Curr. Med. Chem. 4, 313-358 (1997), Pharmacology & Therapeutics 84, 1-111 (1999), J. Med. Chem. 43, 3257-3266 (2000), Tetrahedron 56, 5225-5239 (2000), the disclosures of which documents are hereby incorporated by reference.
When used herein, the term “nitrogen-containing basic group” includes nitrogen-containing compounds that form salts with organic or inorganic acids. As such, the term includes nitrogen-containing groups that, in their neutral state, have a pKa in water of at least 4 (preferably at least 5, 6 or 7, and particularly in the range of 8 to 12). The term therefore specifically includes amidino, guanidino and, particularly, amino groups, any of which may be cyclic or acyclic. Preferred nitrogen-containing basic groups include —N(H)C(═NH)NH2, —C(═NH)NH2 and, particularly, amino groups such as —NH2, alkylamino (e.g. —N(H)CH3) and dialkylamino (e.g. —N(CH3)2) groups and saturated azaheterocyclic groups such as pyrrolidinyl and piperazinyl. Particularly preferred nitrogen-containing basic groups include —N(CH3)2. For the avoidance of doubt, the nitrogen-containing basic group is a separate moiety from the two or more heterocyclic groups mentioned at point (b) above.
When used herein, the term “heterocyclic group” includes 4- to 12-membered (e.g. 5- to 10-membered) heterocyclic groups containing one or more heteroatoms selected from N, O and S. The term therefore includes such groups that are mono- or bicyclic, and which may be saturated, part-unsaturated, aromatic or, where appropriate, part-aromatic. Preferred heterocyclic groups include aromatic or part-aromatic groups such as pyrrolyl, imidazolyl, thiazolyl, oxazolyl, benzoxazolyl, furanyl, thienyl, pyridyl and coumarinyl. Particularly preferred heterocyclic groups include pyrrolyl, imidazolyl, thiazolyl and oxazolyl.
By “substituted in the heterocyclic part”, we mean that each of the essential branched, cyclic or part cyclic C3-5 alkyl groups is a direct substituent on the heterocyclic ring (whether attached to the ring via a heteroatom or otherwise) of each heterocyclic monomer bearing such a group.
In one embodiment of the invention, at least one heterocyclic group that is present (e.g. an imidazolyl, a thienyl or, particularly, a thiazolyl group) is substituted at a ring C-atom by the branched, cyclic or part cyclic C3-5 alkyl group.
In another embodiment of the invention, at least one heterocyclic group that is present is a thiazolyl group (e.g. a 1,3-thiazolyl group that is substituted in the 5-position by the branched, cyclic or part cyclic C3-5 allyl group).
The compounds of the invention may be provided in a form rendering them bioavailable. When used herein, the term “bioavailable” includes compounds that, following administration, are in a form in which they can interact with a biological system, thereby providing a measurable therapeutic response. The term may thus be understood to include compounds that are provided to DNA in a form and/or level that is sufficient to provide a measurable desired or required therapeutic response.
Bioavailability of a compound may be predicted by a number of means known to those skilled in the art including a measurement of a partition coefficient of the compound between water (for example at a pH of between 5 and 9) and an organic, water-immiscible solvent (e.g. octanol), which measurement can be used to predict the behavior in body tissues of the compound in question (for a discussion of which see J. Med. Chem. 43, 3257-3266 (2000)).
Bioavailability may be achieved by providing compounds of the invention in a form (e.g. a pharmaceutical formulation) in which they are presented to DNA at an appropriate concentration to provide a measurable therapeutic response. Bioavailability may alternatively be achieved by changing the physicochemical properties of the active species, for example by improving water solubility by using techniques known to those skilled in the art (e.g. by the introduction of additional basic groups, such as described in J. Med. Chem. 43, 3257-3266 (2000)).
The compounds of the invention may have a high affinity for at least one DNA sequence. When used herein, the term “high affinity for at least one DNA sequence” includes compounds that, when bound to a minor groove of at least one DNA oligomer or polymer, have a dissociation constant of less than 10−5 M, preferably less than 10−6 M (such as 10−7 M) and particularly less than 10−8 M. In this respect, dissociation constants may be measured under conditions know to those skilled in the art, for example in water at room temperature (e.g. at or around 20° C.) in the presence of a buffer (e.g. a buffer that stabilizes the pH at 7.5, such as a borate (e.g. at 0.02M) or Tris/HCl (e.g. at 0.01 M) buffer) and at a DNA concentration of between 10 and 30 μM (e.g. 20 μM). Alternatively, dissociation constants may be estimated by a comparison of the binding affinity of a compound to a set DNA sequence with the binding affinity of a well-known compound (e.g. distamycin) to that same sequence.
Unless otherwise specified, the term “DNA” refers to double-stranded DNA. Further, when used herein, the term “DNA sequence” includes any part of (or the whole of) a DNA oligomer or polymer spanning three or more base pairs.
Preferred compounds of the invention also include those in which each essential branched, cyclic or part cyclic C3-5 alkyl substituent on a heterocyclic monomer is:

    other than cyclopropyl;
    a branched C3-5 alkyl group such as cyclopropylmethyl, cyclopentyl, isopentyl or isopropyl (e.g. isopentyl and, particularly, isopropyl).


According to a further aspect of the invention, there is provided compounds of formula I,




wherein

    R1 represents Het1, R1aC(O)— or D-A-N(H)-[Q]n-C(O)-E-C(O)—;
    R1a represents
    
        H,
        aryl (which latter group is optionally substituted by one or more substituents selected from OH, halo, cyano, nitro, N(R3a)R3b, C1-4 alkyl and C1-4 alkoxy),
        aromatic or part-aromatic C13-14 tricyclic carbocyclyl (which latter group is optionally substituted by one or more substituents selected from OH, halo, cyano, nitro, N(R3a)R3b, C1-4 alkyl and C1-4 alkoxy, and which latter group, if part-aromatic, is optionally substituted in the non-aromatic part by one or two oxo groups) or
        C1-12 alkyl (which latter group is optionally substituted and/or terminated by one or more substituents selected from halo and aryl (which latter group is optionally substituted by one or more substituents selected from OH, halo, cyano, nitro, N(R3a)R3b, C1-4 alkyl and C1-4 alkoxy));
    
    
    A represents, at each occurrence when used herein, C2-6 alkylene or A1-C(O)N(H)-A2, wherein A2 is attached to the group D;
    A1 represents C1-4 alkylene;
    A2 represents C2-5 alkylene;
    D represents, at each occurrence when used herein, —N(R2a)R2b, —C(═NR2c)N(R2d)R2e or —N(R2f)C(═NR2g)N(H)R2h;
    R2a and R2b independently represent H, C1-16 alkyl, Het2 or R2a and R2b together represent (CH2)3-6, which alkylene group is optionally interrupted by NR4 and/or is optionally substituted by one or more C1-4 alkyl groups;
    R4 represents H, C1-6 alkyl or Het3;
    R2c to R2h independently represent H or C1-6 alkyl;


E represents -E1-Het4-, E2a, —(CH2)0-3N(H)C(O)-E2b-C(O)N(H)(CH2)0-3— or a structural fragment of the formula




wherein E3 represents (CH2)1-2, CH═CH, CH═N, CH2—N(Ra), (CH2)0-1C(O), (CH2)0-1O or (CH2)0-1S;

    Ra represents H or C1-6 alkyl;
    E1 represents (CH2)0-2 or CH═CH;
    E2a and E2b independently represent C2-4 alkenylene, C3-6 cycloalkylene, phenylene or naphthylene;
    Het1 to Het4 independently represent four- to twelve-membered heterocyclic groups containing one or more heteroatoms selected from N, O and S, which heterocyclic groups are optionally substituted by one or more substituents selected from ═O, OH, halo, cyano, nitro, N(R3a)R3b, C1-4 alkyl and C1-4 alkoxy;
    R3a and R3b independently represent, at each occurrence when used herein, H or C1-4 alkyl, or R3a represents —C(O)R5;
    R5 represents H or C1-4 alkyl;
    n represents, at each occurrence when used herein, 2, 3, 4 or 5;
    each individual Q independently represents a structural fragment of formula Ia, Ib, Ic, Id, Ie or If






wherein

    R6 represents H or C1-6 alkyl;
    R7 represents C1-12 alkyl;
    R8, R9, R10 and R11 independently represent H or C1-12 alkyl;
    G represents CH or N;
    L represents O or S;
    p, q and r independently represent 0, 1, 2 or 3; and
    provided that the compound comprises at least one structural fragment of formula Ib, Ic, Id, Ie or If in which R6 or R7, R8, R9, R10 or R11, respectively, represents branched, cyclic or part cyclic C3-5 alkyl;
    or a pharmaceutically acceptable derivative thereof,
    which compounds are also referred to hereinafter as “the compounds of the invention”.


Unless otherwise specified, alkyl groups and alkoxy groups as defined herein may be straight-chain or, when there is a sufficient number (i.e. a minimum of three) of carbon atoms, be branched-chain and/or cyclic. Further, when there is a sufficient number (i.e. a minimum of four) of carbon atoms, such alkyl and alkoxy groups may also be part cyclic/acyclic. Such alkyl and alkoxy groups may also be saturated or, when there is a sufficient number (i.e. a minimum of two) of carbon atoms, be unsaturated and/or interrupted by one or more oxygen and/or sulfur atoms. Unless otherwise specified, alkyl and alkoxy groups may also be substituted by one or more halo, and especially fluoro, atoms.
Unless otherwise specified, alkylene groups as defined herein may be straight-chain or, when there is a sufficient number (i.e. a minimum of two) of carbon atoms, be branched-chain. Such alkylene chains may also be saturated or, when there is a sufficient number (i.e. a minimum of two) of carbon atoms, be unsaturated and/or interrupted by one or more oxygen and/or sulfur atoms. Unless otherwise specified, alkylene groups may also be substituted by one or more halo atoms.
The term “aryl”, when used herein, includes C6-10 aryl groups such as phenyl, naphthyl and the like. When substituted, aryl groups are preferably substituted by between one and three substituents.
The term “aromatic or part-aromatic C13-14 tricyclic carbocyclyl”, when used herein includes fluorenyl, anthracenyl, 9,10-dihydroanthracenyl, phenanthrenyl, 9,10-dihydrophenanthrenyl and the like.
The term “halo”, when used herein, includes fluoro, chloro, bromo and iodo.
Het (Het1 to Het4) groups that may be mentioned include those containing 1 to 4 heteroatoms (selected from the group oxygen, nitrogen and/or sulfur) and in which the total number of atoms in the ring system are between five and twelve. Het (Het1 to Het4) groups may be fully saturated, partly unsaturated, wholly aromatic, partly aromatic and/or bicyclic in character. Heterocyclic groups that may be mentioned include benzodioxanyl, benzodioxepanyl, benzodioxolyl, benzofuranyl, benzofurazanyl, benzimidazolyl, benzomorpholinyl, benzothiazolyl, benzothiophenyl, benzoxazolyl, chromanyl, cinnolinyl, coumarinyl, dioxanyl, furanyl, hydantoinyl, imidazolyl, imidazo[1,2-α]pyridinyl, indolyl, isoquinolinyl, isoxazolyl, maleimido, morpholinyl, oxazolyl, phthalazinyl, piperazinyl, piperidinyl, purinyl, pyranyl, pyrazinyl, pyrazolyl, pyridinyl, pyrimindinyl, pyrrolidinonyl, pyrrolidinyl, pyrrolinyl, pyrrolyl, quinazolinyl, quinolinyl, 3-sulfolenyl, tetrahydropyranyl, tetrahydrofuranyl, thiazolyl, thienyl, thiochromanyl, triazolyl and the like. Values of Het1, Het2 and Het3 that may be mentioned include benzoxazolyl. Values of Het4 that may be mentioned include indolyl.
Pharmaceutically acceptable derivatives include salts and solvates. Salts which may be mentioned include acid addition salts.
Compounds of formula I may exhibit tautomerism. All tautomeric forms and mixtures thereof are included within the scope of the invention.
Compounds of formula I may also contain one or more asymmetric carbon atoms and may therefore exhibit optical and/or diastereoisomerism. Diastereoisomers may be separated using conventional techniques, e.g. chromatography or fractional crystallisation. The various stereoisomers may be isolated by separation of a racemic or other mixture of the compounds using conventional, e.g. fractional crystallisation or HPLC, techniques. Alternatively the desired optical isomers may be made by reaction of the appropriate optically active starting materials under conditions which will not cause racemization or epimerization, or by derivatization, for example with a homochiral acid followed by separation of the diastereomeric esters by conventional means (e.g. HPLC, chromatography over silica). All stereoisomers are included within the scope of the invention.
Compounds of formula I that may be mentioned include those in which:

    
    
        R1a represents H or C1-12 alkyl, which latter group is optionally substituted and/or terminated by one or more substituents selected from halo and aryl, which latter group is optionally substituted by one or more substituents selected from OH, halo, cyano, nitro, N(R3a)R3b, C1-4 alkyl and C1-4 alkoxy;
        the compound comprises at least one structural fragment of formula Ib, Ic, Id, Ie or If in which R7, R8, R9, R10 or R11, respectively, represents branched, cyclic or part cyclic C3-5 alkyl.
    
    


Branched, cyclic or part cyclic C3-5 alkyl groups that may be mentioned include isopropyl, cyclopropylmethyl, isopentyl and cyclopentyl.
Preferred compounds of formula I include those in which:

    R1a represents
    
        H,
        phenyl, anthracenyl (which latter two groups are optionally substituted by one to three substituents selected from OH, halo, C1-4 alkyl and C1-4 alkoxy),
        9,10-dihydroanthracenyl (which latter group is optionally substituted by one or two oxo groups and/or one to three substituents selected from OH, halo, C1-4 alkyl and C1-4 alkoxy) or
        optionally unsaturated C1-8 alkyl, which latter group is substituted by one or more halo groups and/or terminated by phenyl, which latter group is optionally substituted by one or more substituents selected from OH, halo, cyano, nitro, N(R3a)R3b, C1-2 alkyl and C1-2 alkoxy;
    
    
    A represents optionally unsaturated C2-5 alkylene or A1-C(O)N(H)-A2;
    A1 represents saturated C1-3 alkylene;
    A2 represents saturated C2-4 alkylene;
    R2a and R2b independently represent H, C1-4 alkyl, Het2 or R2a and R2b together represent (CH2)3-6, which alkylene group is optionally interrupted by NR4 and/or is optionally substituted by a C1-2 alkyl group;
    R4 represents C1-4 alkyl or Het3;
    R2c to R2h independently represent H;
    E represents -E1-Het4-, cis- or trans-ethenylene, cyclopropylene, 1,3- or 1-4-phenylene, —(CH2)1-2N(H)C(O)-phenylene-C(O)N(H)(CH2)1-2— or a structural fragment of the formula






wherein E3 represents (CH2)2, CH═CH, C(O) or S;

    Het1 to Het3 independently represent six- to ten-membered heterocyclic groups containing one or more heteroatoms selected from N, O and S, which heterocyclic groups are optionally substituted by one or more substituents selected from ═O, OH, halo, cyano, nitro, N(R3a)R3b, C1-2 alkyl and C1-2 alkoxy;
    Het4 represents an unsubstituted nine- or ten-membered aromatic heterocyclic group containing one or two N-atoms (e.g. indolyl, such as 2,5- or 2,6-indolyl);
    R3a and R3b independently represent, at each occurrence when used herein, H or C1-2 alkyl, or R3a represents —C(O)R5;
    R5 represents H or C1-2 alkyl;
    R6 represents H or C1-2 alkyl or, when G represents N, R6 may also represent branched, cyclic or part cyclic C3-5 alkyl;
    R7 represents C1-8 alkyl;
    R8, R9, R10 and R11 independently represent H or C1-8 alkyl;
    p, q and r independently represent 0, 1 or 2;
    n represents 3, 4 or 5 or, when R1 represents methyl, Het1 or D-A-N(H)-[Q]n—C(O)-E-C(O)—, then n may also represent 2;
    the compound comprises at least one structural fragment of formula Ib, Ic, Id, Ie or If in which R7, R8, R9, R10 or R11, respectively, represents branched C3-5 alkyl.


More preferred compounds of formula I include those in which:

    R1a represents
    
        H
        phenyl (which latter group is optionally substituted by C1-2 alkoxy), 9,10-dioxo-9,10-dihydroanthracenyl (which latter group is optionally substituted by C1-2 alkoxy),
        saturated, optionally branched C1-6 alkyl or
        saturated C1-3 n-alkyl, which latter group is terminated by phenyl (which latter group is optionally substituted by C1-2 alkoxy);
    
    
    A represents saturated C2-4 alkylene or A1-C(O)N(H)-A2;
    A1 represents (CH2)1-3;
    A2 represents (CH2)2-4;
    D represents —N(R2a)R2b;
    R2a and R2b independently represent C1-3 alkyl or Het2, or R2a and R2b together represent (CH2)3-5, which alkylene group is optionally interrupted by NR4;
    R4 represents C1-3 alkyl or Het3;
    E represents -(2,5-indolyl)-, —(CH2)0-2-(2,6-indolyl)-, —CH═CH-(2,6-indolyl)-, trans-ethenylene, trans-cyclopropylene, 1,3- or 1-4-phenylene, —CH2N(H)C(O)-(1,3- or 1,4-phenylene)-C(O)N(H)CH2— or one of the following structural fragments






    Het1, Het2 and/or Het3 independently represent nine- or ten-membered aromatic heterocycles containing one to three heteroatoms selected from N, O and S;
    R6 represents H or, when G represents N, R6 may also represent branched, cyclic or part cyclic C3-5 alkyl;
    R7, R8, R9, R10 and R11 independently represent saturated, optionally branched C1-6 alkyl or R8 represents H;
    p, q and r independently represent 0 or 1;
    n represents 3 or 4, or, when R1 represents methyl or D-A-N(H)-[Q], —C(O)-E-C(O)—, then n may also represent 2;
    the compound comprises at least one structural fragment of formula Ib, Ic, Id, Ie or If in which R7, R8, R9, R10 or R11, respectively, represents iso- or sec-butyl, isopentyl or, particularly, isopropyl;
    the compound comprises at least one structural fragment of formula Ib, Ic, Id, Ie or If in which R7, R8, R9, R10 or R11, respectively, represents ethyl or, particularly, methyl.


Compounds of formula I that are more preferred still include those in which:

    R1a represents
    
        H
        methoxyphenyl (e.g. p- or, particularly, m-methoxyphenyl), 9,10-dioxo-9,10-dihydroanthracenyl,
        saturated C1-3 alkyl (e.g. methyl) or
        methoxyphenylacetyl (e.g. m- or, particularly, p-methoxyphenyl);
    
    
    Het1 represents a nine-membered aromatic heterocycle containing two heteroatoms selected from N, O and S (e.g. 1,3-benzoxazol-2-yl);
    A represents saturated C2-4 n-alkylene (e.g. n-propylene) or A1-C(O)N(H)-A2;
    A1 represents (CH2)2;
    A2 represents (CH2)3;
    R2a and R2b both represent methyl;
    E represents —CH2N(H)C(O)-(1,3-phenylene)-C(O)N(H)CH2—;
    the —NH— group in the structural fragment of formula Ia is attached in the 6-position of the coumarin ring system;
    R7 represent saturated, optionally branched C1-3 alkyl (e.g. methyl, ethyl or isopropyl);
    R8 represents isopropyl or, particularly, H;
    R8 represents methyl;
    the —NH— and —C(O)— groups in the structural fragment of formula Ic are attached in the 2- and 5-positions, respectively, of the furan or thiophene ring;
    R9, R10 and R11 independently represent saturated, optionally branched C1-3 alkyl (e.g. isopropyl);
    p represents 1;
    q and r represent 0;
    the —C(O)— group in the structural fragment of formula Id is attached in the 4-position of the oxazole ring;
    n represents 3 or, when R1 represents methyl, n represents 2 or 3, or, when
    R1 represents D-A-N(H)-[Q]n—C(O)-E-C(O)—, then n represents 2;
    the compound comprises at least one structural fragment of formula Ib, Ic, Id, Ie or If in which R7, R8, R9, R10 or R11, respectively, represents isopropyl.


Particularly preferred compounds of formula I include those in which:

    each Q independently represents a structural fragment of formula Ib, Id, Ie or If (such as a structural fragment of formula Ib or Ie);
    G represents CH;
    R7 represents methyl or isopropyl.


Compounds of formula I that may be mentioned include those in which each Q does not represent a structural fragment of formula Id.
According to a further aspect of the invention, there is provided compounds of formula I which are compounds of formula II,




wherein

    R1 represents Het1, R1aC(O)— or D-A-N(H)-Q3-Q2-Q1-C(O)-E-C(O)—;
    Q1 is absent or represents a structural fragment of formula Ia, Ib, Ic, Id, Ie or If;
    Q2 represents a structural fragment of formula Ib, Ie or If;
    Q3 represents a structural fragment of formula Ib, Id, Ie or If; and
    Het1, R1a, D, A, E, R2a, R2b, A and the structural fragments of formulae Ia, Ib, Ic, Id, Ie and If are as hereinbefore defined;

provided that:

    (a) at least one of Q1, Q2 and Q3 represents a structural fragment of formula Id, Ie or If; and
    (b) at least one of R6 or R7, R8, R9, R10 and R11 (whichever is/are present) represents branched, cyclic or part cyclic C3-5 alkyl.
    or a pharmaceutically acceptable derivative thereof,
    which compounds are also referred to hereinafter as “the compounds of the invention”.


Compounds of formula II that may be mentioned include those in which at least one of R7, R8, R9, R10 and R11 (whichever is/are present) represents branched, cyclic or part cyclic C3-5 alkyl.
Preferred compounds of formula II include those in which:

    Q1 represents a structural fragment of formula Ic, or, particularly, a is structural fragment of formula Ib, Ie or If, or, when R1 represents methyl or D-A-N(H)-Q3-Q2-Q1-C(O)-E-C(O)—, then Q1 may also be absent;
    Q2 represents a structural fragment of formula Ib in which G represents CH, or a structural fragment of formula Ie in which q represents 0;
    Q3 represents a structural fragment of formula Id, Ie or If;
    at least one of R7, R8, R9, R10 and R11 (whichever is/are present) represents branched C3-5 alkyl.


More preferred compounds of formula II include those in which:

    Q1 represents a structural fragment of formula Ie or, particularly, a structural fragment of formula Ib in which G represents CH, or, when R1 represents methyl, then Q1 may also be absent, or, when R1 represents D-A-N(H)-Q3-Q2-Q1-C(O)-E-C(O)—, then Q1 is absent;
    Q3 represents a structural fragment of formula Ie.
    at least one of R7, R8, R9, R10 and R11 (whichever is/are present) represents isopropyl or isopentyl;
    at least one of R7, R8, R9, R10 and R11 (whichever is/are present) represents ethyl or, particularly, methyl.


Other preferred compounds of formula II include those in which:

    Q1 and Q3 represent a structural fragment of formula Ib in which R6 represents H and R7 represents methyl; and
    Q2 represents a structural fragment of formula Ib in which R6 represents H and R7 represents branched, cyclic or part cyclic C3-5 alkyl (e.g. cyclopropylmethyl, cyclopentyl or, particularly, isopentyl or isopropyl).


In one embodiment of the invention, the compound of formula I or formula II may be one which comprises:

    (a) at least one structural fragment of formula Ib in which G represents N and R6 represents branched, cyclic or part cyclic C3-5 alkyl (e.g. cyclopropylmethyl, isopentyl, cyclopentyl or, particularly, isopropyl);
    (b) at least one structural fragment of formula Id in which p represents 0 and R9 represents branched, cyclic or part cyclic C3-5 alkyl (e.g. cyclopropylmethyl, isopentyl, cyclopentyl or, particularly, isopropyl); and/or, particularly
    (c) at least one structural fragment of formula Ie in which q represents 0 and R10 represents branched, cyclic or part cyclic C3-5 alkyl (e.g. cyclopropylmethyl, isopentyl, cyclopentyl or, particularly, isopropyl).


In this embodiment of the invention, the compound of formula I or formula II may particularly be one which comprises at least one structural fragment of formula Ie in which q represents 0 and R10 represents isopropyl.
Compounds of formulae I and II that may be mentioned include those in which p, q and r, in whichever of structural fragments Id, Ie and If, respectively, are present, represent 0.
Preferred compounds of formulae I and II include those that bind to the minor groove of DNA.
Preferred compounds of the invention include those that have different binding affinities at different minor groove binding sites in double-stranded DNA molecules having more than one minor groove binding site.
When used herein, the term “different minor groove binding sites” includes references to minor grooves that differ with respect to sequences of base pairs that they contain (where the sequences may comprise AT base pairs, GC base pairs or mixtures thereof). However, the term also includes references to minor grooves that, although they may contain the same sequence of base pairs, or very similar sequences (e.g. sequences, such as those comprising solely AT base pairs, differing only with respect to the is order of the base pairs), they differ with respect to:

    (a) the position of the sequence in the minor groove;
    (b) the sequences of base pairs that are at one or both ends of the sequence correlating to the binding site;
    (c) the pitch angle of base pairs in the minor groove;
    (d) the width of the minor groove.


Compounds of the invention that may be mentioned include those that bind to and/or have specificity for DNA sequences that contain at least one GC base pairing.
When used herein, the term “bind to DNA sequences that contain at least one GC base pairing” refers to compounds that, although they bind to DNA minor grooves that contain AT base pairs only, they also bind to DNA minor grooves that contain at least one GC base pairing (i.e. the binding of the compounds to DNA is “tolerant” of the replacement of AT base pairs with GC base pairs).
When used herein, the term “specificity for DNA sequences that contain at least one GC base pairing” refers to compounds that bind with a measurably greater affinity to DNA minor grooves that contain at least one GC base pairing than they do to DNA minor grooves that contain AT base pairs only.
In relation to the above, affinity to DNA may be measured by techniques known to those skilled in the art, such as capillary electrophoresis, for example as described hereinafter. Furthermore, affinity to certain sections of DNA may be determined by techniques known to those skilled in the art, such as DNA footprinting, for example as described hereinafter.
In this respect, preferred compounds of the invention include:

    (i) compounds of formula I, as hereinbefore defined, provided that the compound comprises at least one structural fragment of formula Id, Ie or If;
    (ii) compounds of formula II, as hereinbefore defined.


Preferred compounds of the invention include the compounds of the Examples disclosed hereinafter.
Preparation
Compounds of the invention may be prepared using techniques (e.g. peptide synthesis) known to those skilled in the art, using starting materials that are either commercially available, are known in the literature, or may be obtained either by analogy with the processes described hereinafter, or by conventional synthetic procedures, in accordance with standard techniques; and appropriate reagents and reaction conditions.
According to the invention there is also provided a process for the preparation of compounds of formula I which comprises:

    (a) reaction of a compound of formula III,






wherein Aa represents A or, when a represents 0, then Aa may also represent A2 and Q, D, A and A2 are as hereinbefore defined and a is as defined below, with a compound of formula IV,





wherein Ab represents a direct bond or -A1-C(O)—, as appropriate, L1 represents a suitable leaving group (e.g. halo, such as chloro, C1-6 alkoxy, such as ethoxy, trichloromethyl, hydroxy or an alkoxy group (e.g. a benzyl alkoxy group) that is a functional group of a functionalized polymer (e.g. BALa-PAM resin, or derivatives thereof)), a and b both represent integers from 0 to 5, the sum of the two being 2, 3, 4 or 5, and R1 and Q are as hereinbefore defined, for example under conditions known to those skilled in the art (for example: (i) when L1 represents ethoxy, by reaction at between room and reflux temperature in the presence of ethanol; (ii) when L1 represents halo, by reaction at between −10° C. and room temperature in the presence of a suitable base such as diisopropylamine and an appropriate solvent such as dichloromethane; (iii) when L1 represents hydroxy, by reaction at around room temperature in the presence of an appropriate coupling agent such as HBTU (or a combination of a carbodiimide, such as diisopropylcarbodiimide, and HOBT), a suitable solvent such as DMF, and optionally in the presence of a tertiary amine base such as NMM; and (iv) when L1 represents a benzyl alkoxy group derived from a BALa-PAM resin, by reaction at between room and reflux temperature (e.g. 55° C.) in the presence of a suitable solvent, such as THF); or

    (b) for compounds of formula I in which R1 represents D-A-N(H)-[Q], —C(O)-E-C(O)—, reaction of two equivalents of a compound of formula V,






wherein Q, n, A and D are as hereinbefore defined, with a compound of formula VI,

L2-C(O)-E-C(O)-L2  VI

wherein L2 represents a suitable leaving group (e.g. halo or, particularly, hydroxy), the two L2 groups being the same or different, and E is as hereinbefore defined, for example under conditions known to those skilled in the art (e.g. as described in respect of process (a) above).

Compounds of formulae III, IV, V and VI, and derivatives thereof, are either commercially available, are known in the literature, or may be obtained either by analogy with the processes described herein, or by conventional synthetic procedures, in accordance with standard techniques, from readily available starting materials using appropriate reagents and reaction conditions.
Substituents on the aryl (e.g. phenyl), and heterocyclic, group(s) in compounds defined herein may be converted to other claimed substituents using techniques well known to those skilled in the art. For example, hydroxy may be converted to alkoxy, phenyl may be halogenated to give halophenyl, nitro may be reduced to give amino, halo may be displaced by cyano, etc.
The skilled person will also appreciate that various standard substituent or functional group interconversions and transformations within certain compounds of formula I will provide other compounds of formula I. For example, alkenylene may be reduced to alkylene, carbonyl may be reduced to hydroxy or methylene, etc.
The compounds of the invention may be isolated from their reaction mixtures using conventional techniques.
It will be appreciated by those skilled in the art that, in the process described above, the functional groups of intermediate compounds may be, or may need to be, protected by protecting groups.
Functional groups which it is desirable to protect include hydroxy, amino and carboxylic acid. Suitable protecting groups for hydroxy include trialkylsilyl and diarylalkylsilyl groups (e.g. tert-butytdimethylsilyl, tert-butyldiphenylsilyl or trimethylsilyl), tetrahydropyranyl and alkylcarbonyl groups (e.g. methyl- and ethylcarbonyl groups). Suitable protecting groups for amino include benzyl, tert-butyloxycarbonyl, 9-fluorenylmethoxycarbonyl or benzyloxy-carbonyl. Suitable protecting groups for carboxylic acid include C1-6 alkyl or benzyl esters.
The protection and deprotection of functional groups may take place before or after any of the reaction steps described hereinbefore.
Protecting groups may be removed in accordance with techniques which are well known to those skilled in the art and as described hereinafter.
The use of protecting groups is fully described in “Protective Groups in Organic Chemistry”, edited by J. W. F. McOmie, Plenum Press (1973), and “Protective Groups in Organic Synthesis”, 3rd edition, T. W. Greene & P. G. M. Wutz, Wiley-Interscience (1999).
Persons skilled in the art will appreciate that, in order to obtain compounds of the invention in an alternative, and, on some occasions, more convenient, manner, the individual process steps mentioned herein may be performed in a different order, and/or the individual reactions may be performed at a different stage in the overall route (i.e. substituents may be added to and/or chemical transformations performed upon, different intermediates to those associated hereinbefore with a particular reaction). This will depend inter alia on factors such as the nature of other functional groups present in a particular substrate, the availability of key intermediates and the protecting group strategy (if any) to be adopted. Clearly, the type of chemistry involved will influence the choice of reagent that is used in the said synthetic steps, the need, and type, of protecting groups that are employed, and the sequence for accomplishing the synthesis.
Some of the intermediates referred to hereinbefore are novel. According to a further aspect of the invention there is thus provided a compound of formula V, or a protected derivative thereof.
Uses and Pharmaceutical Preparations
Compounds of the invention are useful because they possess pharmacological activity. They are therefore indicated as pharmaceuticals.
Thus, according to a further aspect of the invention there is provided the compounds of the invention for use as pharmaceuticals.
In particular, compounds of the invention bind to DNA, thereby inhibiting the binding to that DNA of an enzyme necessary for replication, with the effect that DNA replication is inhibited.
Thus, according to a further aspect of the invention there is provided a method of inhibiting DNA replication, which method comprises contacting the DNA with an inhibitory amount of a compound of the invention.
Due to their ability to inhibit DNA replication (e.g. by inhibiting transcription by blocking the binding or displacement of regulatory proteins or DNA-enzyme complexes, such as with reverse transcriptase or topoisomerases), compounds of the invention have utility in the treatment of diseases that rely upon DNA replication for their propagation. Such diseases include cancers and those involving viruses, bacteria, fungi or other microorganisms (e.g. diseases involving parasites, such as malaria).
Thus, according to a further aspect of the invention, there is provided a method of treatment of a disease that relies upon DNA replication for its propagation (e.g. cancer or a viral, bacterial, fungal or other microbial infection), which method comprises administration of a therapeutically effective amount of a compound of the invention to a person suffering from that disease. Such treatment may be particularly useful where the person suffering from that disease is immunocomprorised.
Because they have a different mode of action to many conventional anti-viral, anti-bacterial, anti-fungal or other anti-microbial (e.g. anti-parasitic) agents, compounds of the invention may be particularly useful in the treatment of viral, bacterial, fungal or other microbial (e.g. parasitic) infections where the infective agent is resistant to one or more anti-viral, anti-bacterial, anti-fungal or other anti-microbial (e.g. anti-parasitic) agents having a different mode of action. In this respect, according to a further aspect of the invention there is provided a method of treating a viral, bacterial, fungal or other microbial (e.g. parasitic) infection, where the viral, bacterial, fungal or other microbial (e.g. parasitic) infective agent is resistant to one or more anti-viral, anti-bacterial, anti-fungal or other anti-microbial (e.g. anti-parasitic) agents, respectively, that do not act by inhibiting DNA replication, which method comprises administration of a therapeutically effective amount of a compound of the invention to a person having that infection.
As well as having utility on their own in the treatment of diseases that rely upon DNA replication for their propagation, the compounds of the invention may be used in combination with one or more other compounds or treatment regimes that are used to treat such a disease. Thus, according to a further aspect of the invention, there is provided a method of treatment of a disease that relies upon DNA replication for its propagation (e.g. cancer or a viral, bacterial, fungal or other microbial infection), which method comprises administration, to a person suffering from that disease, of a therapeutically effective amount of a compound of the invention in combination with one or more other agents that are known to be effective in treating that disease.
When used herein, the term “in combination with” includes administration of the other agent(s) that is(are) known to be effective in treating the disease, before, during and/or following administration a compound of the invention. When more than one other agent is administered, the term also includes administration of the different other agents at different times relative to the time of administration of a compound of the invention.
Agents that are known to be effective in treating diseases that rely upon DNA replication for their propagation (e.g. anti-cancer, anti-viral, anti-bacterial, anti-fungal or other anti-microbial (e.g. anti-parasitic) agents) include those listed under the relevant headings in “Martindale: The Complete Drug Reference”, 32nd Edition, the Pharmaceutical Press, London (1999), the disclosures of which document are hereby incorporated by reference.
Anti-cancer agents also include non-chemical agents such as ionizing radiation (e.g. subatomic particle radiation such as α-particles, β-particles, neutrons, protons, mesons and heavy ions or electromagnetic radiation such as high-frequency X-rays or gamma rays). Chemical anti-cancer agents that may be mentioned include:

    (a) Alkylating agents including:
    
        (i) nitrogen mustards such as mechlorethamine (HN2), cyclophosphamide, ifosfamide, melphalan (L-sarcolysin) and chlorambucil;
        (ii) ethylenimines and methylmelamines such as hexamethylmelamine, thiotepa;
        (iii) alkyl sulfonates and thiosulfonates such as busulfan, methyl methanesulfonate WS) and methyl methanethiosulfonate;
        (iv) nitrosoureas and nitrosoguanidines such as carmustine (BCNU), lomustine (CCNU), semustine (methyl-CCNU), streptozocin (streptozotocin) and N-methyl-N′-nitro-N-nitrosoguanidine (MNNG); and
        (v) triazenes such as dacarbazine (DTIC; dimethyltriazenoimidazole-carboxamide).
    
    
    (b) Antimetabolites including:
    
        (i) folic acid analogues such as methotrexate (amethopterin);
        (ii) pyrimidine analogues such as fluorouracil (5-fluorouracil; 5-FU), floxuridine (fluorodeoxyuridine; FUdR) and cytarabine (cytosine arabinoside); and
        (iii) purine analogues and related inhibitors such as mercaptopurine (6-mercaptopurine; 6-MP), thioguanine (6-thioguanine; TG) and pentostatin (2′-deoxycoformycin).
    
    
    (c) Natural Products including:
    
        (i) vinca alkaloids such as vinblastine (VLB) and vincristine;
        (ii) epipodophyllotoxins such as etoposide and teniposide;
        (iii) antibiotics such as dactinomycin (actinomycin A, C, D or F), daunorubicin (daunomycin; rubidomycin), doxorubicin, bleomycin, plicamycin (mithramycin) and mitomycin (mitomycin A, B or C);
        (iv) enzymes such as L-asparaginase; and
        (v) biological response modifiers such as interferon alphenomes.
    
    
    (d) Miscellaneous agents including:
    
        (i) platinum coordination complexes such as cisplatin (cis-DDP) and carboplatin;
        (ii) anthracenedione such as mitoxantrone and anthracycline;
        (iii) substituted urea such as hydroxyurea;
        (iv) methyl hydrazine derivatives such as procarbazine (N-methylhydrazine, MIH);
        (v) adrenocortical suppressants such as mitotane (o,p′-DDD) and amlinoglutethimide;
        (vi) taxol and analogues/derivatives;
        (vii) hormone agonists/antagonists such as flutamide and tamoxifen;
        (viii) photoactivatable compounds (e.g. psoralens);
        (ix) DNA topoisomerase inhibitors (e.g. m-amsacrine and camptothecin);
        (x) anti-angiogenesis agents (e.g. SU6668, SU5416, combretastatin A4, angiostatin and endostatin); and
        (xi) immunotherapeutic agents (e.g. radiolabelled antibodies such as BexxarTM and TheragynTM (PemtumomabTM)).
    
    


Anti-viral agents that may be mentioned include acyclovir, gancyclovir, AZT, ddI, amantadine hydrochloride, inosine pranobex, vidarabine, and the like.
Anti-bacterial agents that may be mentioned include natural and synthetic penicillins and cephalosporins, sulphonamides, erythromycin, kanomycin, tetracycline, chloramphenicol, rifampicin and including gentamicin, ampicillin, benzypenicillin, benethamine penicillin, benzathine penicillin, phenethicillin, phenoxy-methyl penicillin, procaine penicillin, cloxacillin, flucloxacillin, methicillin sodium, amoxicillin, bacampicillin hydrochloride, ciclacillin, mezlocillin, pivampicillin, talampicillin hydrochloride, carfecillin sodium, piperacillin, ticarcillin, mecillinam, pirmecillinan, cefaclor, cefadroxil, cefotaxime, cefoxitin, cefsulodin sodium, ceftazidime, ceftizoxime, cefuroxime, cephalexin, cephalothin, cephamandole, cephazolin, cephradine, latamoxef disodium, aztreonam, chlortetracycline hydrochloride, clomocycline sodium, demeclocydine hydrochloride, doxycycline, lymecycline, minocycline, oxytetracycline, amikacin, framycetin sulphate, neomycin sulphate, netilmicin, tobramycin, colistin, sodium fusidate, polymyxin B sulphate, spectinomycin, vancomycin, calcium sulphaloxate, sulfametopyrazine, sulphadiazine, sulphadimidine, sulphaguanidine, sulphaurea, capreomycin, metronidazole, timidazole, cinoxacin, ciprofloxacin, nitrofurantoin, hexamine, streptomycin, carbenicillin, colistimethate, polymyxin B, furazolidone, nalidixic acid, trimethoprim-sulfamethoxazole, clindamycin, lincomycin, cycloserine, isoniazid, ethambutol, ethionamide, pyrazinamide and the like.
Anti-fungal agents that may be mentioned include miconazole, ketoconazole, itraconazole, fluconazole, fusidic acid, amphotericin, flucytosine, griseofulvin, natamycin, nystatin, and the like.
Anti-parasitic agents (e.g. anti-malarial agents) that may be mentioned include pyrimethamine, proguanil, chloroquine, primaquine, mefloquine, quinine, tetracycline, atovaquone, artemisinin, dihydroartemisinin, artemether, arteether, artesunic acid and its salts, and sulfonamides.
When a compound of the invention is administered to a patient in combination with one or more other agents that are known to be effective in treating diseases that rely upon DNA replication for their propagation, the compound of the invention and the other agent(s) may be administered separately or, conveniently, as a single composition. Thus, according to a further aspect of the invention, there is provided a combination product comprising components:

    (A) a formulation comprising a compound of the invention; and
    (B) a formulation comprising one or more other chemical agents that are known to be effective in treating diseases that rely upon DNA replication for their propagation.


The combination product according to this aspect of the invention provides for the administration of a compound of the invention in conjunction with one or more other chemical agents that are known to be effective in treating diseases that rely upon DNA replication for their propagation, and may thus be presented either as separate components (i.e. (A) and (B) separately), or may be presented (i.e. formulated) as a combined preparation (i.e. presented as a single formulation including a compound of the invention and one or more other chemical agents that are known to be effective in treating diseases that rely upon DNA replication for their propagation). When components (A) and (B) are presented as separate components, the combination product may alternatively be termed “a kit-of-parts”.
In this aspect of the invention, other chemical agents that are known to be effective in treating diseases that rely upon DNA replication for their propagation include those referred to or mentioned hereinbefore. Thus, in a preferred embodiment of this aspect of the invention, the other chemical agents that are known to be effective in treating diseases that rely upon DNA replication for their propagation are one or more chemical anti-cancer, anti-viral, anti-bacterial, anti-fungal and/or anti-parasitic agents (e.g. the agents referred to or mentioned hereinbefore).
In a further preferred embodiment of this aspect of the invention, each of components (A) and (B) is formulated in admixture with a pharmaceutically-acceptable adjuvant, diluent or carrier.
The compounds of the invention will normally be administered orally, subcutaneously, intravenously, intraarterially, transdermally, intranasally, by inhalation, or by any other parenteral route, in the form of pharmaceutical preparations comprising the active ingredient either as a free base or a non-toxic organic or inorganic acid addition salt, in a pharmaceutically acceptable dosage form. Depending upon the disorder and patient to be treated, as well as the route of administration, the compositions may be administered at varying doses.
According to a further aspect of the invention there is thus provided a pharmaceutical formulation including a compound of the invention in admixture with a pharmaceutically acceptable adjuvant, diluent or carrier. Such formulations may be used for the treatment of diseases that rely upon DNA replication for their propagation. Thus, in one embodiment of this aspect of the invention there is provided a pharmaceutical formulation including, in admixture with a pharmaceutically acceptable adjuvant, diluent or carrier, a compound of the invention and one or more other chemical agents that are known to be effective in treating diseases that rely upon DNA replication for their propagation (e.g. one or more chemical anti-cancer, anti-viral, anti-bacterial, anti-fungal and/or anti-parasitic agents, such as the agents referred to or mentioned hereinbefore).
Suitable daily doses of the compounds of the invention in therapeutic treatment of humans are about 1 to 2000 mg/m2.
The most effective mode of administration and dosage regimen for the compounds of the invention depends on several factors, including the particular condition being treated, the extent and localisation of that condition in the patient being treated, as well as the patient's state of health and their reaction to the compound being administered. Accordingly, the dosages of the compounds of the invention should be adjusted to suit the individual patient. Methods for determining the appropriate dose for an individual patient will be known to those skilled in the art.
As well as having utility in the treatment of diseases, compounds of the invention are also useful in various assay methods based upon DNA binding. For example, it is known that compounds that bind to the minor groove of DNA have the ability to stabilise DNA duplexes, as well as to stabilise a fully matched (in terms of base pairs) DNA duplex to a greater extent than a mismatched DNA duplex, thereby enabling easier discrimination between the fully matched and mismatched duplexes (e.g. in terms of the melting temperatures of the duplexes).
Thus, according to a further aspect of the invention, there is provided a method of stabilizing a DNA duplex formed between first and second single strands of DNA, which method comprises contacting that DNA duplex with a compound of the invention.
Further, there is also provided a method of enhancing the difference in melting temperatures between first and second DNA duplexes, wherein each DNA duplex is formed from a first single strand of DNA that is the same in each duplex and a second single strand of DNA that is different in each duplex, which method comprises contacting each DNA duplex with a compound of the invention. In a preferred embodiment, the first DNA duplex has a greater degree of base-pair matching (e.g. it is fully matched) than the second DNA duplex, which has at least one base-pair mismatch.
Compounds that stabilise fully matched DNA duplexes to a greater extent than mismatched DNA duplexes may be used to reduce levels of “false positive” results in DNA hybridization assay techniques, for example as described in U.S. Pat. No. 6,221,589, the disclosures of which are hereby incorporated by reference. The reduction in “false positive” results may be achieved through the use of more stringent conditions (e.g. higher wash temperatures) following a hybridization reaction in the presence of a duplex-stabilizing compound than is possible following a reaction in the absence of such a compound. Thus, there is further provided a method of increasing the maximum temperature of a wash following a DNA hybridization reaction, the method comprising the provision of a compound of the invention to the hybridization reaction mixture. When used herein, the term “maximum temperature of a wash following a DNA hybridization reaction” refers to the highest possible wash temperature that does not result in a substantial loss of the “true positive” results (i.e. the fully or most highly matched DNA duplexes).
When used herein in relation to the above-mentioned methods involving DNA duplexes, the term “contacting” includes admixing of a compound of the invention with a DNA duplex. However, the term also includes attaching (e.g. covalently bonding) a compound of the invention (e.g. a compound of the invention bearing a haloalkyl group), or a derivative thereof (e.g. a compound of formula V) that bears a functional group (e.g. a hydroxy, amino or carboxylic acid group) that may be used to form a suitable attachment, to one or both of the single strands of DNA that form the duplex. Such “labelled” single strands of DNA may be used as primers, capture probes, or in a number of different assays (e.g. capture-detection assays, 5′-nuclease assays and Beacon assays).
Compounds of the invention have the advantage that, compared to corresponding compounds that, in place of the essential branched, cyclic or part cyclic C3-5 alkyl groups of the compounds of the invention, bear methyl substituents (for example compounds known in the prior art), they have a greater affinity and/or selectivity for any given DNA sequence. For example, compared to compounds known in the prior art, compounds of the invention have the advantage that they bind to DNA minor grooves that contain certain DNA sequences (e.g. sequences comprising AT base pairs only) with a measurably greater affinity and/or selectivity.
Compounds of the invention have the advantage in that they can bind to DNA sequences containing AT base pairs only, GC base pairs only, or mixtures of AT and GC base pairs. However, for pharmaceutical applications compounds of the invention (e.g. compounds of formula I comprising at least one structural fragment of formula Id, If or, particularly, Ie, or compounds of formula II) have the further advantage that, compared to corresponding compounds known in the prior art, they bind to DNA minor grooves that contain at least one GC base pairing with a measurably greater affinity and/or selectivity.
Compounds of the invention may also have the advantage that they may be more efficacious than, be less toxic than, have a broader range of activity than, be more potent than, be longer acting than, produce fewer side effects than, be more easily absorbed than, or that they may have other useful pharmacological properties over, compounds known in the prior art.



DESCRIPTION OF THE FIGURES
FIGS. 1 to 6
Capillary electrophoresis was used to study of ligand-DNA binding (see: (i) Hamdan, I. I.; Skellern, G. G.; and Waigh, R. D. “Separation of pd(GC)12 from pd(AT)12 by free solution capillary electrophoresis”, J. Cromatogr. A. 806, 165-168 (1998); (ii) Hamdan, I. I.; Skellern, G. G.; and Waigh, R. D. “Use of capillary electrophoresis in the study of ligand-DNA interactions”, Nucleic Acids Research 26, 3053-3058 (1998); (iii) Hamdan, I. I.; Skellern, G. G.; and Waigh, R. D. “Ligand binding to oligonucleotides” Methods in Molecular Biology, Vol. 163, “Capillary Electrophoresis of Nucleic acids”, Vol 2, pages 379-391, K. R. Mitchelson and J. Cheng Eds., Humana Press, New Jersey, (2000)).



Typically, ligand binding results in a change in migration time of the DNA and sometimes a change in peak shape.
The following are shown in FIGS. 1-6:

    (a) the experimental conditions, including the DNA sequence(s);
    (b) the result of sequential addition of ligand; and
    (c) the structure of the ligand being investigated.

Key to FIGS. 1 to 6:

    r0=electropherogram in the absence of drug
    rX=(where X is 0.5, 1, 2, 3 or 4) electropherogram in the presence of drug, where the drug:DNA ratio (in terms of concentration) is X:1


As can be seen from the figures, the disappearance of a peak corresponding to uncomplexed DNA relates to a measured ratio (rX) of drug to DNA.
This ratio corresponds to the binding ratio.
Double-stranded DNA oligonucleotides having, on one strand, nucleotide sequences AAATTATATTAT (SEQ ID NO:1) (peak 1) and GGGCCGCGCCGC (SEQ ID NO:2) (peak 2) are incubated in the presence of netropsin, a well-documented AT-selective binder. At r0, the two strands are present without any of the drug. At r1, the presence of netropsin (20 μM) causes a new peak (the complex of netropsin and the AT dodecamer) to appear in the trace. Increasing the amount of netropsin in the mixture to 40 μM (r2) causes complete conversion of the free AT dodecamer to its complex with netropsin.
From the traces shown in FIG. 1, it can be determined that:

    (i) netropsin is AT selective; and
    (ii) it has a binding ratio of 2:1 (drug:DNA) with AAATTATATTAT (SEQ ID NO:1) (1 drug molecule to each available binding site).


FIG. 2: Binding studies with 12/41 (the compound of Example 2) Compound 12/41 shows, with AAATTATATTAT (SEQ ID NO:1), the same 2:1 binding ratio as netropsin (as well as similar AT-selectivity).
FIG. 3: Binding studies with 13/20 (the compound of Example 3)
FIG. 3 presents the binding electropherograms of 13/20 in the presence of a double-stranded DNA decamer having, on one strand, the nucleotide sequence CGACTAGTCG (SEQ ID NO:3) the central part of which was indicated to be a high affinity binding site from footprinting studies (see FIG. 7). Here we see that the binding ratio is 4:1 (drug:DNA). This result demonstrates that 13/20 has a strong affinity for the given sequence, and also that the minor groove produced by the DNA decamer accommodates 4 drug-binding molecules in one binding site.
FIG. 4: Binding studies with distamycin
FIG. 4 presents the binding electropherograms of the well-known compound distamycin in the presence of the double-stranded DNA decamer having, on one strand, the nucleotide sequence CGACTAGTCG (SEQ ID NO:3). It can clearly be seen, distamycin has no affinity for the CGACTAGTCG (SEQ ID NO:3) sequence even at a drug to DNA ratio of 4:1 (the trace labelled r4).
FIG. 5: Competitive binding studies with compound 13/20
FIG. 5 presents the binding electropherograms for 13/20 in the presence of a mixture of double-stranded DNA oligonucleotides, one having, on one strand, the dodecameric nucleotide sequence AAATTATATTAT (SEQ ID NO:1) (peak 1) and the other having, on one strand, the decameric nucleotide sequence GGACTAGTCG (SEQ ID NO:4) (peak 2). It can be seen from the results that 13/20 has a greater affinity for the decamer ACTA sequence (as indicated by the earlier disappearance of the peak corresponding to the uncomplexed ACTA sequence).
FIG. 6: Further binding studies with compound 13/20
FIG. 6 presents the binding electropherograms of 13/20 incubated against the double-stranded DNA oligonucleotide having, on one strand, the decameric nucleotide sequence CCACTAGTGG (SEQ ID NO:5) The result obtained for this binding was identical with that achieved with the sequence in FIG. 3, showing that it is the central sequence which dominates binding, as indicated by footprinting.
FIGS. 7 and 8: DNA footprinting studies
DNA footprinting is a well-established technique in which a section of radio-labelled DNA (SEQ ID NO:6) is incubated with a chemical or biological cleaving agent, in the presence and absence of a putative binding ligand. Regions of ligand binding will show as blanks in the ‘ladder’. Knowing the DNA sequence, the binding sites can then be deduced, from the location of these blanks.
The sequence shown in FIGS. 7 and 8 is MS1, which contains all possible four-base-pair binding sites. The procedure used in the footprinting experiments was analogous to that described in J. Med. Chem. 43, 3257 (2000), the disclosures of which document are hereby incorporated by reference. In an analogous manner to the procedure described in J. Med. Chem. 43, 3257 (2000), the MS1 sequence was labelled at the 3′-end with [α-32P]dATP using reverse transcriptase. The agent used to cleave the radio-labelled DNA was DNase I.
Bases that fall within the “footprint” of a compound are indicated by XX . . . XX underneath the sequence. The binding domain that has been confirmed by capillary electrophoresis is indicated by XX. XX.
FIG. 7 shows the results for compound 13/20 (at a concentration of 0.03 μM), whereas FIG. 8 shows the results for compound 13/51 (at the concentrations indicated therein). As can be seen, at the concentration used in the experiment, compound 13/20 produces a footprint that is indicative of binding to only one site on the MS1 sequence. This binding site includes GC base pairs. In contrast, compound 13/51, at the concentrations indicated in FIG. 8, produced footprints over several different “AT-only” binding sites on the MS1 sequence.
FIG. 9: DNA-Binding Assays with Compounds 12/41 and 13/20.
Murine macrophages (obtained and cultured as described in Cell. Signal. 11(7), 491 (1999), hereinafter referred to as “Reference 1”, the disclosures of which document are hereby incorporated by reference) were exposed to vehicle (see Reference 1) or 1 μg/mL lipopolysaccharide (LPS; the active component of gram-negative endotoxin and a strong activator of the Nuclear Factor kappa B (NFκB) pathway; the particular LPS being obtained from Salmonella minnesota) for 1 hour and nuclear extracts prepared by standard procedures (see Brit. J. Pharmacol. 134, 393 (2001), hereinafter referred to as “Reference 2”, the disclosures of which document are hereby incorporated by reference).
Aliquots of compounds (1 μL of a 1 mM solution) were incubated with 1 μL (0.035 pmol) of a 32P-labelled 20 bp double-stranded DNA oligonucleotide (representing the consensus binding sequence for NFκB proteins (see Reference 2 and Brit. J. Pharmacol. 134, 1629-1638 (2001), the disclosures of which latter document are hereby incorporated by reference)) for 30 min at room temperature. Following this, 5 μg of nuclear protein and buffer (the “gel-shift binding buffer” of Reference 2) were added (final volume 10 μL) and the samples incubated for a further 30 min at room temperature prior to their electrophoresis on pre-run non-denaturing polyacrylamide gels for 45-60 min (see Reference 2). Gels were then dried and exposed to X-ray film. The formation of NFκB protein-DNA complexes and potential inhibition of complex formation in the presence of the above compounds was detected by autoradiography.
In FIG. 9, lanes 1 to 4 show the results obtained where the nuclear protein was extracted from the macrophages exposed to vehicle, whereas lanes 5 to 8 show the results obtained where the nuclear protein was extracted from the macrophages exposed to LPS.
From the results presented in FIG. 9, it can be determined that exposure to lipopolysaccharide resulted in an increase in NFκB-DNA-binding activity (lane 1 vs. lane 5). Pre-incubation with the synthetic compounds had no effect upon basal DNA-binding activity (lane 1 vs. lanes 2 to 4). However, compounds 13/51 and 13/20 appeared to inhibit LPS-stimulated NFκB-DNA binding activity (lane 5 vs. lanes 6 and 7). In contrast, compound is 12/41 had little effect (lane 5 vs. lane 8).
Although compound 13/51, which does not bear a branched, cyclic or part cyclic C3-5 alkyl substituent, appears to inhibit LPS-stimulated NFκB-DNA binding activity more strongly than does compound 13/20 (lane 6 vs. lane 7), this might well be expected from the lower binding specificity of compound 13/51 (compare FIGS. 7 and 8).
Biological Tests
Minimum inhibitory concentrations (MICs) against microorganisms (e.g. S. Aureus, E. coli, S. faecalis, P. vulgaris, MRSA, Aspergillus niger, Candida albicans, Klebs. aerogenes, Ent. cloacae, Mycobacterium fortuitum or Aspergillus nidulans) for compounds of the invention may be measured using procedures such as those described in A. J. Drummond and R. D. Waigh “The development of microbiological methods for phytochemical screening” Recent Res. Devel. Phytochem. 4, 143-152 (2000).
EXAMPLES
General Experimental Procedures
Electrospray mass spectra (ES-MS) were obtained on a Fisons® VG Platform Benchtop LC-MS. Electron impact (EI-MS) and fast atom bombardment (FAB-MS) mass spectra were obtained on a Jeol® JMS-AX505HA mass spectrometer.
NMR spectra were obtained on a Bruker® AMX 400 spectrometer operating at 400 MHz for 1H. In 1H NMR spectra, the abbreviation ‘exch.’ signifies that the relevant resonance disappeared on treatment of the solution with D2O.
HPLC purification of the final products was carried out using a Vydac protein and peptide C18 column on a gradient eluting system. The solvents were A: water+0.1% trifluoroacetic acid (TFA), and B: acetonitrile+0.1% TFA.
IR spectra: solids were run as KBr discs and liquids as films, using a Nicolet® Impact 400D.
Column chromatography was performed with silica gel Prolabo® (200-400 mash).
Example 1
N-[5-({[5-({[3-(Dimethylamino)propyl]amino}carbonyl)-1-methyl-1H-pyrrol-3-yl]amino}carbonyl)-1-isopropyl-1-H-pyrrol-3-yl]-4-[(3,3-dimethylbutanoyl)amino]-1-methyl-1H-pyrrole-2-carboxamide
(i) Ethyl 4-nitro-1H-pyrrole-2-carboxylate
The sub-title compound was prepared according to a standard literature procedure (see: Ref. 1: W. J. Hale and W. V. Hoyr, J. Amer. Chem. Soc. 37, 2538-2552 (1915); and Ref. 2: K. J. Morgan and D. P. Morrey, Tetrahedron 22, 57-62 (1966)).
(ii) Ethyl 1-isopropyl-4-nitro-1H-pyrrole-2-carboxylate
Ethyl 4-nitro-1H-pyrrole-2-carboxylate (1.039 g, 5.645 mmol; see step (i) above) was dissolved in DMF (40 mL, dry) to which was added potassium metal (384 mg, 9.831 mmol). The reaction mixture was heated to 100° C. and left at that temperature for 1 h with stirring. The reaction mixture was cooled to 50-60° C. then isopropyl bromide (1.224 g, 9.953 mmol) and potassium iodide (1.714 g, 10.327 mmol) were added and the reaction mixture was again heated with stirring to 100° C. for 5 h, and was then left stirring at room temperature overnight. The solvent was removed under reduced pressure and the residue was diluted with DCM and then extracted with water. The organic extract was dried over MgSO4, filtered and the solvent removed under reduced pressure. The crude product obtained was chromatographed over silica gel eluted with 1/2 pet.ether/DCM. The material (RF=0.26) was collected and the solvent removed under reduced pressure to give white crystalline solid (686 mg, 54% yield), m.p. 60-63° C.
Elemental Analysis:
Found: % C=53.19; % H=6.31; % N=12.30; Calculated for C10H14N2O4: % C=53.10; % H=6.24; % N=12.38. NMR(DMSO-d6): 7.80(1H, d); 7.45(1H, d); 5.55-5.44(1H, qt); 4.36-4.27(2H, q); 1.51(6H, d); 1.40-1.34(3H, t). IR νmax [KBr]: 1714, 1536, 1504, 1440, 1325, 1287, 1223, 1178, 1063 cm−1.
(iii) 1-Isopropyl-4-nitro-1H-pyrrole-2-carboxylic acid
Ethyl 1-isopropyl-4-nitro-1H-pyrrole-2-carboxylate (656 mg, 2.900 mmol; see step (ii) above) was dissolved in ethanol (4 mL) to which was added a solution of NaOH (490 mg, 12.250 mmol in water (10 mL)). The reaction mixture was heated under reflux for 1.5 h and then the ethanol was removed under reduced pressure at 40° C. The reaction mixture was extracted with DCM (10 mL), and the water layer was collected, cooled to 0° C. with ice-water then acidified with HClconc with stirring. The white solid material precipitated was filtered off, washed with water and dried under reduced pressure at 50° C. to give the required product (548 g, 95% yield), m.p. 194-195° C.
Elemental Analysis:
Found: % C=48.40; % H=4.85; % N=14.03; Calculated for C8H10N2O4: % C=48.48; % H=5.09; % N=14.13. NMR(DMSO-d6): 8.37(1H, d); 7.27(1H, d); 5.47-5.36(1H, q); 1.44(6H, d). IR νmax [KBr]: 1676, 1541, 1517, 1483, 1411, 1370, 1250, 1188, 1077 cm−1.
(iv) N-[5-({[3-(Dimethylamino)propyl]amino}carbonyl)-1-methyl-1H-pyrrol-3-yl]-1-isopropyl-4-nitro-1H-pyrrole-2-carboxamide
N-[3-(Dimethylamino)propyl]-1-methyl-4-nitro-1H-pyrrole-2-carboxamide (816 mg, 3.209 mmol; see Tetrahedron 56, 5225-5239 (2000)) was suspended in a mixture of ethanol (30 mL) and HCl (7 mL, dil) to which was added Pd/C (517 mg, 10%) at room temperature. The reaction mixture was hydrogenated at room temperature and atmospheric pressure for 3.5 h. The catalyst was removed by filtration over Kieselguhr and then the solvent was removed under reduced pressure at 50° C. to give the amine as pale yellow solid. The product so formed was dissolved in water (10 mL) to which NaHCO3 (2 g) was added. 1-Isopropyl-4-nitro-1H-pyrrole-2-carboxylic acid (548 mg, 2.631 mmol; see step (iii) above) was dissolved in DME (6 mL, dry) and thionyl chloride (3 mL), then heated under reflux for 2 h. The solvent was removed at room temperature to give the acid chloride which was dissolved in benzene (10 mL) and was added dropwise to the reaction mixture at room temperature with stirring. After addition of the acid chloride solution was finished the reaction mixture was heated under reflux for 30 min. then left to cool to room temperature overnight with continuous stirring. The reaction mixture was extracted with DCM (300 mL), dried and the solvent removed under reduced pressure to give yellow solid material. This material was triturated with a small amount of methanol and filtered to give pale yellow solid (318 mg). The filtrate was concentrated and chromatographed over silica gel using ethyl acetate/methanol/ammonia (49/49/2). Fractions with Rf value of 0.3 were collected. The product was obtained as yellow solid (640 mg, 49% yield in total). M.p. 205-207° C.
Found: C, 56.25; H, 6.78; N, 20.59 Calculated for C19H28N6O4 C, 56.42; H, 6.98; N, 20.78%. 1H-NMR(DMSO-d6) δ 1.42-1.57 (6H, d); 1.60-1.65 (2H, m); 2.12 (6H, s); 2.20-2.25 (2H, t); 3.17-3.22 (2H, q); 3.81 (3H, s); 5.40-5.51 (1H, m); 6.83 (1H, s); 7.22 (1H, s); 7.48 (1H, s); 8.11-8.15 (1H, t, CONH); 8.34 (1H, s); 10.29 (1H, s). IR νmax [KBr]:1640, 1555, 1506, 1480, 1322, 1279, 1240, 1203 cm−1. ESMS: Found: 405.2 Calculated 405.5.
(v) N-[5-({[3-(Dimethylamino)propyl]amino}carbonyl)-1-methyl-1H-pyrrol-3-yl]-1-isopropyl-4-{[(1-methyl-4-nitro-1H-pyrrol-2-yl)carbonyl]-amino)}-1H-pyrrole-2-carboxamide
N-[5-({[3-(Dimethylamino)propyl]amino}carbonyl)-1-methyl-1H-pyrrol-3-yl]-1-isopropyl-4-nitro-1H-pyrrole-2-carboxamide (272 mg, 0.672 mmol; see step (iv) above) and Pd/C (325 mg, 10%) were suspended in isopropanol (30 mL) and hydrogenated at room temperature and atmospheric pressure for 5 h. The catalyst was removed over Kieselguhr and the solvent removed under reduced pressure to give the amine as pale yellow solid, which was used without further purification. The amine was dissolved in THF (5 mL, dry) then 2,2,2-trichloro-1-(1-methyl-4-nitro-1H-pyrrol-2-yl)ethanone (183 mg, 0.674 mmol; see Tetrahedron 56, 5225-5239 (2000)) dissolved in THF (5 mL, dry) was added dropwise with stirring at room temperature. The stirring was continued overnight at room temperature. The solvent was removed under reduced pressure at room temperature to give the crude product, which was purified by silica gel column chromatography ethyl acetate/methanol/ammonia (49/49/2). Fractions containing the product at Rf value of 0.3 were collected. The product was obtained as yellow solid material (221 mg, 63% yield) with no distinct melting point.
1H-NMR(DMSO-d6) δ 1.36-1.38 (6H, d); 1.64-1.71 (2H, m); 2.31 (6H, s); 3.16-3.22 (2H, q); 3.81 (3H, s); 3.96 (3H, s); 5.40-5.50 (1H, m); 6.85 (1H, d J 1.6 Hz); 6.93 (1H, d J 1.6 Hz); 7.18 (1H, d J 1.6 Hz); 7.43 (1H, d J 1.6 Hz); 7.58 (1H, d J 1.6 Hz); 8.07-8.10 (1H, t, CONH); 8.18 (1H, d J 1.6 Hz); 9.96 (1H, s); 10.29 (1H, s). IR νmax [KBr]:1643, 1579, 1534, 1507, 1464, 1407, 1310, 1247 cm−1. HRFABMS: Found: 527.27341 Calculated for C25H35N8O5 527.27304.
(vi) N-[5-({[5-({[3-(Dimethylamino)propyl]amino}carbonyl)-1-methyl-1H-pyrrol-3-yl]amino}carbonyl)-1-isopropyl-1-H-pyrrol-3-yl]-4-[(3,3-dimethylbutanoyl)amino]-1-methyl-1H-pyrrole-2-carboxamide
N-[5-({[3-(Dimethylamino)propyl]amino}carbonyl)-1-methyl-1H-pyrrol-3-yl]-1-isopropyl-4-{[(1-methyl-4-nitro-1H-pyrrol-2-yl)carbonyl]-amino}-1H-pyrrole-2-carboxamide (100 mg, 0.189 mmol; see step (v) above) was dissolved in methanol (20 mL) to which was added Pd/C (114 mg, 10%). The reaction mixture was hydrogenated at room temperature and atmospheric pressure for 6.5 h. The catalyst was removed over Kieselguhr and the solvent removed under reduced pressure. The amine so formed was dissolved in DCM (10 mL, dry) to which was added a solution of 3,3-dimethylbutanoyl chloride (35 μL, 0.260 mmol), which was dissolved in DCM (5 mL, dry). The addition was dropwise with stirring at room temperature. Di-isopropylamine was then added in one portion to the reaction mixture. Stirring was continued at room temperature overnight. The solvent was removed under reduced pressure and the crude product obtained was purified by column chromatography using silica gel and ethyl acetate/methanol/ammonia (49/49/2). The solvent was removed under reduced pressure and the solid material was dissolved in chloroform (100 mL) and extracted with (5%, 50 mL) NaHCO3. The organic layer was dried over Na2SO4, filtered and the solvent removed to give the required product (84 mg, 75% yield) as yellow glassy material with no distinct melting point.
1H-NMR(CDCl3): δ 1.03 (9H, s); 1.29-1.32 (6H, d); 1.68-1.83 (2H, m); 2.15 (2H, s); 2.19 (6H, s); 2.26-2.39 (2H, t); 3.39-3.46 (2H, q); 3.83 (3H, s); 3.84 (3H, s); 5.42-5.51 (1H, m); 6.47 (1H, d J 1.4 Hz); 6.58 (1H, d J 1.4 Hz); 6.67 (1H, d J 1.4 Hz); 7.05 (1H, d J 1.4 Hz); 7.22 (1H, d J 1.4 Hz); 7.37 (1H, d J 1.4 Hz); 7.78 (1H, t CONH); 7.82 (1H, s); 8.18 (1H, s); 8.32 (1H, s). IR νmax [KBr]: 3298, 2960, 1644, 1582, 1538, 1405, 1250 cm−1. ES-MS: Found: M+ 595.1 Calculated for C31H46N8O4 M+ 595.4.
Example 2
N-[5-({[5-({[3-(Dimethylamino)propyl]amino}carbonyl)-1-methyl-1H-pyrrol-3-yl]amino}carbonyl)-1-isopropyl-1H-pyrrol-3-yl]-4-(formylamino)-1-methyl-1H-pyrrole-2-carboxamide
N-[5-({[3-(Dimethylamino)propyl]amino}carbonyl)-1-methyl-1H-pyrrol-3-yl]-1-isopropyl-4-{[(1-methyl-4-nitro-1H-pyrrol-2-yl)carbonyl]-amino}-1H-pyrrole-2-carboxamide (102 mg, 0.194 mmol; see Example 1, step (v) above) was dissolved in methanol (20 mL), to which was added Pd/C (106 mg, 10%). The reaction mixture was hydrogenated for 5 h at room temperature and atmospheric pressure. The catalyst was removed over Kieselguhr and then ethyl formate (10 mL) was added to the filtrate. The reaction mixture was then heated until reflux for 72 h. The solvent was removed under reduced pressure and the crude product obtained was purified by HPLC. The product was obtained as white solid material after freeze-drying (64 mg, 51% yield as TFA salt).
1H-NMR(DMSO-d6) δ1.35-1.37(6H, d); 1.81-1.85(2H, m); 2.78-2.79(6H, d); 3.05(2H, m); 3.23-3.25(2H, q); 3.81(3H, s); 3.84(3H, s); 5.40-5.46(1H, m); 6.92(1H, s); 6.94(1H, s); 6.96(1H, s); 7.17(1H, s); 7.19(1H, s); 7.38(1H, s); 8.12(1H, s); 8.15(1H, t, CONH); 9.3(1H, broad, TFA); 9.85(1H, s); 9.91(1H, s); 10.05(1H, s). IR νmax [KBr]: 1673, 1644, 1582, 1540, 1470, 1441, 1402, 1204, 1139 cm−1. ES-MS: Found: M+ 524.9 Calculated 525.6.
Example 3
N-[3-(Dimethylamino)propyl]-2-({[4-({[4-(formylamino)-1-methyl-1H-pyrrol-2-yl]carbonyl}amino)-1-methyl-1H-pyrrol-2-yl]carbonyl}amino)-5-isopropyl-1,3-thiazole-4-carboxamide
(i) Methyl 2-amino-5-isopropyl-1,3-thiazole-4-carboxylate
The sub-title compound was prepared in 41% yield according to the procedure described in J. Chem. Soc., Perkin Trans. I 159 (1982).
m.p. 151-152° C. (Lit. 150-151° C.).
(ii) Methyl 5-isopropyl-2-{[(1-methyl-4-nitro-1H-pyrrol-2-yl)carbonyl]-amino}-1,3-thiazole-4-carboxylate
1-Methyl-4-nitro-1H-pyrrole-2-carboxylic acid (520 mg, 3.057 mmol; see Tetrahedron 56, 5225-5239 (2000)) was dissolved in thionyl chloride (10 mL). The reaction mixture was heated under reflux overnight. Excess thionyl chloride was removed under reduced pressure to give the acid chloride, which was used without further purification. The acid chloride was dissolved in DCM (20 mL, dry), to which NMM (1.214 g, 12.000 mmol). The reaction mixture was cooled to 0° C. and kept under N2. A solution of methyl 2-amino-5-isopropyl-1,3-thiazole-4-carboxylate (0.612 g, 3.057 mmol; see step (i) above) in DCM (20 mL, dry) was then added dropwise with stirring over a period of 10 min. The temperature was left to rise to room temperature overnight. DCM (10 mL) was added to the reaction mixture then HCl (50 mL, dil.) was added and the reaction mixture was extracted. The organic layer was washed with brine (50 mL), dried over MgSO4 and the solvent removed under reduced pressure to give the crude product. Column chromatography over flash silica gel [1/1 ethyl acetate/pet.ether] gave the required product as white crystalline solid (460 mg, 43% yield), m.p. 118-120° C. (softening).
NMR(CDCl3): 1.33-1.35(6H, CH—(CH3)2, d, J=6.4 Hz); 3.89(3H, s, CO2Me); 4.09(3H, s, NMe); 4.11-4.18(1H, m); 7.24(1H, pyrrole, d, J=1.4 Hz); 7.67(1H, pyrrole, d, J=1.4 Hz); 9.85(1H, broad, CONH, exch.). IR νmax [KBr]: 3557, 3119, 2975, 1712, 1646, 1574, 1509, 1319, 1208 cm−1. HREIMS: Found: 352.08579 calculated for C14H16N4O5S 352.08414.
(iii) 5-Isopropyl-2-{[(1-methyl-4-nitro-1H-pyrrol-2-yl)carbonyl]amino}-1,3-thiazole-4-carboxylic acid
Methyl 5-isopropyl-2-{[(1-methyl-4-nitro-1H-pyrrol-2-yl)carbonyl]amino}-1,3-thiazole-4-carboxylate (480 mg, 1.363 mmol; see step (ii) above) was suspended in ethanolic KOH (0.5 M, 25 mL). The reaction mixture was heated under reflux for 4 h, then cooled to 0° C. HCl (conc.) was added dropwise with stirring until pH 2. The pale yellow solid obtained was filtered off, washed with de-ionised water and dried under reduced pressure at 45° C. overnight to give the required material (440 mg, 96% yield), m.p. 315-319° C.[decomp.].
NMR(DMSO-d6) 1.23-1.25(6H, CH—(CH3)2, d, J=6.4 Hz); 3.98(3H, s, NMe); 4.01-4.08(1H, m); 7.99(1H, pyrrole, d, J=1.4 Hz); 8.29(1H, pyrrole, d, J=1.4 Hz); 12.5-13.2(1H, broad, CO2H, exch.). IR νmax [KBr]: 3189, 3132, 2972, 1668, 1566, 1537, 1512, 1497, 1319, 1231 cm−1. HRFABMS: Found: 337.06396 calculated for C13H13O5N4S 337.06067
(iv) N-[3-(Dimethylamino)propyl]-5-isopropyl-2-{[(1-methyl-4-nitro-1H-pyrrol-2-yl)carbonyl]amino}-1,3-thiazole-4-carboxamide
5-Isopropyl-2-{[(1-methyl-4-nitro-1H-pyrrol-2-ylcarbonyl]amino}-1,3-thiazole-4-carboxylic acid (440 mg, 1.301 mmol; see step (iii) above) was suspended in thionyl chloride (6 mL) and heated until reflux for 3 h. Solvent (excess thionyl chloride) was removed under reduced pressure and the acid chloride so formed was dissolved in THF (20 mL, dry) then NMM (330 μL) was added. A solution of 3-(dimethylamino)propylamine (270 mg, 2.602 mmol) in THF (5 mL, dry) was added dropwise with stirring at room temperature under nitrogen. The stirring was continued at room temperature overnight. The solvent was removed under reduced pressure and the residue was purified by column chromatography using (1:1 methanol/ethyl acetate containing 1% TEA). The product was obtained as yellow glassy material (159 mg, 29% yield), m.p. 85-90° C. [softening].
NMR(CDCl3): 1.27-1.29(6H, CH—(CH3)2, d, J=6.4 Hz); 1.79-1.86(2H, CH2, qt, J=6.9 Hz); 2.31(6H, s, NMe2); 2.45-2.49(2H, CH2, t, J=6.9 Hz); 3.44-3.50(2H, CH2, q, J=6.9 Hz); 4.10(3H, s, NMe); 4.38-4.45(1H, CH(CH3)2), m); 7.56(1H, pyrrole, d, J=1.4 Hz); 7.62(1H, s, CONH, exch.); 7.69(1H, pyrrole, d, J=1.4 Hz). IR νmax [KBr]: 3131, 2959, 1668, 1551, 1500, 1418, 1310, 1286 cm4. HREIMS: Found: 422.17695 calculated for C18H26O4N6S 422.17363.
(v) N-[3-(Dimethylamino)propyl]-5-isopropyl-2-{[(1-methyl-4-{[(1-methyl-4-nitro-1H-pyrrol-2-yl)carbonyl]amino}-1H-pyrrol-2-yl)carbonyl]-amino}-1,3-thiazole-4-carboxamide
N-[3-(Dimethylamino)propyl]-5-isopropyl-2-{[(1-methyl-4-nitro-1H-pyrrol-2-yl)carbonyl]amino}-1,3-thiazole-4-carboxamide (159 mg, 0.376 mmol; see step (iv) above) was dissolved in methanol (25 mL), cooled with ice, and then Pd/C (158 mg, 10%) was added under nitrogen. The reaction mixture was hydrogenated for 4 h at room temperature and atmospheric pressure. The catalyst was removed over Kieselguhr and the solvent was then removed under reduced pressure to give the amine. This amine was dissolved in THF (25 mL, dry) to which was added 2,2,2-trichloro-1-(1-methyl-4-nitro-1H-pyrrol-2-yl)ethanone (134 mg, 0.494 mmol; see Tetrahedron 56, 5225-5239 (2000)) dissolved in THF (5 mL, dry), dropwise with stirring, at room temperature. Stirring was continued at room temperature overnight. The solvent was removed under reduced pressure and the residue was chromatographed using 49/49/2 methanol/ethyl acetate/TEA. The product obtained was dissolved in DCM and extracted with a solution of sodium carbonate (10 mL, 5%), then dried and the solvent removed under reduced pressure. The product was obtained as yellow solid (90 mg, 44% yield). M.p. 138-141° C.
1H-NMR(DMSO-d6) δ 1.26 & 1.28(6H, d, 2xMe); 1.65(2H, m, CH2); 2.19(6H, s, NMe2); 2.32(2H, t, CH2); 3.26(2H, q, CH2); 3.90(3H, s, NMe); 3.97(3H, s, NMe); 4.19(1H, m, CH); 7.36(1H, d, PyrH); 7.47(1H, d, pyrH); 7.62(1H, d, PyrH); 7.81(1H, t, CONH exch.); 8.19(1H, d, PyrH); 10.35(1H, s, CONH exch.); 12.10(1H, broad exch.). IR νmax [KBr]: 1651, 1552, 1506, 1464, 1421, 1398, 1311, 1288, 1202 cm−1. HRFABMS: Found: 545.22931 Calculated for C24H33N8O5S 545.22946.
(vi) N-[3-(Dimethylamino)propyl]-2-({[4-({[4-(formylamino)-1-methyl-1H-pyrrol-2-yl]carbonyl}amino)-1-methyl-1H-pyrrol-2-yl]carbonyl}amino)-5-isopropyl-1,3-thiazole-4-carboxamide
N-[3-(Dimethylamino)propyl]-5-isopropyl-2-{[(1-methyl-4-{[(1-methyl-4-nitro-1H-pyrrol-2-yl)carbonyl]amino}-1H-pyrrol-2-yl)carbonyl]amino}-1,3-thiazole-4-carboxamide (90 mg, 0.165 mmol; see step (v) above) was suspended in ethanol (20 mL) then Pd/C (97 mg, 10%) was added at 0° C. under nitrogen. The reaction mixture was hydrogenated at room temperature and atmospheric pressure for 5 h. The catalyst was removed under reduced pressure then ethyl formate (20 mL) was added to the ethanolic solution of the amine. The reaction mixture was heated under reflux for 3 days, then the solvent was removed under reduced pressure. The crude product was dissolved in water (2 mL) containing 0.1% TFA, then purified by HPLC. The fractions collected were freeze-dried to give the desired product as pale yellow solid (55 mg, 51%) with no distinct m.p.
1H-NMR(DMSO-d6) δ 1.27-1.29(6H, d, J=6.9 Hz), 1.86(2H, m), 2.78-2.79(6H, d, J=4.0 Hz), 3.07(2H, m), 3.37(2H, m), 3.84(3H, s), 3.88(3H, s), 4.19(1H, m), 6.94(1H, d, J=1.6 Hz), 7.19(1H, s), 7.38(1H, s), 7.40(1H, s), 7.96(1H, t), 8.13(1H, d, J=1.6 Hz), 9.30(1H, broad, TFA), 9.99(1H, s), 10.04(1H, s), 12.02(1H, s). IR νmax [KBr]: 1664, 1555, 1465, 1399, 1294, 1209, 1130 cm−1. HRFABMS: Found: 544.25962 Calculated for C25H36N8O4S 544.25802
Example 4
N-[5-({[3-(Dimethylamino)propyl]amino}carbonyl)-1-isopropyl-1H-pyrrol-3-yl]-4-({[4-(formylamino-1-isopropyl-1H-pyrrol-2-yl]carbonyl}amino)-1-isopropyl-1H-pyrrole-2-carboxamide
(i) N-[3-(Dimethylamino)propyl]-1-isopropyl-4-nitro-1H-pyrrole-2-carboxamide
1-Isopropyl-4-nitro-1H-pyrrole-2-carboxylic acid (312 mg, 1.574 mmol; see Example 1, step (iii) above) was dissolved in thionyl chloride (5 mL) and heated until reflux for 4 h. The excess thionyl chloride was removed under reduced pressure at 50° C. to give the acid chloride as white solid material that was used without further purification. 3-(Dimethylamino)propylamine (250 μL) was dissolved in THF (250 mL, dry) to which NMM (250 μL) was added at room temperature with stirring. The acid chloride was dissolved in THF (5 mL, dry) and added dropwise to the amine solution at room temperature with stirring. The reaction mixture was then left stirring at room temperature overnight. Following this the solvent was removed under reduced pressure at 50° C. and then the crude product was extracted with K2CO3 (25 mL, 10%) and DCM (2×50 mL). The organic layer was collected, dried over Na2SO4, filtered and the solvent removed under reduced pressure. The crude product was purified by chromatography over silica gel using 49.5:49.5:1 methanol/ethyl acetate/TEA to give the product as pale yellow oil, Rf=0.25, (400 mg, 90% yield).
NMR(CDCl3): 1.46&1.48(6H, d, J=6.7 Hz), 1.71-1.77(2H, qt, J=6.0 Hz), 2.32(6H, s), 2.51(2H, t, J=5.7 Hz), 3.49(2H, qt, J=5.0 Hz), 5.62(1H, qt, J=6.7 Hz), 6.92(1H, d, J=1.6 Hz), 7.73(1H, d, J=1.6 Hz), 8.58(1H, s). IR νmax [KBr]: 3330, 3136, 2979, 1650, 1535, 1430, 1279, 1258 cm−1. HREIMS: Found: 282.16908 Calculated for C13H22N4O3 282.16919
(ii) N-[5-({[3-Dimethylamino)propyl]amino}carbonyl)-1-isopropyl-1H-pyrrol-3-yl]-1-isopropyl-4-nitro-1H-pyrrole-2-carboxamide
N-[3-(Dimethylamino)propyl]-1-isopropyl-4-nitro-1H-pyrrole-2-carboxamide (400 mg, 1.417 mmol; see step (i) above) was dissolved in ethanol (20 mL) then cooled to 0° C. Pd/C-10% (343 mg) was added portion-wise under N2 with stirring. The reaction mixture was hydrogenated at room temperature and atmospheric pressure for 4 h. The catalyst was removed over Kieselguhr, and the solvent removed under reduced pressure at 50° C. to give an oil which was used in the next step without further purification. 1-Isopropyl-4-nitro-1H-pyrrole-2-carboxylic acid (281 mg, 1.417 mmol; see Example 1, step (iii) above) was suspended in thionyl chloride (5 mL) then heated under reflux for 4 h. The excess thionyl chloride was removed under reduced pressure at 50° C. and then it was dissolved in THF (5 mL, dry). The amine was dissolved in TH (20 mL, dry) to which was added NMM (250 μL) followed by the acid chloride solution. The addition was dropwise at room temperature with stirring. The reaction mixture was left stirring at room temperature overnight. The solvent was removed under reduced pressure and the crude product dissolved in DCM (50 mL) and extracted with Na2CO3 (5%, 25 mL). The organic layer was dried over Na2SO4, filtered and the solvent removed under reduced pressure. The crude product was chromatographed over silica gel using 50:50:0.5 methanol/ethyl acetate/TEA. Fractions with Rf value of 0.1 were collected. The solvent was removed at 50° C. under reduced pressure to give the product as yellow glassy material (471 mg, 77% yield), m.p. 86-90° C. (softening).
NMR(CDCl3):1.42(6H, d, 6.7 Hz), 1.75(6H, d, J=6.7 Hz), 1.72-1.77(2H, m), 2.31(6H, s), 2.46(2H, t, J=6.1 Hz), 3.44-3.49(2H, q, J=6.0 Hz), 5.51-5.64(2H, m), 6.45(1H, d, 1.6 Hz), 7.17(1H, d, J=1.6 Hz), 7.40(1H, d, J=1.6 Hz), 7.69(1H, s, broad, CONH), 7.79(1H, d, J=1.6 Hz). IR νmax [KBr]: 2974, 2927, 1636, 1574, 1531, 1507, 1407, 1282, 1237, 1170 cm−1. HREIMS: Found: 432.24833 Calculated for C21H32N6O4 432.24850
(iii) N-[5-({[3-(Dimethylamino)propyl]amino}carbonyl)-1-isopropyl-1H-pyrrol-3-yl]-1-isopropyl-4-{[(1-isopropyl-4-nitro-1H-pyrrol-2-yl)carbonyl]-amino}-1H-pyrrole-2-carboxamide
N-[5-({[3-(Dimethylamino)propyl]amino}carbonyl)-1-isopropyl-1H-pyrrol-3-yl]-1-isopropyl-4-nitro-1H-pyrrole-2-carboxamide (209 mg, 0.483 mmol; see step (ii) above) was dissolved in ethanol (20 mL) at 0° C. with stirring. Pd/C-10% (180 mg) was added to the solution at 0° C. and under N2 with stirring. The reaction mixture was hydrogenated for 4 h then the catalyst was removed by filtration over Kieselguhr and the solvent removed under reduced pressure at 50° C. to give the amine. 1-Isopropyl-4-nitro-1H-pyrrole-2-carboxylic acid (92 mg, 0.462 mmol; see Example 1, step (iii) above) was dissolved in thionyl chloride (3 mL) and heated under reflux for 3 h. Excess thionyl chloride was removed under reduced pressure at 50° C. to give the acid chloride. The amine was dissolved in THF (20 mL, dry) to which the acid chloride [dissolved in THF (20 mL, dry)] was added dropwise with stirring at room temperature. The reaction mixture was left stirring at room temperature overnight. The solvent was removed under reduced pressure and the crude product dissolved in DCM (2×50 mL) after which it was extracted with Na2CO3 (50 mL, 5%). The organic layer was dried and then the solvent removed. The crude product was chromatographed over silica gel using 49.5:49.5:1 ethyl acetate/methanol/TEA as eluant. The product was obtained as yellow glassy material Rf=0.15, (230 mg, 82% yield), m.p. 130-133° C. (softening).
NMR(CDCl3): 1.43(6H, d, J=6.7 Hz), 1.47(6H, d, J=6.7 Hz), 1.52(6H, d, J=6.7 Hz), 1.73-1.79(2H, m), 2.32(6H, s), 2.47-2.50(2H, t, 6.1 Hz), 3.46-3.50(2H, q, 6.0 Hz), 5.53-5.61(3H, m), 6.42(1H, d, J=1.6 Hz), 6.60(1H, d, J=1.6 Hz), 7.28(1H, d, J=1.6 Hz), 7.40(1H, d, J=1.6 Hz), 7.41(1H, s), 7.44(1H, s), 7.63(1H, s, broad, CONH), 7.81(1H, d, J=1.6 Hz), 8.02(1H, s). IR νmax [KBr]: 2979, 2937, 1645, 1593, 1525, 1504, 1410, 1279, 1237, 1190 cm−1. HRFABMS: Found: 583.33440 Calculated for C29H43N8O5 583.33564
(iv) N-[5-({[3-(Dimethylamino)propyl]amino}carbonyl)-1-isopropyl-1H-pyrrol-3-yl]-4-({[4-(formylamino)-1-isopropyl-1H-pyrrol-2-yl]carbonyl}-amino)-1-isopropyl-1H-pyrrole-2-carboxamide
N-[5-({[3-(Dimethylamino)propyl]amino}carbonyl)-1-isopropyl-1H-pyrrol-3-yl]-1-isopropyl-4-{[(1-isopropyl-4-nitro-1H-pyrrol-2-yl)carbonyl]amino}-1H-pyrrole-2-carboxamide (105 mg, 0.180 mmol; see step (iii) above) was suspended in ethanol (20 mL) to which Pd/C-10% (80 mg) was added under nitrogen at 0° C. The reaction mixture was hydrogenated at room temperature and atmospheric pressure for 4 h. The catalyst was removed over Kieselguhr and the ethanolic solution was then used in the second part of the experiment. Ethyl formate (20 mL) was added to the ethanolic solution of the amine. The reaction mixture was heated under reflux for 4 days. The solvents were removed under reduced pressure at 40° C. and then the crude product was purified by reverse phase HPLC. The fractions obtained were freeze-dried to give the required material as white solid (71 mg, 57% yield) as TFA salt with no distinct m.p.
NMR(DMSO-d6): 1.14-1.36(18H, m), 1.82-1.91(2H, m), 2.78(6H, d, J=4.62 Hz), 3.04-3.09(2H, m), 3.22-3.26(2H, m), 5.42-5.51(3H, m), 6.82(1H, d, J=1.6 Hz), 5.89(1H, d, J=1.6 Hz), 6.97(1H, d, J=1.6 Hz), 7.35(1H, d, J=1.6 Hz), 7.34(1H, s), 8.12-8.14(2H, s&t), 9.25(1H, s, broad, TFA), 9.91(1H, s), 9.93(1H, s), 10.03(1H, s). IR νmax [KBr]: 3285, 2953, 1650, 1580, 1525, 1460, 1402, 1260 cm−. HREIMS: Found: 580.35047 Calculated for C30H44O4N8 580.34855.
Example 5
N-[5-({[5-({[3-(Dimethylamino)propyl]amino}carbonyl)-1-isopentyl-1H-pyrrol-3-yl]amino}carbonyl)-1-isopentyl-1H-pyrrol-3-yl]-4-(formylamino-1-isopentyl-1H-pyrrole-2-carboxamide
(i) Ethyl 1-isopentyl-4-nitro-1H-pyrrole-2-carboxylate
Ethyl 4-nitro-1H-pyrrole-2-carboxylate (2.022 g, 10.983 mmol; see Example 1, step (i) above) was dissolved in DMF (30 mL, dry) to which potassium (0.569 g, 14.552 mmol) was added with stirring under nitrogen. The reaction mixture was heated at 100° C. for 1 h and then the temperature was allowed to reach 50° C. Isoamyl bromide (2.498 g, 16.538 mmol) was then added, followed by KI (2.197 g, 14.552 mmol). The temperature was raised to 100° C. and stirring continued for 5 h, after which time the temperature was allowed to return to room temperature. The reaction mixture was then stirred overnight, following which the solvent was removed under reduced pressure at 50° C. The crude product was dissolved in DCM and the salt extracted with water. The organic extract was dried over MgSO4, filtered and the solvent removed under reduced pressure at 30° C. The crude product obtained was chromatographed over silica gel using 1/2 n-hexane/DCM as eluant. Material with Rf=0.3 was collected and the solvent was removed under reduced pressure to give white crystalline material (2.377 g, 85% yield). M.p. 46-47° C. (Lit. m.p. 46-47° C.).
Reference: Turchin, K. F.; Grokhovskii, S. L.; Zhuze, A. L.; Gottikh, B. P., Soviet Journal of Bioorganic Chemistry (English Translation) 1978, 4, 780-790.
NMR(CDCl3): 0.97(6H, d, J=6.45 Hz), 1.38(3H, t, J=7.2 Hz), 1.61-1.73(3H, m), 4.30-4.39(4H, m), 7.43(1H, d, J=1.6 Hz), 7.63(1H, d, J=1.6 Hz). IR νmax [KBr]: 3138, 2970, 1707, 1539, 1510, 1487, 1426, 1389, 1321, 1259, 1204, 1130, 1097 cm−1.
(ii) 1-Isopentyl-4-nitro-1H-pyrrole-2carboxylic acid
Ethyl 1-isopentyl-4-nitro-1H-pyrrole-2-carboxylate (2.377 g, 9.329 mmol; see step (i) above) was suspended in ethanol (5 mL), then a solution of NaOH (955 mg dissolved in 20 mL of water) was added. The reaction mixture was reduced by half under reduced pressure at 50° C., and then the cooled solution was extracted with ether. The water layer was cooled to 0° C. then conc. HCl was added dropwise with vigorous stirring until pH 2. The white solid material was filtered off, washed with water, dried at 60° C. under reduced pressure for 2 h then left at room temperature overnight. The product was obtained as white solid (2.008 g, 95% yield), m.p. 154-157° C. [Lit.m.p. 154-156° C.].
Reference: Turchin, K. F.; Grokhovskii, S. L.; Zhuze, A. L.; Gottikh, B. P., Soviet Journal of Bioorganic Chemistry (English Translation) 1978, 4, 780-790.
NMR(CDCl3): 0.98(6H, d, J=6.46 Hz), 1.62-1.75(3H, m), 4.38(2H, t, J=7.5 Hz), 7.58(1H, d, J=1.98 Hz), 7.69(1H, d, J=1.97 Hz). IR νmax [KBr]: 3120, 1677, 1540, 1517, 1480, 1315, 1250 cm−1.
(iii) N-[3-(Dimethylamino)propyl]-1-isopentyl-4-nitro-1H-pyrrole-2-carboxamide
1-Isopentyl-4-nitro-1H-pyrrole-2-carboxylic acid (315 mg, 1.388 mmol; see step (ii) above) was dissolved in thionyl chloride (5 mL) and the reaction mixture heated under reflux for 4 h. Excess thionyl chloride was removed under reduced pressure and the acid chloride so formed was used without further purification. 3-(Dimethylamino)propyl-amine (250 μL, 2.471 mmol) was dissolved in THF (20 mL, dry) to which NMM (250 μL, 2.472 mmol) was added. The acid chloride was dissolved in THF (5 mL, dry) then it was added dropwise to the amine solution at room temperature with stirring, which was continued at room temperature overnight. The solvent was removed under reduced pressure and the crude product dissolved in DCM (50 mL) then extracted with aqueous sodium carbonate (540 mg of Na2CO3 in 25 mL of water). The organic layer was dried over silica gel using 100:100:1 ethyl acetate/methanol/TFA to give the required product as pale yellow solid (Rf=0.15), (410 mg, 95% yield), m.p. 72-73° C.
NMR(CDCl3): 0.95(6H, d, J=6.5 Hz), 1.57-1.76(5H, m), 2.32(6H, s), 2.51(2H. t, J=10.3 Hz), 3.47-3.51(2H, qt, J=4.8 Hz), 4.40-4.44(2H, q, J=7.5 Hz), 6.92(1H, d, J=1.88 Hz), 7.56(1H, d, J=1.90 Hz), 8.61(1H, s, broad, CONH). IR νmax [KBr]: 1656, 1637, 1565, 1534, 1498, 1417, 1333 cm−1. HREIMS: Found: 310.20031 Calculated for C15H26O4N3 310.20049.
(iv) N-[3-(Dimethylamino)propyl]-1-isopentyl-4-{[(1-isopentyl-4-nitro-1H-pyrrol-2-yl)carbonyl]amino}-1H-pyrrole-2-carboxamide
N-[3-(Dimethylamino)propyl]-1-isopentyl-4-nitro-1H-pyrrole-2-carboxamide (151 mg, 0.486 mmol; see step (iii) above) was dissolved in ethanol (20 mL). The reaction mixture was cooled to 0° C. then Pd/C-10% (98 mg) was added to the reaction mixture under N2. The reaction mixture was then hydrogenated at room temperature and atmospheric pressure for 4 h. The catalyst was removed over Kieselguhr and the solvent removed under reduced pressure at 50° C. to give the amine as pale yellow oil that was used in the next step without further purification. 1-Isopentyl-4-nitro-1H-pyrrole-2-carboxylic acid (100 mg, 0.441 mmol; see step (ii) above) was dissolved in thionyl chloride (3 mL) and the reaction mixture heated under reflux for 4 h. Excess thionyl chloride was removed under reduced pressure at 50° C. and the acid chloride so formed was used without further purification. The amine was dissolved in THF (20 mL, dry) to which NMM (200 μL) was added at room temperature with stirring. The acid chloride was dissolved in THF (15 mL, dry) then added to the amine solution dropwise with stirring at room temperature. The stirring was continued at room temperature overnight. The solvent was removed under reduced pressure at 50° C., then the crude product was dissolved in DCM (50 mL) and extracted with sodium carbonate solution (612 mg in 20 mL of water). The organic layer was collected, dried and the solvent removed under reduced pressure. The crude product was purified by column chromatography using ethyl acetate/methanol/TEA 100:100:1 ratio. Fractions containing the required material were collected and the solvent was then removed under reduced pressure and co-evaporated with n-hexane to give the pure product as glassy yellow material Rf=0.34, (223 mg, 94% yield), m.p. 57-60° C. [Transparent].
NMR[CDCl3]: 0.93(6H, d, J=4.5 Hz), 0.95(6H, d, J=4.5 Hz), 1.57-1.83(4H, m), 2.35(6H, s), 2.52(2H, t, J=6.1 Hz), 3.45-3.49(2H, q, J=5.6 Hz), 4.36(2H, t, J=7.4 Hz), 4.43(2H, t, J=7.4 Hz), 6.51(1H, d, J=1.9 Hz), 7.20(1H, d, J=1.9 Hz), 7.22(1H, d, J=1.9 Hz), 7.64(1H, d, J=1.9 Hz), 7.77(2H, s &t). IR νmax [KBr]: 2953, 1633, 1592, 1573, 1539, 1525, 1503, 1312 cm−1. HREIMS: Found: 488.31163 Calculated for C25H40O4N6 488.31110.
(v) N-[5-({[5-({[3-(Dimethylamino)propyl]amino}carbonyl)-1-isopentyl-1H-pyrrol-3-yl]amino}carbonyl)-1-isopentyl-1H-pyrrol-3-yl]-1-isopentyl-4-nitro-1H-pyrrole-2-carboxamide
N-[3-(Dimethylamino)propyl]-1-isopentyl-4-{[(1-isopentyl-4-nitro-1H-pyrrol-2-yl)carbonyl]amino}-1H-pyrrole-2-carboxamide (200 mg, 0.410 mmol; see step (iv) above) was dissolved in ethanol (20 mL) at 0° C. Pd/C-10° C. (164 mg) was added to the reaction mixture at 0° C. and under N2. The reaction mixture was hydrogenated at room temperature and atmospheric pressure for 4 h. The catalyst was removed over Kieselguhr and the solvent removed under reduced pressure to give the amine, which was used in the next step without further purification. 1-Isopentyl-4-nitro-1H-pyrrole-2-carboxylic acid (110 mg, 0.485 mmol; see step (ii) above) was dissolved in thionyl chloride (3 mL) and heated under reflux for 3 h. Excess thionyl chloride was removed under reduced pressure to give the acid chloride that was used without further purification. The acid chloride was dissolved in THF (20 mL, dry) and added dropwise at room temperature to the amine which was dissolved in THF (20 mL, dry) containing NMM (200 μL). Stirring was continued overnight at room temperature and then the solvent was removed under reduced pressure at 50° C. The residue was dissolved in DCM (50 mL) and extracted with K2CO3 (270 mg, in water 20 mL). The organic layer was dried over MgSO4, filtered and the solvent removed under reduced pressure. The crude product was purified by column chromatography using methanol/ethyl acetate/TEA (100:100:1) to give the product as yellow glassy material (Rf=0.20), 223 mg, 82% yield. M.p. 110-115° C. [Transparent].
NMR[CDCl3]: 0.93(6H, d, J=1.6 Hz), 0.95(6H, d, J=5.6 Hz), 0.98(6H, d, J=3.7 Hz), 1.57-1.78(5H, m), 2.47(6H, s), 2.70(2H, m), 3.49(2H, m), 4.31-4.49(6H, m), 6.57(1H, s), 7.28(1H, s), 7.33(1H, s), 7.41(1H, s), 7.44(1H, s), 7.61(1H, s), 7.64(1H, d, J=1.8 Hz), 7.75(1H, s), 8.22(1H, s). IR νmax [KBr]: 2953, 1646, 1583, 1534, 1505, 1464, 1422, 1311 cm−1. HRPABMS: Found: 667.42932 Calculated for C35H55O5N8 667.42954.
(vi) N-[5-({[5-({[3-(Dimethylamino)propyl]amino}carbonyl)-1-isopentyl-1H-pyrrol-3-yl]amino}carbonyl)-1-isopentyl-1H-pyrrol-3-yl]-4-(formyl-amino)-1-isopentyl-1H-pyrrole-2-carboxamide
N-[5-({[5-({[3-(Dimethylamino)propyl]amino}carbonyl)-1-isopentyl-1H-pyrrol-3-yl]amino}carbonyl)-1-isopentyl-1H-pyrrol-3-yl]-1-isopentyl-4-nitro-1H-pyrrole-2-carboxamide (119 mg, 0.178 mmol; see step (v) above) was dissolved in ethanol (20 mL) and Pd/C-10% (104 mg) was added at 0° C. under N2 with stirring. The reaction mixture was hydrogenated at room temperature and atmospheric pressure for 3 h. The catalyst was removed over Kieselguhr, then ethyl formate (15 mL) was added to the ethanolic solution of the amine. The reaction mixture was heated under reflux for 4 days. The solvent was removed under reduced pressure and the crude product was chromatographed over silica gel using ethyl acetate/methanol/TEA (100:100:1). The product was obtained as light brown solid with no distinct m.p., Rf=0.15, (84 mg, 71%). Some of this material was purified further by HPLC.
NMR[DMSO-d6]: 0.87-0.90(18H, m), 1.47-1.53(9H, m), 1.75(2H, m), 2.78(6H, d, J=4.8 Hz), 3.06(2H, m), 3.25(2H, m), 4.31(6H, qt, J=7.2 Hz), 6.88(1H, d, J=1.8 Hz), 6.92(1H, d, J=1.8 Hz), 7.02(1H, d, J=1.8 Hz), 7.19(1H, d, J=1.8 Hz), 7.23(2H, s&d), 8.13(2H, s&t), 9.21(1H, s, broad, TFA), 9.88(1H, s), 9.89(1H, s), 10.05(1H, s). IR νmax [KBr]: 2953, 1650, 1580, 1525, 1461, 1402, 1260, 1221 cm−1. HRFABMS: Found: 665.44877 Calculated for C36H57O4N8 665.45028.
Example 6
N-[5-({[5-({[3-(Dimethylamino)propyl]amino}carbonyl)-1-isopropyl-1H-pyrrol-3-yl]amino}carbonyl)-1-methyl-1H-pyrrol-3-yl]-4-(formylamino)-1-isopropyl-1H-pyrrole-2-carboxamide
(i) N-[3-(Dimethylamino)propyl]-1-isopropyl-4-nitro-1H-pyrrole-2-carboxamide
1-Isopropyl-4-nitro-1H-pyrrole-2-carboxylic acid (312 mg, 1.574 mmol; see Example 1, step (iii) above) was dissolved in thionyl chloride (5 mL) and heated until reflux for 4 h. The excess thionyl chloride was removed under reduced pressure at 50° C. to give the acid chloride as white solid material, which was used without further purification. 3-(Dimethylamino)propyl-amine (250 μL) was dissolved in THF (20 mL, dry) to which was added NMM (250 μL, dry) at room temperature with stirring. The acid chloride was dissolved in THF (5 mL, dry) and added dropwise to the amine solution at room temperature with stirring. The stirring was continued at room temperature overnight and then the solvent was removed under reduced pressure at 50° C. The crude product was extracted with K2CO3 (25 mL, 10%) and DCM (2×50 mL). The organic layer was collected, dried over Na2SO4, filtered and the solvent removed under reduced pressure. The crude product obtained as pale yellow oil was purified over silica gel using 49.5/49.5/1% methanol/ethyl acetate/TEA to give the pure product as pale yellow oil, RF=0.25, (400 mg, 90% yield).
NMR[CDCl3]: 8.59(1H, broad); 7.74(1H, d); 6.92(1H, d); 5.65-5.59(1H, qt); 3.51-3.46(2H, q); 2.51(2H, t); 2.32(6H, s); 1.77-1.71(2H, qt); 1.48(6H, d). IR νmax [NaCl]: 3330, 3136, 2979, 1650, 1535, 1430, 1341, 1279 cm−1. HREIMS: Found: 282.16908 calculated for C13H22N4O3 282.16919.
(ii) N-[5-({[3-(Dimethylamino)propylamino}carbonyl)-1-isopropyl-1H-pyrrol-3-yl]-1-methyl-4-nitro-1H-pyrrole-2-carboxamide
N-[3-(Dimethylamino)propyl]-1-isopropyl-4-nitro-1H-pyrrole-2-carboxamide (120 mg, 0.425 mmol; see step (i) above) was dissolved in methanol (25 mL) to which Pd/C-10% (52 mg) was added at 0° C. under nitrogen. The reaction mixture was hydrogenated at room temperature and atmospheric pressure. The catalyst was removed over Kieselguhr and the solvent was then removed under reduced pressure at 40° C. This gave the amine (as pale yellow oil), which was then dissolved in DCM (25 mL, dry). 1-Methyl-4-nitro-1H-pyrrole-2-carboxylic acid (90 mg, 0.529 mmol; see Tetrahedron 56, 5225-5239 (2000)) was suspended in thionyl chloride (4 mL) then heated until reflux for 4 h. The excess thionyl chloride was removed under reduced pressure at 40° C. The acid chloride so obtained was dissolved in DCM (25 mL, dry) then added dropwise with stirring at room temperature to the amine solution. The reaction mixture was left stirring at room temperature overnight. K2CO3 solution (232 mg, in water 10 mL) was added and the mixture was extracted with DCM (3×25 mL). The organic layers were combined, dried over MgSO4, filtered and the solvent removed under reduced pressure. The crude product was purified by flash chromatography using silica gel, methanol/ethyl acetate/TEA [1/3 containing 1% TEA]. The product was obtained as micro-crystalline yellow solid (165 mg, 96%), m.p. 161-163° C.
NMR(CDCl3): 1.43-1.44(6H, d, J=6.4 Hz, 2xMe); 1.72-1.79(2H, quintet, J=6.2 Hz, CH2); 2.33(6H, s, NMe2); 2.47-2.50(2H, t, J=6.2 Hz, CH2); 3.45-3.49(2H, q, J=5.7 Hz, CH2); 4.04(3H, s, NMe); 5.57-5.62(1H, m); 6.46(1H, d, 1.8J=Hz); 7.22(1H, d, J=1.7 Hz); 7.39(1H, d, J=1.7 Hz); 7.60(1H, d, J=1.7 Hz); 7.73(1H, t, J=5.6 Hz, CONH, exch.); 7.77(1H, s, CONH, exch.). IR νmax [KBr]: 3281, 3110, 2967, 1640, 1557, 1532, 1503, 1468, 1409, 1310 cm−1. HRFABMS: Found: 405.22501 Calculated for C19H29N6O4 405.22503.
(iii) N-[5-({[5-({[3-(Dimethylamino)propyl]amino}carbonyl)-1-isopropyl-1H-pyrrol-3-yl]amino}carbonyl)-1-methyl-1H-pyrrol-3-yl]-1-isopropyl-4-nitro-1H-pyrrole-2-carboxamide
N-[5-({[3-(Dimethylamino)propyl]amino}carbonyl)-1-isopropyl-1H-pyrrol-3-yl]-1-methyl-4-nitro-1H-pyrrole-2-carboxamide (160 mg, 0.395 mmol; see step (ii) above) was suspended in methanol (25 mL) to which was added Pd/C-10% (112 mg) at 0° C. under nitrogen with stirring. The reaction mixture was hydrogenated at room temperature and atmospheric pressure for 4 h. The catalyst was removed over Kieselguhr and the solvent removed under reduced pressure at 40° C. to give the amine. 1-Isopropyl-4-nitro-1H-pyrrole-2-carboxylic acid (94 mg, 0.552 mmol; see Example 1, step (iii) above) was suspended in thionyl chloride (4 mL) and heated until reflux for 2 h. Excess thionyl chloride was removed under reduced pressure at 40° C., and the acid chloride so formed was used without further purification. The amine was dissolved in DCM (25 mL, dry) to which TEA (40 μL, dry) was added at room temperature with stirring. The acid chloride was dissolved in DCM (15 mL, dry) after which it was added to the amine solution dropwise with stirring at room temperature. The stirring was continued overnight. Na2CO3 solution (280 mg, in water 5 mL) was added to the reaction mixture. The organic layers obtained from the extraction were combined and dried over MgSO4, filtered and the solvent removed under reduced pressure. The crude product was purified using flash chromatography. Silica gel and methanol/ethyl acetate/TEA [1/3 containing 1% TEA, Rf=0.1] were used to give the product as yellow solid (152 mg, 69%), m.p. 145-148° C.
NMR(DMSO-d6): 1.32-1.34(6H, d, J=6.4 Hz, 2xMe); 1.45-1.46(6H, d, J=6.4 Hz, 2xMe); 1.69-1.73(2H, quintet, J=6.2 Hz, CH2); 2.38(6H, s, NMe2); 2.47-2.50(2H, t, J=6.2 Hz, CH2); 3.19-3.24(2H, m, CH2); 3.86(3H, s, NMe); 5.42-5.50(1H, m); 6.80(1H, s); 7.05(1H, d, J=1.6 Hz); 7.26(1H, d, J=1.6 Hz); 7.36(1H, d, J=1.6 Hz); 7.50(1H, d, J=1.6 Hz); 8.08-8.11(1H, t, J=5.6 Hz, CONH, exch.); 8.33(1H, d, J=1.6 Hz); 9.92(1H, s, CONH, exch.); 10.33(1H, s, CONH, exch.). IR νmax [KBr]: 2943, 2860, 1638, 1593, 1524, 1456, 1403, 1316, 1251, 1187, 1170 cm−1. HRFABMS: Found: 555.30593 Calculated for C27H39N8O5 555.30434.
(iv) N-[5-({[5-({[3-(Dimethylamino)propyl]amino}carbonyl)-1-isopropyl-1H-pyrrol-3-yl]amino}carbonyl)-1-methyl-1H-pyrrol-3-yl]-4-(formyl-amino)-1-isopropyl-1H-pyrrole-2-carboxamide
N-[5-({[5-({[3-(Dimethylamino)propyl]amino}carbonyl)-1-isopropyl-1H-pyrrol-3-yl]amino}carbonyl)-1-methyl-1H-pyrrol-3-yl]-1-isopropyl-4-nitro-1H-pyrrole-2-carboxamide (150 mg, 0.291 mmol; see step (iii) above) was dissolved in ethanol (15 mL). The solution was cooled to 0° C. under N2 then Pd/C-10% (120 mg) was added. The reaction mixture was hydrogenated at room temperature and atmospheric pressure for 4 h. The catalyst was removed over Kieselguhr and then ethyl formate (20 mL) was added to the ethanolic solution. The reaction mixture was heated under reflux overnight and then the solvent was removed under reduced pressure at 40° C. The product was purified by HPLC to give the product as white solid material (71 mg, 40% yield) with no distinct melting point.
NMR[DMSO-d6]: 10.0564(1H, s); 9.96(1H, s); 9.90(1H, s); 9.24(1H, s, broad, TFA); 8.16-8.14(2H, m); 7.34(2H, s); 7.22(1H, s); 7.06(1H, s); 6.89(1H, s); 6.68(1H, s); 5.49-5.42(1H, m); 3.84(3H, s); 3.25(2H, m); 3.06(2H, m); 2.79(6H, d, J=4.76 Hz); 1.84(2H, m); 1.36-1.33(12H, m). IR νmax [KBr]: 3425, 3285, 2972, 1676, 1639, 1579, 1533, 1465, 1439, 1404, 1257, 1200, 1180, cm−1. HRFABMS: Found 554.33484 calculated for C28H42N8O4 554.33290
Example 7
N-[5-({[3-(Dimethylamino)propyl]amino}carbonyl)-1-methyl-1H-pyrrol-3-yl]-2-({[4-(formylamino)-1-methyl-1H-pyrrol-2-yl]carbonyl}amino)-5-isopropyl-1,3-thiazole-4-carboxamide
(i) N-[5-({[3-(Dimethylamino)propyl]amino}carbonyl)-1-methyl-1H-pyrrol-3-yl]-5-isopropyl-2-{[(1-methyl-4-nitro-1H-pyrrol-2-yl)carbonyl]amino}-1,3-thiazole-4-carboxamide
N-[3-(Dimethylamino)propyl]-1-methyl-4-nitro-1H-pyrrole-2-carboxamide (270 mg, 1.062 mmol; see Tetrahedron 56, 5225-5239 (2000)) was dissolved in methanol (25 mL), to which Pd/C-10% (236 mg) was added at 0° C. under N2 with stirring. The reaction mixture was hydrogenated at room temperature and atmospheric pressure for 4 h after which the catalyst was removed over Kieselguhr and the solvent was then removed under reduced pressure to give the amine. 5-Isopropyl-2-{[(1-methyl-4-nitro-1H-pyrrol-2-yl)carbonyl]amino}-1,3-thiazole-4-carboxylic acid (359 mg, 1.062 mmol; see Example 3, step (iii) above) was dissolved in DMF (4 mL, dry) to which NMM (0.5 mL, dry) was added followed by HBTU (721 mg, 1.901 mmol). The amine was dissolved in DMF (2 mL, dry) and then added to the reaction mixture at room temperature with stirring. The stirring was continued at room temperature overnight. NMM was removed under reduced pressure. The reaction mixture was diluted with ethyl acetate then NaHCO3 saturated was added with stirring. The organic layer was separated, dried over MgSO4 and the solvent was removed under reduced pressure. The crude product obtained was chromatographed over silica gel using 1:1:0.2 methanol/ethyl acetate/TEA. The product was obtained as yellow glassy material (415 mg, 72% yield) with no distinct melting point.
NMR[DMSO-d6]: 9.60(1H, s); 8.23(1H, s); 8.09-8.036(1H, t); 7.83(1H, s); 7.25(1H, d); 6.91(1H, d); 4.22-4.16(1H, qt); 4.00(3H, s); 3.82(3H, s); 3.25-3.18(2H, q); 2.38-2.34(2H, t); 2.23(6H, s); 1.68-1.61(2H, qt); 1.30-1.28(6H, d). IR νmax [KBr]: 1644, 1551, 1500, 1465, 1402, 1309, 1283, 1194, 1100 cm−1. HRFABMS: Found: 545.22962 calculated for C24H33N8O5S 545.22946.
(ii) N-[5-({[3-(Dimethylamino)propyl]amino}carbonyl)-1-methyl-1H-pyrrol-3-yl]-2-({[4-(formylamino)-1-methyl-1H-pyrrol-2-yl]carbonyl}-amino)-5-isopropyl-1,3-thiazole-4-carboxamide
N-[5-({[3-(Dimethylamino)propyl]amino}carbonyl)-1-methyl-1H-pyrrol-3-yl]-5-isopropyl-2-{[(1-methyl-4-nitro-1H-pyrrol-2-yl)carbonyl]amino}-1,3-thiazole-4-carboxamide (137 mg, 0.252 mmol; see step (i) above) was dissolved in ethanol (15 mL), to which Pd/C-10% (121 mg) was added under N2 at 0° C. The reaction mixture was hydrogenated at room temperature and atmospheric pressure for 2.5 h. The catalyst was removed over Kieselguhr and then ethyl formate (25 mL) was added to the ethanolic solution. The reaction mixture was heated under reflux overnight, following which the solvent was removed under reduced pressure and the product was then purified by HPLC. The product was obtained after freeze-drying as white solid material (41 mg, 25% yield) [TFA salt] with no distinct melting point.
NMR[DMSO-d6]: 12.0971(1H, s); 10.1404(1H, s); 9.5957(1H, s); 9.2310(1H, broad, TFA); 8.3533-8.3249(1H, d and 1H, t); 7.3982(1H, s); 7.2894(1H, d); 7.2046(1H, d); 7.0146(1H, d); 4.1717-4.1200(1H, m); 3.8841(3H, s); 3.8274(3H, s); 3.2577(2H, m); 3.0646(2H, m); 2.7987(6H, d, NMe2); 1.8612-1.8231(2H, m); 1.3135(6H, d). IR νmax [KBr]: 3428, 1662, 1545, 1467, 1401, 1284, 1201, 1134 cm−1. HRFABMS: Found: 543.24988 calculated for C25H35N8O4S 543.25020.
Example 8
4-({[4-(Formylamino)-1-methyl-1H-pyrrol-2-yl]carbonyl}amino)-1-iso-propyl-N-[1-methyl-5-({[3-(4-morpholinyl)propyl]amino}carbonyl)-1H-pyrrol-3-yl]-1H-pyrrole-2-carboxamide
(i) 1-Isopropyl-N-[1-methyl-5-({[3-(4-morpholinyl)propyl]amino}-carbonyl)-1H-pyrrol-3-yl]-4-nitro-1H-pyrrole-2-carboxamide
1-Methyl-N-[3-(4-morpholinyl)propyl]-4-nitro-1H-pyrrole-2-carboxamide (214 mg, 0.805 mmol; see Tetrahedron 56, 5225-5239 (2000)) was dissolved in methanol (25 mL). The solution was cooled to 0° C. under N2 then Pd/C-10% (192 mg) was added. The reaction mixture was hydrogenated at room temperature and atmospheric pressure for 3 h. The catalyst was removed over Kieselguhr and the solvent was removed under reduced pressure at 50° C. The amine so formed was dissolved in DMF (2 mL, dry), to which 1-isopropyl-4-nitro-1H-pyrrole-2-carboxylic acid (160 mg, 0.805 mmol; see Example 1, step (iii) above) was added followed HBTU (610 mg, 1.608 mmol) and NMM (100 μL, dry). Additional amount of DMF (2 mL, dry) was added with stirring at room temperature and was continued for 72 h. The reaction mixture was diluted with ethyl acetate and NaHCO3 solution with stirring. The organic layer was separated, dried MgSO4, filtered and the solvent removed under reduced pressure. The crude product was chromatographed over flash silica gel using 1/3 methanol/ethyl acetate. Fractions containing the product [RF=0.30] were collected and the solvents were removed under reduced pressure at 50° C. The product was obtained as glassy yellow material [hygroscopic] (260 mg, 73% yield) with no distinct melting point.
NMR[DMSO-d6]: 10.28(1H, s); 8.33(1H, d); 8.08-8.05(1H, t); 7.48(1H, d); 7.20(1H, d); 6.85(1H, d); 5.89-5.42(1H, qt); 3.80(3H, s); 3.58-3.56(4H, t); 3.22-3.17(2H, q); 2.32-2.28(6H, m); 1.67-1.62(2H, qt); 1.45-1.43(6H, d). IR νmax [KBr]: 1661, 1582, 1540, 1441, 1389, 2326, 1284, 1242, 1116, 850, 755 cm−1. HREIMS: found 446.22568 calculated for C21H30N6O5 446.22777.
(ii) 1-Isopropyl-N-[1-methyl-5-({[3-(4-morpholinyl)propyl]amino}-carbonyl)-1H-pyrrol-3-yl]-4-{[(1-methyl-4-nitro-1H-pyrrol-2-yl)carbonyl]-amino}-1H-pyrrole-2-carboxamide
1-Isopropyl-N-[1-methyl-5-({[3-(4-morpholinyl)propyl]amino}carbonyl)-1H-pyrrol-3-yl]-4-nitro-1H-pyrrole-2-carboxamide (250 mg, 0.560 mmol; see step (i) above) was dissolved at 0° C. under N2. Pd/C-10% (220 mg) was added and the reaction mixture was hydrogenated for 3.5 h. The catalyst was removed over Kieselguhr and the solvent was removed under reduced pressure. The amine so formed was dissolved in DMF (2 mL, dry), to which was NMM (100 μL, dry) was added followed by HBTU (425 mg, 1.069 mmol) and 1-methyl-4-nitro-1H-pyrrole-2-carboxylic acid (95 mg, 0.560 mmol; see Tetrahedron 56, 5225-5239 (2000)) with stirring at room temperature. The stirring was continued overnight. The reaction mixture was diluted with ethyl acetate and a saturated solution of sodium hydrogen carbonate. The organic layer was separated, dried over MgSO4 and filtered. The solvent was removed under reduced pressure and the crude product was chromatographed using flash silica gel and 1:3:0.1 methanol/ethyl acetate/TEA. Fractions containing the pure material were collected [RF=0.3] solvents were removed under reduced pressure at 40° C. to give semi-solid glassy yellow material (170 mg, 53%) with no distinct melting point.
NMR[DMSO-d6]: 10.31(1H, s); 9.98(1H, s); 8.20(1H, s); 8.04-8.01(1H, t); 7.59(1H, s); 7.44(1H, s); 7.18(1H, s); 6.92(1H, s); 6.86(1H, s); 5.49-5.42(1H, qt); 3.97(3H, s); 3.80(3H, s); 3.58-3.57(4H, t); 3.22-3.17(2H, q); 2.33-2.29(2H, d); 1.68-1.61(2H, qt); 1.38-1.36(6H, d); 1.05-1.01(2H, m). IR νmax [KBr]:3425, 2927, 1662, 1653, 1582, 1543, 1502, 1410, 1307, 1251, 1203, 1115, 848 cm−1. HRFABMS: found 569.28147 calculated for C27H37N8O6 569.28361.
(iii) 4-({[4-(Formylamino)-1-methyl-1H-pyrrol-2-yl]carbonyl}amino)-1-isopropyl-N-[1-methyl-5-({[3-(4-morpholinyl)propyl]amino}carbonyl)-1H-pyrrol-3-yl]-1H-pyrrole-2-carboxamide
1-Isopropyl-N-[1-methyl-5-({[3-(4-morpholinyl)propyl]amino}carbonyl)-1H-pyrrol-3-yl]-4-{[(1-methyl-4-nitro-1H-pyrrol-2-yl)carbonyl]amino}-1H-pyrrole-2-carboxamide (160 mg, 0.282 mmol; see step (ii) above) was dissolved in ethanol (25 mL) to which Pd/C-10% (150 mg) was added at 0° C. under nitrogen with stirring. The reaction mixture was hydrogenated for 2 h at room temperature and atmospheric pressure. The catalyst was removed over Kieselguhr. Ethyl formate (25 mL) was added to the ethanolic solution, then the reaction mixture was heated under reflux overnight. Ethanol and excess ethyl formate were removed under reduced pressure and the crude product was purified by HPLC to give the required material as white solid (40.1 mg, 21% yield) with no distinct melting point.
NMR[DMSO-d6]: 10.05(1H, s); 9.93(1H, s); 9.92(1H, s); 9.58(1H, broad, TFA); 8.17(1H, t); 8.13(1H, s); 7.39(1H, s); 7.19(1H, s); 7.17(1H, s); 6.97(1H, s); 6.95(1H, s); 6.92(1H, s); 3.84(3H, s); 3.81(3H, s); 3.56-3.60(4H, t); 3.49-3.43(4H, t); 3.26-3.24(2H, q); 3.12-3.06(4H, m); 1.87(2H, qt); 1.37-1.36(6H, d). IR νmax [KBr]: 3423, 1672, 1644, 1581, 1536, 1462, 1440, 1407, 1254, 1200, 1134 cm−1. HRFABMS: found: 567.30312 calculated for C28H39N8O5 567.30434.
Example 9
4-(Formylamino)-N-[1-isopropyl-5-({[1-methyl-5-({[3-(1-pyrrolidinyl)-propyl]amino}carbonyl)-1H-pyrrol-3-yl]amino}carbonyl)-1H-pyrrol-3-yl]-1-methyl-1H-pyrrole-2-carboxamide
(i) 1-Methyl-4-nitro-N-[3-(1-pyrrolidinyl)propyl]-H-pyrrole-2-carboxamide
3-(1-Pyrrolidino)propylamine (236 mg, 1.842 mmol (Lancaster Synthesis Ltd.)) was dissolved in THF (25 mL, dry) to which a solution of 2,2,2-trichloro-1-(1-methyl-4-nitro-1H-pyrrol-2-yl)ethanone (508 mg, 1.842 mmol; see Tetrahedron 56, 5225-5239 (2000)) was added in THF (2 mL, dry) at room temperature with stirring. The reaction mixture was left stirring at room temperature overnight. The solvent was removed under reduced pressure and the crude product was purified by column chromatography using 49.5:49.5:1 ethyl acetate/methanol/TEA. The product was obtained as glassy yellow solid, Rf=0.1 (503 mg, 98% yield), m.p. 113-115° C.
1H-NMR(DMSO-d6) δ 1.70-1.79(6H, m), 2.48-2.51(6H, m), 3.28-3.51(2H, q, J=6.85 Hz), 3.89(3H, s), 7.45(1H, d, J=1.6 Hz), 8.18(1H, d, J=1.6 Hz), 8.51(1H, t, J=5.37 Hz). IR νmax [KBr]: 3131, 2966, 2794, 1654, 1545, 1525, 1492, 1305 cm−1. HRFABMS: Found: 281.16249 Calculated for C13H21N4O3 281.16137.
(ii) 1-Isopropyl-N-[1-methyl-5-({[3-(1-pyrrolidinyl)propyl]amino}-carbonyl)-1H-pyrrol-3-yl]-4-nitro-1H-pyrrole-2-carboxamide
1-Methyl-4-nitro-N-[3-(1-pyrrolidinyl)propyl]-1H-pyrrole-2-carboxamide (227 mg, 0.811 mmol; see step (i) above) was dissolved in methanol (25 mL) to which Pd/C-10% (160 mg) was added at 0° C. under nitrogen with stirring. The reaction mixture was hydrogenated for 2 h at room temperature and atmospheric pressure. The catalyst was removed over Kieselguhr and the solvent was removed under reduced pressure at 40° C. to give the amine. 1-Isopropyl-4-nitro-1H-pyrrole-2-carboxylic acid (161 mg, 0.811 mmol; see Example 1, step (iii)) was dissolved in DMF (1 mL, dry) to which HBTU (615 mg, 1.622 mmol) and NMM (100 μL, dry) were added. The amine was dissolved in DMF (2 mL, dry) and added to the reaction mixture at room temperature with stirring. The stirring was continued at room temperature overnight. The reaction mixture was diluted with ethyl acetate and a saturated solution of sodium hydrogen carbonate. The organic layer was separated, dried over magnesium sulphate, filtered and the solvent removed under reduced. The product was purified by column chromatography using 1/2/0.1 methanol/ethyl acetate/TEA. The product was obtained as yellow material (300 mg, 86% yield) with no distinct melting point. Some of this material was further purified by HPLC.
NMR[DMSO-d6]: 10.31(1H, s); 9.48(1H, broad, TFA); 8.34(1H, d); 8.21-8.18(1H, t); 7.48(1H, d); 7.28(1H, d); 6.92(1H, d); 5.48-5.42(1H, qt); 3.82(3H, s); 3.56-3.55(2H, m); 3.27-3.23(2H, q); 3.17-3.12(2H, m); 2.99-2.97(2H, m); 2.01(2H, m); 1.86-1.83(4H, m); 1.45-1.44(6H, d). IR νmax [KBr]: 3433, 1672, 1650, 1535, 1462, 1426, 1371, 1321, 1283, 1237, 1200, 1178, 1131 cm−1. HRFABMS: found: 430.23179 calculated for C21H30N6O4 430.23285.
(iii) N-[1-Isopropyl-5-({[1-methyl-5-({[3-(1-pyrrolidinyl)propyl]amino}-carbonyl)-1H-pyrrol-3-yl]amino}carbonyl)-1H-pyrrol-3-yl]-1-methyl-4-nitro-1H-pyrrole-2-carboxamide
1-Isopropyl-N-[1-methyl-5-({[3-(1-pyrrolidinyl)propyl]amino}carbonyl)-1H-pyrrol-3-yl]-4-nitro-1H-pyrrole-2-carboxamide (300 mg, 0.697 mmol; see step (ii) above) was dissolved in methanol (25 mL) to which Pd/C-10% (235 mg) was added at 0° C. under nitrogen with stirring. The reaction mixture was hydrogenated for 3 h at room temperature and atmospheric pressure. The catalyst was removed over Kieselguhr and the solvent was removed under reduced pressure at 40° C. to give the amine. 1-Methyl-4-nitro-1H-pyrrole-2-carboxylic acid (119 mg, 0.699 mmol; see Tetrahedron 56, 5225-5239 (2000)) was dissolved in DMF (2 mL, dry) to which HBTU (529 mg, 1.394 mmol) and NMM (100 μL, dry) were added. The amine was dissolved in DMF (2 mL, dry) and added to the reaction mixture at room temperature with stirring. The stirring was continued at room temperature overnight. The reaction mixture was diluted with ethyl acetate and a saturated solution of sodium hydrogen carbonate. The organic layer was separated, dried over magnesium sulphate, filtered and the solvent removed under reduced pressure. The product was purified by column chromatography using 1/2/0.1 methanol/ethyl acetate/TEA. The product was obtained as yellow material (239 mg, 62% yield) with no distinct melting point. Some of this material was further purified by HPLC.
NMR[DMSO-d6]: 10.28(1H, s); 9.98(1H, s); 9.46(1H, broad, TFA); 8.19(1H, s); 8.14(1H, t); 7.58(1H, s); 7.43(1H, s); 7.18(1H, s); 6.94(2H, s); 5.46-5.43(1H, m); 3.97(3H, s); 3.82(3H, s); 3.55(2H, m); 3.27(2H, m); 3.14(2H, m); 3.00(2H, m); 2.02(2H, m); 1.86(4H, m); 1.38-1.37(6H, d). IR νmax [KBr]: 3419, 3136, 1673, 1645, 1586, 1531, 1463, 1409, 1311, 1247, 1199, 1130 cm−1. HRFABMS: found: 553.29109 calculated for C27H37N8O5 553.28869.
(iv) 4-(Formylamino)-N-[1-isopropyl-5-({[1-methyl-5-({[3-(1-pyrrolidinyl)-propyl]amino}carbonyl)-1H-pyrrol-3-yl]amino}carbonyl)-1H-pyrrol-3-yl]-1-methyl-1H-pyrrole-2-carboxamide
N-[1-Isopropyl-5-({[1-methyl-5-({[3-(1-pyrrolidinyl)propyl]amino}-carbonyl)-1H-pyrrol-3-yl]amino}carbonyl)-1H-pyrrol-3-yl]-1-methyl-4-nitro-1H-pyrrole-2-carboxamide (224 mg, 0.406 mmol; see step (iii) above) was dissolved in ethanol (25 mL) to which Pd/C-10% (224 mg) was added at 0° C. under nitrogen with stirring. The reaction mixture was hydrogenated for 2.5 h at room temperature and atmospheric pressure. The catalyst was removed over Kieselguhr. Ethyl formate (15 mL) was added to the ethanolic solution, then the reaction mixture was heated under reflux overnight. Ethanol and excess ethyl formate were removed under reduced pressure and the crude product was purified by HPLC to give the required material as white solid (42.7 mg, 16% yield) with no distinct melting point.
NMR[DMSO-d6]: 10.07(1H, s); 9.94(1H, s); 9.92(1H, s); 9.42(1H, broad, TFA); 8.17-8.13(1H, 2H, m); 7.39(1H, d); 7.19(1H, d); 7.17(1H, d); 6.97(1H, d); 6.95(1H, d); 6.92(1H, d); 3.84(3H, s); 3.61(3H, s); 3.55(2H, m); 3.26-3.24(2H, m); 3.17-3.12(2H, m); 3.00(2H, m); 2.01(2H, m); 1.86(4H, m); 1.37-1.36(6H, d). IR νmax [KBr]: 3429, 1675, 1645, 1582, 1534, 1462, 1440, 1407, 1252, 1200, 1132 cm−1. HRFABMS: found: 551.31199 calculated for C28H39N8O4 551.30943.
Example 10
N-[5-({[5-({[3-(Dimethylamino)propyl]amino}carbonyl)-1-methyl-1H-pyrrol-3-yl]amino}carbonyl)-1-isopentyl-1H-pyrrol-3-yl]-4-(formylamino)-1-methyl-1H-pyrrole-2-carboxamide
(i) N-[5-({[3-(Dimethylamino)propyl]amino}carbonyl)-1-methyl-1H-pyrrol-3-yl]-1-isopentyl-4-nitro-1H-pyrrole-2-carboxamide
N-[3-(Dimethylamino)propyl]-1-methyl-4-nitro-1H-pyrrole-2-carboxamide (253 mg, 0.995 mmol; see Tetrahedron 56, 5225-5239 (2000)) was dissolved in methanol (25 mL) to which Pd/C-10% (162 mg) was added at 0° C. under nitrogen. The reaction mixture was hydrogenated for 4 h. The catalyst was removed over Kieselguhr and the solvent was removed under reduced pressure at 50° C. to give the amine. 1-Isopentyl-4-nitro-1H-pyrrole-2-carboxylic acid (228 mg, 1.005 mmol; prepared according to the procedure described in Soviet Journal of Bioorganic Chemistry (English Translation) 4, 780-790 (1978)) was dissolved in thionyl chloride (4 mL) and the reaction mixture was heated under reflux for 4 h. Excess thionyl chloride was removed under reduced pressure and the acid chloride so formed was dissolved in DCM (10 mL, dry). The amine was dissolved in DCM (10 mL, dry) to which NMM (200 μL, dry) was added at room temperature with stirring. The acid chloride solution was added dropwise to the amine solution at room temperature with stirring. The stirring was continued overnight at room temperature. The reaction mixture was diluted with DCM (25 mL) and saturated solution of sodium hydrogen carbonate (25 mL). After the extraction, the organic layer was collected, dried over magnesium sulphate, filtered and the solvent removed under reduced pressure. The product was purified by column chromatography using 1/3/0.030 methanol/ethyl acetate/TEA. Fractions containing the product (RF=0.20) were collected and the solvents were removed under reduced pressure at 50° C. to give the product as yellow powder (347 mg, 81% yield), m.p. 148-151° C.
NMR[DMSO-d6]: 10.23(1H, s); 8.23(1H, d); 8.14-8.11(1H, t); 7.55(1H, d); 7.19(1H, d); 6.82(1H, d); 4.45-4.41(2H, t); 3.81(3H, s); 3.22-3.17(2H, q); 2.35-2.31(2H, t); 2.20(6H, s); 1.67-1.58(4H, m); 1.56-1.46(1H, m); 0.89-0.87(6H, d). IR νmax [KBr]: 1665, 1642, 1599, 1528, 1499, 1425, 1312 cm−1. HRFABMS: found 433.25630 calculated for C21H33N6O4 433.25633.
(ii) N-[5-({[5-({[3-(Dimethylamino)propyl]amino}carbonyl)-1-methyl-1H-pyrrol-3-yl]amino}carbonyl)-1-isopentyl-1H-pyrrol-3-yl]-1-methyl-4-nitro-1H-pyrrole-2-carboxamide
N-[5-({[3-(Dimethylamino)propyl]amino}carbonyl)-1-methyl-1H-pyrrol-3-yl]-1-isopentyl-4-nitro-1H-pyrrole-2-carboxamide (335 mg, 0.775 mmol; see step (i) above) was dissolved in methanol (25 mL) to which Pd/C-10% (213 mg) was added at 0° C. under nitrogen. The reaction mixture was hydrogenated for 5 h. The catalyst was removed over Kieselguhr and the solvent was removed under reduced pressure at 50° C. to give the amine. 1-Methyl-4-nitro-1H-pyrrole-2-carboxylic acid (210 mg, 1.234 mmol; see Tetrahedron 56, 5225-5239 (2000)) was dissolved in thionyl chloride (3 mL) and the reaction mixture was heated under reflux for 5 h. Excess thionyl chloride was removed under reduced pressure and the acid chloride so formed was dissolved in DCM (10 mL, dry). The amine was dissolved in DCM (10 mL, dry) to which NMM (200 μL, dry) was added at room temperature with stirring. The acid chloride solution was added dropwise to the amine solution at room temperature with stirring. The stirring was continued overnight at room temperature. The reaction mixture was diluted with DCM (25 mL) and saturated solution of sodium hydrogen carbonate (25 mL). After the extraction, the organic layer was collected, dried over magnesium sulphate, filtered and the solvent removed under reduced pressure. The product was purified by column chromatography using 1/3/0.030 methanol/ethyl acetate/TEA. Fractions containing the product (RF=0.20) were collected and the solvents were removed under reduced pressure at 50° C. to give the product as yellow solid material (335 mg, 78% yield), m.p. 110-115° C.[transparent].
NMR[DMSO-d6]: 10.28(1H, s); 9.92(1H, s); 8.18(1H, d); 8.10-8.07(1H, t); 7.59(1H, d); 7.32(1H, d); 7.18(1H, d); 6.98(1H, d); 6.91(1H, d); 6.83(1H, d); 4.35-4.32(2H, t); 3.97(3H, s); 3.80(3H, s); 3.22-3.17(2H, q); 2.36-2.32(2H, t); 2.21(6H, s); 1.68-1.62(2H, q); 1.61-1.45(3H, m); 1.05-0.99(2H, m); 0.90-0.88(6H, d). IR νmax [KBr]: 3401, 3289, 1643, 1582, 1533, 1594, 1463, 1400, 1309, 1253 cm−1. HRFABMS: found 555.30169 calculated for C27H39N8O5 555.30434.
(iii) N-[5-({[5-({[3-(Dimethylamino)propyl]amino}carbonyl)-1-methyl-1H-pyrrol-3-yl]amino}carbonyl)-1-isopentyl-1H-pyrrol-3-yl]-4-(formylamino)-1-methyl-1H-pyrrole-2-carboxamide
N-[5-({[5-({[3-(Dimethylamino)propyl]amino}carbonyl)-1-methyl-1H-pyrrol-3-yl]amino}carbonyl)-1-isopentyl-1H-pyrrol-3-yl]-1-methyl-4-nitro-1H-pyrrole-2-carboxamide (89 mg, 0.160 mmol; see step (ii) above) was dissolved in ethanol (25 mL) to which Pd/C-10% (95 mg) was added at 0° C. under nitrogen with stirring. The reaction mixture was hydrogenated for 2 h at room temperature and atmospheric pressure. The catalyst was removed over Kieselguhr. Ethyl formate (25 mL) was added to the ethanolic solution, then the reaction mixture was heated under reflux overnight. Ethanol and excess ethyl formate were removed under reduced pressure and the crude product was purified by HPLC to give the required material as pale yellow solid (37.4 mg, 35% yield) with no distinct melting point.
NMR[DMSO-d6]: 10.04(1H, s); 9.90(1H, s); 9.88(1H, s); 9.63(1H, broad, TFA); 8.15-8.13(2H, s & t); 7.26(1H, s); 7.18(1H, s); 7.16(1H, s); 7.01(1H, s); 6.92(1H, s); 6.92(1H, s); 4.31-4.30(2H, t); 3.84(3H, s); 3.82(3H, s); 3.25-3.24(2H, m); 3.07(2H, m); 2.79(6H, d); 1.84-1.82(2H, m); 1.57-1.48(3H, m); 0.90(6H, d). IR νmax [KBr]: 3428, 3315, 1676, 1644, 1582, 1538, 1464, 1438, 1403, 1262, 1201, 1132 cm−1. HRFABMS: found 553.32520 calculated for C28H41N8O4 553.32508.
Example 11
2-(Acetylamino)-N-[5-({[5-({[3-(dimethylamino)propyl]amino}carbonyl)-1-methyl-1H-pyrrol-3-yl]amino}carbonyl)-1-methyl-1H-pyrrol-3-yl]-5-isopropyl-1,3-thiazole-4-carboxamide
(i) Methyl 2-(acetylamino)-5-isopropyl-1,3-thiazole-4-carboxylate
Methyl 2-amino-5-isopropyl-1,3-thiazole-4-carboxylate (500 mg, 2.497 mmol; see Example 3, step (i) above) was dissolved in DCM (10 mL, dry) to which NMM (300 μL, dry) was added at room temperature with stirring. Acetyl chloride (300 μL, 330 mg, 4.204 mmol) was added dropwise to the reaction mixture with stirring. The stirring was continued at room temperature overnight. Brine (25 mL) was added to the reaction mixture and the product was then extracted with DCM (2×50 mL). The organic layers were combined and dried over MgSO4, filtered and the solvent removed under reduced pressure to give the crude product which was purified by column chromatography over silica gel using 1/1 ethyl acetate/n-hexane [RF=0.22]. The product was obtained as white fine needles (432 mg, 72% yield), m.p. 170-172° C.
NMR(DMSO-d6): 12.31(1H, s); 4.01-3.94(1H, quintet); 3.78(3H, s); 2.11(3H, s); 1.27(6H, d). IR νmax [KBr]: 3277, 2971, 1752, 1694, 1543, 1202 cm−1. HRFABMS: Found 243.08074 calculated for C10H15N2O3S 243.08034.
(ii) 2-(Acetylamino)-5-isopropyl-1,3-thiazole-4-carboxylic acid
Methyl 2-(acetylamino)-5-isopropyl-1,3-thiazole-4-carboxylate (242 mg, 1.00 mmol; see step (i) above) was dissolved in ethanol (10 mL) to which ethanolic sodium hydroxide [0.5 M, 10 mL] was added. The reaction mixture was heated under reflux for 30 min following which it was cooled to 0° C. and then dilute HCl was added with stirring until pH 2. Water (50 mL) was added and the white precipitate was filtered off and dried under reduced pressure at 45° C. overnight. The product was obtained as micro-crystalline white solid (166 mg, 73% yield), m.p.>230° C.
NMR(DMSO-d6): 12.65(1H, br); 12.23(1H, s); 4.04-3.97(1H, quintet); 2.11(3H, s); 1.26(6H, d). IR νmax [KBr]: 3076, 2971, 2868, 1699, 1671, 1568, 1543, 1301, 1221 cm−1. HRFABMS: Found 229.06408 calculated for C9H13N2O3S 229.06469.
(iii) 2-(Acetylamino)-N-[5-({[5-({[3-(dimethylamino)propyl]amino}-carbonyl)-1-methyl-1H-pyrrol-3-yl]amino}carbonyl)-1-methyl-1H-pyrrol-3-yl]-5-isopropyl-1,3-thiazole-4-carboxamide
N-[5-({[3-Dimethylamino)propyl]amino}carbonyl)-1-methyl-1H-pyrrol-3-yl]-1-methyl-4-nitro-1H-pyrrole-2-carboxamide (105 mg, 0.279 mmol; see Tetrahedron 56, 5225-5239, (2000)) was dissolved in methanol (25 mL). The solution was cooled to 0° C. under N2 then Pd/C-10% (82 mg) was added. The reaction mixture was hydrogenated at room temperature and atmospheric pressure for 3 h. The catalyst was removed over Kieselguhr and then the solvent was removed under reduced pressure at 50° C. The amine thus formed was dissolved in DMF (2 mL, dry), to which 2-(acetylamino)-5-isopropyl-1,3-thiazole-4-carboxylic acid (96 mg, 0.418 mmol; see step (ii) above) was added, followed by HBTU (211 mg, 0.556 mmol) and NMM (300 μL, dry). The reaction mixture was left stirring at room temperature overnight after which it was diluted with ethyl acetate and NaHCO3 solution with stirring. The organic layer was separated, dried MgSO4, filtered and the solvent removed under reduced pressure. The product was purified by HPLC to give the pure material as white solid (71.3 mg, 38% yield) with no distinct melting point.
NMR[DMSO-d6]: 12.31(1H, s); 8.87(1H, s); 9.57(1H, s); 9.24(1H, broad); 8.14(1H, t); 7.26(1H, d); 7.17(1H, d); 7.12(1H, d); 6.94(1H, d); 4.19-4.12(1H, m); 3.85(3H, s); 3.81(3H, s); 3.25(2H, m); 3.07(2H, m); 2.79(6H, d); 2.16(3H, s); 1.83(2H, qt); 1.29(6H, d). IR νmax [KBr]: 1676, 1644, 1550, 1465, 1435, 1404, 1202, 1136 cm−1. HRFABMS: found 557.26442 calculated for C26H37N8O4S 557.26585.
Example 12
2-(Acetylamino)-N-[5-({[4-({[3-(dimethylamino)propyl]amino}carbonyl)-5-isopropyl-1,3-thiazol-2-yl]amino}carbonyl)-1-methyl-1H-pyrrol-3-yl]-5-isopropyl-1,3-thiazole-4-carboxamide
N-[3-(Dimethylamino)propyl]-5-isopropyl-2-{[(1-methyl-4-nitro-1H-pyrrol-2-yl)carbonyl]amino}-1,3-thiazole-4-carboxamide (100 mg, 0.236 mmol; see Example 3, step (iv) above) was dissolved in methanol (25 mL). The solution was cooled to 0° C. under N2 then Pd/C-10% (82 mg) was added. The reaction mixture was hydrogenated at room temperature and atmospheric pressure for 3 h. The catalyst was removed over Kieselguhr and the solvent was then removed under reduced pressure at 50° C. The amine so formed was dissolved in DMF (2 mL, dry), to which 2-(acetylamino)-5-isopropyl-1,3-thiazole-4-carboxylic acid (64 mg, 0.356 mmol; see Example 11, step (ii) above) was added, followed by HBTU (135 mg, 0.356 mmol) and NMM (200 μL, dry). The reaction mixture was left stirring at room temperature overnight, after which it was diluted with ethyl acetate and NaHCO3 solution with stirring. The organic layer was separated, dried MgSO4, filtered and the solvent removed under reduced pressure. The product was purified by HPLC to give the pure material as white solid (78.8 mg, 47% yield) with no distinct melting point.
NMR[DMSO-d6]: 12.11(1H, s); 12.01(1H, s); 9.64(1H, s); 9.27(1H, broad); 7.96(1H, t); 7.51(1H, d); 7.42(1H, d); 4.22-4.11(2H, m); 3.90(3H, s); 3.34(2H, m); 3.08(2H, m); 2.79(6H, d); 2.16(3H, s); 1.91-1.85(2H, qt); 1.30-1.27(12H, 2xd). IR νmax [KBr]: 1666, 1549, 1508, 1466, 1398, 1286, 1201, 1134 cm−1. HRFABMS: found 603.25162 calculated for C27H39N8O4S2 603.25357.
Example 13
2-(Acetylamino)-N-(5-{[(3-{[3-(dimethylamino)propyl]amino}-3-oxopropyl)amino]carbonyl}-1-methyl-1H-pyrrol-3-yl-5-isopropyl-1,3-thiazole-4-carboxamide
Samples of Boc-BALa-PAM resin (100 mg of 100-200 mesh (Novabiochem)) were placed in 10 separate vials to each of which was added DCM (0.5 mL, dry). TFA (80%) in DCM (3 mL, dry) was then added to each vial. The reactions were carried out under nitrogen and the reaction mixture agitated for 15 min. Following this, the solvents were drained and the resin washed with DMF (2×2 mL, dry) and they were then agitated for 5 min and then drained. 4-[(tert-Butoxycarbonyl)amino]-1-methyl-1H-pyrrole-2-carboxylic acid (180 mg, 0.750 mmol; see J. Med. Chem. 46(17), 3492-3497 (1981)) was dissolved in DMF (15 mL, dry) and then (1.5 mL) of this solution was added to each vial. HBTU (284 mg, 0.748 mmol) was dissolved in DMF (15 mL, dry) then (1.5 mL) of this solution was added to each vial followed by diisopropylethylamine (0.5 mL, dry). The agitation was continued for 30 min after which the solvents and reagents were drained. TFA (80%) in DCM (3 mL, dry) were added to each vial. The reaction mixture was agitated for a further 15 min. The solvents were drained and the resin was then washed with DMF (2×2 mL, dry) and agitated for 5 min and then drained. 2-(Acetylamino)-5-isopropyl-1,3-thiazole-4-carboxylic acid (171 mg, 0.750 mmol; see Example 11, step (ii) above) was dissolved in DMF (15 mL, dry) then (1.5 mL) of this solution was added to each vial. HBTU (284 mg, 0.748 mmol) was dissolved in DMF (15 mL, dry) then 1.5 mL of this solution, followed by diisopropylethylamine (0.5 mL, dry), was added to each vial. Agitation was continued for 30 min after which the solvents and reagents were drained. The resin in each vial was washed successively with DMF (3 mL, dry) for min with agitation, drained and then followed by DCM (3 mL, dry), drained again and finally washed with THF (3 mL, dry) and drained again. To each vial THF (3 mL, dry) was added followed by 3-(dimethylamino)-propylamine (0.5 mL, dry). Agitation was continued overnight at 55° C., then the solvent was filtered. The combined filtrate was collected and the solvent and reagent were removed under reduced pressure to give the crude product as brown oil. This material was further purified by HPLC and the fractions containing the required material were freeze-dried. The pure product was obtained as white solid (92 mg, 20% yield) with no distinct melting point.
NMR[DMSO-d6]: 12.07(1H, s); 9.51(1H, s); 9.24(1H, broad); 8.03(2H, t); 7.21(1H, d); 6.91(1H, d); 4.17-4.11(1H, m); 3.81(3H, s); 3.41-3.38(2H, m); 3.13-3.09(2H, m); 3.01(2H, m); 2.74(6H, t); 2.35(2H, t); 2.15(3H, s); 1.77-1.71(2H, qt); 1.28(6H, d). IR νmax [KBr]: 1673, 1548, 1465, 1438, 1404, 1286, 1201, 1180, 1131 cm−1. HRFABMS: Found 506.25688 calculated for C23H36N7O4S 506.25495.
Example 14
N1,N3-Bis(2-{[5-({[4-({[3-(dimethylamino)propyl]amino}carbonyl)-5-isopropyl-1,3-thiazol-2-yl]amino}carbonyl)-1-methyl-1H-pyrrol-3-yl]amino}-2-oxoethyl)isophthalamide
N-[3-(Dimethylamino)propyl]-5-isopropyl-2-{[(1-methyl-4-nitro-1H-pyrrol-2-yl)carbonyl]amino}-1,3-thiazole-4-carboxamide (100 mg, 0.236 mmol; see Example 3, step (iv) above) was dissolved in methanol (25 mL). The solution was cooled to 0° C. under N2 then Pd/C-10% (86 mg) was added. The reaction mixture was hydrogenated at room temperature and atmospheric pressure for 5 h. The catalyst was removed over Kieselguhr and the solvent was then removed under reduced pressure at 50° C. The amine so formed was dissolved in DMF (2 mL, dry), to which [(3-{[(carboxymethyl)amino]carbonyl}benzoyl)amino]acetic acid (33 mg, 0.118 mmol; see J. Med. Chem. 43, 3257-3266 (2000)) was added followed by HBTU (270 mg, 0.710 mmol) and NMM (300 μL, dry). An additional amount of DMF (2 mL, dry) was added with stirring at room temperature and the stirring was continued for 72 h. The reaction mixture was diluted with ethyl acetate/methanol (40 mL/10 mL) and brine with stirring. After extraction the organic layers were collected and the solvents removed under reduced pressure. The product was purified by HPLC and the fractions containing the desired material were freeze-dried. The product was obtained as white solid material (25 mg, 16% yield) with no distinct melting point.
NMR[DMSO-d6]: 12.03(2H, s); 10.08(2H, s); 9.24(2H, broad); 8.93(2H, t); 8.05(2H, d); 7.94(2H, t); 7.61(1H, t); 7.39(2H, d); 7.25(2H, d); 4.21-4.15(2H, m); 4.06(2H, d); 3.87(6H, s); 3.30(4H, m); 3.07(4H, m); 2.79(6H, d); 1.86(4H, qt); 1.28(12H, d). IR νmax [KBr]: 1655, 1548, 1467, 1403, 1288, 1202, 1132 cm−1. LRLCMS: Found 1029.3 calculated for C48H65N14O8S2 1029.5.
Example 15
The following compounds were prepared using analogous techniques to those described hereinbefore:

    N-[5-({[5-({[3-(Dimethylamino)propyl]amino}carbonyl)-1-methyl-1H-pyrrol-3-yl]amino}carbonyl)-1-isopropyl-1H-pyrrol-3-yl]-4-(acetylamino)-1-methyl-1H-pyrrole-2-carboxamide; and
    N-[5-({[5-({[3-(Dimethylamino)propyl]amino}carbonyl)-1-methyl-1H-pyrrol-3-yl]amino}carbonyl)-1-isopentyl-1H-pyrrol-3-yl]-4-(acetylamino)-1-methyl-1H-pyrrole-2-carboxamide.


Example 16
N2,N5-Bis[5-({[4-({[3-(dimethylamino)propyl]amino}carbonyl)-5-isopropyl-1,3-thiazol-2-yl]amino}carbonyl)-1-methyl-1H-pyrrol-3-yl]-1H-indole-2,5-dicarboxamide
N-[3-(Dimethylamino)propyl]-5-isopropyl-2-{[(1-methyl-4-nitro-1H-pyrrol-2-yl)carbonyl]amino}-1,3-thiazole-4-carboxamide (122 mg, 0.284 mmol; see Example 3, step (iv) above) and Pd/C-10% (110 mg) were suspended in methanol (20 mL) and hydrogenated for 2.5 h at room temperature. Filtration of catalyst over Kieselguhr under N2, followed by removal of the solvent under reduced pressure gave the amine as an off-white solid, which was used without further purification. Indole-2,5-dicarboxylic acid (29 mg, 0.142 mmol; prepared according to a standard literature procedure (see H. G. Lindwall and G. J. Mantell J. Org. Chem. 18, 345-356 (1953))) was dissolved in DMF (0.5 mL, dry), to which was added a solution of HBTU (107 mg, 0.284 mmol) and NMM (0.2 mL, dry) in DMF (1 mL, dry) at room temperature with stirring. The stirring was continued for 30 min. at room temperature. This mixture was added to the amine with stirring at room temperature and stirring was continued at room temperature overnight, followed by purification by HPLC to give the desired material as bis-TFA salt (32 mg, 23% yield) with no distinct melting point.
NMR [DMSO-d6]: 1.3(12H, s, isopropylMe2); 2.08(1H, m, isopropylCH); 1.85-1.92(4H, m, 2xCH2); 2.80(6H, s, NMe2); 2.81(6H, s, NMe2); 3.07(4H, m, 2xCH2); 3.23(4H, m, 2xCH2); 3.93(6H, s, NMe); 7.46(2H, m); 7.54(2H, m); 7.85(1H, m); 7.99(2H, m); 8.35(1H, s); 9.37(2H, br, 2xTFA, exch); 10.32(1H, s); 10.52(1H, s); 11.95(1H, s); 12.09(1H, s); 12.15(1H, s). IR [KBr]: 3415, 2960, 2362, 1654, 1549, 1467, 1398, 1287, 1200, 1134 cm−1. HRFABMS: found 953.42; calculated for C46H59N13O6S2 953.42.
Example 17
N2,N5-Bis[1-isopentyl-5-({[1-methyl-5-({[3-(4-morpholinyl)propyl]amino}-carbonyl)-1H-pyrrol-3-yl]amino}carbonyl)-1H-pyrrol-3-yl]-1H-indole-2,5-dicarboxamide
1-Isopentyl-N-[1-methyl-5-({[3-(4-morpholinyl)propyl]amino}carbonyl)-1H-pyrrol-3-yl]-4-nitro-1H-pyrrole-2-carboxamide (120 mg, 0.25 mmol; see Example 30, step (i) below) and Pd/C-10% (110 mg) were suspended in methanol (20 mL) and hydrogenated for 2.5 h at room temperature. Filtration of catalyst over Kieselguhr under N2, followed by removal of the solvent under reduced pressure gave the amine as an off-white solid, which was used without further purification. Indole-2,5-dicarboxylic acid (26 mg, 0.125 mmol; see Example 16 above) was dissolved in DMF (0.5 mL, dry), to which was added a solution of HBTU (137 mg, 0.36 mmol) and NMM (0.2 mL, dry) in DMF (1 mL, dry) at room temperature with stirring. The stirring was continued for 30 min. at room temperature. This mixture was added to amine with stirring at room temperature and stirring was continued at room temperature overnight, followed by purification by HPLC to give the desired material as bis-TFA salt (15 mg, 12% yield) with no distinct melting point.
NMR [DMSO-d6]: 11.95(1H, s); 10.47(1H, s); 10.28(1H, s); 10.02(1H, s); 9.99(1H, s); 9.66(2H, br, TFA); 8.39(1H, s); 8.24(2H, t, unresolved, 2xCONH); 7.88(1H, d, J=8.7 Hz); 7.49(1H, s); 7.43(2H, s); 7.23(2H, s); 7.14(2H, s); 7.02(2H, s); 4.43(4H, m); 4.06(4H, m); 3.89(6H, s); 3.71(4H, t, J=4.6 Hz); 3.49(4H, m); 3.31(4H, m); 3.19(8H, m); 1.94(4H, m); 1.66-1.57(6H, m); 0.98(12H, d, J=6.5 Hz). IR [KBr]: 1677, 1646, 1533, 1443, 1403, 1198, 1134 cm−1. LRESMS: Found 1058.6; calculated for C56H76N13O8 1058.6
Example 18
N2,N5-Bis[5-({[5-({[3-(dimethylamino)propyl]amino}carbonyl)-1-methyl-1H-pyrrol-3-yl]amino}carbonyl)-1-isopentyl-1H-pyrrol-3-yl]-1H-indole-2,5-dicarboxamide
N-[5-({[3-(Dimethylamino)propyl]amino}carbonyl)-1-methyl-1H-pyrrol-3-yl]-1-isopentyl-4-nitro-1H-pyrrole-2-carboxamide (110 mg, 0.25 mmol; see Example 10, step (i) above) and Pd/C-10% (110 mg) were suspended in methanol (20 mL) and hydrogenated for 2.5 h at room temperature. Filtration of catalyst over Kieselguhr under N2, followed by removal of the solvent under reduced pressure gave the amine as an off-white solid, which was used without further purification. Indole-2,5-dicarboxylic acid (26 mg, 0.125 mmol) was dissolved in DMF (0.5 mL, dry), to which was added a solution of HBTU (137 mg, 0.36 mmol) and NMM (0.2 mL, dry) in DMF (1 mL, dry) at room temperature with stirring. The stirring was continued for 30 min. at room temperature. This mixture was added to amine with stirring at room temperature and stirring was continued at room temperature overnight, followed by purification by HPLC to give the desired material as bis-TFA salt (36 mg, 30% yield) with no distinct melting point.
NMR [DMSO-d6]: 11.95(1H, s); 10.47(1H, s); 10.28(1H, s); 10.02(1H, s); 9.99(1H, s); 9.39(2H, br, 2xTFA); 8.39(1H, s); 8.22(2H, t, unresolved, 2xCONH); 7.91(1H, d, J=8.7 Hz); 7.61(1H, d, J=8.7 Hz); 7.49(1H, s); 7.43(2H, s); 7.23(2H, s); 7.13(2H, s); 7.01(2H, s); 4.43(4H, m); 3.89(6H, s); 3.31(4H, m); 3.14(4H, m); 2.86(12H, d, J=3.8 Hz); 1.91(4H, m); 1.66-1.55(6H, m); 0.98(12H, d, J=6.5 Hz). IR [KBr]: 1677, 1647, 1583, 1533, 1443, 1404, 1199, 1135 cm1. HRFABMS: Found 974.6; calculated for C52H72N13O6 974.5
Example 19
N2,N5-Bis[1-isopentyl-5-({[1-methyl-5-({[3-(4-methyl-1-piperazinyl)-propyl]amino}carbonyl)-1H-pyrrol-3-yl]amino}carbonyl)-1H-pyrrol-3-yl]-1H-indole-2,5-dicarboxamide
1-Isopentyl-N-[1-methyl-5-({[3-(4-methyl-1-piperazinyl)propyl]amino]-carbonyl)-1H-pyrrol-3-yl]-4-nitro-1H-pyrrole-2-carboxamide (122 mg, 0.25 mmol; see Example 29, step (i) below) and Pd/C-10% (110 mg) were suspended in methanol (20 mL) and hydrogenated for 2.5 h at room temperature. Filtration of catalyst over Kieselguhr under N2, followed by removal of the solvent under reduced pressure gave the amine as an off-white solid, which was used without further purification. Indole-2,5-dicarboxylic acid (26 mg, 0.125 mmol) was dissolved in DMF (0.5 mL, dry), to which was added a solution of HBTU (137 mg, 0.36 mmol) and NMM (0.2 mL, dry) in DMF (1 mL, dry) at room temperature with stirring. The stirring was continued for 30 min. at room temperature. This mixture was added to amine with stirring at room temperature and stirring was continued at room temperature overnight, followed by purification by HPLC to give the desired material as bis-TFA salt (17 mg, 13% yield) with no distinct melting point.
NMR [DMSO-d6]: 11.95(1H, s); 10.47(1H, s); 10.27(1H, s); 10.01(1H, s); 9.97(1H, s); 9.60(2H, br, TFA); 8.39(1H, s); 8.13(2H, br); 7.91(1H, d, J=8.7 Hz); 7.61(1H, d, J=8.7 Hz); 7.49(1H, s); 7.43(2H, s); 7.21(2H, s); 7.14(2H, s); 6.98(2H, s); 4.43(4H, m); 3.88(6H, s); 3.29(4H, m); 3.20-2.73(20H, m); 1.80(4H, m); 1.66-1.55(6H, m); 0.96(12H, d, J=6.5 Hz). IR [KBr]: 1676, 1647, 1584, 1533, 1443, 1404, 1200, 1136 cm−1. HRFABMS: Found 1084.6; calculated for C58H82N15O6 1084.6
Example 20
2-({[4-({4-(Acetylamino)-1-methyl-1H-imidazol-2-yl]carbonyl}amino)-1-methyl-1H-pyrrol-2-yl]carbonyl}amino)-N-[3-(dimethylamino)propyl]-5-isopropyl-1,3-thiazole-4-carboxamide
N-[3-(Dimethylamino)propyl]-5-isopropyl-2-{[(1-methyl-4-nitro-1H-pyrrol-2-yl)carbonyl]amino}-1,3-thiazole-4-carboxamide (105 mg, 0.25 mmol; see Example 3, step (iv) above) and Pd/C-10% (100 mg) were suspended in methanol (20 mL) and hydrogenated for 2.5 h at room temperature. Filtration of catalyst over Kieselguhr under N2, followed by removal of the solvent under reduced pressure gave the amine as an off-white solid, which was used without further purification. 4-Acetamido-1-methyl-2-imidazolecarboxylic acid sodium salt (120 mg, 0.7 mmol; prepared according to a standard literature procedure (see Tao, Z.; Fujiwara, T.; Saito, I.; Sugiyama, H. Angew. Chem. Int. Ed. EN 38(5), 650-653 (1999))) was dissolved in DMF (0.5 mL, dry), to which was added a solution of HBTU (137 mg, 0.36 mmol) and NMM (0.2 mL, dry) in DMF (1 mL, dry) at room temperature with stirring. The stirring was continued for 30 min. at room temperature. This mixture was added to the amine with stirring at room temperature and stirring was continued at room temperature overnight, followed by purification by HPLC to give the desired material as bis-TFA salt (30 mg, 22% yield) with no distinct melting point.
NMR [DMSO-d6]: 1.27-1.28(6H, d, J=6.8 Hz, isopropyl); 1.87(2H, m); 2.02(3H, s); 2.78(6H, s, NMe2); 3.07(2H, m); 3.32(2H, m); 3.89(3H, s, NMe); 3.95(3H, s, COMe); 4.19(1H, m, isopropyl); 7.44(2H, m); 7.48(1H, m); 7.97(1H, m); 9.3(1H, br); 10.00(1H, s); 10.23(1H, s); 12.03(1H, s). IR [KBr]: 1667, 1550, 1470, 1288, 1198, 1133 cm−1. HRFABMS: Found 558.26332 calculated for C25H36N9O4S 558.26110.
Example 21
4-(Acetylamino)-N-[1-isopentyl-5-({[1-methyl-5-({[3-(4-methyl-1-piperazinyl)propyl]amino}carbonyl)-1H-pyrrol-3-yl]amino}carbonyl)-1H-pyrrol-3-yl]-1-methyl-1H-pyrrole-2-carboxamide
N-[1-Isopentyl-5-({[1-methyl-5-({[3-(4-methyl-1-piperazinyl)propyl]-amino}carbonyl)-1H-pyrrol-3-yl]amino}carbonyl)-1H-pyrrol-3-yl]-1-methyl-4-nitro-1H-pyrrole-2-carboxamide (186 mg, 0.305 mmol; see Example 29, step (ii) below) was dissolved in methanol at 0° C. under N2 with stirring to which Pd/C-10% (136 mg) was added. The reaction mixture was hydrogenated for 3 h at room temperature and atmospheric pressure with stirring. The catalyst was removed over Kieselguhr and the solvent was removed under reduced pressure. The amine so formed was dissolved in dichloromethane (10 mL) and this solution was divided in half. Acetyl chloride (12 mg, 12 μL, 0.153 mmol) was added dropwise with stirring at room temperature to the first half. The stirring was continued at room temperature overnight. The solvent was removed under reduced pressure and the crude product formed was dissolved in small amount of acetonitrile/water containing 0.1% TFA and purified by HPLC. Fractions containing the pure material were combined and freeze-dried to give off-white solid (45.5 mg, 40% yield) with no distinct melting point.
NMR [DMSO-d6]: 9.87(1H, s); 9.86(1H, s); 9.79(1H, s); 8.09(1H, t, unresolved); 7.26(1H, d, J=1.7 Hz); 7.14(1H, d, J=1.7 Hz); 7.13(1H, d, J=1.7 Hz); 7.01(1H, d, J=1.7 Hz); 6.91(1H, d, J=1.7 Hz); 6.86(1H, d, J=1.7 Hz); 4.31(2H, t, J=6.9 Hz); 3.83(3H, s); 3.81(3H, s); 3.24(2H, q, J=6.4 Hz); 3.10-2.60(8H, br, & 3H, s); 1.97(3H, s); 1.77(2H, m); 1.58-1.46(3H, m); 0.90(6H, d, J=6.4 Hz). IR [KBr]: 1675, 1647, 1584, 1535, 1459, 1436, 1402, 1197, 1132 cm−1. HRFABMS: Found 622.38301; calculated for C32H48N9O4 622.38293.
Example 22
N-[1-Isopentyl-5-({[1-methyl-5-({[3-(4-methyl-1-piperazinyl)propyl]-amino}carbonyl)-1H-pyrrol-3-yl]amino}carbonyl)-1H-pyrrol-3-yl]-4-[(3-methoxybenzoyl)amino]-1-methyl-1H-pyrrole-2-carboxamide
To the second half of the amine solution (see Example 21 above) was added m-methoxybenzoyl chloride (26 mg, 26 μL, 0.153 mmol) was added dropwise at room temperature with stirring. The stirring was continued overnight at room temperature. The solvent was removed under reduced pressure and the crude product was purified by HPLC. The product was obtained as light brown solid (60.8 mg, 48% yield).
NMR [DMSO-d6]: 10.28(1H, s); 9.95(1H, s); 9.88(1H, s); 8.09(1H, t, unresolved); 7.53-7.47(2H, m); 7.43(1H, t, J=7.8 Hz); 7.32(1H, d, J=1.7 Hz); 7.29(1H, d, J=1.7 Hz); 7.15-7.11(3H, m); 7.02(1H, d, J=1.7 Hz); 6.92(1H, d, J=1.7 Hz); 4.32(2H, t, J=6.6 Hz); 3.88(3H, s); 3.83(3H, s); 3.81(3H, s); 3.24(2H, q, J=6.0 Hz); 3.10-2.40(8H, br, & 3H, s); 1.77(2H, br); 1.59-1.47(3H, m); 0.91(6H, d, J=6.4 Hz). IR [KBr]: 1677, 1645, 1583, 1535, 1462, 1435, 1402, 1263, 1197, 1132 cm−1. HRFABMS: Found 714.40764; calculated for C38H52N9O5 714.40914.
Example 23
N-[5-({[3-(Dimethylamino)propyl]amino}carbonyl)-1-methyl-1H-pyrrol-3-yl]-4-({[5-(formylamino)-2-methyl-3-thienyl]carbonyl}amino)-1-isopentyl-1H-pyrrole-2-carboxamide
(i) Ethyl 2-methyl-4,5-dihydro-3-thiophenecarboxylate
A standard procedure was employed (see Pallab Chatterjee, Patrick J. Murphy, Rosanna Pepe and Michael Shaw J. Chem. Soc., Perkin Trans. 1 17, 2403-2406 (1994)) to give the product as colorless oil (96% yield).
(ii) Ethyl 2-methyl-3-thiophenecarboxylate
A standard procedure was employed (see Pallab Chatteree, Patrick J. Murphy, Rosanna Pepe and Michael Shaw J. Chem. Soc., Perkin Trans. 1 17, 2403-2406 (1994)) to give the product as colorless oil (82% yield).
(iii) 2-Methyl-3-thiophenecarboxylic acid
Ethyl 2-methyl-3-thiophenecarboxylate (3.42 g, 20.09 mmol; see step (ii) above) was dissolved in ethanol (5 mL) to which was added a solution of sodium hydroxide (3.2145 mg, 80.362 mmol) in water (10 mL). The reaction mixture was heated under reflux for 2 h. The volume was reduced to half under reduced pressure at 40° C. and the residue was cooled with ice water. Dilute HCl was added dropwise with stirring until pH 2. The white solid material was filtered off, washed with water and dried under reduced pressure at 50° C. to give the required material (2.1850 mg, 77% yield), m.p. 115-117° C., lit. m.p. 116-117° C. (see D. W. Knight, A. P. Nott J. Chem. Soc., Perkin Trans. 1 791-794 (1983)).
(iv) 2-Methyl-5-nitro-3-thiophenecarboxylic acid
A mixture of concentrated nitric acid (10 mL, sp.gr. 1.42) and concentrated sulphuric acid (6 mL) was mechanically stirred in a round-bottomed flask and cooled to (−10° C.) by a dry ice methanol bath. The temperature was kept below (−5° C.) while 2-methyl-3-thiophenecarboxylic acid (996 mg, 7.006 mmol; see step (iii) above) was added in small portions. The reaction mixture was stirred at the same temperature for 15 min. and then was poured over ice water. The solid material that precipitated was filtered off, washed with water and dried to give light brown solid (883 mg; 67% yield), m.p. 177-180° C.
NMR [DMSO-d6]: 13.35(1H, br); 8.11(1H, s); 2.76(3H, s). IR [KBr]: 1706, 1543, 1514, 1457, 1335, 1257 cm−1. HREIMS: Found 186.99431; calculated for C6H5NO4S 186.99393.
(v) N-[5-({[3-(Dimethylamino)propyl]amino}carbonyl)-1-methyl-1H-pyrrol-3-yl]-1-isopentyl-4-{[(2-methyl-5-nitro-3-thienyl)carbonyl]amino}-1H-pyrrole-2-carboxamide
N-[5-({[3-(Dimethylamino)propyl]amino}carbonyl)-1-methyl-1H-pyrrol-3-yl]-1-isopentyl-4-nitro-1H-pyrrole-2-carboxamide (204 mg, 0.463 mmol; see Example 10, step (i) above) was dissolved in methanol (25 mL). The reaction mixture was cooled to 0° C. and then Pd/C-10% (121 mg) was added portion-wise under N2 with stirring. The reaction mixture was hydrogenated for 5 h at room temperature and atmospheric pressure. The catalyst was removed over Kieselguhr and the solvent was then removed under reduced pressure. 2-Methyl-5-nitro-3-thiophenecarboxylic acid (87 mg, 0.463 mmol; see step (iv) above) was dissolved in thionyl chloride (2 mL) then heated until reflux for 5 h. The excess thionyl chloride was is removed under reduced pressure to give the acid chloride, which was dissolved in DCM (5 mL). The amine was dissolved in DCM (5 mL) to which N-methyl morpholine (0.1 mL) was added followed by the acid chloride, which was added dropwise at room temperature with stirring. The stirring was continued at room temperature overnight. The volatile material was removed under reduced pressure and the crude product was then purified by column chromatography using 2.5/2.5/0.6 mL ethyl acetate/methanol/TEA) RF=0.5. The product was obtained as amorphous yellow material (237 mg, 90% yield) with no distinct melting point.
NMR [DMSO-d6]: 10.37(1H, s); 9.94(1H, s); 8.58(1H, s); 8.12(1H, t, J=5.6 Hz); 7.35(1H, d, J=1.7 Hz); 7.18(1H, d, J=1.7 Hz); 7.14(1H, d, J=1.7 Hz); 7.01(1H, d, J=1.7 Hz); 6.86(1H, d, J=1.7 Hz); 4.34(1H, t, J=6.9 Hz); 3.80(3H, s); 3.22(2H, q, J=6.5 Hz); 2.77(3H, s); 2.64(2H, m); 2.44(6H, s); 1.73(2H, quintet, J=6.7 Hz); 1.59-1.45(3H, m); 0.90(6H, d, J=6.4 Hz). IR [KBr]: 1675, 1650, 1583, 1537, 1465, 1437, 1403, 1263, 1202, 1133 cm−1. HRFABMS: Found: 572.26551; calculated for C27H37N7O5S 572.26580.
(vi) N-[5-({[3-(Dimethylamino)propyl]amino}carbonyl)-1-methyl-1H-pyrrol-3-yl]-4-({[5-(formylamino)-2-methyl-3-thienyl]carbonyl}amino-1-isopentyl-1-pyrrole-2-carboxamide
N-[5-({[3-(dimethylamino)propyl]amino}carbonyl)-1-methyl-1H-pyrrol-3-yl]-1-isopentyl-4-{[(2-methyl-5-nitro-3-thienyl)carbonyl]amino}-1H-pyrrole-2-carboxamide (110 mg, 0.193 mmol; see step (v) above) was dissolved in ethanol (20 mL) and cooled to 0° C. Pd/C-10% (120 mg) was added under N2 with stirring and the reaction was hydrogenated at room temperature and atmospheric pressure for 3 h. The catalyst was removed over Kieselguhr then ethyl formate (20 mL) was added to the ethanolic solution. The reaction mixture was heated under reflux for 3 days. The volatile material was then removed under reduced pressure and the crude product was purified by HPLC. The product was obtained as solid material with no distinct melting point (23 mg, 17.4% yield).
NMR [DMSO-d6]: 11.32(1H, s); 9.94(1H, s); 9.88(1H, s); 9.24(1H, br, TFA); 8.29(1H, s); 8.14(1H, t, J=5.9 Hz); 7.29(1H, d, J=1.7 Hz); 6.95(1H, s); 6.93(1H, d, J=1.7 Hz); 4.32(1H, t, J=7.0 Hz); 3.81(3H, s); 3.25(2H, q, J=5.1 Hz); 3.06(2H, m); 2.79(6H, d, J=3.5 Hz); 2.5(3H, s); 1.83(2H, quintet, J=6.7 Hz); 1.57-1.49(3H, m); 0.90(6H, d, J=6.4 Hz). IR [KBr]: 1671, 1651, 1582, 1537, 1464, 1403, 1200, 1179, 1132 cm−1. HRFABMS: Found: 570.28565; calculated for C28H40N7O4S 570.28625.
Example 24
N-[5-({[5-({[3-(dimethylamino)propyl]amino}carbonyl)-1-methyl-1H-pyrrol-3-yl]amino}carbonyl)-1-methyl-1H-pyrrol-3-yl]-5-isopropyl-2-[(3-methoxybenzoyl)amino]-1,3-thiazole-4-carboxamide
(i) Methyl 5-isopropyl-2-[(3-methoxybenzoyl)amino]-1,3-thiazole-4-carboxylate
Methyl 2-amino-5-isopropyl-1,3-thiazole-4-carboxylate (383 mg, 1.913 mmol; see Example 3, step (i) above) was dissolved in DCM (10 mL) at room temperature with stirring. N-methyl morpholine (0.3 mL) was added followed by 3-methoxybenzoyl chloride (326 mg, 1.913 mmol) at room temperature with stirring. The reaction mixture was heated until reflux for 10 min. and then was left stirring at room temperature overnight. The solvent was removed under reduced pressure and the crude product was purified by column chromatography using silica gel and 1:2 ethyl acetate/petroleum ether. Fractions containing the required material (RF=0.4) were collected and the solvents were removed under reduced pressure to give the product as white solid material (530 mg, 83% yield), m.p. 60-63° C.
NMR [CDCl3]: 9.89(1H, s); 7.45-7.38(3H, m); 7.16-7.13(1H, m); 4.16(1H, heptet, J=6.8 Hz); 3.86(3H, s); 3.85(3H, s); 1.40(6H, d, J=6.8 Hz). IR [KBr]: 2958, 1720, 1669, 1547, 1463, 1298, 1208, 1045, 822, 743 cm−1. HRFABMS: Found: 335.10620; calculated for C16H19N2O4S 335.10655.
(ii) 5-Isopropyl-2-[(3-methoxybenzoyl)amino]-1,3-thiazole-4-carboxylic acid
Methyl 5-isopropyl-2-[(3-methoxybenzoyl)amino]-1,3-thiazole-4-carboxylate (330 mg, 0.998 mmol; see step (i) above) was dissolved in ethanolic KOH (561 mg, in 10 mL ethanol; 10 mmol). The reaction mixture was heated under reflux for 3 h, and then it was cooled to 0° C. HCl(conc.) was added dropwise with stirring at 0° C. and the resulting solid was filtered off, washed with water and dried under reduced pressure at 45° C. overnight. The product was obtained as white solid material (290 mg, 91% yield), m.p.>230° C. [sublimation].
NMR [DMSO-d6]: 7.69(2H, m); 7.44(1H, t, J=3.9 Hz); 7.19(1H, m); 4.06(1H, heptet, J=6.8 Hz); 3.84(3H, s); 1.31(6H, d, J=6.8 Hz). IR [KBr]: 2963, 1672, 1555, 1463, 1306, 1221, 1043, 936, 820, 736 cm−1. HRFABMS: Found: 321.09056; calculated for C15H17N2O4S 321.09090.
(iii) N-[5-({[5-({[3-(dimethylamino)propyl]amino}carbonyl)-1-methyl-1H-pyrrol-3-yl]amino}carbonyl)-1-methyl-1H-pyrrol-3-yl]-5-isopropyl-2-[(3-methoxybenzoyl)amino]-1,3-thiazole-4-carboxamide
N-[5-({[3-(Dimethylamino)propyl]amino}carbonyl)-1-methyl-1H-pyrrol-3-yl]-1-methyl-4-nitro-1H-pyrrole-2-carboxamide (113 mg, 0.300 mmol; see Tetrahedron 56, 5225-5239, (2000)) was suspended in methanol (25 mL) at 0° C. with stirring under N2. Pd/C-10% (61 mg) was added with stirring under N2 and then the reaction mixture was hydrogenated at room temperature and atmospheric pressure for 3 h. The catalyst was removed over Kieselguhr and the solvent was then removed under reduced pressure to give the amine, which was used in the coupling reaction without further purification. 5-Isopropyl-2-[(3-methoxybenzoyl)amino]-1,3-thiazole-4-carboxylic acid (96 mg, 3.00 mmol; see step (ii) above) was dissolved in thionyl chloride (2 mL) then heated under reflux for 3 h. The excess thionyl chloride was removed under reduced pressure and the acid chloride so formed was dissolved in DCM (5 mL). The amine was dissolved in DCM (5 mL), to which N-methyl morpholine (0.2 mL) was added. The acid chloride solution was added dropwise at room temperature with stirring and then the stirring was continued overnight at room temperature. The volatile material was removed under reduced pressure and the crude product was purified by HPLC. Fractions containing the required material were collected and freeze-dried to give the product as pale yellow solid (73 mg, 32% yield) with no distinct melting point.
NMR [DMSO-d6]: 12.63(1H, s); 9.88(1H, s); 9.55(1H, s); 9.29(1H, br); 8.14(1H, t, 5.8 Hz); 7.69(1H, s); 7.67(1H, s); 7.48(1H, t, J=5.9 Hz); 7.26(1H, d, 1.7 Hz); 7.23(1H, m); 7.18(1H, d, J=1.7 Hz); 7.13(1H, d, J=1.7 Hz); 6.94(1H, d, 1.7 Hz); 4.19(1H, heptet, J=6.8 Hz); 3.86(6H, s); 3.82(3H, s); 3.24(2H, q, J=6.7 Hz); 3.07(2H, m); 2.79(6H, d, J=3.8 Hz); 1.86(2H, quintet, J=6.7 Hz); 1.33(6H, d, J=6.8 Hz). IR [KBr]: 1660, 1547, 1466, 1436, 1403, 1286, 1199, 1137, 1043 cm−1. HRFABMS: Found: 649.29379; calculated for C32H41N8O5S 649.29206.
Example 25
N-[5-({[3-(Dimethylamino)propyl]amino}carbonyl)-1-methyl-1H-pyrrol-3-yl]-4-{[(5-{[(9,10-dioxo-9,10-dihydro-2-anthracenyl)carbonyl]amino}-2-methyl-3-thienyl)carbonyl]amino}-1-isopentyl-1H-pyrrole-2-carboxamide
N-[5-({[3-(Dimethylamino)propyl]amino}carbonyl)-1-methyl-1H-pyrrol-3-yl]-1-isopentyl-4-{[(2-methyl-5-nitro-3-thienyl)carbonyl]amino}-1H-pyrrole-2-carboxamide (127 mg, 0.223 mmol; see Example 23, step (v) above) was dissolved in methanol (25 mL) at 0° C. under N2 with stirring. Pd/C-10% (114 mg) was added and the reaction mixture was hydrogenated at room temperature and atmospheric pressure for 3.5 h. The catalyst was removed over Kieselguhr and the solvent was removed under reduced pressure to give the amine, which was used in the subsequent coupling reaction. 9,10-Dioxo-9,10-dihydro-2-anthracenecarboxylic acid (Aldrich) (56 mg, 0.223 mmol) was dissolved in DMF (1 mL, dry), to which HBTU (127 mg, 0.335 mmol) and N-methyl morpholine (0.2 mL, dry) were added with stirring under N2. The amine was dissolved in DMF (1 mL, dry) and was added dropwise to the reaction mixture. The reaction mixture was left stirring at room temperature overnight. The reaction mixture was then diluted with a mixture made of ethyl acetate/methanol 9:1 (50 mL), after which it was extracted with water. The organic layer was dried over MgSO4, filtered and the solvents removed under reduced pressure. The crude product obtained was purified by HPLC to give the pure material as brown solid with no distinct melting point (33 mg, 19% yield).
NMR [DMSO-d6]: 21.04(1H, s); 10.04(1H, s); 9.91(1H, s); 9.23(1H, br, TFA); 8.83(1H, d, J=1.7 Hz); 8.50(1H, dd, J=1.8 Hz & J=8.1 Hz); 8.42(1H, d, J=8.1 Hz); 8.29-8.25(2H, m); 8.15(1H, t, J=5.9 Hz); 8.00-7.97(2H, m); 7.33(1H, d, J=1.7 Hz); 7.21(1H, s); 7.17(1H, d, J=1.7 Hz); 7.02(1H, d, J=1.7 Hz); 6.94(1H, d, J=1.7 Hz); 4.33(2H, t, J=7.1 Hz); 3.82(3H, s); 3.24(2H, q, J=5.1 Hz); 3.08(2H, m); 2.79(6H, d, J=3.5 Hz); 2.59(3H, s); 1.84(2H, quintet, J=6.7 Hz); 1.60-1.50(3H, m); 0.91(6H, d, J=6.4 Hz). IR [KBr]: 1674, 1653, 1585, 1539, 1464, 1404, 1487, 1200, 1177, 1135 cm−1. HRFABMS: Found: 776.32284; calculated for C42H46N7O6S 776.32303.
Example 26
N-[1-(Cyclopropylmethyl)-5-({[5-({[3-(dimethylamino)propyl]amino}-carbonyl)-1-methyl-1H-pyrrol-3-yl]amino}carbonyl)-1H-pyrrol-3-yl]-4-(formylamino)-1-methyl-1H-pyrrole-2-carboxamide
(i) Ethyl 1-(cyclopropylmethyl)-4-nitro-1H-pyrrole-2-carboxylate
Ethyl 4-nitro-1H-pyrrole-2-carboxylate (1.042 g, 5.626 mmol; see Example 1, step (i) above) was dissolved in DMF (20 mL, dry) to which potassium metal (0.435 g, 11.124 mmol) was added. The reaction mixture was heated to 100° C. with stirring and it was left at that temperature for 1 h. The reaction mixture was cooled to 50-60° C. then (chloromethyl)cyclopropane (1.000 g, 11.044 mmol) [purchased from Aldrich] and KI (1.349 g, 8.127 mmol) were added and the reaction mixture was heated again with stirring to 80° C. for 5 h, after which time it was left stirring overnight at room temperature. The reaction mixture was diluted with brine (50 mL) and extracted with ethyl acetate (3×100 mL). The combined organic extracts were collected and the solvent was removed under reduced pressure. The crude product obtained (containing some DMF) was purified by flash chromatography using silica gel and 1/10 ethyl acetate/n-hexane. The product as white microcrystalline solid [RF=0.2] was obtained (1.070 g, 80% yield), m.p. 65-66° C.
NMR [DMSO-d6]: 8.34(1H, d, J=1.3 Hz); 7.35(1H, d, J=1.3 Hz); 4.30-4.24(2H, q, J=7.1 Hz); 4.21(2H, d, J=7.2 Hz); 1.34-1.23(2H; t, J=7.1 Hz & 1H, m); 0.53-0.45(2H, m); 0.42-0.38(2H, m). IR [KBr]: 3142, 2996, 2921, 1704, 1502, 1310, 1270, 1225, 1184, 1091 cm−1. HREIMS: Found 238.09585; calculated for C11H14N2O4 238.09536.
(ii) 1-(Cyclopropylmethyl-4-nitro-1H-pyrrole-2-carboxylic acid
Ethyl 1-(cyclopropylmethyl)-4-nitro-1H-pyrrole-2-carboxylate (482 mg, 2.023 mmol; see step (i) above) was dissolved in ethanol (4 mL) to which a solution of NaOH (393 mg, 9.825 mmol) in water (10 mL) was added. The reaction mixture was heated under reflux for 2 h then cooled to 0° C. HCl conc. was added dropwise with stirring until the solution reached pH 2. The white solid material, which precipitated was filtered off, washed with water and dried under reduced pressure at 60° C. overnight. The product was obtained as white solid material (382 mg, 90% yield), m.p. 215-217° C.
NMR [DMSO-d6]: 13.14(1H, br); 8.29(1H, d, J=2.4 Hz); 7.29(1H, d, J=2.1 Hz); 4.20(2H, d, J=2.2 Hz); 1.34-1.27(1H, m); 0.52-0.38(4H, m). IR [KBr]: 3115, 3005, 2922, 2854, 1680, 1540, 1517, 1481, 1420, 1314 cm−1. HREIMS: Found 210.06469; calculated for C9H10N2O4 210.06406.
(iii) 1-(Cyclopropylmethyl)-N-[5-({[3-(dimethylamino)propyl]amino}-carbonyl)-1-methyl-1H-pyrrol-3-yl]-4-nitro-1H-pyrrole-2-carboxamide
N-[3-(Dimethylamino)propyl]-1-methyl-4-nitro-1H-pyrrole-2-carboxamide (100 mg, 0.393 mmol; see Tetrahedron 56, 5225-5239 (2000)) was dissolved in methanol (25 mL) to which Pd/C-10% (75 mg) was added at 0° C. under N2 with stirring. The reaction mixture was hydrogenated for 2 h at room temperature and atmospheric pressure. The catalyst was removed over Kieselguhr and the solvent was removed under reduced pressure. The amine so formed was dissolved in DMF (2 mL, dry) to which was added 1-(cyclopropylmethyl)-4-nitro-1H-pyrrole-2-carboxylic acid (83 mg, 0.393 mmol; see step (ii) above), HBTU (298 mg, 0.786 mmol), NMM (200 μL, dry) with stirring at room temperature. The stirring was continued for 48 h. The reaction mixture was diluted with ethyl acetate (50 mL) and extracted with NaHCO3 (25 mL, saturated). The water layer was extracted again with ethyl acetate (50 mL). The combined organic extract was dried over MgSO4, filtered and the solvent removed under reduced pressure to give the crude product as pale yellow oil. Purification by flash column chromatography over silica gel using 1/2/0.1 methanol/ethyl acetate/TEA gave the required product as glassy yellow material [RF=0.5] (130 mg, 80% yield) with no distinct melting point.
NMR [DMSO-d6]: 10.26(1H, s); 8.24(1H, d, J=1.9 Hz); 8.10(1H, t, J=5.6 Hz); 7.57(1H, d, J=1.9 Hz); 7.21(1H, d, J=1.9 Hz); 6.83(1H, d, J=1.9 Hz); 4.27(2H, d, J=7.2 Hz); 3.81(3H, s); 3.21-3.16(2H, q, J=6.9 Hz); 2.28(2H, t, J=7.1 Hz); 2.17(6H, s); 1.65-1.59(2H, quintet, J=7.1 Hz); 1.34-1.29(1H, m); 0.51-0.38(4H, m). IR [KBr]: 3283, 3126, 2944, 1642, 1573, 1532, 1504, 1463, 1427, 1389, 1309, 1233 cm−1. HRFABMS: Found 417.22460; calculated for C20H29N6O4 417.22503.
(iv) N-[1-(Cyclopropylmethyl)-5-({[5-({[3-(dimethylamino)propyl]amino}-carbonyl)-1-methyl-1H-pyrrol-3-yl]amino}carbonyl)-1H-pyrrol-3-yl]-1-methyl-4-nitro-1H-pyrrole-2-carboxamide
1-(Cyclopropylmethyl)-N-[5-({[3-(dimethylamino)propyl]amino}carbonyl)-1-methyl-1H-pyrrol-3-yl]-4-nitro-1H-pyrrole-2-carboxamide (120 mg, 0.288 mmol; see step (iii) above) was dissolved in methanol (25 mL) to which Pd/C-10% (97 mg) was added at 0° C. under N2 with stirring. The reaction mixture was hydrogenated for 4 h at room temperature and atmospheric pressure. The catalyst was removed over Kieselguhr and the solvent was removed under reduced pressure to give the amine, which was used in the next step without any purification. The amine so formed was dissolved in DMF (2 mL, dry) to which 1-methyl-4-nitro-1H-pyrrole-2-carboxylic acid (57 mg, 0.288 mmol; see Tetrahedron 56, 5225-5239 (2000)), HBTU (218 mg, 0.576 mmol), and NMM (200 μL, dry) were added at room temperature with stirring. The stirring was continued at room temperature overnight. The reaction mixture was diluted with ethyl acetate (50 mL) and extracted with NaHCO3 (25 mL, sat.). The water layer was extracted again with ethyl acetate (50 mL). The combined organic extract was dried over MgSO4, filtered and the solvent was removed under reduced pressure. The crude product obtained was purified by column chromatography using silica gel and 1/2/0.1 methanol/ethyl acetate/TEA. Fractions containing the pure product [RF=0.4] were collected and the solvents were removed under reduced pressure at 50° C. to give the required product as glassy yellow solid (110 mg, 71% yield) with no distinct melting point.
NMR [DMSO-d6]: 10.27(1H, s); 9.94(1H, s); 8.18(1H, d, J=1.7 Hz); 8.06(1H, t, J=5.2 Hz); 7.59(1H, d, J=1.9 Hz); 7.36(1H, d, 1.9 Hz); 7.18(1H, d, J=1.9 Hz); 7.02(1H, d, J=1.9 Hz); 6.83(1H, d, J=1.9 Hz); 4.19(2H, d, J=7.0 Hz); 3.97(3H, s); 3.80(3H, s); 3.21-3.16(2H, q, J=6.9 Hz); 2.26(2H, t, J=7.1 Hz); 2.15(6H, s); 1.65-1.58(2H, quintet, J=7.1 Hz); 1.26-1.13(1H, m); 0.47-0.42(2H, m); 0.33-0.31(2H, m). IR [KBr]: 3286, 3126, 2938, 1646, 1580, 1531, 1462, 1439, 1400, 1309, 1248 cm−1. HRFABMS: Found 539.27295; calculated for C26H35N8O5 539.27304.
(v) N-[1-(Cyclopropylmethyl)-5-({[5-({[3-(dimethylamino)propyl]amino}-carbonyl)-1-methyl-1H-pyrrol-3-yl]amino}carbonyl)-1H-pyrrol-3-yl]-4-(formylamino)-1-methyl-1H-pyrrole-2-carboxamide
N-[1-(Cyclopropylmethyl)-5-({[5-({[3-(dimethylamino)propyl]amino}-carbonyl)-1-methyl-1H-pyrrol-3-yl]amino}carbonyl)-1H-pyrrol-3-yl]-1-methyl-4-nitro-1H-pyrrole-2-carboxamide (100 mg, 0.186 mmol; see step (iv) above) was dissolved in ethanol (25 mL) to which Pd/C-10% (78 mg) was added at 0° C. under N2 with stirring. The reaction mixture was hydrogenated for 3 h at room temperature and atmospheric pressure. The catalyst was removed over Kieselguhr. Ethyl formate was added to the ethanolic solution of the amine and the reaction mixture was heated under reflux for 48 h. Ethanol and excess ethyl formate were removed under reduced pressure and the crude product was purified by HPLC. The product was obtained as pale yellow solid (52 mg, 42% yield) after freeze drying with no distinct melting point.
NMR [DMSO-d6]: 10.04(1H, s); 9.91(1H, s); 9.90(1H, s); 9.28(1H, br, TFA); 8.16-8.13(2H, t&d); 7.31(1H, d, J=1.7 Hz); 7.19(1H, d, J=1.7 Hz); 7.16(1H, d, J=1.7 Hz); 7.05(1H, d, J=1.7 Hz); 6.95(1H, d, 1.7 Hz); 6.93(1H, d, J=1.7 Hz); 4.18(2H, d, J=7.0 Hz); 3.85(3H, s); 3.81(3H, s); 3.26-3.22(2H, q, J=6.3 Hz); 3.07(2H, m); 2.79(2H, d, J=4.3 Hz); 1.87-1.82(2H, quintet, J=6.6 Hz); 1.23(1H, m); 0.47-0.42(2H, m); 0.33-0.29(2H, m). IR[KBr]: 3410, 3294, 1674, 1649, 1582, 1533, 1464, 1438, 1403, 1201, 1132 cm−1. HRFABMS: Found 537.29360; calculated for C27H37N8O4 537.29378.
Example 27
1-Cyclopentyl-N-[5-({[3-(dimethylamino propyl]amino}carbonyl-1-methyl-1H-pyrrol-3-yl]-4-({[4-(formylamino)-1-methyl-1H-pyrrol-2-yl]-carbonyl}amino)-1H-pyrrole-2-carboxamide
(i) Ethyl 1-cyclopentyl-4-nitro-1H-pyrrole-2-carboxylate
Ethyl 4-nitro-1H-pyrrole-2-carboxylate (1.006 g, 5.432 mmol; see Example 1, step (i) above) was dissolved in DMF (20 mL, dry) to which was added potassium metal (0.492 g, 12.582 mmol) then it was heated to 80° C. and then it was left at that temperature for 1 h with stirring. The reaction mixture was cooled to 50-60° C. after which bromocyclopentane (1 mL, 1.390 g, 9.326 mmol) was added followed by KI (1.548 g, 9.326 mmol). The reaction mixture was heated again for 5 h with stirring at 80° C., after which time it was left stirring at room temperature under N2, overnight. The reaction mixture was diluted with brine under N2, at room temperature, and then it was extracted with ethyl acetate (3×100 mL). The combined organic extract was dried over MgSO4, filtered and the solvent removed under reduced pressure to give the crude product (containing some DME). The product was purified using column chromatography [silica gel, 1/10 ethyl acetate/n-hexane (RF=0.24)]. Fractions containing the pure material were collected and the solvent removed to give pale yellow oil (440 mg, 32% yield).
NMR [CDCl3]: 7.77(1H, d, J=2.0 Hz); 7.45(1H, d, J=2.0 Hz); 5.57-5.50(1H, quintet, J=6.6 Hz); 4.33(2H, q, J=7.1 Hz); 2.30-2.24(2H, m); 1.98-1.75(6H, m); 1.37(3H, t, J=7.1 Hz). IR[KBr]: 2965, 2875, 1717, 1534, 1508, 1426, 1335, 1294, 1222, 1187, 1084 cm−1. HRFABMS: Found 253.11824; calculated for C12H17N2O4 253.11883.
(ii) 1-Cyclopentyl-4-nitro-1H-pyrrole-2-carboxylic acid
Ethyl 1-cyclopentyl-4-nitro-1H-pyrrole-2-carboxylate (430 mg, 1.706 mmol; see step (i) above) was dissolved in ethanol (4 mL) to which a solution of NaOH (408 mg, 10.20 mmol) in water (10 mL) was added. The reaction mixture was heated under reflux for 2 h, and then it was cooled to 0° C. Hydrochloric acid (conc.) was added dropwise with stirring until pH 2. The solid was filtered off, washed with water and dried at 45° C. for 48 h to give white solid material (340 mg, 89% yield). Mp 195-198° C.
NMR [DMSO-d6]: 13.13(1H, br); 8.27(1H, d, J=2.0 Hz); 7.29(1H, d, J=2.0 Hz); 5.45(1H, quintet, J=7.1 Hz); 2.16-2.07(2H, m); 1.88-1.78(4H, m); 1.65-1.61(2H, m). IR [KBr]: 3152, 2964, 2880, 1683, 1508, 1430, 1331, 1292, 1078, 911 cm−1. HREIMS: Found 224.07926; calculated for C10H12N2O4 224.07971.
(iii) 1-Cyclopentyl-N-[5-({[3-(dimethylamino)propyl]amino}carbonyl)-1-methyl-1H-pyrrol-3-yl]-4-nitro-1H-pyrrole-2-carboxamide
N-[3-(Dimethylamino)propyl]-1-methyl-4-nitro-1H-pyrrole-2-carboxamide (100 mg, 0.393 mmol; see Tetrahedron 56, 5225-5239 (2000)) was dissolved in methanol (25 mL) to which Pd/C-10% (90 mg) was added at 0° C. under N2 with stirring. The reaction mixture was hydrogenated for 3 h at room temperature and atmospheric pressure. The catalyst was removed over Kieselguhr and the solvent was removed under reduced pressure. The amine so formed was dissolved in DMF (2 mL, dry) to which 1-(cyclopentyl-4-nitro-1H-pyrrole-2-carboxylic acid (88 mg, 0.393 mmol; see step (ii) above) was added followed by HBTU (298 mg, 0.786 mmol) and NMM (200 μL, dry) with stirring at room temperature. The reaction mixture was diluted with ethyl acetate (50 mL) and extracted with NaHCO3(sat.) (25 mL). The water layer was extracted again with ethyl acetate (50 mL). The combined organic extract was dried over MgSO4, filtered and the solvent removed under reduced pressure to give the crude product which was purified by column chromatography using silica gel and 1/2/0.1 methanol/ethyl acetate/TEA. The product was obtained as yellow oil RF=0.45 (157 mg, 93% yield).
NMR [DMSO-d6]: 10.27(1H, s); 8.24(1H, d, J=1.7 Hz); 8.11(1H, t, J=5.2 Hz); 7.47(1H, s); 7.20(1H, d, J=1.7 Hz); 6.83(1H, d, J=1.7 Hz); 5.48(1H, quintet, J=7.4 Hz); 3.80(3H, s); 3.18(2H, q, J=6.6 Hz); 2.66(2H, m); 2.30(2H, t, J=7.1 Hz); 2.14(6H, s); 2.12(2H, m); 1.82(4H, m); 1.62(2H, quintet, J=7.1 Hz). IR [KBr]: 1644, 1575, 1534, 1504, 1437, 1401, 1313, 1287, 748 cm1. HRFABMS: Found 431.24204; calculated for C21H31N6O4 431.24068.
(iv) 1-Cyclopentyl-N-[5-({[3-(dimethylamino)propyl]amino}carbonyl)-1-methyl-1H-pyrrol-3-yl]-4-{[(1-methyl-4-nitro-1H-pyrrol-2-yl)carbonyl]-amino}-1H-pyrrole-2-carboxamide
1-Cyclopentyl-N-[5-({[3-(dimethylamino)propyl]amino}carbonyl)-1-methyl-1H-pyrrol-3-yl]-4-nitro-1H-pyrrole-2-carboxamide (157 mg, 0.365 mmol; see step (iii) above) was dissolved in methanol (25 mL) at 0° C. under N2 with stirring, to which Pd/C-10% (80 mg) was added. The reaction mixture was hydrogenated for 2 h at room temperature and atmospheric pressure. The catalyst was removed over Kieselguhr and the solvent was removed under reduced pressure. The amine so formed was dissolved in DMF (2 mL, dry) to which 1-methyl-4-nitro-1H-pyrrole-2-carboxylic acid (62 mg, 0.365 mmol; see Tetrahedron 56, 5225-5239 (2000)), HBTU (277 mg, 0.730 mmol) and NMM (200 μL, dry) were added with stirring at room temperature. The stirring was continued overnight. The reaction mixture was diluted with ethyl acetate (50 mL) and extracted with NaHCO3(sat) (25 mL). The water layer was extracted again with ethyl acetate (50 mL). The combined organic extract was dried over MgSO4, filtered and the solvent removed under reduced pressure to give the crude product, which was purified by column chromatography using silica gel and 1/2/0.1 methanol/ethyl acetate/TEA, RF=0.40. The product was obtained as glassy solid material with no distinct melting point (110 mg, 55% yield).
NMR [DMSO-d6]: 10.28(1H, s); 9.96(1H, s); 8.18(1H, d, J=1.8 Hz); 8.07(1H, t, J=5.2 Hz); 7.58(1H, d, J=1.8 Hz); 7.41(1H, d, J=1.8 Hz); 7.18(1H, d, J=1.8 Hz); 6.93(1H, d, J=1.8 Hz); 6.85(1H, d, J=1.8 Hz); 5.53(1H, quintet, J=7.3 Hz); 3.97(3H, s); 3.80(3H, s); 3.20(2H, m); 2.83(2H, m); 2.42(2H, t, J=7.2 Hz); 2.27(6H, s); 2.09(2H, m); 1.79-1.64(6H, m). IR [KBr]: 1642, 1584, 1529, 1505, 1403, 1309 cm−1. HRFABMS: Found 553.28890; calculated for C27H37N8O5 553.28869.
(v) 1-Cyclopentyl-N-[5-({[3-(dimethylamino)propyl]amino}carbonyl)-1-methyl-1H-pyrrol-3-yl]-4-({[4-(formylamino)-1-methyl-1H-pyrrol-2-yl]-carbonyl}amino)-1H-pyrrole-2-carboxamide
1-Cyclopentyl-N-[5-({[3-(dimethylamino)propyl]amino}carbonyl)-1-methyl-1H-pyrrol-3-yl]-4-{[(1-methyl-4-nitro-1H-pyrrol-2-yl)carbonyl]-amino}-1H-pyrrole-2-carboxamide (100 mg, 0.181 mmol; see step (iv) above) was dissolved in ethanol (20 mL) at 0° C. under N2 with stirring, to which Pd/C-10% (92 mg) was added. The reaction mixture was hydrogenated at room temperature and atmospheric pressure for 3 h. The catalyst was removed over Kieselguhr and ethyl formate (25 mL) was added to the ethanolic solution. The reaction mixture was heated under reflux for 24 h. The solvent was removed under reduced pressure to give the crude product, which was purified by HPLC. Fractions containing the required material were collected and freeze dried to give the product as pale yellow solid (21 mg, 18% yield) with no distinct melting point.
NMR [DMSO-d6]: 10.06(1H, s); 9.95(1H, s); 9.91(1H, s); 9.21(1H, br, TFA); 8.14(1H, t, J=6.0 Hz); 8.13(1H, d, J=1.7 Hz); 7.36(1H, d, J=1.7 Hz); 7.19(1H, d, J=1.7 Hz); 7.17(1H, d, J=1.7 Hz); 6.97(1H, d, J=1.7 Hz); 6.95(1H, d, J=1.7 Hz); 6.92(1H, d, J=1.7 Hz); 5.52(1H, quintet, J=7.5 Hz); 3.84(3H, s); 3.81(3H, s); 3.24(2H, m); 3.06(2H, m); 2.79(6H, d, J=3.3 Hz); 2.08(2H, m); 1.83(4H, m); 1.64(4H, m). IR [KBr]: 1674, 1647, 1582, 1536, 1463, 1440, 1406, 1201, 1131 cm−1. HRFABMS: Found 551.30950; calculated for C28H39N8O4 551.30943.
Example 28
N2,N7-Bis[5-({[4-({[3-(dimethylamino)propyl]amino}carbonyl)-5-isopropyl-1,3-thiazol-2-yl]amino}carbonyl)-1-methyl-1H-pyrrol-3-yl]-9,10-dihydro-2,7-phenanthrenedicarboxamide
N-[3-(Dimethylamino)propyl]-5-isopropyl-2-{[(1-methyl-4-nitro-1H-pyrrol-2-yl)carbonyl]amino}-1,3-thiazole-4-carboxamide (170 mg, 0.402 mmol; see Example 3, step (iv) above) was suspended in methanol (25 mL) at 0° C. under N2 with stirring, to which Pd/C-10% (104 mg) was added. The reaction mixture was hydrogenated for 6 h at room temperature and atmospheric pressure. The catalyst was removed over Kieselguhr and the solvent was removed under reduced pressure. The amine so formed was dissolved in DMF (2 mL, dry), to which 9,10-dihydro-2,7-phenanthrene-dicarboxylic acid (54 mg, 0.201 mmol; see Tetrahedron 56, 5225-5239 (2000)), HBTU (610 mg, 1.608 mmol) and NMM (200 mL, dry) were added at room temperature with stirring. The reaction mixture was stirred overnight at room temperature. The reaction mixture was diluted with ethyl acetate containing 5% methanol and NaHCO3(sat). The organic layer was dried over MgSO4, filtered and the solvent removed under reduced pressure to give the crude product, which was purified by HPLC. Fractions containing the required material were collected and freeze dried to give pale yellow solid with distinct melting point (46.3 mg, 19% yield).
NMR [DMSO-d6]: 12.11(2H, s); 10.46(2H, s); 9.26(2H, br, TFA); 8.07-7.91(6H, m); 7.53(2H, s); 7.46(2H, s); 4.20(2H, quintet, J=6.9 Hz); 3.92(6H, s); 3.33(4H, m); 3.07(4H, m); 2.97(2H, s); 2.96(2H, s); 2.80(12H, d, J=4.1 Hz); 1.87(4H, quintet, J=7.7 Hz); 1.27(12H, d, J=6.9 Hz). IR [KBr]: 1660, 1548, 1468, 1284, 1199, 1132, 832, 800, 721 cm−1. LRESMS: Found M+H=1017.4; [M+2]/2=509.5; calculated for C52H66N12O6S2 M+H=1017.4; [M+2H]/2=509.3.
Example 29
4-(Formylamino)-N-[1-isopentyl-5-({[1-methyl-5-({[3-(4-methyl-1-piperazinyl)propyl]amino}carbonyl)-1H-pyrrol-3-yl]amino}carbonyl)-1H-pyrrol-3-yl]-1-methyl-1H-pyrrole-2-carboxamide
(i) 1-Isopentyl-N-[1-methyl-5-({[3-(4-methyl-1-piperazinyl)propyl]amino}-carbonyl)-1H-pyrrol-3-yl]-4-nitro-1H-pyrrole-2-carboxamide
1-Methyl-N-[3-(4-methyl-1-piperazinyl)propyl]-4-nitro-1H-pyrrole-2-carboxamide (209 mg, 0.676 mmol; see Tetrahedron 56, 5225-5239 (2000)) was dissolved in methanol (25 mL) to which Pd/C-10% (182 mg) was added at 0° C. under N2 with stirring. The reaction mixture was hydrogenated for 3 h at room temperature and atmospheric pressure. The catalyst was removed over Kieselguhr and the solvent was removed under reduced pressure to give the amine, which was used without further purification. 1-Isopentyl-4-nitro-1H-pyrrole-2-carboxylic acid (153 mg, 0.676 mmol; prepared according to the procedure described in Soviet Journal of Bioorganic Chemistry (English Translation) 4, 780-790 (1978)) was dissolved in thionyl chloride 4 mL and heated under reflux for 3 h. Excess thionyl chloride was removed under pressure at 50° C. and the acid chloride was dissolved in DCM (5 mL). The amine was dissolved in DCM (10 mL) to which NMM (200 μL) was added followed by the acid chloride at room temperature with stirring. The stirring was continued at room temperature overnight. KOH 10% (5 mL) was added and the mixture was extracted. The organic layer was collected, dried over MgSO4, filtered and the solvent was removed under reduced pressure to give the crude product, which was purified by column chromatography using silica gel and 1/2/0.1 methanol/ethyl acetate/TEA. The product was obtained as glassy yellow material (RF=0.45), (278 mg, 84% yield) with no distinct melting point.
NMR [DMSO-d6]: 10.21(1H, s); 8.23(1H, d, J=1.8 Hz); 8.05(1H, t, J=5.4 Hz); 7.54(1H, d, J=1.8 Hz); 7.18(1H, d, J=1.8 Hz); 6.82(1H, d, J=1.8 Hz); 4.43(2H, t, J=7.4 Hz); 3.81(3H, s); 3.21-3.16(2H, q, J=6.6 Hz); 2.32-2.28(10H, m); 2.15(3H, s); 1.66-1.59(4H, quintet, J=6.7 Hz); 1.55-1.47(1H, m); 0.90(6H, d, J=6.5 Hz). IR [KBr]: 2951, 2805, 1642, 1575, 1532, 1506, 1437, 1312 cm−1. HRFABMS: Found 488.29707; calculated for C24H38N7O4 488.29853.
(ii) N-[1-Isopentyl-5-({[1-methyl-5-({[3-(4-methyl-1-piperazinyl)propyl]-amino}carbonyl)-1H-pyrrol-3-yl]amino}carbonyl)-1H-pyrrol-3-yl]-1-methyl-4-nitro-1H-pyrrole-2-carboxamide
1-Isopentyl-N-[1-methyl-5-({[3-(4-methyl-1-piperazinyl)propyl]amino}-carbonyl)-1H-pyrrol-3-yl]-4-nitro-1H-pyrrole-2-carboxamide (140 mg, 0.287 mmol; see step (i) above) was dissolved in methanol (25 mL) to which Pd/C-10% (100 mg) was added at 0° C. under N2 with stirring. The reaction mixture was hydrogenated at room temperature and atmospheric pressure for 3 h. The catalyst was removed over Kieselguhr and the solvent was removed under reduced pressure. 1-Methyl-4-nitro-1H-pyrrole-2-carboxylic acid (49 mg, 0.287 mmol; see Tetrahedron 56, 5225-5239 (2000)) was dissolved in thionyl chloride (4 mL) and the reaction mixture was heated under reflux for 3 h. Excess thionyl chloride was removed under reduced pressure to give the acid chloride, which was dissolved in DCM (5 mL). The amine was dissolved in DCM (10 mL) to which NMM (0.1 mL) was added at room temperature with stirring followed by the acid chloride solution. The stirring was continued overnight at room temperature. KOH (5 mL, 10%) was added and the reaction mixture was extracted, and the organic layer collected, dried over MgSO4, filtered and the solvent removed under reduced pressure. Column chromatography (silica gel, 1/2/0.1 methanol/ethyl acetate/TEA) was used to purify the required material, which was obtained as yellow glassy material (131 gm, 75% yield), RF=0.15 with no distinct melting point.
NMR [DMSO-d6]: 10.27(1H, s); 9.90(1H, s); 8.18(1H, d, J=1.8 Hz); 8.01(1H, t, J=5.6 Hz); 7.59(1H, d, J=1.8 Hz); 7.31(1H, d, J=1.8 Hz); 7.16(1H, d, J=1.8 Hz); 6.98(1H, J=1.8 Hz); 6.84(1H, d, J=1.8 Hz); 4.33(1H, t, J=6.9 Hz); 3.96(3H, s); 3.79(3H, s); 3.17(2H, q, J=6.5 Hz); 2.32-2.29(10 mH, m); 2.16(3H, s); 1.66-1.46(5H, m); 0.89(6H, d, J=6.4 Hz). IR [KBr]: 2949, 2803, 1650, 1588, 1531, 1506, 1399, 1309 cm−1. HRFABMS: Found 610.34797; calculated for C30H44N9O5 610.34654.
(iii) 4-(Formylamino)-N-[1-isopentyl-5-({[1-methyl-5-({[3-(4-methyl-1-piperazinyl)propyl]amino}carbonyl)-1H-pyrrol-3-yl]amino}carbonyl)-1H-pyrrol-3-yl]-1-methyl-1H-pyrrole-2-carboxamide
N-[1-Isopentyl-5-({[1-methyl-5-({[3-(4-methyl-1-piperazinyl)propyl]-amino}carbonyl)-1H-pyrrol-3-yl]amino}carbonyl)-1H-pyrrol-3-yl]-1-methyl-4-nitro-1H-pyrrole-2-carboxamide (120 mg, 0.197 mmol; see step (ii) above) was dissolved in ethanol (20 mL) to which Pd/C-10% (77 mg) was added at 0° C. under N2 with stirring. The reaction mixture was hydrogenated for 3 h at room temperature and atmospheric pressure. The catalyst was removed over Kieselguhr and ethyl formate (20 mL) was added to the ethanolic solution. The reaction mixture was heated under reflux for 48 h. Ethanol and excess ethyl formate were removed under reduced pressure and the crude product was purified by HPLC. The product was obtained as yellow solid with no distinct melting point (75 mg, 53% yield) after freeze-drying.
NMR [DMSO-d6]: 10.03(1H, s); 9.89(1H, s); 9.87(1H, s); 8.13(1H, d, J=1.6 Hz); 8.09(1H, t, J=5.6 Hz); 7.26(1H, d, J=1.6 Hz); 7.18(1H, d, J=1.6 Hz); 7.14(1H, d, J=1.6 Hz); 7.01(1H, d, J=1.6 Hz); 6.92(1H, d, J=1.6 Hz); 6.91(1H, d, J=1.6 Hz); 4.31(2H, t, J=6.9 Hz); 3.83(3H, s); 3.81(3H, s); 3.23(2H, q, J=6.5 Hz); 3.10-2.72(8H, br & 3H, s); 1.77(2H, s, br); 1.58-1.46(3H, m); 0.90(6H, d, J=6.4 Hz). IR[KBr]: 1675, 1584, 1535, 1403, 1199, 1132 cm−1. HRFABMS: Found 608.36634; calculated for C31H46N9O4 608.36728.
Example 30
4-(Acetylamino)-N-[1-isopentyl-5-({[1-methyl-5-({[3-(4-morpholinyl)-propyl]amino}carbonyl)-1H-pyrrol-3-yl]amino}carbonyl)-1H-pyrrol-3-yl]-1-methyl-1H-pyrrole-2-carboxamide
(i) 1-Isopentyl-N-[1-methyl-5-({[3-(4-morpholinyl)propyl]amino}-carbonyl)-1H-pyrrol-3-yl]-4-nitro-1H-pyrrole-2-carboxamide
1-Methyl-N-[3-(4-morpholinyl)propyl]-4-nitro-1H-pyrrole-2-carboxamide (500 mg, 1.688 mmol; see Tetrahedron 56, 5225-5239 (2000)) was dissolved in methanol (25 mL) at 0° C. under N2 with stirring to which was added Pd/C-10% (272 mg). The reaction mixture was hydrogenated for 4 h. The catalyst was removed over Kieselguhr and the solvent was removed under reduced pressure. The amine so formed was dissolved in DCM (10 mL). 1-Isopentyl-4-nitro-1H-pyrrole-2-carboxylic acid (445 mg, 1.966 mmol; prepared according to the procedure described in Soviet Journal of Bioorganic Chemistry (English Translation) 4, 780-790 (1978)) was dissolved in thionyl chloride (5 mL) and the reaction mixture was heated under reflux for 4 h. Excess thionyl chloride was removed under reduced pressure and the acid chloride was dissolved in DCM (10 mL). NMM (0.2 mL) was added to the amine solution followed by the acid chloride solution at room temperature with stirring. The stirring was continued at room temperature overnight. DCM was removed under reduced pressure and the crude product was purified by column chromatography using silica gel and 1/2/0.1 methanol/ethyl acetate/TEA. Fractions containing the pure material (RF=0.45) were collected and the solvents removed under reduced pressure to give yellow glassy material, which was dissolved in small amount of ethyl acetate and precipitated with n-hexane to give the required product as yellow powder (670 mg, 79% yield), m.p. 155-158° C.
NMR [CDCl3]: 7.64(1H, d, J=1.7 Hz); 7.60(1H, s); 7.22(1H, unresolved triplet); 7.18(1H, d, J=1.7 Hz); 7.07(1H, d, J=1.7 Hz); 6.66(1H, d, J=1.6 Hz); 4.43(2H, t, J=7.5 Hz); 3.93(3H, s); 3.77(2H, t, J=4.6 Hz); 3.49(2H, q, J=5.6 Hz); 2.52(6H, m); 1.80-1.58(5H, m); 0.97(6H, d, J=6.5 Hz). IR[KBr]: 1647, 1589, 1513, 1399, 1309, 1252, 1114 cm−1. HRFABMS: Found 475.26789; calculated for C23H35N6O5 475.26689.
(ii) N-[1-Isopentyl-5-({[1-methyl-5-({[3-(4-morpholinyl)propyl]amino}-carbonyl)-1H-pyrrol-3-yl]amino}carbonyl)-1H-pyrrol-3-yl]-1-methyl-4-nitro-1H-pyrrole-2-carboxamide
1-Isopentyl-N-[1-methyl-5-({[3-(4-morpholinyl)propyl]amino}carbonyl)-1H-pyrrol-3-yl]-4-nitro-1H-pyrrole-2-carboxamide (136 mg, 0.286 mmol; see step (i) above) was dissolved in methanol (25 mL) at 0° C. under N2 with stirring to which was added Pd/C-10% (98 mg). The reaction mixture was hydrogenated at room temperature and atmospheric pressure for 2 h. The catalyst was removed over Kieselguhr and the solvent was removed under reduced pressure. The amine so formed was dissolved in DCM (5 mL). 1-Methyl-4-nitro-1H-pyrrole-2-carboxylic acid (48 mg, 0.282 mmol; see Tetrahedron 56, 5225-5239 (2000)) was dissolved in thionyl chloride (3 mL) and heated until reflux for 2 h. Excess thionyl chloride was removed under reduced pressure and the acid chloride so formed was dissolved in DCM (5 mL) and then added dropwise to the amine solution with stirring at room temperature. The stirring was continued overnight. The solvent was removed and the crude product was purified by column chromatography (1/2/0.1 methanol/ethyl acetate/TEA, RF=0.7). Fractions containing the required material were collected and the solvents were removed under reduced pressure. The yellow glassy material was dissolved in DCM (25 mL) and extracted with KOH (10%, 5 mL). The organic layer was collected, dried over MgSO4, filtered and the solvent removed under reduced pressure to give yellow glassy material (115 mg, 67% yield) with no distinct melting point.
NMR [Acetone-d6]: 9.52(1H, s); 9.26(1H, s); 7.95(1H, d, J=1.7 Hz); 7.55(1H, t, unresolved); 7.38(1H, d, J=1.9 Hz); 7.33(1H, d, J=1.9 Hz); 7.20(1H, d, J=1.9 Hz); 6.91(1H, d, J=1.9 Hz); 6.84(1H, d, J=1.9 Hz); 4.44(2H, t, J=7.2 Hz); 4.08(3H, s); 3.89(3H, s); 3.64(4H, m); 3.37(2H, t, J=6.7 Hz); 2.42(6H, m); 1.77-1.56(5H, m); 0.95(6H, d, J=6.5 Hz). IR [KBr]: 1640, 1588, 1524, 1464, 1399, 1310, 1252, 1114 cm−1. HRFABMS: 597.31332; calculated for C29H41N8O6 597.31491.
(iii) 4-(Acetylamino)-N-[1-isopentyl-5-({[1-methyl-5-({[3-(4-morpholinyl)-propyl]amino}carbonyl)-1H-pyrrol-3-yl]amino}carbonyl)-1H-pyrrol-3-yl]-1-methyl-1H-pyrrole-2-carboxamide
N-[1-Isopentyl-5-({[1-methyl-5-({[3-(4-morpholinyl)propyl]amino}-carbonyl)-1H-pyrrol-3-yl]amino}carbonyl)-1H-pyrrol-3-yl]-1-methyl-4-nitro-1H-pyrrole-2-carboxamide (115 mg, 0.193 mmol; see step (ii) above) was dissolved in ethanol (20 mL) to which was added Pd/C-10% (104 mg) at 0° C. under N2 with stirring. The reaction mixture was hydrogenated for 3 h at room temperature and atmospheric pressure. The catalyst was removed over Kieselguhr and the ethanolic solution was divided into two equal volumes (i.e. 10 mL). Ethanol was removed from one of the fractions under reduced pressure and DCM (2 mL) was added to the amine with stirring. NMM (0.1 mL) was added followed by acetyl chloride (0.01 mL) at room temperature with stirring. The stirring was continued overnight. All volatile materials were removed under reduced pressure and the crude product was purified by HPLC. Fractions containing the required material were collected and freeze-dried to give white solid material (25.7 mg, 35% yield) as TFA salt with no distinct melting point.
NMR [DMSO-d6]: 9.87(2H, s); 9.79(1H, s); 9.55(1H, br, TFA); 8.16(1H, t, unresolved); 7.26(1H, d, J=1.8 Hz); 7.15(1H, d, J=1.8 Hz); 7.13(1H, d, J=1.8 Hz); 7.01(1H, d, J=1.8 Hz); 6.94(1H, d, J=1.8 Hz); 6.87(1H, d, J=1.8 Hz); 4.31(2H, t, J=6.9 Hz, isopentyl); 4.00(2H, d, J=12.4 Hz, morpho); 3.83(3H, s); 3.81(3H, s); 3.64(2H, t, J=12.0 Hz, morpho); 3.45(2H, d, J=12.0 Hz, morpho); 3.24(2H, q, J=6.2 Hz); 3.12-3.06(2H, m, side chain & 2H morpho); 1.97(3H, s); 1.87(2H, m, isopentyl); 1.58-1.48(2H, m, side chain & 1H isopentyl); 0.90(6H, d, J=6.4 Hz, isopentyl). IR [KBr]: 2925, 2858, 1655, 1583, 1526, 1465, 1400, 1260, 1200, 1131 cm−1. HRFABMS: Found 609.34957; calculated for C31H45N8O5 609.35129.
Example 31
4-(Formylamino)-N-[1-isopentyl-5-({[1-methyl-5-({[3-(4-morpholinyl)-propyl]amino}carbonyl)-1H-pyrrol-3-yl]amino}carbonyl)-1H-pyrrol-3-yl]-1-meth-1H-pyrrole-2-carboxamide
To the second half of the amine solution (10 mL) (see Example 30, step (iii) above), ethyl formate was added (10 mL) and the reaction mixture was heated under reflux for 48 h. Volatile solvents were removed under reduced pressure and the crude product was purified by HPLC. Fractions containing the required material were collected and freeze-dried to give white solid material (22.7 mg, 32% yield) as TFA salt with no distinct melting point.
NMR [DMSO-d6]: 10.03(1H, s); 9.89(1H, s); 9.87(1H, s); 9.56(1H, br, TFA); 8.16(1H, t, unresolved); 8.12(1H, d, J=1.7 Hz); 7.26(1H, d, J=1.7 Hz); 7.18(1H, d, J=1.7 Hz); 7.15(1H, d, J=1.7 Hz); 7.02(1H, d, J=1.7 Hz); 6.93(1H, d, J=1.7 Hz); 6.92(1H, d, J=1.7 Hz); 4.31(2H, t, J=7.1 Hz); 4.00(2H, d, J=11.8 Hz); 3.84(3H, s); 3.81(3H, s); 3.64(2H, t, J=11.9 Hz); 3.46(2H, d, J=12.8 Hz); 3.26(2H, q, J=6.1 Hz); 3.12-3.06(4H, m); 1.87(2H, m); 1.58-1.46(3H, m); 0.90(6H, d, J=6.3 Hz). IR [KBr]: 1682, 1640, 1584, 1529, 1403, 1263, 1202, 1132, 803 cm−1. HRFABMS: Found 595.33717; calculated for C30H43N8O5 595.33564.
Example 32
N-[5-({[5-({[3-(Dimethylamino)propyl]amino}carbonyl)-1-methyl-1H-pyrrol-3-yl]amino}carbonyl)-1-isopentyl-1H-pyrrol-3-yl]-4-[(3-methoxybenzoyl)amino]-1-methyl-1H-pyrrole-2-carboxamide
N-[5-({[5-({[3-(Dimethylamino)propyl]amino}carbonyl)-1-methyl-1H-pyrrol-3-yl]amino}carbonyl)-1-isopentyl-1H-pyrrol-3-yl]-1-methyl-4-nitro-1H-pyrrole-2-carboxamide (260 mg, 0.469 mmol; see Example 10, step (ii) above) was dissolved in methanol (25 mL) to which Pd/C-10% (132 mg) was added at 0° C. under N2 with stirring. The reaction mixture was hydrogenated for 3 h. The catalyst was removed over Kieselguhr and the solvent was removed under reduced pressure to give the amine, which was dissolved in DCM (5 mL). This solution was divided to two each (2.5 mL). m-Anisoyl chloride (50 mg, 0.293 mmol) was added dropwise at room temperature with stirring. The stirring was continued overnight. The solvent was removed under reduced pressure and the residue was dissolved in acetonitrile containing (0.1% TFA) and purified by HPLC. Fractions containing the required material were collected and freeze-dried to give the product as light pink solid with no distinct melting point (72.3 mg, 40% yield).
NMR [DMSO-d6]: 10.29(1H, s); 9.96(1H, s); 9.89(1H, s); 9.27(1H, br, TFA); 8.15(1H, t, J=5.6 Hz); 7.53-7.37(3H, m); 7.32(1H, d, J=1.6 Hz); 7.29(1H, d, J=1.6 Hz); 7.16(1H, d, J=1.6 Hz); 7.14-7.10(2H, m); 7.02(1H, d, J=1.6 Hz); 6.93(1H, d, J=1.6 Hz); 4.32(1H, t, J=6.9 Hz); 3.88(3H, s); 3.83(3H, s); 3.82(3H, s); 3.25(2H, q, J=6.2 Hz); 3.07(2H, m); 2.79(6H, d, J=4.5 Hz); 1.84(2H, quintet, J=7.3 Hz); 1.59-1.47(3H, m); 0.90(6H, d, J=6.3 Hz). IR [KBr]: 1644, 1583, 1533, 1464, 1436, 1402, 1260, 1200, 801, 778 cm−1. HRFABMS: Found 659.36784; calculated for C35H47N8O5 659.36694.
Example 33
N-[5-({[5-({[3-(Dimethylamino)propyl]amino}carbonyl)-1-methyl-1H-pyrrol-3-yl]amino}carbonyl)-1-isopentyl-1H-pyrrol-3-yl]-4-{[(4-methoxy-phenyl)acetyl]amino}-1-methyl-1H-pyrrole-2-carboxamide
The second half of the amine (see Example 32 above) was used in this experiment. To the amine (2.5 mL) in DCM was added (4-methoxy-phenyl)acetyl chloride (50 mg, 0.270 mmol) at room temperature, dropwise with stirring. The stirring was continued overnight. The solvent was removed under reduced pressure and the crude product so formed was purified by HPLC. Fractions containing the required material were collected and freeze-dried to give white solid material (51 mg, 28% yield) with no distinct melting point.
NMR [Acetone-d6]: 12.15(1H, br); 9.18(1H, s); 9.11(1H, s); 9.05(1H, s); 7.67(1H, t, unresolved); 7.29-7.24(4H, m); 7.13(1H, d, J=1.7 Hz); 6.89-6.85(4H, m); 6.78(1H, d, J=1.7 Hz); 4.41(2H, t, J=6.5 Hz); 3.90(6H, s); 3.77(3H, s); 3.58(2H, s); 3.45(2H, q, J=6.1 Hz); 3.26(2H, t, J=6.1 Hz); 2.93(6H, s); 1.69-1.56(3H, m); 0.95(6H, d, J=6.6 Hz). IR [KBr]: 1650, 1588, 1515, 1465, 1402, 1251, 1203, 1133, 826, 779 cm−1. HRFABMS: Found 673.38492; calculated for C3H19N8O5 673.38259.
Example 34
Compounds of the examples were found to bind to the minor groove of DNA, as determined by the capillary electrophoresis and/or DNA footprinting methods described hereinbefore.
Example 35
Experiments that probe the binding of compounds to DNA by using n.m.r. methods are well known to those skilled in the art (see, for example: (a) J. Bunkenborg, C. Behrens, J. P. Jacobsen “NMR characterization of the DNA binding properties of a novel Hoechst 33258 analogue peptide building block” Bioconjugate Chemistry 13(5), 927-936 (2002); (b) G. A Morris, K. T. Douglas “Binding of a porphyrin conjugate of Hoechst 33258 to DNA. II. NMR spectroscopic studies detect multiple binding modes to a 12-mer nonself-complementary duplex DNA” Nucleosides Nucleotides & Nucleic Acids 20(1-2), 145-156 (2001); and (c) X. G. Han, X. L. Gao “Sequence specific recognition of ligand-DNA complexes studied by NMR” Current Medicinal Chemistry 8(5) 551-581 (2001)).
Compounds of the examples were found to bind to the minor groove of DNA, as determined by experiments in which the compounds were mixed under standard conditions with DNA duplexes (e.g. d(CGACTAGTCG)2) and binding was confirmed by changes observed in the n.m.r. spectra of the compound and the DNA duplex, as well as by nOe measurements on the complex formed between the compound and the DNA duplex. Narrow lines and strong cross-peaks were observed for the complex formed between the compound of Example 3 and d(CGACTAGTCG)2, which is consistent with the compound of Example 3 binding with high affinity.
Example 36
Compounds of the examples were found to bind to DNA, as determined by melting temperature (Tm) measurements. Tm measurements are well known in the art as a method for investigating the stability of a DNA duplex (see V. A Bloomfield, D. M. Crothers and I. Tenneco “Nucleic Acids: Structures, Properties and Functions ” University Science Books, Sausalito, Calif. (2000), and in particular pages 176-180 and 561-564 of that book). If a ligand stabilises the duplex, an increase in Tm is recorded. Compounds of the examples demonstrated large increases in Tm for DNA duplexes. For example, when the DNA used was a duplex of AAATTATATTAT, the compounds of Examples 2, 10 and 26 gave an increase in melting point of greater than 10° C.
Example 37
Compounds of the examples were found to inhibit the growth of microorganisms, for example as indicated in Tables A to G below.









TABLE A






MIC (μM)
MIC (μM)



Organism:
Organism:


Example No.
S. aureus
E. coli

















 7
4.8
>152.4


17
19.4
>77.7


28
80
>80.3


 3
4.7
>152.3


Antibiotic control
0.49
2.0


Amoxicillin


















TABLE B






MIC (μM)
MIC (μM)



Organism:
Organism:


Example No.
S. faecalis
P. vulgaris

















 7
9.5
152.4


17
77.7
77.7


28
10.0
>80.3


 3
9.5
152.2


Antibiotic control
0.49
8.1


Amoxicillin



















TABLE C








MIC (μM)



Example No.
Organism: MRSA



















 7
19.1



17
>77.7



28
10.0



 3
38.1



Antibiotic control
16.1



Amoxicillin



















TABLE D






MIC (μM)
MIC (μM)



Organism:
Organism:


Example No.
Aspergillus niger
Candida albicans

















 7
38.1
38.1


17
>77.7
>77.7


28
>80.3
>80.3


 3
76.1
76.1


Anti fungal control
>326.6
81.6


Fluconazole


















TABLE E






MIC (μM)
MIC (μM)



Organism: Klebs.
Organism:


Example No.
aerogenes
Ent. cloacae

















 7
38.1
9.5


17
38.9
>77.7


28
>80.3
>80.3


 3
76.2
76.2


Control
32.3
4.0


Amoxicillin



















TABLE F








MIC (μM)




Organism:



Example No.
Mycobacterium fortuitum



















 7
19.0



17
>77.7



28
40.1



 3
19.0



Control
21.5



Streptomycin




















TABLE G








MIC (μM)



Example
Organism:



No.
Aspergillus nidulans



















 7
9.5



17
77.7



28
20.1



 3
38.1



Control
40.8



Fluconazole










Abbreviations

    br=broad (in relation to NMR)
    CE=capillary electrophoresis
    d=doublet (in relation to NMR)
    DCM=dichloromethane
    DMF=N,N-dimethylformamide
    DMSO=dimethylsulfoxide
    eq.=equivalents
    h=hour(s)
    HBTU=O-benzotriazol-1-yl-N,N,N′,N′-tetramethyluronium hexafluorophosphate
    HCl=hydrochloric acid
    HOBT=1-hydroxybenzotriazole
    HPLC=high performance liquid chromatography
    HREIMS=high resolution electron ionisation mass spectrometry
    HRFABMS=high resolution fast atom bombardment mass spectrometry
    IR=infra red (in relation to spectroscopy)
    LRESMS=low resolution electrospray mass spectrometry
    m=multiplet (in relation to NMR)
    Me=methyl
    mi.=minute(s)
    m.p.=melting point
    MS=mass spectroscopy
    νmax=wave number (in relation to infra red spectroscopy)
    NMM=N-methylmorpholine
    Pd/C=palladium on carbon
    q=quartet (in relation to NMR)
    s=singlet (in relation to NMR)
    t=triplet (in relation to NMR)
    TEA=triethylamine
    THF=tetrahydrofuran
    TFA=trifluoroacetic acid


Prefixes n-, s-, i-, t- and tert- have their usual meanings: normal, secondary, iso, and tertiary.

## Claims

1. A compound of formula I,




wherein
R1 represents Het1, R1aC(O)— or D-A-N(H)-[Q]n-C(O)-E-C(O)—;
R1a represents:
H,
aryl optionally substituted by one or more substituents selected from the group consisting of OH, halo, cyano, nitro, N(R3a)R3b, C1-4 alkyl and C1-4 alkoxy),
aromatic or part-aromatic C13-14 tricyclic carbocyclyl optionally substituted by one or more substituents selected from the group consisting of OH, halo, cyano, nitro, N(R3a)R3b,C1-4 alkyl and C1-4 alkoxy, and when the C13-14 tricyclic carbocyclyl is part-aromatic, a non-aromatic part of the C13-14 tricyclic carbocyclyl is optionally substituted by one or two oxo groups or
C1-12 alkyl optionally substituted and/or terminated by one or more substituents selected from the group consisting of halo and aryl, wherein the aryl is optionally substituted by one or more substituents selected from the group consisting of OH, halo, cyano, nitro, N(R3a)R3b, C1-4 alkyl and C1-4 alkoxy;

A represents C2-6 alkylene or A1-C(O)N(H)-A2, wherein A2 is attached to D;
A1 represents C1-4 alkylene;
A2 represents C2-5 alkylene;
D represents —N(R2a)R2b, —C(═NR2c)N(R2d)R2e or —N(R2f)C(═NR2g)N(H)R2h;
R2a and R2b independently represent H, C1-6 alkyl, Het2 or R2a and R2b together represent (CH2)3-6, wherein the (CH2)3-6 is optionally interrupted by NR4 and/or is optionally substituted by one or more C1-4 alkyl groups;
R4 represents H, C1-6 alkyl or Het3;
R2c to R2h independently represent H or C1-6 alkyl;
E represents -E1-Het4-, E2a, —(CH2)0-3N(H)C(O)-E2b-C(O)N(H)(CH2)0-3— or is represented by the formula




E3 represents (CH2)1-2, CH═CH, CH═N, CH2—N(Ra), (CH2)0-1C(O), (CH2)0-1O or (CH2)0-1S;
Ra represents H or C1-6 alkyl;
E1 represents (CH2)0-2 or CH═CH;
E2a and E2b independently represent C2-4 alkenylene, C3-6 cycloalkylene, phenylene or naphthylene;
Het1 to Het4 independently represent four- to twelve-membered heterocyclic groups containing one or more heteroatoms selected from N, O and S, which heterocyclic groups are optionally substituted by one or more substituents selected from the group consisting of ═O, OH, halo, cyano, nitro, N(R3a)R3b, C1-4 alkyl and C1-4 alkoxy;
R3a and R3b independently represent, H or C1-4 alkyl, or R3a represents —C(O)R5;
R5 represents H or C1-4 alkyl;
n represents, 2, 3, 4 or 5;
each individual Q independently represents a structure represented by formula Ia, Ib, Ic, Id, Ie or If





wherein
R6 represents H or C1-6 alkyl;
R7 represents C1-12 alkyl;
R8, R9, R10 and R11 independently represent H or C1-12 alkyl;
G represents CH or N;
L represents O or S; and
p, q and r independently represent 0, 1, 2 or 3;
provided that the compound comprises at least one structure represented by formula Ib, Ic, Id, Ie or If in which R6 or R7, R8, R9, R10 or R11, respectively, represents branched, cyclic or part cyclic C3-5 alkyl; or a pharmaceutically acceptable derivative thereof.

2. A compound as claimed in claim 1, wherein:
R1a represents H or C1-12 alkyl, optionally substituted and/or terminated by one or more substituents selected from halo and aryl optionally substituted by one or more substituents selected the group consisting of OH, halo, cyano, nitro, N(R3a)R3b, C1-4 alkyl and C1-4 alkoxy; and
the compound comprises at least one structure represented by formula Ib, Ic, Id, Ie or If in which R7, R8, R9, R10 or R11, respectively, represents branched, cyclic or part cyclic C3-5 alkyl.

3. A compound as claimed in claim 1, wherein aryl is phenyl or naphthyl.

4. A compound as claimed in claim 1, wherein alkyl and alkoxy groups are:
(a) straight-chain;
(b) branched-chain and/or cyclic; or
(c) part cyclic/acyclic.

5. A compound as claimed in claim 1, wherein alkyl and alkoxy groups are:
(a) saturated or unsaturated;
(b) interrupted by one or more oxygen and/or sulfur atoms; and/or
(c) unless otherwise specified, substituted by one or more halo atoms.

6. A compound as claimed in claim 1, which is a compound of formula II,




wherein
R1 represents Het1, R1aC(O)— or D-A-N(H)-Q3-Q2-Q1-C(O)-E-C(O)—;
Q1 is absent or represents a structure represented by formula Ia, Ib, Ic, Id, Ie or If;
Q2 represents a structure represented by formula Ib, Ie or If; and
Q3 represents a structure represented by formula Ib, Id, Ie or If; provided that:
(a) at least one of Q1, Q2 and Q3 represents a structure represented by formula Id, Ie or If; and
(b) at least one of R6 or R7, R8, R9, R10 and R11 represents branched, cyclic or part cyclic C3-5 alkyl, or a pharmaceutically acceptable derivative thereof.

7. A compound as claimed in claim 1, wherein the compound comprises:
(a) at least one structure represented by formula Ib in which G represents N and R6 represents branched, cyclic or part cyclic C3-5 alkyl;
(b) at least one structure represented by formula Id in which p represents 0 and R9 represents branched, cyclic or part cyclic C3-5 alkyl; and/or
(c) at least one structure represented by formula Ie in which q represents 0 and R10 represents branched, cyclic or part cyclic C3-5 alkyl.

8. A compound as claimed in claim 1, wherein each of the at least one branched, cyclic or part cyclic C3-5 alkyl groups independently represents isopropyl, cyclopropylmethyl, isopentyl or cyclopentyl.

9. A compound as claimed in claim 1, wherein the compound comprises at least one structure represented by formula Ib, Ic, Id, Ie or If in which R7, R8, R9, R10 or R11, respectively, represents isopropyl.

10. A compound as claimed in claim 1, which compound comprises at least one structure represented by the formula

11. A compound of formula IIa,




wherein
R1 represents
a nine-membered aromatic heterocycle containing two heteroatoms selected from N, O and S,
R1aC(O)— or
D-A-N(H)-Q3-Q2-Q1-C(O)-E-C(O)—;

R1a represents
H,
phenyl optionally substituted by C1-2 alkyoxy,
9,10-dioxo-9,10-dihydroanthracenyl optionally substituted by C1-2 alkoxy,
saturated, optionally branched C1-6 alkyl or
saturated C1-3 n-alkyl, terminated by phenyl optionally substituted by C1-2 alkoxy;

A represents saturated C2-4 alkylene or (CH2)1-3—C(O)N(H)—(CH2)2-4; 
D represents —N(R2a)R2b;
R2a and R2b independently represent
C1-3 alkyl or a nine- or ten-membered aromatic heterocycle containing one to three heteroatoms selected from N, O and S, or
R2a and R2b together represent (CH2)3-5 optionally interrupted by NR4;

R4 represents
C1-3 alkyl or a nine- or ten-membered aromatic heterocycle containing one to three heteroatoms selected from N, O and S;

E represents
-(2,5-indolyl-,
—(CH2)0-2-(2,6-indolyl)-,
—CH═CH-(2,6-indolyl)-,
trans-ethenylene,
trans-cyclopropylene,
1,3- or 1-4-phenylene,
—CH2N(H)C(O)-(1,3- or 1,4-phenylene)-C(O)N(H)CH2—,
or one of the following structures





Q1 is absent or represents a structure represented by formula Ia, Ib, Ic, Id, Ie or If;
Q2 represents a structure represented by formula Ib, Ie or If;
Q3 represents a structure represented by formula Ib, Id, Ie or If;
wherein the structures of formulae Ia, Ib, Ic, Id, Ie and If are as follows





wherein
R6 represents H or, when G represents N, R6 represents H or branched, cyclic or part cyclic C3-5 alkyl;
R7, R8, R9, R10 and R11 independently represent saturated, optionally branched C1-6 alkyl or represents H;
provided that the compound comprises at least one structure represented by formula Ie in which R10 represents branched, cyclic or part cyclic C3-5 alkyl.

12. A compound as claimed in claim 11, wherein the compound comprises at least one structure represented by formula Ie in which R10 represents cyclopropylmethyl, isopentyl, cyclopentyl or isopropyl.

13. A compound as claimed in claim 11, wherein the compound comprises at least one structure represented by formula Ie in which R10 represents isopropyl.

14. A compound of formula IIb,




wherein
R1 represents
a nine-membered aromatic heterocycle containing two heteroatoms selected from N, O and S.
HC(O)—,
(methoxyphenyl)C(O)—,
(9,10-dioxo-9,10-dihydroanthracenyl)C(O)—,
(saturated C1-3 alkyl)C(O)—,
(methoxyphenylacetyl)C(O)—, or
(CH3)2N-A-N(H)-Q3-Q2-Q1-C(O)-E-C(O)—;

A represents saturated C2-4 n-alkylene or (CH2)2—C(O)N(H)—(CH2)3;
E represents —CH2N(H)C(O)-(1,3-phenylene)-C(O)N(H)CH2—;
Q1 is absent or represents a structure represented by formula Ia, Ib, Ic, Id, Ie or If;
Q2 represents a structure represented by formula Ib, Ie or If;
Q3 represents a structure represented by formula Ib, Id, Ie or If;
wherein the structures of formulae Ia, Ib, Ic, Id, Ie and If are as follows





wherein
R6 represents H or, when G represents N, R6 represents H or branched, cyclic or part cyclic C3-5 alkyl;
R7, R9, R10 and R11 independently represent saturated, optionally branched C1-3 alkyl;
provided that the compound comprises at least one structure represented by formula Ie in which R10 represents branched, cyclic or part cyclic C3-5 alkyl.

15. A compound as claimed in claim 14, wherein the compound comprises at least one structure represented by formula Ie in which R10 represents cyclopropylmethyl, isopentyl, cyclopentyl or isopropyl.

16. A compound as claimed in claim 14, wherein the compound comprises at least one structure represented by formula Ie in which R10 represents isopropyl.

17. A compound as claimed in claim 1, which compound is selected from the following:
(i) N-[5-({[5-({[3-(Dimethylamino)propyl]amino}carbonyl)-1-methyl-1H-pyrrol3-yl]amino}carbonyl)-1-isopropyl-1-H-pyrrol-3-yl]-4-[(3,3-dimethylbutanoyl)amino]-1-methyl-1H-pyrrole-2-carboxamide;
(ii) N-[5-({[5-({[3-(Dimethylamino)propyl]amino}carbonyl) -1-methyl-1H-pyrrol-3-yl]amino}carbonyl)-1-isopropyl-1H-pyrrol-3-yl]-4-(formylamino)-1-methyl-1H-pyrrole-2-carboxamide;
(iii) N-[3-(Dimethylamino)propyl]-2-({[4-({[4-(formylamino)-1-methyl-1H-pyrrol-2-yl]carbonyl}amino)-1-methyl-1H-pyrrol-2-yl]carbonyl}-amino)-5-isopropyl-1,3-thiazole-4-carboxamide;
(iv) N-[5-({[3-(Dimethylamino)propyl]amino}carbonyl)-1-isopropyl-1H-pyrrol-3-yl]-4-({[4-(formylamino)-1-isopropyl-1H-pyrrol-2-yl]carbonyl}-amino)-1-isopropyl-1H-pyrrole-2-carboxamide
(v) N-[5-({[5-({[3-(Dimethylamino)propyl]amino}carbonyl)-1-isopentyl-1H-pyrrol-3-yl]amino}carbonyl)-1-isopentyl-1H-pyrrol-3-yl]-4-(formyl-amino)-1-isopentyl-1H-pyrrole-2-carboxamide;
(vi) N-[5-({[5-({[3-(Dimethylamino)propyl]amino}carbonyl)-1-isopropyl-1H-pyrrol-3-yl]amino}carbonyl)-1-methyl-1H-pyrrol-3-yl]-4-(formyl-amino)-1-isopropyl-1H-pyrrole-2-carboxamide;
(vii) N-[5-({[3-(Dimethylamino)propyl]amino}carbonyl)-1-methyl-1H-pyrrol-3-yl]-2-({[4-(formylamino)-1-methyl-1H-pyrrol-2-yl]carbonyl}-amino)-5-isopropyl-1,3-thiazole-4-carboxamide;
(viii) 4-({[4-(Formylamino)-1-methyl-1H-pyrrol-2-yl]carbonyl}amino)-1-iso-propyl-N-[1-methyl-5-({[3-(4-morpholinyl)propyl]amino}carbonyl)-1H-pyrrol-3-yl]-1H-pyrrole-2-carboxamide;
(ix) 4-(Formylamino)-N-[1-isopropyl-5-({[1-methyl-5-({[3-(1-pyrrolidinyl)-propyl]amino}carbonyl)-1H-pyrrol-3-yl]amino}carbonyl)-1H-pyrrol-3-yl]-1-methyl-1H-pyrrole-2-carboxamide;
(x) N-[5-({[5-({[3-(Dimethylamino)propyl]amino}carbonyl)-1-methyl-1H-pyrrol-3-yl]amino}carbonyl)-1-isopentyl-1H-pyrrol-3-yl]-4-(formylamino)-1-methyl-1H-pyrrole-2-carboxamide;
(xi) 2-(Acetylamino)-N-[5-({[5({[3-(dimethylamino) propyl]amino}-carbonyl)-1-methyl-1H-pyrrol-3-yl]amino}carbonyl)-1-methyl-1H-pyrrol-3-yl]5-isopropyl-1,3-thiazole-4-carboxamide;
(xii) 2-(Acetylamino-)-N-[5-({[4-({[3-(dimethylamino)propyl]amino}-carbonyl)-5-isopropyl-1,3-thiazol-2-yl]amino}carbonyl)-1-methyl-1H-pyrrol-3-yl]-5-isopropyl-1,3-thiazole-4-carboxamide;
(xiii) 2-(Acetylamino)-N-(5-{[(3-{[3-(dimethylamino)propyl]amino}-3-oxo-propyl)amino]carbonyl}-1-methyl-1H-pyrrol-3-yl)-5-isopropyl-1,3-thiazole-4-carboxamide;
(xiv) N1,N3-Bis(2-{[5({[4({[3-(dimethylamino)propyl]aminol}carbonyl)-5-isopropyl-1,3-thiazol-2-yl]amino}carbonyl)-1-methyl-1H-pyrrol-3-yl]-amino}-2-oxoethyl) isophthalamide;
(xv) N-[5-({[5-({[3-(Dimethylamino)propyl]amino}carbonyl)-1-methyl-1H-pyrrol-3-yl]amino}carbonyl)-1-isopropyl-1H-pyrrol-3-yl]-4-(acetylamino)-1-methyl-1H-pyrrole-2-carboxamide;
(xvi) N-[5-({[5-({[3-(Dimethylamino)propyl]amino}carbonyl)-1-methyl-1H-pyrrol-3-yl]amino}carbonyl)-1-isopentyl-1H-pyrrol-3-yl]-4-(acetyl-amino)-1-methyl-1H-pyrrole-2-carboxamide;
(xvii) N2,N5-Bis[5({[4({[3-(dimethylamino)propyl]amino}carbonyl)-5-isopropyl-1,3-thiazol-2-yl]amino}carbonyl)-1-methyl-1H-pyrrol-3-yl]-1H-indole-2,5-dicarboxamide;
(xviii) N2,N5-Bis[1-isopentyl-5-({[1-methyl-5-({[3(4-morpholinyl)propyl]-amino}carbonyl)-1H-pyrrol-3-yl]amino}carbonyl)-1H-pyrrol-3-yl]-1H-indole-2,5-dicarboxamide;
(xix) N2,N5-Bis[5({[5({[3-(dimethylamino)propyl]amino}carbonyl)-1-methyl-1H-pyrrol-3-yl]amino}carbonyl)-1-isopentyl-1H-pyrrol-3-yl]-1H-indole-2,5-dicarboxamide;
(xx) N2, N5Bis[1isopentyl-5({[1methyl5({[3(4methyl-1-piperazinyl)-propyl]amino}carbonyl)-1H-pyrrol-3-yl]amino}carbonyl)-1H-pyrrol-3-yl]-1H-indole-2,5-dicarboxamide;
(xxi) 2-({[4-({[4-(Acetylamino)-1-methyl-1H-imidazol-2-yl]carbonyl}-amino)-1-methyl-1H-pyrrol-2-yl]carbonyl}amino)-N-[3-(dimethylamino)-propyl]-5-isopropyl-1,3-thiazole-4-carboxamide;
(xxii) 4-(Acetylamino)-N-[1-isopentyl-5-({[1-methyl-5-({[3-(4-methyl-1-piperazinyl)propyl]amino}carbonyl)-1H-pyrrol-3-yl]amino}carbonyl)-1H-pyrrol-3-yl]-1-methyl-1H-pyrrole-2-carboxamide;
(xxiii) N-[1-Isopentyl-5-({[1-methyl-5-({[3-(4-methyl-1-piperazinyl)-propyl]amino}carbonyl)-1H-pyrrol-3-yl]amino}carbonyl)-1H-pyrrol-3-yl]-4-[(3-methoxybenzoyl) amino]-1-methyl-1H-pyrrole-2-carboxamide;
(xxiv) N-[5-({[3-(Dimethylamino)propyl]amino}carbonyl)-1-methyl-1H-pyrrol-3-yl]-4-({[5-(formylamino)-2-methyl-3-thienyl]carbonyl}amino)-1-isopentyl-1H-pyrrole-2-carboxamide;
(xxv) N-[5-({[5-({[3-(dimethylamino)propyl]amino}carbonyl)-1-methyl-1H-pyrrol-3-yl]amino}carbonyl)-1-methyl-1H-pyrrol-3-yl]-5-isopropyl-2-[(3-methoxybenzoyl)amino]-1,3-thiazole-4-carboxamide;
(xxvi) N-[5-({[3-(Dimethylamino)propyl]amino}carbonyl)-1-methyl-1H-pyrrol-3-yl]-4-{[(5-{[(9,10-dioxo-9,10-dihydro-2-anthracenyl)carbonyl]-amino}-2-methyl-3-thienyl)carbonyl]amino}-1-isopentyl-1H-pyrrole-2-carboxamide;
(xxvii) N-[1-(Cyclopropylmethyl)-5-({[5-({[3-(dimethylamino)propyl]-amino}carbonyl)-1-methyl-1H-pyrrol-3-yl]amino}carbonyl)-1H-pyrrol-3-yl]-4-(formylamino)-1-methyl-1H -pyrrole-2-carboxamide;
(xxviii) 1-Cyclopentyl-N-[5-({[3-(dimethylamino)propyl]amino}carbonyl)-1-methyl-1H-pyrrol-3-yl]-4-({[4-(formylamino)-1-methyl-1H-pyrrol-2-yl]-carbonyl}-amino)-1H-pyrrole-2-carboxamide;
(xxix) N2,N7-Bis[5({[4({[3-(dimethylamino)propyl]amino}carbonyl)-5-isopropyl-1,3-thiazol-2-yl]amino}carbonyl)-1-methyl-1H-pyrrol-3-yl]-9,10-dihydro-2,7-phenanthrenedicarboxamide;
(xxx) 4-(Formylamino)-N-[1-isopentyl-5-({[1-methyl-5-({[3-(4methyl-1-piperazinyl)propyl]amino}carbonyl)-1H-pyrrol-3-yl]amino}carbonyl)-1H-pyrrol-3-yl]-1-methyl-1H-pyrrole-2-carboxamide;
(xxxi) 4-(Acetylamino)-N-[1-isopentyl-5-({[1-methyl5({[3-(4-morpholinyl) propyl]amino}carbonyl)-1H-pyrrol-3-yl]amino}carbonyl)-1H-pyrrol-3-yl]-1-methyl-1H-pyrrole-2-carboxamide;
(xxxii) 4-(Formylamino)-N-[1-isopentyl-5-({[1-methyl-5-({[3-(4-morpholinyl) propyl]amino}carbonyl)-1H-pyrrol-3-yl]amino}carbonyl)-1H-pyrrol-3-yl]-1-methyl-1H-pyrrole-2-carboxamide;
(xxxiii) N[5({[5({[3-(Dimethylamino)propyl]amino}carbonyl)-1-methyl-1H-pyrrol-3-yl]amino}carbonyl)-1-isopentyl-1H-pyrrol-3-yl]-4-[(3-methoxybenzoyl)amino]-1-methyl-1H-pyrrole-2-carboxamide; and
(xxxiv) N[5({[5({[3-(Dimethylamino)propyl]amino}carbonyl)-1-methyl-1H-pyrrol-3-yl]amino}carbonyl)-1-isopentyl-1H-pyrrol-3-yl]-4-{[(4-methoxyphenyl)acetyl]amino}-1-methyl-1H-pyrrole-2-carboxamide.

18. A compound as claimed in claim 17 which is:
(a) N-[5-({[5({[3-(Dimethylamino)propyl]amino}carbonyl)-1-methyl-1H-pyrrol-3-yl]amino}carbonyl)-1-isopropyl-1H-pyrrol-3-yl]-4-(formylamino)-1-methyl-1H-pyrrole-2-carboxamide;
(b) N-[3-(Dimethylamino)propyl]-2-({[4-({[4-(formylamino)-1-methyl-1H-pyrrol-2yl]carbonyl}amino)-1-methyl-1H-pyrrol-2-yl]carbonyl}-amino)-5-isopropyl-1,3-thiazole-4-carboxamide;
(c) N-[5-({[3-(Dimethylamino)propyl]amino}carbonyl)-1-methyl-1H-pyrrol-3yl]-2-({[4-(formylamino)-1-methyl-1H-pyrrol-2-yl]carbonyl}-amino)-5-isopropyl-1,3-thiazole-4-carboxamide;
(d) N-[5-({[5-({[3-(Dimethylamino)propyl]amino}carbonyl)-1-methyl-1H-pyrrol-3-yl]amino}carbonyl)-1-isopentyl-1H-pyrrol-3-yl]-4-(formylamino)-1-methyl-1H-pyrrole-2-carboxamide;
(e) N2,N5-Bis[1-isopentyl-5-({[1-methyl-5-({[3-(4-morpholinyl)propyl]-amino}carbonyl)-1H-pyrrol-3-yl]amino}carbonyl)-1H-pyrrol-3-yl]-1H-indole-2,5-dicarboxamide;
(f) N-[1-(Cyclopropylmethyl)-5-({[5-({[3-(dimethylamino)propyl]-amino}carbonyl)-1-methyl-1H-pyrrol-3-yl]amino}carbonyl)-1H-pyrrol-3-yl]-4-(formylamino)-1-methyl-1H -pyrrole-2-carboxamide; or
(g) N2, N7-Bis[5-({[4({[3-(dimethylamino)propyl]amino}carbonyl)-5-isopropyl-1,3-thiazol-2-yl]amino}carbonyl)-1-methyl-1H-pyrrol-3-yl]-9,10-dihydro-2,7-phenanthrenedicarboxamide.

19. A compound as claimed in claim 11 which is N-[3-(dimethylamino)propyl]-2-({[4-({[4-(formylamino)-1-methyl-1H-pyrrol-2-yl]carbonyl}-amino)-1-methyl-1H-pyrrol-2-yl]carbonyl}amino)-5-isopropyl-1,3-thiazole-4-carboxamide.

20. A compound as claimed in claim 1, which binds to and/or has specificity for DNA sequences that contain at least one GC base pairing.

21. A compound as claimed in claim 11 or 14, which binds to and/or has specificity for DNA sequences that contain at least one GC base pairing, provided that the compound comprises at least one structure represented by formula Id, Ie or If.

22. A compound as claimed in claim 1 which has different binding affinities at different minor groove binding sites in double-stranded DNA molecules having more than one minor groove binding site.

23. A compound as claimed in claim 22, wherein the different minor groove binding sites comprise solely AT base pairs.

24. A pharmaceutical formulation including a compound as defined in claim 1 in admixture with a pharmaceutically-acceptable adjuvant, diluent or carrier.

25. A method of stabilising a DNA duplex formed between first and second single strands of DNA, which method comprises contacting that DNA duplex with a compound as defined in claim 1.

26. A method of enhancing the difference in melting temperatures between first and second DNA duplexes, wherein each DNA duplex is formed from a first single strand of DNA that is the same in each duplex and a second single strand of DNA that is different in each duplex, which method comprises contacting each DNA duplex with a compound as defined in claim 1.

27. A process for the preparation of compounds of formula I as defined in claim 1 which comprises:
(a) reaction of a compound of formula III,





wherein Aa represents A or, when a represents 0, then Aarepresents A or A2, a is as defined below, with a compound of formula IV,




wherein Ab represents a direct bond or -A1-C(O)—, L1 represents a leaving group, a and b both represent integers from 0 to 5, the sum of a and b being 2, 3, 4 or 5;
(b) for compounds of formula I in which R1 represents D-A-N(H) -[Q]n-C(O)-E-C(O)—, reaction of two equivalents of a compound of formula V,





with a compound of formula VI,


L2-C(O)-E-C(O)-L2  VI


wherein L2 represents a leaving group, the two L2 groups being the same or different; or
(c) deprotection of a protected derivative of a compound of formula I.

28. A compound of formula V, as defined in claim 27, or a protected derivative thereof.