Current Topics in Medicinal Chemistry - Volume 5, Issue 13, 2005

Recent developments in nucleoside/nucleotide therapeutics and antiviral drug targets are described covering progress in the development of nucleoside/nucleotide mimetics for the treatment of influenza virus, human immunodeficiency virus type 1, hepatitis B and C virus, herpes virus infections; including herpes simplex virus, cytomegalovirus and varicella zoster virus infections, and the highly pathogenic poxviruses (variola, vaccinia and mokey pox) and filoviruses (Ebola and Marburg).

Mitochondrial thymidine kinase or TK-2 belongs to the family of mammalian deoxynucleoside kinases (dNKs) that catalyze the phosphorylation of deoxynucleosides to their corresponding deoxynucleoside monophosphates by γ- phosphoryl transfer of ATP. These enzymes are instrumental in the activation of deoxynucleoside analogues with biological and therapeutic properties. Moreover, dNKs are fundamental to maintain dNTPs pools for DNA synthesis and repair. TK-2 has a mitochondrial localization and is the only thymidine kinase that is physiologically active in nonproliferating and resting cells. Several recent investigations point to an important role of TK-2 in the maintenance of mitochondrial dNTPs pools. Indeed, mutations in the gene encoding TK-2 have been associated with mitochondrial DNA (mtDNA) depletion that mostly affects skeletal muscle. Moreover, TK-2 has been suggested to be implicated in mitochondrial toxicity associated to prolonged treatments with nucleoside analogues (i.e AZT for the treatment of AIDS patients). In this scenario, TK-2 inhibitors could be a useful tool to further clarify both the physiological role of TK-2 in the maintenance of mitochondrial dNTP pools, and the possible contribution of TK-2 to the mitochondrial toxicity of pyrimidine nucleoside analogues. In the present article we review the most recent literature covering different aspects of TK-2 as well as published TK-2 inhibitors, with special emphasis on acyclic nucleoside analogues that have been described by our research groups and whose prototype compound is 1-[(Z)-4-(triphenylmethoxy)-2-butenyl]thymine.

MraY presents all necessary biological requirements to be considered as a target of interest for the discovery of novel antibacterials. Furthermore, several inhibitors aimed at this enzyme have been discovered. Amphomycin, which is currently used as a topical antibacterial in the veterinary industry is one of them, but the major source of future developments resides in the nucleoside based inhibitors group. This group has been subdivided into classes: Tunicamycins, Ribosamino-uridines, Uridylpeptides and Capuramycins. Analysis of pharmacological behaviours observed with several compounds within these classes, shows that broad-spectrum antibacterial activity, including relevant resistant strains and in vivo efficacy without toxicity are achievable. Among them, Caprazamycins, Muraymycins, Riburamycins and Capuramycins present the most promising profiles.

Purine nucleoside phosphorylase (PNP), an enzyme involved in the catabolism and recycling of nucleosides, is under investigation for the development of novel antibiotics. One method used for the design of inhibitors is transition state analysis. Chemically stable analogues of a transition state complex are predicted to convert the energy of enzymatic rate acceleration (kcat/knon) into binding energy. Transition state structures have been reported for the bovine (Bos taurus), human (Homo sapiens), and malarial (Plasmodium falciparum) PNPs. All three enzymes proceed through SN1-like mechanisms and have transition states with substantial ribooxocarbenium ion character. Bovine PNP proceeds through an early SN1-like transition state, whereas the human and malarial PNPs proceed through more dissociative transition state. Transition state analogues developed for PNP exhibit differential inhibition specificity for these three enzymes based upon their distinct reaction rates (kcat), mechanisms, and substrate specificity. The most powerful inhibitors of these three enzymes have picomolar dissociation constants, two of which are Immucillin-H and DADMe-Immucillin-H. MTImmucillin- H was also developed as a specific inhibitor for P. falciparum PNP by virtue of its unique utilization of 5'- methylthio substrates. Although the transition state for tuberculosis (Mycobacterium tuberculosis) PNP is yet to be determined, inhibition values support a mechanism with a dissociative transition state like those of its human and plasmodial counterparts. Comparison of the transition states and substrate specificity of various PNPs permits the design of species-specific inhibitors for use as therapeutic agents.

Escherichia coli purine nucleoside phosphorylase (PNP) catalyzes the cleavage of 9-(2-deoxy-β-Dribofuranosyl)- 6-methylpurine (MeP-dR), while human PNP does not. MeP-dR is well tolerated while the cleavage product, 6-methylpurine (MeP), is highly cytotoxic. This clinical profile suggests an anticancer gene therapy strategy in which solid tumors are transfected with the gene for E. coli PNP. Tumor cells expressing E. coli PNP will liberate MeP and be killed. Furthermore, MeP released from the cell via the purine transport system will enter nearby cells, resulting in bystander killing of tumor cells. To reduce toxicity resulting from activation of MeP-dR by intestinal tract flora, we redesigned the E. coli PNP active site to cleave prodrugs that are not cleaved by wild type E. coli PNP. It is possible that the variation of substrate specificity among enzymes that cleave nucleosides will have broader application in the gene therapy approach to prodrug activation. Here we review progress in the development of E. coli PNP anticancer gene therapy. We also review the structural basis for activity of nucleoside phosphorylases and suggest future directions for the development of activating enzymes for suicide gene therapy.

Selective agonists and antagonists for A3 adenosine receptors (ARs) are being explored for the treatment of a variety of disorders, including brain and heart ischemic conditions, cancer, and rheumatoid arthritis. This review covers both the structure activity relationships of nucleoside agonist ligands and selected antagonists acting at this receptor and the routes of synthesis. Highly selective agonists have been designed, using both empirical approaches and a semi-rational approach based on molecular modeling. The prototypical A3 agonists IB-MECA 10 and the more receptor-subtypeselective Cl-IB-MECA 11, both of which have affinity in binding to the receptor of ∼ 1 nM, have been used widely as pharmacological probes in the elucidation of the physiological role of this receptor. In addition to the exploration of the effects of structural modification of the adenine and ribose moieties on A3AR affinity, the effects of these structural changes on the intrinsic efficacy have also been studied in a systematic fashion. Key structural features determining A3AR interaction include the N6-benzyl group, 2-position substitution such as halo, substitution of ribose (e.g., the (N)- methanocarba ring system, various 2¢- and 3 ¢-substitutions and 4¢-thio substitution of oxygen). Conformational studies of the ribose moiety and its equivalents indicate that the ring oxygen is not required and the North (N) ring conformation is preferred in binding to the A3AR. Using these observations, a series of ring constrained (N)-methanocarba 5¢-uronamide derivatives was recently reported to be highly selective A3AR agonists, the most notable amongst them was MRS3558 113 having a Ki value in binding to the human A3 receptor of 0.3 nM.