Compositions and methods to reduce mutagenesis

This application is a divisional application and claims the benefit of U.S. application Ser. No. 10/994,215, filed Nov. 19, 2004, which claims benefit under 35 U.S.C. § 119(e) of U.S. Provisional Application No. 60/608,949, filed Nov. 19, 2003, which is hereby incorporated herein by reference in its entirety for all purposes.

Drug resistance is an ever increasing problem in modern medicine impacting the treatment of conditions as diverse as bacterial infections, viral infections, protozoan infections, fungal infections, and cancer.

In particular, the worldwide emergence of antibiotic-resistant bacteria threatens to undo the dramatic advances in human health that followed the discovery of these drugs. Antibiotic drug resistance is especially acute with tuberculosis, which infects one-third of all humans, most of whom live in the developing world. The health care establishment is countering this challenge by trying to create new antibiotics and by limiting the use of those already available. However, this approach has not yet produced the desired effect, as the prevalence of resistant strains continues to increase.

Drug resistance is also a problem with viruses, including the human immunodeficiency virus (“HIV”). In fact, HIV drug resistance is rapidly becoming an epidemic. One study of HIV infected patients between 1996 and 1999, shows that about 78% of patients harbored viruses that were resistant to at least one class of drugs, 51% had viruses that were resistant to two classes of drugs, and 18% had viruses that were resistant to three classes of drugs. Thus, HIV drug therapies must constantly evolve to keep pace with the evolution of resistance.

Drug resistance is also a problem during cancer therapy. It is estimated that half of all cancer patients are cured, mostly by a combination of surgery, radiotherapy and/or chemotherapy. However, some cancers can only be treated by chemotherapy, and in those cases, only one in five patients survives long-term. It is believed that the overriding reason for this poor result is drug resistance, wherein the tumors are either innately resistant to the drugs available, or else are initially sensitive but evolve resistance during treatment and eventually re-grow. Allen J D, et al. Cancer Research (2002) 62, 2294-2299.

Drug resistance also occurs with protozoa such as Plasmodium spp., the genus of protozoa responsible for malaria. In recent years, drug resistance has become one of the most important problems in malaria control. Resistance in vivo has been reported to all anti-malaria drugs except artemisinin and its derivatives. This necessitates the use of drugs which are more expensive and may have dangerous side effects.

Thus, there is a great need for compounds that inhibit the mutations that confer drug resistance and methods for using such compounds to treat and prevent drug resistant conditions.

The present invention relates to compositions comprising, consisting essentially of, or consisting of achaogens. Achaogens are compounds that reduce the rate of induced mutagenesis. Achaogens can include nucleic acids, peptide nucleic acids, phage, phagemids, polypeptides, peptidomimetics, antibodies, small or large organic or inorganic molecules or any combination of the above. Achaogens can be naturally occurring or non-naturally occurring (e.g., recombinant) and are preferably isolated and/or purified.

In preferred embodiments an achaogen interacts with or binds to a gene product that increases rate of mutation in a cell or an organism. Examples of such gene products include RecA, RecB, RecC, RecD, RecF, RecG, Rec N, LexA, UmuC, UmuD, PolB, PolIV, PolV, PriA, RuvA, RuvB, RuvC, UmuC, UmuD, UvrA, UvrB, UvrD or any homologs or analogs thereof.

In some embodiments, an achaogen interacts with or binds to LexA or any homolog or analog thereof to reduce the rate of mutation in a cell or an organism. Such an achaogen can, for example, interact with or bind to LexA\'s (or homolog of LexA\'s) cleavage site or active site. In some embodiments, an achaogen interferes with LexA\'s (or a homolog of LexA\'s) autocleavage, which is required for induced mutagenesis by binding to the active site of LexA (or homolog of LexA).

Such an achaogen can comprise, consist essentially of, or consist of a polypeptide or peptidomimetic of a polypeptide that binds LexA, thus preventing LexA\'s autoproteolysis activity. Examples of such polypeptide (and peptidomimetics thereof) include those comprising, consisting essentially of, or consisting of dipeptide Ala-Ala, tripeptide Val-Ala-Ala, or SEQ ID NO: 1, 2, or 3. In some embodiments wherein the achaogen comprises an Ala-Gly bond, the bond may be modified so that it is not cleavable under normal physiological conditions. In some embodiments, the polypeptide or peptidomimetic is C-terminally modified, e.g., such that it is electrophilic.

In some embodiments, an achaogen of the present invention is one of Formula I,

wherein where R₁, R₂, R₃, R₄, R₅, and R₆ are each independently selected from the group consisting of —(CHR_a)_x-L-R_b, where x is selected from the group consisting of 0, 1, 2, 3, or 4; L is a single bond or —C(O)—, —NHC(O)—, —OC(O)—, —S(O)_j, where j is 0, 1, or 2; R_a is a moiety selected from the group consisting of H, (C₁-C₆)alkyl, halogen, (C₁-C₆)fluoroalkyl, (C₁-C₆)alkoxy, —C(O)OH, —C(O)—NH₂, —(C₁-C₆)alkylamine, —C(O)—(C₁-C₆)alkyl, —C(O)—(C₁-C₆)fluoroalkyl, —C(O)—(C₁-C₆)alkylamine, and —C(O)—(C₁-C₆)alkoxy; and R_b is H, OH, halogen, NH₂, CN, N₃, or a moiety, optionally substituted with 1-3 independently selected substituents, selected from the group consisting of alkyl, alkenyl, alkoxy, mercaptyl, alkylamine, alkynyl, aryl, cycloalkyl, cycloalkenyl, and a heterocycle; in addition, R₁ and R₂, R₂ and R₃, R₃ and R₄, and R₅ and R₆, can optionally form a substituted or unsubstituted ring structure.

In some embodiments, an achaogen is an isolated and purified serine protease inhibitor.