1.  Field of the Invention
This invention relates to halogen-substituted thienyl compounds, in particular ones binding to nucleic acids and having anti-microbial properties, and methods for their use. 
2.  Description of the Related Art
A number of naturally occurring or synthetic compounds bind to double stranded nucleic acid, especially double stranded DNA (“dsDNA”).  Some bind to the major groove, while others bind to the minor groove.  Still others intercalate between adjacent base pairs.  Combination binding modes are known, in which a compound has binding interactions with more than one nucleic acid site. 
It has been proposed to use dsDNA binding compounds to regulate the expression of genes for medical purposes.  If a disease is characterized by the overexpression or undesired expression of a gene (e.g., an oncogene), in principle the disease can be treated by suppressing wholly or partially the gene's expression via the binding of a compound to the gene or a promoter site thereof and interfering with transcription.  Infections by pathogens such as fungi, bacteria, and viruses can be treated with compounds that affect the expression of genes essential for the pathogen's proliferation.  Or, in a disease characterized by non- or under-expression of a beneficial gene, the expression of the beneficial gene can be up-regulated with a compound that binds to binding site of a repressor. 
The natural products distamycin and netropsin represent a class of DNA-binding compounds that has been studied over the years:
Distamycin and netropsin may be viewed as heteroaromatic polyamides, having as their core structural motif N-methylpyrrole carboxamide residues.  They bind to the minor groove, their crescent molecular shapes providing a conformational fit within the groove.  The binding occurs with a preference for A,T rich dsDNA tracts. 
A number of heteroaromatic polyamides have been synthesized elaborating on the distamycin/netropsin motif, with the objective of enhancing or varying biological properties, increasing binding affinity to dsDNA, and/or improving specificity in base pair sequence recognition.  The use of synthetic heteroaromatic polyamides in therapeutics has been proposed, for example, in Dervan et al.,  U.S. Pat.  No.  5,998,140 (1999); Dervan et al.,  WO 00/15209 (2000); Dervan, WO 00/15773 (2000); and Gottesfeld et al.,  WO 98/35702 (1998).  In many instances the structural variable investigated has been the heteroaromatic ring.  Alternative heteroaromatic rings disclosed in the art include furan, imidazole, isoxazole, oxazole, pyrazole, pyridine, thiophene, and triazole rings. 
Disclosures relating to heteroaromatic polyamides having thiophene rings include Arcamone et al.,  Anti-Cancer Drug Design, 1986, 1, 235-244; Nielsen, Bioconjugate Chemistry, January/February 1991, 2(1), p. 1; Bailly et al.,  Bioconjugate Chemistry, 1998, 9 (5), p. 513; Dickerson et al.,  Structure, 1997, 5, p. 1033; Khalaf et al.,  Tetrahedron 2000, 56, 5225-5239; Lown et al.,  U.S. Pat.  No.  4,912,199 (1990); Lazzari et al.,  U.S. Pat.  No.  5,017,599 (1991); Lazzari et al.,  U.S. Pat.  No.  5,049,579 (1991); Lazzari et al.,  U.S. Pat.  No.  5,310,752 (1994); Animati et al.,  U.S. Pat.  No.  5,472,976 (1995); Lown et al.,  U.S. Pat.  No.  5,502,068 (1996); U.S. Pat.  No.  5,616,606 (1997); Bruice et al.,  U.S. Pat.  No.  5,698,674 (1995); Beria et al.,  U.S. Pat.  No.  5,753,629 (1998); Lown et al.,  WO 92/13838 (1992); and Animati et al.,  WO 94/20463 (1994).  Matsumoto et al.,  Heterocycles 1992, 34, p. 1697, discloses halogenated oligo-N-methylpyrrole carboxamide derivatives, including those having halogenated thiophene groups.  El-Naggar et al, J. Indian Chem.  Soc.,  1982, LIX, p. 783, have reported on investigations on the anti-microbial properties of 5-bromo-2-thienyl carboxylic acid dipeptide derivatives.