US20180169083A1 - Inhibitors of nucleotidyl transferases and use in herpes and hepatitis viral infections therefor - Google Patents

Inhibitors of nucleotidyl transferases and use in herpes and hepatitis viral infections therefor Download PDF

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US20180169083A1
US20180169083A1 US15/735,197 US201615735197A US2018169083A1 US 20180169083 A1 US20180169083 A1 US 20180169083A1 US 201615735197 A US201615735197 A US 201615735197A US 2018169083 A1 US2018169083 A1 US 2018169083A1
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herpesvirus
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John Edwin Tavis
Lynda Anne Morrison
Marvin Meyers
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St Louis University
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    • A61K31/395—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
    • A61K31/435—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with one nitrogen as the only ring hetero atom
    • A61K31/44—Non condensed pyridines; Hydrogenated derivatives thereof
    • A61K31/4412—Non condensed pyridines; Hydrogenated derivatives thereof having oxo groups directly attached to the heterocyclic ring
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    • A61K31/4353—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with one nitrogen as the only ring hetero atom ortho- or peri-condensed with heterocyclic ring systems
    • A61K31/4375—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with one nitrogen as the only ring hetero atom ortho- or peri-condensed with heterocyclic ring systems the heterocyclic ring system containing a six-membered ring having nitrogen as a ring heteroatom, e.g. quinolizines, naphthyridines, berberine, vincamine
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    • A61K31/505—Pyrimidines; Hydrogenated pyrimidines, e.g. trimethoprim
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    • A61K31/7052—Compounds having saccharide radicals and heterocyclic rings having nitrogen as a ring hetero atom, e.g. nucleosides, nucleotides
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    • A61K31/7068—Compounds having saccharide radicals and heterocyclic rings having nitrogen as a ring hetero atom, e.g. nucleosides, nucleotides containing six-membered rings with nitrogen as a ring hetero atom containing condensed or non-condensed pyrimidines having oxo groups directly attached to the pyrimidine ring, e.g. cytidine, cytidylic acid
    • A61K31/7072—Compounds having saccharide radicals and heterocyclic rings having nitrogen as a ring hetero atom, e.g. nucleosides, nucleotides containing six-membered rings with nitrogen as a ring hetero atom containing condensed or non-condensed pyrimidines having oxo groups directly attached to the pyrimidine ring, e.g. cytidine, cytidylic acid having two oxo groups directly attached to the pyrimidine ring, e.g. uridine, uridylic acid, thymidine, zidovudine
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    • A61K31/7064—Compounds having saccharide radicals and heterocyclic rings having nitrogen as a ring hetero atom, e.g. nucleosides, nucleotides containing six-membered rings with nitrogen as a ring hetero atom containing condensed or non-condensed pyrimidines
    • A61K31/7076—Compounds having saccharide radicals and heterocyclic rings having nitrogen as a ring hetero atom, e.g. nucleosides, nucleotides containing six-membered rings with nitrogen as a ring hetero atom containing condensed or non-condensed pyrimidines containing purines, e.g. adenosine, adenylic acid
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    • A61K38/19—Cytokines; Lymphokines; Interferons
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    • A61P31/00—Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
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    • A61P31/22—Antivirals for DNA viruses for herpes viruses
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    • C07D213/02—Heterocyclic compounds containing six-membered rings, not condensed with other rings, with one nitrogen atom as the only ring hetero atom and three or more double bonds between ring members or between ring members and non-ring members having three double bonds between ring members or between ring members and non-ring members
    • C07D213/89—Heterocyclic compounds containing six-membered rings, not condensed with other rings, with one nitrogen atom as the only ring hetero atom and three or more double bonds between ring members or between ring members and non-ring members having three double bonds between ring members or between ring members and non-ring members with hetero atoms directly attached to the ring nitrogen atom
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    • C07D471/02—Heterocyclic compounds containing nitrogen atoms as the only ring hetero atoms in the condensed system, at least one ring being a six-membered ring with one nitrogen atom, not provided for by groups C07D451/00 - C07D463/00 in which the condensed system contains two hetero rings
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Definitions

  • the disclosure relates to the fields of pathology, virology, molecular biology and pharmaceuticals. More specifically, the disclosure relates to the identification of candidate inhibitors for the treatment and prevention of herpesvirus and hepatitis B diseases. Also provided are compounds having such activity.
  • Herpesviridae is a large family of DNA viruses that cause diseases in vertebrates, including humans. These viruses are significant pathogens and, in addition to primary infections, cause latent, recurring infections. At least six species of Herpesviridae—herpes simplex virus 1 (HSV-1) and HSV-2 (both of which can cause orolabial herpes and genital herpes), Varicella-zoster virus (which causes chickenpox and shingles), Epstein-Barr virus (which causes mononucleosis), Cytomegalovirus (which causes mental retardation and deafness in neonates), and Human herpesvirus 6B (which causes roseola infantum and febrile seizures)—are extremely widespread among humans.
  • HSV-1 herpes simplex virus 1
  • HSV-2 both of which can cause orolabial herpes and genital herpes
  • Varicella-zoster virus which causes chickenpox and shingles
  • Epstein-Barr virus which causes mononu
  • viruses with human tropism include human herpesvirus 6A, human herpesvirus 7 and Kaposi's sarcoma-associated herpesvirus.
  • herpesviruses There are more than 130 herpesviruses, including those that infect non-human mammals, birds, fish, reptiles, amphibians, and mollusks.
  • the drugs, acyclovir and ganciclovir are considered the standard treatments and prophylactic agents for infections caused by HSV, VZV and CMV.
  • acyclovir Until a decade ago, the impact of acyclovir on the control of severe and life-threatening herpesvirus infections was unprecedented.
  • new drugs i.e., penciclovir and the oral prodrugs, valaciclovir, famciclovir, cidofovir, fomivirsen, and foscamet
  • Newer agents, such as brivudin and benzimidavir are in ongoing clinical development, while others have been suspended because of safety concerns. Regardless, new anti-herpes agents are needed to face clinical issues such as drug resistance, increased use of anti-herpes prophylaxis, and safety concerns in small children or pregnant women.
  • hepatitis B virus is a hepatotropic DNA virus that replicates by reverse transcription (Hostomsky et al., 1993). It chronically infects >350 million people world-wide and kills up to 1.2 million patients annually by inducing liver failure and liver cancer (Steitz, 1995; Katayanagi et al., 1990; Yang et al., 1990; Lai et al., 2000).
  • Reverse transcription is catalyzed by a virally-encoded polymerase that has two enzymatic activities: a DNA polymerase that synthesizes new DNA and a ribonuclease H (RNAseH) that destroys the viral RNA after it has been copied into DNA (Hostomsky et al., 1993; Rice et al., 2001; Hickman et al., 1994; Ariyoshi et al., 1994). Both activities are essential for viral replication.
  • RNAseH ribonuclease H
  • HBV infections are treated with interferon ⁇ or one of five nucleos(t)ide analogs (Parker et al., 2004; Song et al., 2004; Lima et al., 2001).
  • Interferon ⁇ leads to sustained clinical improvement in 20-30% of patients, but the infection is very rarely cleared (Hostomsky et al., 1993; Katayanagi et al., 1990; Braunshofer-Reiter et al., 1998).
  • the nucleos(t)ide analogs are used more frequently than interferon.
  • Antiviral resistance was a major problem with the earlier nucleos(t)ide analogs, but resistance to the newer drugs entecavir and tenofovir is very low (Parker et al., 2004; Keck et al., 1998; Goedken et al., 2001; Li et al., 1995). This has converted HBV from a steadily worsening disease into a controllable condition for most individuals (McClure, 1993). The cost of this control is indefinite administration of the drugs (probably life-long; (Song et al., 2004), with ongoing expenses of $400-600/month (Poch et al., 1989; Hu et al. 1996; Hu et al., 1997) and unpredictable adverse effects associated with decades-long exposure to the drugs.
  • a method of inhibiting a cellular or herpesvirus nucleic acid metabolism enzyme comprising contacting said enzyme with a compound having the formula:
  • the compound is further defined as:
  • the compound is further defined as:
  • the compound is further defined as:
  • the salt maybe an ethanolamine salt.
  • the method may further comprise contacting said enzyme with a second inhibitor of said enzyme, or further comprise contacting said enzyme with said compound a second time.
  • the enzyme may be located in a cell, which cell may be located in vitro or located in a living subject.
  • the subject may be a vertebrate infected with a herpesvirus.
  • the compound may be administered intravenously, intraarterially, ocularly, orally, buccally, nasally, rectally, vaginally, topically, intramuscularly, intradermally, cutaneously or subcutaneously.
  • the subject may be further administered a second anti-herpesvirus therapy distinct from the compound.
  • the second anti-herpesvirus therapy may be foscarnet or a nucleoside analog, such as acyclovir, famciclovir, valaciclovir, penciclovir, or ganciclovir.
  • the second anti-herpesvirus therapy may be administered to the subject before or after said compound.
  • the second anti-herpesvirus therapy may be administered to said subject at the same time as said compound.
  • the subject may have previously received a first-line anti-herpesvirus therapy, and further may have developed resistance to said first-line anti-herpesvirus therapy.
  • the herpevirus may be selected from a human alpha herpesvirus, a human beta herpesvirus or a human gamma herpesvirus.
  • the human alpha herpesvirus may be selected from herpes simplex virus 1 (HSV-1), herpes simplex virus 2 (HSV-2), and Varicella-Zoster virus (VZV).
  • the human beta herpesvirus may be selected from human cytomegalovirus (HCMV), human herpesvirus 6A, (HHV-6A), human herpesvirus 6B (HHV-6B), and human herpesvirus 7 (HHV-7).
  • the human gamma herpesvirus may be selected from Epstein-Barr virus (EBV) and Kaposi's sarcoma herpesvirus (KSHV).
  • the herpesvirus may be a non-human herpesvirus, such as Marek's disease virus, equine herpesviruses, Bovine herpeviruses, or pseudorabies virus.
  • the present disclosure provides a pharmaceutical composition
  • a pharmaceutical composition comprising a compound of the formula:
  • the pharmaceutical composition is formulated for administration: orally, nasally, ocularly, buccally, corneally, rectally, vaginally, or topically. In other embodiments, the pharmaceutical composition formulated for administration via injection. In some embodiments, the injection is formulated for administration: intradermally, cutaneously, subcutaneously, intramuscularly, intraperitoneally, intraarterially, or intravenously.
  • R 2 , R 5 , or R 10 is hydrogen. In some embodiments, R 2 , R 5 , and R 10 are hydrogen. In some embodiments, R 1 is aralky (C ⁇ 18) , aralkylamino (C ⁇ 18) , or a substituted version of either group. In some embodiments, R 6 is hydroxy. In some embodiments, R 7 is aryl (C ⁇ 12) . In some embodiments, R 11 is Y 1 —O—X 1 —OR 12 ; wherein:
  • Y 1 is alkanediyl (C ⁇ 8) ;
  • X 1 is arenediyl (C ⁇ 12) , or a substituted version of either of these groups;
  • R 12 is aryl (C ⁇ 12) or substituted aryl (C ⁇ 12) .
  • the compounds are further defined as:
  • the present disclosure provides a compound of the formula:
  • compositions comprising:
  • the pharmaceutical composition is formulated for administration: orally, nasally, buccally, corneally, rectally, vaginally, topically, intradermally, cutaneously, ocularly, subcutaneously, intramuscularly, intraperitoneally, intraarterially, or intravenously.
  • the pharmaceutical composition is formulated as a unit dose.
  • the present disclosure provides methods of inhibiting a hepatitis B virus RNaseH comprising administering an effective amount of a compound or composition described herein.
  • the method is performed in vitro.
  • the method is performed in vivo.
  • the method is performed ex vivo.
  • the methods are sufficient to inhibit viral replication.
  • the present disclosure provides methods of inhibiting replication of a hepatitis B virus comprising contacting the virus with an effective amount of a compound or composition described herein.
  • the method is performed in vitro.
  • the method is performed in vivo.
  • the method is performed ex vivo.
  • the methods are sufficient to treat an infection of a hepatitis B virus.
  • the present disclosure provides methods of treating an infection of a hepatitis B virus in a patient comprising administering a therapeutically effective amount of a compound or composition described herein.
  • the method further comprises a second antiviral treatment.
  • the second antiviral therapy is interferon alfa-2b, lamivudine, adefovir, telbivudine, entercavir, or tenofovir.
  • the patient is a mammal such as a human.
  • the term “about” is used to indicate that a value includes the inherent variation of error for the device, the method being employed to determine the value, or the variation that exists among the study subjects, or +/ ⁇ 5% of the stated value.
  • FIG. 1 Structure of Piroctone Olamine.
  • FIG. 2 Compound #191 inhibits replication of HSV-2 primary clinical isolates. Vero cell monolayers were infected with the indicated patient isolates at moi of 0.1 in the presence of piroctone olamine (#191) or DMSO control at 5 ⁇ M. Cultures were collected 24 hours post-infection and infectious virus titers were determined by plaque assay. Titers in #191-treated samples were subtracted from DMSO-treated samples. Values are the averages of duplicate cultures.
  • FIG. 3 Sensitivity of thymidine kinase-deficient HSV-2 to piroctone olamine.
  • Vero cell monolayers were infected with the indicated wild-type or mutant HSV-1 or HSV-2 strains at moi of 0.1 in the presence of DMSO control or piroctone olamine at 5 ⁇ M.
  • Duplicate cultures were collected 24 hours post-infection and infectious virus titers were determined by plaque assay. Titers in compound-treated samples were subtracted from DMSO-treated samples. Values are the averages ⁇ one standard error of the mean.
  • FIGS. 4A & 4B RNAseH inhibitors work synergistically with Lamivudine against HBV replication. Chou-Talaly combination indexes for compounds #1 ( FIG. 4A ) and #46 ( FIG. 4B ) together with Lamivudine. Additive interactions are shown with the red line, synergistic interactions below the line, and antagonistic interactions are above the line.
  • FIGS. 5A & 5B HBV's genetic variation is unlikely to present a barrier to RNAseH drug development.
  • Four variant patient-derived RNAseH enzymes were expressed as recombinant enzymes, purified, and tested in an RNAseH assay with compounds #1 ( FIG. 5A ) and #46 ( FIG. 5B ) at their respective IC 50 s.
  • NTS nucleotidyl-transferase superfamily
  • the compounds described herein may be used from a variety of different viral infections including herpesvirus and hepatitis B virus.
  • Inhibitors of NTS enzymes like this compound may well have a high barrier to development of antiviral resistance, and its unique mode of action suggests that it should be a good candidate for combination therapy with the existing antiviral drugs to improve overall efficacy of antiviral therapy.
  • Herpesviruses are a diverse group of enveloped viruses having a large, double-stranded DNA genome enclosed in an icosahedral capsid (Pellet & Roizman 2013).
  • the herpesviruses rely on the host cell RNA polymerase II for transcription, but encode all of the enzymes needed for replication of their genomes, including DNA polymerase, helicase, primase, terminase, ribonucleotide reductase, and thymidine kinase. All herpesviruses share the capacity to establish latency in host cells, allowing them to maintain the infection for the life of the host. Periodic reactivation from latency in response to cues in the cellular environment leads to lytic replication at mucosal surfaces, causing recurrent disease and providing the opportunity for transmission to uninfected individuals.
  • the herpesviruses are divided into three subclasses based primarily on their cellular tropism and characteristics of the latent infection.
  • the human alpha herpesviruses herpes simplex virus 1 (HSV-1) (Roizman et al., 2013), herpes simplex virus 2 (HSV-2) (Roizman et al., 2013) and Varicella-Zoster virus (VZV) (Arvin & Gilden 2013) establish latency in sensory neurons where they may remain quiescent for long periods of time.
  • HSV-1 herpes simplex virus 1
  • HSV-2 herpes simplex virus 2
  • VZV Varicella-Zoster virus
  • HSV-1 and HSV-2 are similar viruses with colinear genomes and 83% nucleotide sequence identity in protein coding regions (Dolan et al., 1998); VZV contains a smaller, less homologous genome.
  • the human beta herpesviruses human cytomegalovirus (HCMV), human herpesvirus 6A (HHV-6A), human herpesvirus 6B (HHV-6B) and human herpesvirus 7 (HHV-7) (Yamanishi et al., 2013) establish latency predominantly in mononuclear cells.
  • Epstein-Barr virus (EBV) (Longnecker et al., 2013) and Kaposi's sarcoma herpesvirus (KSHV) (Damania & Cesarman 2013) stimulate cellular proliferation upon infection.
  • EBV Epstein-Barr virus
  • KSHV Kaposi's sarcoma herpesvirus
  • EBV infects B lymphocytes, where it establishes latency, and also epithelial cells.
  • endothelial cells harbor the latent reservoir of KSHV, although the virus infects numerous other cell types as well.
  • the genomes of latent beta and gamma herpesviruses are replicated as the host cell divides in order to maintain latent infection.
  • HSV-1 causes numerous maladies (Roizman et al., 2013): gingivostomatitis; eczema herpeticum; herpes gladiatorum; less common but frequently fatal encephalitis; and an increasing proportion of ulcerative anogential lesions (Gilbert et al., 2011; Horowitz et al., 2011; Pena et al., 2010; Smith & Roberts 2009). Nearly two-thirds of the U.S. population has been exposed to HSV-1 (Xu et al., 2006).
  • HSV-2 infects approximately 17% of Americans (Xu et al., 2006) and up to 75% of some demographics world-wide (Obasi et al., 1999 and Kamali et al., 1999), with an estimated global disease burden of more than half a billion people (Looker, et al., 2008).
  • HSV-2 is the primary cause of ulcerative anogenital lesions.
  • HSV-1 and HSV-2 may be transmitted from a pregnant woman to her child during birth, often causing potentially fatal disseminated disease in the newborn (Kimberlin 2007).
  • HCMV is the most common in utero virus infection (Manicklal et al., 2013), and approximately 8,000 HCMV-infected infants born each year in the U.S.
  • HCMV can cause mononucleosis, retinitis, colitis, pneumonitis, and esophagitis. These serious HCMV infections are associated with increased morbidity and mortality (Komatsu et al., 2014). EBV causes the vast majority of infectious mononucleosis, which strikes nearly half of young adults (Luzuriaga & Sullivan 2010). Notably, of the eight human herpesviruses, a vaccine is available only for VZV.
  • HSV-1 causes recurrent cold sores; a significant proportion of devastating viral encephalitis; and corneal scarring known as herpetic stromal keratitis which is the most frequent infectious cause of blindness, afflicting nearly 400,000 persons annually in the U.S. (Roizman et al., 2013).
  • HSV-2 frequently reactivates to cause genital ulcers and prior HSV-2 infection is associated with an increased risk of human immunodeficiency virus (HIV) acquisition (Roizman et al., 2013).
  • HIV human immunodeficiency virus
  • Latent EBV infection is associated with a variety of cancers including Burkitt's lymphoma, two types of Hodgkin's lymphoma, non-Hodgkin's lymphoma, nasopharyngeal carcinoma, and post-transplant lymphoproliferative disease.
  • Latent KSHV infection can lead to three types of cancer: Kaposi's sarcoma, pleural effusion lymphoma, and Castleman's disease (Damania & Cesarman 2013).
  • Marek's disease is highly contagious, spreading rapidly through flocks of chickens that have not been vaccinated. It causes T cell lymphoma with infiltration of nerves and somatic organs, leading to paralysis and death in up to 80% of infected birds (Hirari, 2001).
  • vaccine efficacy has declined with a concomitant increase in Marek's virus virulence (Gimeno, 2008).
  • Pseudorabies (PRV) is the second most economically important viral disease of swine. Although PRV does not cause illness in adult swine, infection of pregnant sows results in a high incidence of abortion or resorption (Smith, 1997).
  • Piglets infected with PRV suffer coughing, sneezing, fever, constipation, and a variety of neurologic symptoms. Mortality in piglets less than one month of age is close to 100%, but declines rapidly with age (Nauwynck et al., 2007). Ruminants and dogs and cats are also susceptible to lethal PRV infection (Fenner et al., 1993). In cattle, symptoms include intense itching followed by neurological signs and death. In dogs, intense itching is accompanied by jaw and pharyngeal paralysis and subsequent death (Decaro et al., 2008). In cats, usually no symptoms are observed because the disease is so rapidly fatal (Gaskell et al., 2007).
  • Bovine herpesviruses cause a variety of illnesses in young cattle, and can also cause abortion. Although the illnesses caused by BHV's are mostly not life-threatening, they cause important diseases because infection may trigger a decline in meat and milk production and affect trade restrictions (Nandi et al., 2009). Equine herpesviruses typically cause respiratory disease, but certain species also cause myeloencephalopathy in horses, abortion and occasionally neonatal mortality due to pneumonia (Fortier et al., 2010). The herpesviruses of various fish species can cause significant mortality in aquaculture settings, particularly at the fingerling stage (Hanson et al., 2011).
  • NTS inhibitors may be promising candidates for pan anti-herpesvirus drug development due to similarities in replication mechanisms of all the herpesviruses.
  • Enveloped herpesvirus particles fuse with the plasma membrane of a cell, releasing viral regulatory proteins and the viral capsid containing the linear double-stranded DNA genome into the cytoplasm.
  • the capsids deliver the viral genome to the nucleus via release through nuclear pores, whereupon the genome circularizes and becomes transcriptionally active.
  • Viral infection at this point can proceed by two patterns, lytic or latent. In the lytic cycle, coordinated phases of viral transcription lead to expression of the viral regulatory proteins, viral enzymes, and concurrently with the onset of DNA replication, the viral structural proteins.
  • Nascent viral capsids assemble in the nucleus and then bud through the nuclear membranes to acquire their envelope (Mettenleiter et al., 2009).
  • the virus Release from the cells is primarily lytic, resulting in the death of the cell.
  • the virus may enter a latent state, where transcription is limited to a few viral regulatory loci and viral DNA replication is strictly limited. Upon recognition of appropriate cellular stimuli, viral transcription reverts to the lytic pattern and productive viral replication occurs.
  • Initial infections with alpha herpesviruses are lytic, resulting in dispersion of the virus to other cells and organs. These viruses establish latency in the unique environment of the neuron, and also in satellite cells in the case of VZV. During latency, replication of alpha herpesvirus DNA may occur at a low level because latently infected neurons contain multiple copies of the genome (Chen et al., 2002; Wang et al., 2005). Once latency is established, DNA replication increases markedly only during a reactivation event.
  • Initial infections with beta herpesviruses are typically non-lytic but may cause cell-cell fusion.
  • the gamma herpesviruses stimulate proliferation of infected cells, replicating their DNA along with cellular DNA replication to transmit copies of the viral genome to daughter cells (Longnecker et al., 2013). All the herpesviruses cause episodic lytic infection of at least some cell types, allowing them to be shed from mucosal surfaces to facilitate transmission to uninfected individuals.
  • Circularization of the linear double-stranded herpesvirus DNA occurs in the nucleus shortly after viral uncoating, presumably through a recombination-mediated event.
  • Replication of the viral DNA occurs in the nucleus within three-dimensional domains termed replication compartments (Quinlan et al., 1984).
  • DNA replication is thought to employ a double-stranded rolling circle mechanism [reviewed in (Weller & Coen 2012; Lehman & Boehmer 1999)].
  • virus-encoded transcriptional activators upregulate expression of proteins involved in nucleic acid metabolism.
  • DNA replication then initiates at one of three viral origins of DNA replication and is mediated through action of the viral ICP6 origin binding protein.
  • DNA synthesis is primed by the viral helicase/primase complex (pUL5, pUL8, and pUL52). DNA elongation occurs by coupled leading- and lagging-strand DNA synthesis through formation of a replication fork that is grossly similar to the forks that replicate cellular DNA. DNA synthesis is catalyzed by the pUL30 DNA polymerase/UL42 processivity protein complex that also possesses 5′-3′ exonuclease, 3′-5′ exonuclease, and RNase H activities.
  • Helical torsion is relieved by the viral helicase/primase complex, and proper replication fork initiation, architecture and dynamics are promoted by the ICP8 single-stranded DNA binding protein.
  • the initial product of DNA replication is a head-to-tail concatamer, but later in the replication cycle complex branched concatamers accumulate through recombination and/or re-initiation mechanisms.
  • the concatamer is cleaved to unit length by the terminase complex (pUL15, pUL28, and pUL33) (Selvarajan et al., 2013) during encapsidation of the viral genome into pre-formed viral capsids. Without wishing to be bound by any theory, it is believed that some of the compounds described herein inhibit the activity of pUL15 terminase.
  • nucleotidyl transferase superfamily inhibitors in the herpesvirus genomes.
  • the inhibitors screened here function against HIV by binding to the viral RNase H or integrase active sites and chelating the essential divalent cations within the active site (Fuji et al., 2009; Su et al., 2010; Chung et al., 2011; Billamboz et al., 2011; Himmel et al., 2009; Kirschberg et al., 2009).
  • Other compounds screened here are chemically related to inhibitors of the HIV RNase H and integrase. Therefore, their presumed mechanism of action is to inhibit one or more of the viral and/or cellular NTS enzymes essential for herpesviral genomic replication. This mechanism has not yet been tested.
  • candidate genes include the RNase H activity of the pUL30 DNA polymerase (Liu et al., 2006), the 3′-5′ exonuclease activity of pUL30 (Coen 1996), the strand transfer activity of ICP8 (Bortner et al., 1993; Nimonkar & Boehmer, 2003), or the 5′-3′ exonuclease activity of the pUL12 polymerase accessory protein (Schumacher et al., 2012) that are directly involved in virus replication (Weller & Coen 2012).
  • the pUL15 terminase protein that cleaves the concatameric viral DNA produced by DNA replication into the mature linear monomers is also a prime candidate (Selvarajan et al., 2013).
  • herpesviruses encode proteins with functions consistent with NTS enzymes that could be plausible targets.
  • pUL98 is the HCMV ortholog of HSV pUL12 and is functionally conserved, as demonstrated by trans-complementation experiments (Gao et al., 1998). At least two of the seven HCMV proteins involved in encapsidation form an essential terminase complex which likely functions as both an endonuclease and a DNA translocase during DNA cleavage and packaging (Bogner, 2002; Hwang & Bogner, 2002; Scheffczik et al., 2002; Scholz et al., 2003).
  • HCMV human cytomegalovirus
  • pUL56 mediates the specific binding to pac sequences on DNA concatamers and provides energy and structural assistance for DNA translocation into the procapsids
  • pUL89 cleaves the DNA concatomers (Bogner, 2002). These are the orthologs of HSV terminase subunits pUL15 and pUL28.
  • Cellular proteins are also plausible targets for the action of the NTS inhibitors, especially because DNA recombination events appear to be important during productive replication (Weller & Coen 2012). These proteins include the human RNase H1 that could assist in removal of RNA primers for DNA synthesis. Other candidates include the Fen1 endonuclease that may assist in removal of primers (Zhu et al., 2010), and the double-stranded break repair enzymes Mre11, Rad50, NBS1, Rad51 (Weizman & Weller 2011), and Rad52 (Schumacher et al., 2012). The base-excision repair enzymes SSH2 and MLH1 which form complexes that are recruited to viral replication sites and contribute to HSV genomic replication (Mohni et al., 2011) are also plausible targets.
  • Herpesvirus DNA polymerase inhibitors include acyclovir, famciclovir, valaciclovir, penciclovir, and ganciclovir are the most common forms of treatment.
  • a pyrophosphate analog, foscarnet also inhibits the herpesvirus DNA polymerases.
  • a DNA helicase-primase inhibitor, AIC316 (pritelivir), was shown to reduce HSV-2 shedding and number of days without lesions in a phase 2 clinical trial (Wald et al., 2014). However, a subsequent double-blind trial by the same group was terminated by the sponsor because of concurrent findings of toxicity in monkeys (De et al., 2015).
  • CMX001 brincidofovir
  • cidofovir an orally bioavailable lipid conjugate of cidofovir, potentiates the antiviral effect of acyclovir in mice inoculated intranasally with HSV-1 or HSV-2 (Prichard et al., 2011).
  • N-Methanocarbathymidine reduces lethality in a mouse model of HSV-2 infection (Quenelle et al., 2011) and a guinea pig model of neonatal herpes (Bernstein et al., 2011). N-MCT also reduces acute and recurrent disease caused by HSV-2 in an adult guinea pig model.
  • the monoamine oxidase inhibitor tranylcypromine (TCP), which also blocks the activity of histone demethylase LSD1 reduces HSV-1 infection of the cornea, trigeminal ganglia and brain of mice, corneal disease, and percentage of mice shedding virus upon induced reactivation (Yao et al., 2014).
  • TCP has also been tested in a rabbit eye model of recurrent infection with HSV-1 and the mouse and guinea pig models of HSV-2 genital infection.
  • An acyclic nucleoside phosphonate, PMEO-DAPym inhibits HSV replication in a variety of cultured cell types by targeting the viral DNA polymerase (Balzarini et al., 2013).
  • the HIV integrase inhibitor, Raltegravir has a small amount of inhibitory activity against replication of several herpesviruses in cultured cells (Zhou et al., 2014; Yan et al., 2014) and appears to target the polymerase processivity factor UL42 (Zhou et al., 2014).
  • XZ15 and XZ45 Two other integrase inhibitors, XZ15 and XZ45, reduce replication of HSV-1 in cell culture by approximately 800- to 8000-fold, respectively (Yan et al., 2014).
  • XZ45 also inhibits HCMV replication and KSHV gene expression (Yan et al., 2014).
  • Acyclovir resistant variants are particularly prevalent among children, the immunocompromised, and patients with herpetic stromal keratitis (Duan et al., 2008; Wang et al., 2011; Field & Vere Hodge, 2013; Morfin & Thouvenot, 2003; Andrei & Snoeck, 2013).
  • Ganciclovir-resistant variants occur in the naturally circulating viral population (Drew et al., 1993) and can be selected in patients over time (Marfori et al., 2007; Imai et al., 2004; Drew et al., 2001; Drew et al., 1999).
  • Hepatitis B virus is a species of the genus Orthohepadnavirus, which is likewise a part of the Hepadnaviridae family of viruses. This virus causes the disease hepatitis B. In addition to causing hepatitis B, infection with HBV can lead to hepatic fibrosis, cirrhosis and hepatocellular carcinoma. It has also been suggested that it may increase the risk of pancreatic cancer.
  • the hepatitis B virus is classified as the type species of the Orthohepadnavirus, which contains at least five other species: the pomona roundleaf bat hepatitis virus, long-fingered bat hepatitis virus, the Ground squirrel hepatitis virus, Woodchuck hepatitis virus, and the Woolly monkey hepatitis B virus.
  • the genus is classified as part of the Hepadnaviridae family along with Avihepadnavirus. This family of viruses have not been assigned to a viral order.
  • Viruses similar to hepatitis B have been found in all the Old World apes (orangutan, gibbons, gorillas and chimpanzees) and from a New World woolly monkey suggesting an ancient origin for this virus in primates.
  • the virus is divided into four major serotypes (adr, adw, ayr, ayw) based on antigenic epitopes present on its envelope proteins, and into eight genotypes (A-H) according to overall nucleotide sequence variation of the genome.
  • the genotypes have a distinct geographical distribution and are used in tracing the evolution and transmission of the virus. Differences between genotypes affect the disease severity, course and likelihood of complications, and response to treatment and possibly vaccination.
  • the virus particle (virion) consists of an outer lipid envelope and an icosahedral nucleocapsid core composed of protein.
  • the nucleocapsid encloses the viral DNA and a DNA polymerase that has reverse transcriptase activity similar to retroviruses.
  • the outer envelope contains embedded proteins which are involved in viral binding of, and entry into, susceptible cells.
  • the virus is one of the smallest enveloped animal viruses with a virion diameter of 42 nm, but pleomorphic forms exist, including filamentous and spherical bodies that both lack a core.
  • HBV virus itself is called a Dane particle and consists of HBsAg, a lipid envelope, the core protein (HBcAg), the viral genome, and the Hepatitis B virus DNA polymerase.
  • the functions of the small regulatory protein (HBx) are not yet well known but may be related to interfering with transcription, signal transduction, signal transduction, cell cycle progress, protein degradation, apoptosis, or chromosomal stability.
  • the virus also produces a secreted protein called HBeAg that is an amino-terminal extension of HBcAg initiating from an upstream start codon that is involved in suppressing antiviral immune responses.
  • the genome of HBV is made of circular DNA, but it is unusual because the DNA is not fully double-stranded in the virion.
  • One end of the full length strand is linked to the viral DNA polymerase.
  • the genome is 3020-3320 nucleotides long (for the full length strand) and 1700-2800 nucleotides long (for the short length strand).
  • the negative-sense, (non-coding), strand is the complete strand and it is complementary to the viral mRNA.
  • the viral DNA is found in the nucleus soon after infection of the cell.
  • the partially double-stranded DNA is rendered fully double-stranded shortly after infection of a cell by completion of the (+) sense strand and removal of a protein molecule from the ( ⁇ ) sense strand and a short sequence of RNA from the (+) sense strand. A short terminal duplication of are removed from the ends of the ( ⁇ ) sense strand and the ends are rejoined.
  • the mature nuclear form of the genome is called the “cccDNA.”
  • the cccDNA is the template for transcription of all of the viral mRNAs.
  • the core protein (HBcAg) is coded for by gene C, and its start codon is preceded by an upstream in-frame AUG start codon from which the pre-core protein is produced.
  • HBeAg is produced by proteolytic processing of the pre-core protein.
  • the DNA polymerase is encoded by gene P.
  • Gene S is the gene that codes for the surface antigens (HBsAg).
  • the HBsAg gene is one long open reading frame but contains three in frame “start” (ATG) codons that divide the gene into three sections, pre-S1, pre-S2, and S.
  • polypeptides of three different sizes called large, middle, and small are produced.
  • the function of the protein coded for by gene X is not fully understood, but it has pleiotropic regulatory functions in both the cytoplasm and nucleus.
  • genotypes There are at least eight known genotypes labeled A through H.
  • a possible new “I” genotype has been described, but acceptance of this notation is not universal. Different genotypes may respond to treatment in different ways.
  • the genotypes differ by at least 8% of the sequence and have distinct geographical distributions and this has been associated with anthropological history.
  • Type F which diverges from the other genomes by 14% is the most divergent type known.
  • Type A is prevalent in Europe, Africa and South-east Asia, including the Philippines.
  • Type B and C are predominant in Asia; type D is common in the Mediterranean area, the Middle East and India; type E is localized in sub-Saharan Africa; type F (or H) is restricted to Central and South America.
  • Type G has been found in France and Germany.
  • Genotypes A, D and F are predominant in Brazil and all genotypes occur in the United States with frequencies dependent on ethnicity.
  • the E and F strains appear to have originated in aboriginal populations of Africa and the New World, respectively.
  • 24 subtypes have been described which differ by 4-8% of the genome:
  • Hepatitis B is one of a few known non-retroviral viruses which use reverse transcription as a part of its replication process:
  • Intron A® Interferon Alpha
  • Pegasys® Pegasys®
  • Epivir HBV® Livudine
  • Hepsera® Adefovir
  • Baraclude® Enterecavir
  • Tyzeka® Telbivudine
  • Viread® Teenofovir
  • Adefovir is an orally-administered nucleotide analog reverse transcriptase inhibitor (ntRTI). It can be formulated as the pivoxil prodrug adefovir dipivoxil. Adefovir works by blocking reverse transcriptase, the enzyme that is crucial for the hepatitis B virus (HBV) to reproduce in the body because it synthesizes the viral DNA. It is approved for the treatment of chronic hepatitis B in adults with evidence of active viral replication and either evidence of persistent elevations in serum aminotransferases (primarily ALT) or histologically active disease.
  • HBV hepatitis B virus
  • Adefovir dipivoxil contains two pivaloyloxymethyl units, making it a prodrug form of adefovir.
  • Lamivudine (2′,3′-dideoxy-3′-thiacytidine, commonly called 3TC) is a potent nucleoside analog reverse transcriptase inhibitor (nRTI). It is marketed by GlaxoSmithKline with the brand names Zeffix®, Heptovir®, Epivir®, and Epivir-HBV®. Lamivudine has been used for treatment of chronic hepatitis B at a lower dose than for treatment of HIV. It improves the seroconversion of HBeAg positive hepatitis B and also improves histology staging of the liver.
  • lamivudine Long term use of lamivudine unfortunately leads to emergence of a resistant hepatitis B virus mutants with alterations to the key YMDD motif in the reverse transcriptase active site. Despite this, lamivudine is still used widely as it is well tolerated and as it is less expensive than the newer drugs and is the only anti-HBV drug many people in emerging economies can afford.
  • Lamivudine is an analogue of cytidine. It can inhibit both types (1 and 2) of HIV reverse transcriptase and also the reverse transcriptase of hepatitis B. It is phosphorylated to active metabolites that compete for incorporation into viral DNA. It inhibits the HIV reverse transcriptase enzyme competitively and acts as a chain terminator of DNA synthesis. The lack of a 3′—OH group in the incorporated nucleoside analogue prevents the formation of the 5′ to 3′ phosphodiester linkage essential for DNA chain elongation, and therefore, the viral DNA growth is terminated. Lamivudine is administered orally, and it is rapidly absorbed with a bio-availability of over 80%. Some research suggests that lamivudine can cross the blood-brain barrier.
  • Entecavir is an oral antiviral drug used in the treatment of hepatitis B infection. It is marketed under the trade names Baraclude® (BMS) and Entaliv® (DRL). Entecavir is a nucleoside analog (more specifically, a guanosine analogue) that inhibits reverse transcription and DNA replication thus preventing transcription in the viral replication process. The drug's manufacturer claims that entecavir is more efficacious than previous agents used to treat hepatitis B (lamivudine and adefovir). Entecavir was approved by the U.S. FDA in March 2005 and is used to treat chronic hepatitis B. It also helps prevent the hepatitis B virus from multiplying and infecting new liver cells. Entecavir is also indicated for the treatment of chronic hepatitis B in adults with HIV/AIDS infection. However, entecavir is not active against HIV.
  • Telbivudine is an antiviral drug used in the treatment of hepatitis B infection. It is marketed by Swiss pharmaceutical company Novartis under the trade names Sebivo® (Europe) and Tyzeka® (United States). Clinical trials have shown it to be significantly more effective than lamivudine or adefovir, and less likely to cause resistance. Telbivudine is a synthetic thymidine nucleoside analogue; it is the L-isomer of thymidine. It is taken once daily.
  • Tenofovir disoproxil fumarate (TDF or PMPA), marketed by Gilead Sciences under the trade name Viread®, it is also a nucleotide analogue reverse transcriptase inhibitor (nRTIs) which blocks the HBV reverse transcriptase, an enzyme crucial to viral production.
  • Tenofovir disoproxil fumarate is a prodrug form of tenofovir.
  • Tenofovir is indicated in combination with other antiretroviral agents for the treatment of HIV-1 infection in adults. This indication is based on analyses of plasma HIV-1 RNA levels and CD4 cell counts in controlled studies of tenofovir in treatment-naive and treatment-experienced adults. There are no study results demonstrating the effect of tenofovir on the clinical progression of HIV. It also has activity against wild-type and lamivudine-resistant HBV.
  • RNAse H and integrase are members of the nucleotidyl transferase superfamily (NTS) whose members share a similar protein fold and enzymatic mechanisms (Yang 1995). Therefore, the presumed targets of the anti-herpesvirus compounds claimed here are viral and/or cellular NTS enzymes.
  • NTS nucleotidyl transferase superfamily
  • RNA primers during DNA synthesis, removal of abortive transcription products, and removal of RNA strands following reverse transcription by viruses or retrotransposons.
  • Integrase enzymes cleave DNA strands and catalyze the covalent insertion of another DNA strand at the cleavage site. Consequently, the presumed mechanism of action for the herpesvirus inhibitors is through suppression of one or more of the nucleolytic or recombination-related activities essential for replication of the herpesvirus DNA.
  • the NTS family of enzymes includes E. coli RNase H I and II (Katayanagi et al., 1990, Yang et al., 1990 and Lai et al., 2000); human RNase H 1 and 2 (Lima et al., 2001, Frank et al., 1998 and Frank et al., 1998); the RuvC Holiday junction resolvase (Ariyoshi et al., 1994); and the Argonaute RNAse (Parker et al., 2004 and Song et al., 2004); retroviral RNase H enzymes including the HIV enzyme (Nowotny 2009); retroviral integrases including the HIV integrase (Dyda et al., 1994); and the hepatitis B virus (HBV) RNase H (Tavis et al., 2013).
  • E. coli RNase H I and II Keratayanagi et al., 1990, Yang et al.
  • RNA and DNA digestion contains about 100 amino acids that fold into a 5-stranded ⁇ -sheet overlaid with 3 ⁇ -helices arranged like an “H”.
  • the canonical RNase H structure contains about 100 amino acids that fold into a 5-stranded ⁇ -sheet overlaid with 3 ⁇ -helices arranged like an “H”.
  • Within the active site are four conserved carboxylates (the “DEDD” motif) that coordinate two divalent cations (Nowotny et al., 2005).
  • RNA binding by the “stand-alone” class typified by E. coli RNAse H I is promoted by a basic “handle” region (Hostomsky et al., 1993; Kwun et al., 2001).
  • Eukaryotic RNase Hs typically contain a “RHBD” domain that influences nucleic acid binding.
  • substrate binding by the retroviral enzymes can either be a property of the RNase H domain itself (e.g., Moloney murine leukemia virus) or may require the reverse transcriptase domain to provide sufficient affinity for the nucleic acid substrate (e.g., HIV) (Hostomsky et al., 1993; Smith et al., 1994).
  • RNase H domain itself
  • reverse transcriptase domain to provide sufficient affinity for the nucleic acid substrate
  • the HBV RNase H is a NTS enzyme. Mutational analysis of the HBV RNase H revealed the DEDD active site residues to be D702, E731, D750, and D790 (numbering for HBV strain adw2) (Gerelsaikhan et al., 1996; Tavis et al., 2013). Data obtained with the HBV RNase H will be used as an example to establish how anti-RNase H drug discovery can be conducted and to establish utility of the claimed compounds against HBV replication.
  • HIV reverse transcription requires a virally encoded RNase H activity to remove the viral RNA after it has been copied into DNA (Freed and Martin, 2007). Consequently, the HIV RNase H activity has attracted much attention as a drug target (Billamboz et al., 2011; Bokesch et al., 2008; Budihas et al., 2005; Chung et al., 2011; Chung et al., 2010; Di et al., 2010; Didierjean et al., 2005; Fuji et al., 2009; Himmel et al., 2009; Himmel et al., 2006; Kirschberg et al., 2009; Klarmann et al., 2002; Klumpp et al., 2003; Klumpp and Mirzadegan, 2006; Shaw-Reid et al., 2003; Su et al., 2010; Takada et al., 2007; Wendeler et al., 2008; Williams et al., 2010).
  • the large majority of these compounds inhibit the RNase H by chelating divalent cations in the active site (Billamboz et al., 2011; Chung et al., 2011; Fuji et al., 2009; Himmel et al., 2009; Kirschberg et al., 2009; Su et al., 2010), but compounds that alter the enzyme's conformation or its interaction with nucleic acids have also been reported (Himmel et al., 2006; Wendeler et al., 2008).
  • the inhibitors typically have EC 50 values ⁇ 10 ⁇ higher than the IC 50 values, and they often cause modest cytotoxicity, leading to therapeutic indexes (TI) that are usually ⁇ 10.
  • Second-generation inhibitors with substantially improved efficacy have been reported, (Billamboz et al., 2011; Chung et al., 2011; Williams et al., 2010), and compounds with efficacy and TI values appropriate for a human drug exist (Himmel et al., 2006; Williams et al., 2010).
  • RNase H and integrase are NTS enzymes
  • some anti-RNase H compounds can inhibit the HIV integrase
  • some anti-integrase compounds can inhibit the RNase H (Klarmann et al., 2002, Williams et al., 2010 and Billamboz et al., 2011).
  • resistance mutations to HIV DNA polymerase or integrase drugs have not led to cross-resistance to RNase H inhibitors (Billamboz et al., 2011 and Himmel et al., 2006).
  • HBV reverse transcription requires two viral enzymatic activities that are both located on the viral reverse transcriptase protein.
  • the DNA polymerase activity synthesizes new DNA and is targeted by the nucleos(t)ide analogs.
  • the RNase H destroys the viral RNA after it has been copied into DNA. Inhibiting the RNAse H would block DNA synthesis and consequently halt viral replication, but anti-HBV RNase H drugs have not been developed because enzyme suitable for drug screening could not be readily made.
  • the compound of the present disclosure appears to inhibit a different enzymatic activity than the existing anti-hepatitis or anti-herpesvirus drugs, and does so with a striking capacity to suppress virus replication at very low toxicity to uninfected cells. This implies that it will be effective against viral isolates resistant to the existing drugs and suggests that these drugs could be combined effectively with the existing drugs to both increase efficacy and to reduce the rate of resistance development to either drug. Furthermore, the compound was more effective against HSV-2 than a currently accepted first line therapy, acyclovir, indicating that it may be more effective than the existing drugs when formulated for pharmaceutical delivery. In other embodiments, the present compounds may be used to treat infections of hepatitis B virus or used in combination with other hepatitis B virus therapies.
  • the compound of the disclosure contains one or more asymmetrically-substituted carbon or nitrogen atoms, and may be isolated in optically active or racemic form.
  • optically active or racemic form all chiral, diastereomeric, racemic form, epimeric form, and all geometric isomeric forms of the chemical formula are intended, unless the specific stereochemistry or isomeric form is specifically indicated.
  • the compound may occur as a racemate and racemic mixtures, single enantiomers, diastereomeric mixtures and individual diastereomers. In some embodiments, a single enantiomer or diastereomer is obtained.
  • the chiral centers of the compound of the present disclosure can have the S or the R configuration.
  • Chemical formulas used to represent the compound of the disclosure will typically only show one of possibly several different tautomers. For example, many types of ketone groups are known to exist in equilibrium with corresponding enol groups. Regardless of which tautomer is depicted for a given compound, and regardless of which one is most prevalent, all tautomers of a given chemical formula are intended.
  • the compound of the disclosure may also have the advantage of being more efficacious than, be less toxic than, be longer acting than, be more potent than, produce fewer side effects than, be more easily absorbed than, and/or have a better pharmacokinetic profile (e.g., higher oral bioavailability and/or lower clearance) than, and/or have other useful pharmacological, physical, or chemical properties over, compounds known in the prior art, whether for use in the indications stated herein or otherwise.
  • a better pharmacokinetic profile e.g., higher oral bioavailability and/or lower clearance
  • atoms making up the compound of the present disclosure are intended to include all isotopic forms of such atoms.
  • Isotopes include those atoms having the same atomic number but different mass numbers.
  • isotopes of hydrogen include tritium and deuterium
  • isotopes of carbon include 13 C and 14 C.
  • one or more carbon atom(s) of a compound of the present disclosure may be replaced by a silicon atom(s).
  • one or more oxygen atom(s) of a compound of the present disclosure may be replaced by a sulfur or selenium atom(s).
  • the compound of the present disclosure may also exist in prodrug form. Since prodrugs are known to enhance numerous desirable qualities of pharmaceuticals (e.g., solubility, bioavailability, manufacturing, etc.), the compound employed in some methods of the disclosure may, if desired, be delivered in prodrug form. Thus, the disclosure contemplates prodrugs of the compound of the present disclosure as well as methods of delivering prodrugs. Prodrugs of the compound employed in the disclosure may be prepared by modifying functional groups present in the compound in such a way that the modifications are cleaved, either in routine manipulation or in vivo, to the parent compound. Accordingly, prodrugs include, for example, compounds described herein in which a hydroxy group is bonded to any group that, when the prodrug is administered to a subject, cleaves to form a hydroxy group.
  • any salt of this disclosure is not critical, so long as the salt, as a whole, is pharmacologically acceptable. Additional examples of pharmaceutically acceptable salts and their methods of preparation and use are presented in Handbook of Pharmaceutical Salts: Properties, and Use (2002), which is incorporated herein by reference.
  • hydroxo means —O
  • carbonyl means —C( ⁇ O)—
  • carboxy means —C( ⁇ O)OH (also written as —COOH or —CO 2 H);
  • halo means independently —F, —Cl, —Br or —I;
  • amino means —NH 2 ;
  • hydroxyamino means —NHOH;
  • nitro means —NO 2 ;
  • imino means ⁇ NH;
  • cyano means —CN;
  • isocyanate means —N ⁇ C ⁇ O;
  • zido means —N 3 ; in a monovalent context “phosphate” means —OP(O)(OH) 2 or a deprotonated form thereof; in a divalent context “phosphate” means —OP(O)(OH)O— or a deprotonated form thereof; “mercapto”
  • the symbol “ ” means a single bond where the group attached to the thick end of the wedge is “out of the page.”
  • the symbol “ ” means a single bond where the group attached to the thick end of the wedge is “into the page”.
  • the symbol “ ” means a single bond where the geometry around a double bond (e.g., either E or Z) is undefined. Both options, as well as combinations thereof are therefore intended. Any undefined valency on an atom of a structure shown in this application implicitly represents a hydrogen atom bonded to that atom. A bold dot on a carbon atom indicates that the hydrogen attached to that carbon is oriented out of the plane of the paper.
  • R may replace any hydrogen atom attached to any of the ring atoms, including a depicted, implied, or expressly defined hydrogen, so long as a stable structure is formed.
  • R may replace any hydrogen atom attached to any of the ring atoms, including a depicted, implied, or expressly defined hydrogen, so long as a stable structure is formed.
  • R may replace any hydrogen attached to any of the ring atoms of either of the fused rings unless specified otherwise.
  • Replaceable hydrogens include depicted hydrogens (e.g., the hydrogen attached to the nitrogen in the formula above), implied hydrogens (e.g., a hydrogen of the formula above that is not shown but understood to be present), expressly defined hydrogens, and optional hydrogens whose presence depends on the identity of a ring atom (e.g., a hydrogen attached to group X, when X equals —CH—), so long as a stable structure is formed.
  • R may reside on either the 5-membered or the 6-membered ring of the fused ring system.
  • the subscript letter “y” immediately following the group “R” enclosed in parentheses represents a numeric variable. Unless specified otherwise, this variable can be 0, 1, 2, or any integer greater than 2, only limited by the maximum number of replaceable hydrogen atoms of the ring or ring system.
  • the number of carbon atoms in the group or class is as indicated as follows: “Cn” defines the exact number (n) of carbon atoms in the group/class. “C ⁇ n” defines the maximum number (n) of carbon atoms that can be in the group/class, with the minimum number as small as possible for the group/class in question, e.g., it is understood that the minimum number of carbon atoms in the group “alkenyl (C ⁇ 8) ” or the class “alkene (C ⁇ 8) ” is two. Compare with “alkoxy (C ⁇ 10) ”, which designates alkoxy groups having from 1 to 10 carbon atoms.
  • Cn-n′ defines both the minimum (n) and maximum number (n′) of carbon atoms in the group.
  • alkyl (C ⁇ 10) designates those alkyl groups having from 2 to 10 carbon atoms. These carbon number indicators may precede or follow the chemical groups or class it modifies and it may or may not be enclosed in parenthesis, without signifying any change in meaning.
  • the terms “C5 olefin”, “C5-olefin”, “olefin (C5) ”, and “olefin C5 ” are all synonymous.
  • any of the chemical groups or compound classes defined herein is modified by the term “substituted”, any carbon atom(s) in a moiety replacing a hydrogen atom is not counted.
  • methoxyhexyl which has a total of seven carbon atoms, is an example of a substituted alkyl (C1-6) .
  • saturated when used to modify a compound or chemical group means the compound or chemical group has no carbon-carbon double and no carbon-carbon triple bonds, except as noted below.
  • the term when used to modify an atom, it means that the atom is not part of any double or triple bond.
  • substituted versions of saturated groups one or more carbon oxygen double bond or a carbon nitrogen double bond may be present. And when such a bond is present, then carbon-carbon double bonds that may occur as part of keto-enol tautomerism or imine/enamine tautomerism are not precluded.
  • saturated when used to modify a solution of a substance, it means that no more of that substance can dissolve in that solution.
  • aliphatic when used without the “substituted” modifier signifies that the compound or chemical group so modified is an acyclic or cyclic, but non-aromatic hydrocarbon compound or group.
  • the carbon atoms can be joined together in straight chains, branched chains, or non-aromatic rings (alicyclic).
  • Aliphatic compounds/groups can be saturated, that is joined by single carbon-carbon bonds (alkanes/alkyl), or unsaturated, with one or more carbon-carbon double bonds (alkenes/alkenyl) or with one or more carbon-carbon triple bonds (alkynes/alkynyl).
  • aromatic when used to modify a compound or a chemical group refers to a planar unsaturated ring of atoms with 4n+2 electrons in a fully conjugated cyclic it system.
  • alkyl when used without the “substituted” modifier refers to a monovalent saturated aliphatic group with a carbon atom as the point of attachment, a linear or branched acyclic structure, and no atoms other than carbon and hydrogen.
  • the groups —CH 3 (Me), —CH 2 CH 3 (Et), —CH 2 CH 2 CH 3 (n-Pr or propyl), —CH(CH 3 ) 2 (i-Pr, i Pr or isopropyl), —CH 2 CH 2 CH 2 CH 3 (n-Bu), —CH(CH 3 )CH 2 CH 3 (sec-butyl), —CH 2 CH(CH 3 ) 2 (isobutyl), —C(CH 3 ) 3 (tert-butyl, t-butyl, t-Bu or t Bu), and —CH 2 C(CH 3 ) 3 (neo-pentyl) are non-limiting examples of alkyl groups.
  • alkanediyl when used without the “substituted” modifier refers to a divalent saturated aliphatic group, with one or two saturated carbon atom(s) as the point(s) of attachment, a linear or branched acyclic structure, no carbon-carbon double or triple bonds, and no atoms other than carbon and hydrogen.
  • the groups —CH 2 -(methylene), —CH 2 CH 2 —, —CH 2 C(CH 3 ) 2 CH 2 —, and —CH 2 CH 2 CH 2 — are non-limiting examples of alkanediyl groups.
  • alkylidene when used without the “substituted” modifier refers to the divalent group ⁇ CRR′ in which R and R′ are independently hydrogen or alkyl.
  • alkylidene groups include: ⁇ CH 2 , ⁇ CH(CH 2 CH 3 ), and ⁇ C(CH 3 ) 2 .
  • An “alkane” refers to the class of compounds having the formula H—R, wherein R is alkyl as this term is defined above.
  • the following groups are non-limiting examples of substituted alkyl groups: —CH 2 OH, —CH 2 Cl, —CF 3 , —CH 2 CN, —CH 2 C(O)OH, —CH 2 C(O)OCH 3 , —CH 2 C(O)NH 2 , —CH 2 C(O)CH 3 , —CH 2 OCH 3 , —CH 2 OC(O)CH 3 , —CH 2 NH 2 , —CH 2 N(CH 3 ) 2 , and —CH 2 CH 2 Cl.
  • aryl when used without the “substituted” modifier refers to a monovalent unsaturated aromatic group with an aromatic carbon atom as the point of attachment, said carbon atom forming part of a one or more six-membered aromatic ring structure, wherein the ring atoms are all carbon, and wherein the group consists of no atoms other than carbon and hydrogen. If more than one ring is present, the rings may be fused or unfused. As used herein, the term does not preclude the presence of one or more alkyl or aralkyl groups (carbon number limitation permitting) attached to the first aromatic ring or any additional aromatic ring present.
  • Non-limiting examples of aryl groups include phenyl (Ph), methylphenyl, (dimethyl)phenyl, —C 6 H 4 CH 2 CH 3 (ethylphenyl), naphthyl, and a monovalent group derived from biphenyl.
  • the term “arenediyl” when used without the “substituted” modifier refers to a divalent aromatic group with two aromatic carbon atoms as points of attachment, said carbon atoms forming part of one or more six-membered aromatic ring structure(s) wherein the ring atoms are all carbon, and wherein the monovalent group consists of no atoms other than carbon and hydrogen.
  • the term does not preclude the presence of one or more alkyl, aryl or aralkyl groups (carbon number limitation permitting) attached to the first aromatic ring or any additional aromatic ring present. If more than one ring is present, the rings may be fused or unfused. Unfused rings may be connected via one or more of the following: a covalent bond, alkanediyl, or alkenediyl groups (carbon number limitation permitting).
  • arenediyl groups include:
  • an “arene” refers to the class of compounds having the formula H—R, wherein R is aryl as that term is defined above. Benzene and toluene are non-limiting examples of arenes. When any of these terms are used with the “substituted” modifier one or more hydrogen atom has been independently replaced by —OH, —F, —Cl, —Br, —I, —NH 2 , —NO 2 , —CO 2 H, —CO 2 CH 3 , —CN, —SH, —OCH 3 , —OCH 2 CH 3 , —C(O)CH 3 , —NHCH 3 , —NHCH 2 CH 3 , —N(CH 3 ) 2 , —C(O)NH 2 , —C(O)NHCH 3 , —C(O)N(CH 3 ) 2 , —OC(O)CH 3 , —NHC(O)CH 3 , —S(O) 2
  • aralkyl when used without the “substituted” modifier refers to the monovalent group -alkanediyl-aryl, in which the terms alkanediyl and aryl are each used in a manner consistent with the definitions provided above.
  • Non-limiting examples are: phenylmethyl (benzyl, Bn) and 2-phenyl-ethyl.
  • aralkyl When the term aralkyl is used with the “substituted” modifier one or more hydrogen atom from the alkanediyl and/or the aryl group has been independently replaced by —OH, —F, —Cl, —Br, —I, —NH 2 , —NO 2 , —CO 2 H, —CO 2 CH 3 , —CN, —SH, —OCH 3 , —OCH 2 CH 3 , —C(O)CH 3 , —NHCH 3 , —NHCH 2 CH 3 , —N(CH 3 ) 2 , —C(O)NH 2 , —C(O)NHCH 3 , —C(O)N(CH 3 ) 2 , —OC(O)CH 3 , —NHC(O)CH 3 , —S(O) 2 OH, or —S(O) 2 NH 2 .
  • substituted aralkyls are:
  • heteroaryl when used without the “substituted” modifier refers to a monovalent aromatic group with an aromatic carbon atom or nitrogen atom as the point of attachment, said carbon atom or nitrogen atom forming part of one or more aromatic ring structures wherein at least one of the ring atoms is nitrogen, oxygen or sulfur, and wherein the heteroaryl group consists of no atoms other than carbon, hydrogen, aromatic nitrogen, aromatic oxygen and aromatic sulfur. If more than one ring is present, the rings may be fused or unfused. As used herein, the term does not preclude the presence of one or more alkyl, aryl, and/or aralkyl groups (carbon number limitation permitting) attached to the aromatic ring or aromatic ring system.
  • heteroaryl groups include furanyl, imidazolyl, indolyl, indazolyl (Im), isoxazolyl, methylpyridinyl, oxazolyl, phenylpyridinyl, pyridinyl (pyridyl), pyrrolyl, pyrimidinyl, pyrazinyl, quinolyl, quinazolyl, quinoxalinyl, triazinyl, tetrazolyl, thiazolyl, thienyl, and triazolyl.
  • N-heteroaryl refers to a heteroaryl group with a nitrogen atom as the point of attachment.
  • a “heteroarene” refers to the class of compounds having the formula H—R, wherein R is heteroaryl. Pyridine and quinoline are non-limiting examples of heteroarenes. When these terms are used with the “substituted” modifier one or more hydrogen atom has been independently replaced by —OH, —F, —Cl, —Br, —I, —NH 2 , —NO 2 , —CO 2 H, —CO 2 CH 3 , —CN, —SH, —OCH 3 , —OCH 2 CH 3 , —C(O)CH 3 , —NHCH 3 , —NHCH 2 CH 3 , —N(CH 3 ) 2 , —C(O)NH 2 , —C(O)NHCH 3 , —C(O)N(CH 3 ) 2 , —OC(O)CH 3 , —NHC(O)CH 3 , —S(O) 2 OH, or —S
  • acyl when used without the “substituted” modifier refers to the group —C(O)R, in which R is a hydrogen, alkyl, cycloalkyl, or aryl as those terms are defined above.
  • the groups, —CHO, —C(O)CH 3 (acetyl, Ac), —C(O)CH 2 CH 3 , —C(O)CH(CH 3 ) 2 , —C(O)CH(CH 2 ) 2 , —C(O)C 6 H 5 , and —C(O)C 6 H 4 CH 3 are non-limiting examples of acyl groups.
  • a “thioacyl” is defined in an analogous manner, except that the oxygen atom of the group —C(O)R has been replaced with a sulfur atom, —C(S)R.
  • aldehyde corresponds to an alkyl group, as defined above, attached to a —CHO group.
  • one or more hydrogen atom (including a hydrogen atom directly attached to the carbon atom of the carbonyl or thiocarbonyl group, if any) has been independently replaced by —OH, —F, —Cl, —Br, —I, —NH 2 , —NO 2 , —CO 2 H, —CO 2 CH 3 , —CN, —SH, —OCH 3 , —OCH 2 CH 3 , —C(O)CH 3 , —NHCH 3 , —NHCH 2 CH 3 , —N(CH 3 ) 2 , —C(O)NH 2 , —C(O)NHCH 3 , —C(O)N(CH 3 ) 2 , —OC(O)CH 3 , —NHC(O)CH 3 , —S(O) 2 OH, or —S(O) 2 NH 2 .
  • the groups, —C(O)CH 2 CF 3 , —CO 2 H (carboxyl), —CO 2 CH 3 (methylcarboxyl), —CO 2 CH 2 CH 3 , —C(O)NH 2 (carbamoyl), and —CON(CH 3 ) 2 are non-limiting examples of substituted acyl groups.
  • alkoxy when used without the “substituted” modifier refers to the group —OR, in which R is an alkyl, as that term is defined above.
  • R is an alkyl
  • Non-limiting examples include: —OCH 3 (methoxy), —OCH 2 CH 3 (ethoxy), —OCH 2 CH 2 CH 3 , —OCH(CH 3 ) 2 (isopropoxy), —OC(CH 3 ) 3 (tert-butoxy), —OCH(CH 2 ) 2 , —O-cyclopentyl, and —O-cyclohexyl.
  • cycloalkoxy when used without the “substituted” modifier, refers to groups, defined as —OR, in which R is cycloalkyl, alkenyl, alkynyl, aryl, aralkyl, heteroaryl, heterocycloalkyl, and acyl, respectively.
  • alkylthio and “acylthio” when used without the “substituted” modifier refers to the group —SR, in which R is an alkyl and acyl, respectively.
  • alcohol corresponds to an alkane, as defined above, wherein at least one of the hydrogen atoms has been replaced with a hydroxy group.
  • ether corresponds to an alkane, as defined above, wherein at least one of the hydrogen atoms has been replaced with an alkoxy group.
  • alkylamino when used without the “substituted” modifier refers to the group —NHR, in which R is an alkyl, as that term is defined above. Non-limiting examples include: —NHCH 3 and —NHCH 2 CH 3 .
  • dialkylamino when used without the “substituted” modifier refers to the group —NRR′, in which R and R′ can be the same or different alkyl groups, or R and R′ can be taken together to represent an alkanediyl.
  • dialkylamino groups include: —N(CH 3 ) 2 and —N(CH 3 )(CH 2 CH 3 ).
  • cycloalkylamino when used without the “substituted” modifier, refers to groups, defined as —NHR, in which R is cycloalkyl, alkenyl, alkynyl, aryl, aralkyl, heteroaryl, heterocycloalkyl, alkoxy, and alkylsulfonyl, respectively.
  • a non-limiting example of an arylamino group is —NHC 6 H 5 .
  • a non-limiting example of an amido group is —NHC(O)CH 3 .
  • alkylimino when used without the “substituted” modifier refers to the divalent group ⁇ NR, in which R is an alkyl, as that term is defined above.
  • the term “about” is used to indicate that a value includes the inherent variation of error for the device, the method being employed to determine the value, or the variation that exists among the study subjects, or +/ ⁇ 5% of the stated value.
  • “effective,” as that term is used in the specification and/or claims, means adequate to accomplish a desired, expected, or intended result. “Effective amount,” “Therapeutically effective amount” or “pharmaceutically effective amount” when used in the context of treating a patient or subject with a compound means that amount of the compound which, when administered to a subject or patient for treating a disease, is sufficient to effect such treatment for the disease.
  • IC 50 refers to an inhibitory dose which is 50% of the maximum response obtained. This quantitative measure indicates how much of a particular drug or other substance (inhibitor) is needed to inhibit a given biological, biochemical or chemical process (or component of a process, i.e. an enzyme, cell, cell receptor or microorganism) by half.
  • An “isomer” of a first compound is a separate compound in which each molecule contains the same constituent atoms as the first compound, but where the configuration of those atoms in three dimensions differs.
  • the term “patient” or “subject” refers to a living vertebrate organism, such as a human, monkey, cow, sheep, goat, dog, cat, mouse, rat, guinea pig, bird, fish or transgenic species thereof.
  • the patient or subject is a primate.
  • Non-limiting examples of human subjects are adults, juveniles, infants and fetuses.
  • “pharmaceutically acceptable” refers to those compounds, materials, compositions, and/or dosage forms which are, within the scope of sound medical judgment, suitable for use in contact with the tissues, organs, and/or bodily fluids of human beings and animals without excessive toxicity, irritation, allergic response, or other problems or complications commensurate with a reasonable benefit/risk ratio.
  • “Pharmaceutically acceptable salts” means salts of the compound of the present disclosure which are pharmaceutically acceptable, as defined above, and which possess the desired pharmacological activity. Such salts include acid addition salts formed with inorganic acids such as hydrochloric acid, hydrobromic acid, sulfuric acid, nitric acid, phosphoric acid, and the like; or with organic acids such as 1,2-ethanedisulfonic acid, 2-hydroxyethanesulfonic acid, 2-naphthalenesulfonic acid, 3-phenylpropionic acid, 4,4′-methylenebis(3-hydroxy-2-ene-1-carboxylic acid), 4-methylbicyclo[2.2.2]oct-2-ene-1-carboxylic acid, acetic acid, aliphatic mono- and dicarboxylic acids, aliphatic sulfuric acids, aromatic sulfuric acids, benzenesulfonic acid, benzoic acid, camphorsulfonic acid, carbonic acid, cinnamic acid, citric acid
  • Pharmaceutically acceptable salts also include base addition salts which may be formed when acidic protons present are capable of reacting with inorganic or organic bases.
  • Acceptable inorganic bases include sodium hydroxide, sodium carbonate, potassium hydroxide, aluminum hydroxide and calcium hydroxide.
  • Acceptable organic bases include ethanolamine, diethanolamine, triethanolamine, tromethamine, N-methylglucamine and the like. It should be recognized that the particular anion or cation forming a part of any salt of this disclosure is not critical, so long as the salt, as a whole, is pharmacologically acceptable. Additional examples of pharmaceutically acceptable salts and their methods of preparation and use are presented in Handbook of Pharmaceutical Salts: Properties, and Use (2002).
  • Prevention includes: (1) inhibiting the onset of a disease in a subject or patient which may be at risk and/or predisposed to the disease but does not yet experience or display any or all of the pathology or symptomatology of the disease, and/or (2) slowing the onset of the pathology or symptomatology of a disease in a subject or patient which may be at risk and/or predisposed to the disease but does not yet experience or display any or all of the pathology or symptomatology of the disease, including reactivation.
  • Prodrug means a compound that is convertible in vivo metabolically into an inhibitor according to the present disclosure.
  • the prodrug itself may or may not also have activity with respect to a given target protein.
  • a compound comprising a hydroxy group may be administered as an ester that is converted by hydrolysis in vivo to the hydroxy compound.
  • esters that may be converted in vivo into hydroxy compounds include acetates, citrates, lactates, phosphates, tartrates, malonates, oxalates, salicylates, propionates, succinates, fumarates, maleates, methylene-bis- ⁇ -hydroxynaphthoate, gentisates, isethionates, di-p-toluoyltartrates, methanesulfonates, ethanesulfonates, benzenesulfonates, p-toluenesulfonates, cyclohexylsulfamates, quinates, esters of amino acids, and the like.
  • a compound comprising an amine group may be administered as an amide that is converted by hydrolysis in vivo to the amine compound.
  • a “stereoisomer” or “optical isomer” is an isomer of a given compound in which the same atoms are bonded to the same other atoms, but where the configuration of those atoms in three dimensions differs.
  • “Enantiomers” are stereoisomers of a given compound that are mirror images of each other, like left and right hands.
  • “Diastereomers” are stereoisomers of a given compound that are not enantiomers.
  • Chiral molecules contain a chiral center, also referred to as a stereocenter or stereogenic center, which is any point, though not necessarily an atom, in a molecule bearing groups such that an interchanging of any two groups leads to a stereoisomer.
  • the chiral center is typically a carbon, phosphorus or sulfur atom, though it is also possible for other atoms to be stereocenters in organic and inorganic compounds.
  • a molecule can have multiple stereocenters, giving it many stereoisomers.
  • the total number of hypothetically possible stereoisomers will not exceed 2 n , where n is the number of tetrahedral stereocenters.
  • Molecules with symmetry frequently have fewer than the maximum possible number of stereoisomers.
  • a 50:50 mixture of enantiomers is referred to as a racemic mixture.
  • a mixture of enantiomers can be enantiomerically enriched so that one enantiomer is present in an amount greater than 50%.
  • enantiomers and/or diasteromers can be resolved or separated using techniques known in the art. It is contemplated that for any stereocenter or axis of chirality for which stereochemistry has not been defined, that stereocenter or axis of chirality can be present in its R form, S form, or as a mixture of the R and S forms, including racemic and non-racemic mixtures.
  • the phrase “substantially free from other stereoisomers” means that the composition contains ⁇ 15%, more preferably ⁇ 10%, even more preferably ⁇ 5%, or most preferably ⁇ 1% of another stereoisomer(s).
  • Effective amount means that amount which, when administered to a subject or patient for treating a disease, is sufficient to effect such treatment for the disease.
  • Treatment includes (1) inhibiting a disease in a subject or patient experiencing or displaying the pathology or symptomatology of the disease (e.g., arresting further development of the pathology and/or symptomatology), (2) ameliorating a disease in a subject or patient that is experiencing or displaying the pathology or symptomatology of the disease (e.g., reversing the pathology and/or symptomatology), and/or (3) effecting any measurable decrease in a disease in a subject or patient that is experiencing or displaying the pathology or symptomatology of the disease.
  • treatment of a patient afflicted with one of the pathological conditions described herein comprises administering to such a patient an amount of compound described herein which is therapeutically effective in controlling the condition or in prolonging the survivability of the patient beyond that expected in the absence of such treatment.
  • the term “inhibition” of the condition also refers to slowing, interrupting, arresting or stopping the condition and does not necessarily indicate a total elimination of the condition. It is believed that prolonging the survivability of a patient, beyond being a significant advantageous effect in and of itself, also indicates that the condition is beneficially controlled to some extent.
  • a pharmaceutical composition appropriate for the intended application.
  • this will entail preparing a pharmaceutical composition that is essentially free of pyrogens, as well as any other impurities or contaminants that could be harmful to humans or animals.
  • One also will generally desire to employ appropriate buffers to render the complex stable and allow for uptake by target cells.
  • compositions of the present disclosure comprise an effective amount of the active compound, as discussed above, further dispersed in pharmaceutically acceptable carrier or aqueous medium. Such compositions also are referred to as inocula.
  • pharmaceutically or pharmacologically acceptable refers to compositions that do not produce an adverse, allergic or other untoward reaction when administered to an animal, or a human, as appropriate, as well as the requisite sterility for in vivo uses.
  • “pharmaceutically acceptable carrier” includes any and all solvents, dispersion media, coatings, antibacterial and antifungal agents, isotonic and absorption delaying agents and the like. The use of such media and agents for pharmaceutically active substances is well known in the art. Except insofar as any conventional media or agent is incompatible with the active ingredient, its use in the therapeutic compositions is contemplated. Supplementary active ingredients also can be incorporated into the compositions.
  • Solutions of therapeutic compositions can be prepared in water suitably mixed with a surfactant, such as hydroxypropylcellulose.
  • Dispersions also can be prepared in glycerol, liquid polyethylene glycols, mixtures thereof and in oils. Under ordinary conditions of storage and use, these preparations contain a preservative to prevent the growth of microorganisms.
  • compositions of the present disclosure are advantageously administered in the form of injectable compositions either as liquid solutions or suspensions; solid forms suitable for solution in, or suspension in, liquid prior to injection may also be prepared. These preparations also may be emulsified.
  • a typical composition for such purpose comprises a pharmaceutically acceptable carrier.
  • the composition may contain 10 mg, 25 mg, 50 mg or up to about 100 mg of human serum albumin per milliliter of phosphate buffered saline.
  • Other pharmaceutically acceptable carriers include aqueous solutions, non-toxic excipients, including salts, preservatives, buffers and the like.
  • non-aqueous solvents examples include propylene glycol, polyethylene glycol, vegetable oil and injectable organic esters such as ethyloleate.
  • Aqueous carriers include water, alcoholic/aqueous solutions, saline solutions, parenteral vehicles such as sodium chloride, Ringer's dextrose, etc.
  • Intravenous vehicles include fluid and nutrient replenishers.
  • Preservatives include antimicrobial agents, anti-oxidants, chelating agents and inert gases. The pH and exact concentration of the various components the pharmaceutical composition are adjusted according to well-known parameters.
  • Oral formulations include such typical excipients as, for example, pharmaceutical grades of mannitol, lactose, starch, magnesium stearate, sodium saccharine, cellulose, magnesium carbonate and the like.
  • the compositions take the form of solutions, suspensions, tablets, pills, capsules, sustained release formulations or powders.
  • the route is topical, the form may be a cream, ointment, a controlled release patch, salve or spray.
  • the topical formulation by used for administration to the skin, to mucosa membranes such as the eye, eye lids, the genitals, the anus, or the inside of the mouth or nose, and in particular to the cornea.
  • unit dose refers to physically discrete units suitable for use in a subject, each unit containing a predetermined quantity of the therapeutic composition calculated to produce the desired responses, discussed above, in association with its administration, i.e., the appropriate route and treatment regimen.
  • the quantity to be administered both according to number of treatments and unit dose, depends on the protection desired.
  • Precise amounts of the therapeutic composition also depend on the judgment of the practitioner and are peculiar to each individual. Factors affecting dose include physical and clinical state of the patient, the route of administration, the intended goal of treatment and the potency, stability and toxicity of the particular therapeutic substance.
  • Formulations of the present disclosure are suitable for oral administration.
  • the therapeutic compositions of the present disclosure may be administered via any common route so long as the target tissue is available via that route. This includes nasal, buccal, corneal, ocularly, rectal, vaginal, or topical administration, and intradermal, subcutaneous, intramuscular, intraperitoneal or intravenous injection.
  • compositions would be formulated pharmaceutically in route-acceptable compositions that include physiologically acceptable carriers, buffers or other excipients.
  • the timing of delivery depends on the judgment of the practitioner and are peculiar to each individual. Factors affecting dose include physical and clinical state of the patient, the route of administration, the intended goal of treatment and the potency, stability and toxicity of the particular therapeutic substance.
  • Combinations may be achieved by administering a single composition or pharmacological formulation that includes both agents, or with two distinct compositions or formulations, at the same time, wherein one composition includes the agents of the present disclosure and the other includes the standard therapy.
  • standard therapy may precede or follow the present agent treatment by intervals ranging from minutes to weeks to months.
  • Drugs suitable for such combinations include, but are not limited to, DNA polymerase inhibitors (nucleoside analogs), including acyclovir, famciclovir, valaciclovir, penciclovir, and ganciclovir. Additionally, it is contemplated that other antiviral agents such as a pegylated interferon, interferon alfa-2b, lamivudine, adefovir, telbivudine, entercavir, or tenofovir may be used in combination with the compounds described herein.
  • Vero cells were maintained in Dulbecco's modified Eagle's medium (DMEM) containing 3% newborn calf serum, 3% bovine growth serum, 2 mM L-glutamine and 100 IU/mL penicillin and 0.1 mg/mL streptomycin (P/S).
  • DMEM Dulbecco's modified Eagle's medium
  • HSV-1 #6 and HSV-2 #1 are de-identified clinical isolates from the Saint Louis University Hospital. Stocks were prepared after a single passage in cell culture and were titered by standard plaque assay (Knipe and Spang, 1982). Wild-type HSV-2 used in FIG. 3 was laboratory strain 333.
  • TK-deficient mutant of HSV-2 strain 333 contains a 180-bp KpnI-KpnI deletion in the UL23 open reading frame that abrogates TK activity (McDermott, et al, 1984).
  • ⁇ TK ⁇ was the generous gift of Jim Smiley. Virus stocks were grown and titered on Vero cells (Morrison and Knipe, 1996).
  • the compound was selected for evaluation of its ability to inhibit HSV replication based on one or more of the following criteria:
  • Compounds to be screened were diluted in PBS supplemented to contain 2% newborn calf serum and 1% glutamine, and added in 100 ⁇ L volume to confluent cell monolayers in 24-well cluster plates. Immediately thereafter HSV-1 and HSV-2, diluted in the supplemented PBS medium, were added to the wells in 50 ⁇ l volume such that the final concentration of compound was 50 ⁇ M, 5 ⁇ M and 1 ⁇ M and the multiplicity of infection was 0.1. The plates were incubated at 37° C. for 1 hour and then virus-containing inoculum was removed and the wells were washed once in PBS.
  • Mitochondrial toxicity was measured by incubating the cells with 0.25 mg/mL thiazolyl blue tetrazolium bromide (MTT, SigmaAldrich Chemical Co.), the cultures were incubated for 60 min, metabolites were solubilized in acidic isopropanol, and absorbance was read at 570 nm. CC 50 values were calculated by non-linear curve fitting using GraphPad Prism.
  • Microsomal incubations are run at a final P450 concentration of 0.25 ⁇ M.
  • the microsomal mixture is composed of 0.1M potassium phosphate containing 3.3 mM MgCl and 1 ⁇ M compound (final concentration). The mixture is prewarmed for 5 min at 37° C.
  • a 12 mM stock of NAPDH (1.2 mM, final concentration) is added to the warmed microsomal mixture and aliquots are removed at 0, 5, 10, 20 and 30 min. Samples are quenched with ice cold acetonitrile containing internal standard and either 1.8 mM EDTA or EGTA (final concentration). Samples are vortexed and spun down at 3200 rpm for 5 min. The supernant is transferred to 96-deep well plates and run on LC/MS/MS.
  • Recombinant HBV RNaseH and human RNaseH1 were expressed in E. coli and partially purified by nickel-affinity chromatography as previously described in Tavis, et al. (2013).
  • the enriched extracts were dialyzed into 50 mM HEPES pH 7.3, 300 mM NaCl, 20% glycerol, and 5 mM DTT and stored in liquid nitrogen.
  • Oligonucleotide-Directed RNA Cleavage Assay Oligonucleotide-Directed RNA Cleavage Assay.
  • RNaseH activity was measured using an oligonucleotide-directed RNA cleavage assay as previously described in Hu, et al., Tavis, et al., and Cai, et al. (2013; 2013; and 2014, respectfully). Briefly, 6 ⁇ L protein extract was mixed on ice with an internally 32 P-labeled 264 nt RNA derived from the Duck Hepatitis B Virus genome (DRF+ RNA) plus 3 ⁇ g oligonucleotide D2507- or its inverse-complement oligonucleotide D2526+ as a negative control.
  • DRF+ RNA Duck Hepatitis B Virus genome
  • HBV replication was measured in HepDES19 cells as previously described in Cai, et al. (2014).
  • Cells were seeded into 6-well plates and incubated in DMEM/F12, 10% fetal bovine serum (FBS), 1% penicillin/streptomycin (P/S) with 1 ⁇ g/mL tetracycline. Tetracycline was withdrawn after 24 hours.
  • the test compound was applied to duplicate wells 48 hours later in medium containing a final DMSO concentration of 1%, and medium containing the compound was refreshed daily for the following two days.
  • Cells were harvested and non-encapsidated nucleic acids were digested with micrococcal nuclease (New England Biolabs).
  • HBV DNA was purified from capsids using QIAamp Cador Pathogen Mini Kit (Qiagen) with proteinase K incubation overnight at 37° C.
  • TaqMan PCR was performed for 40 cycles at an annealing temperature of 60° C.
  • Primers and probe (IDT Inc.) for the plus-polarity strand were: 5′CATGAACAAGAGATGATTAGGCAGAG3′; 5′GGAGGCTGTAGGCATAAATTGG3′; 5′/56-FAM/CTGCGCACC/ZEN/AGCACCATGCA/3IABkFQ.
  • Primers and probe for the minus-polarity strand were: 5′ GCAGATGAGAAGGCACAGA3′; 5′CTTCTCCGTCTGCCGTT3′; 5′/56-FAM/AGTCCGCGT/ZEN/AAAGAGAGGTGCG/3IABkFQ.
  • This compound was selected based on its structural similarity to polyoxygenated heterocycle compounds with anti-microbial activity.
  • Piroctone olamine (octopirox; #191) is an approved antifungal in Europe. Its structure is shown in FIG. 1 .
  • octopirox octopirox
  • FIG. 1 Nine napthyridinones were tested for capacity to inhibit the nuclease activity of pUL15C (Masaoka et al., 2016). Seven of these inhibited nuclease activity with IC 50 values ⁇ 2 ⁇ M, and two of the seven compounds (#151 and 155) strongly suppressed HSV-1 and HSV-2 replication in cell culture at 5 ⁇ M or less (Table 2).
  • Efficacy of this compound against both HSV-1 and HSV-2 was initially assessed at 50, 5 and 1 ⁇ M in a semi-quantitative replication inhibition assay. Inhibition was categorized as negligible ( ⁇ 1 log 10 at 50 ⁇ M relative to the DMSO-treated control), intermediate (1 to 3 log 10 suppression, which equals 10- to 1,000-fold reduction), or strong (3 to 6 log 10 suppression, or 1,000- to 1,000,000-fold reduction).
  • Compound #191 piroctone olamine or octopirox
  • Compound #191 maintained intermediate inhibition of HSV-1 and HSV-2 even at 1 ⁇ M (Table 2).
  • HSV-1 inhibited HSV-1 by 3.61 log 10 (4,074-fold) and HSV-2 by 4.59 log 10 (39,000-fold) at 5 ⁇ M.
  • the approved anti-HSV drug acyclovir inhibited HSV-1 replication in this assay by 4.22 log 10 (16,600-fold) and HSV-2 by only 3.6 log 10 (3,980-fold) at 5 ⁇ M. Therefore, this polyoxygenated heterocycle compound inhibits both HSV-1 and HSV-2 replication as well as or better than acyclovir.
  • a quantitative toxicity measurement was conducted. Toxicity was assessed by measuring release of intracellular proteases into the culture medium due to cellular lysis. Cells were plated in 96-well plates at 1.0 ⁇ 10 4 per well. The next day compound was added in concentrations ranging from 0.78 to 100 ⁇ M in a final concentration of 1% (v/v) DMSO. The cells were incubated for 24 hours under conditions identical to those employed for the viral replication inhibition assays, and then mitochondrial activity was measured with the MTT assay (Sigma Aldrich) according to the manufacturer's instructions. Percent viability was determined for each compound concentration from the luminosity data, and then 50% cytotoxic concentration (CC 50 ) value was calculated by non-linear curve fitting using GraphPad Prism. Consistent with the subjective assessments of toxicity, #191 had a CC 50 value >100 ⁇ M under these conditions (Table 1). #191 did not inhibit the activity of human RNaseH1 (Table 1), another indicator of low toxicity.
  • Compound #191 suppressed replication of three primary clinical isolates of HSV-2 by >4.7 log 10 at 5 ⁇ M ( FIG. 2 ), indicating that it is active against a range of clinically relevant virus strains.
  • ACV is a nucleoside analog prodrug that must be phosphorylated by the viral thymidine kinase (TK) for it to become a substrate for the viral DNA polymerase (Elion, et al., 1977). HSV TK-deficient mutants are therefore insensitive to ACV.
  • TK viral thymidine kinase
  • the cells were treated with 5 ⁇ M ACV or compound #191 as was done in the primary screening assays, and viral yields 24 hours post-infection were measured by plaque assay.
  • ACV 5 ⁇ M inhibited wild-type HSV-2 replication 100-fold, but it had little effect on the TK ⁇ mutant ( FIG. 3 ).
  • compound #191 efficiently inhibited the wild-type HSV-2 and the TK ⁇ mutant strain. Therefore, this compound does not require phosphorylation by the viral TK gene to be active, confirming that compound #191 suppress HSV-2 replication in a different manner than ACV.
  • Table 3 shows the elimination profile of compounds #191, #41, and #208.
  • the table shows the half life, the intrinsic clearance, the hepatic clearance, extraction ratio, and methods of turnover.
  • Several compounds tested in mouse liver microsomes had long half-lives, low extraction ratios, and no evidence of non-P450 turnover (Table 3), suggesting their capacity to resist rapid degradation and elimination by the liver.
  • the inventors here demonstrate that a polyoxygenated heterocycle compound profoundly suppresses replication of HSV-1 and HSV-2 with no measurable toxicity in a short-term cell culture assay. Inhibition by this primary screening hit is equal or superior to the approved anti-herpesvirus drug acyclovir, particularly against HSV-2.
  • the existing compound may already be superior to the drugs that are used for HSV-2 infection, and improved efficacy can readily be envisioned through standard medicinal chemistry approaches.
  • Its structural dissimilarity to the nucleoside analogs implies a novel mode of action, suggesting it would be a good candidate for combination therapy with the existing anti-herpesvirus drugs to improve efficacy of antiviral therapy.
  • HBV activity of some of the compounds described herein is shown in Table 4 below.
  • HBV Activity Com- Qualitative HBV pound EC 50 CC 50 replication Number Compound ( ⁇ M) ( ⁇ M) inhibition assay 151 4.7 15 ** 153 4.1 10 ** 210 1.5 71 ** 208 0.69 15 ** 211 13 30 ** 49 ND 9 — ** + DNA suppression ⁇ 25% and ⁇ DNA suppression >60% *+ DNA suppression ⁇ 50% of ⁇ DNA suppression ND - not determined
  • RNAseH inhibitors from two different chemical classes were employed, compound #1 [2-hydroxyisoquinoline-1,3(2H,4H)-dione], an HID, and #46 ( ⁇ -thujaplicinol), an ⁇ -hydroxytropolone, were tested. Chou-Talaly analysis yields a combination index (CI). CI values ⁇ 1.0 indicate synergy, CIs of approximately 1.0 indicate additive interactions, and CI values >1.0 indicate antagonism. CI values are calculated at various efficacy levels (EC 50 , EC 75 , EC 90 , and EC 95 ), and a weighted CI value favoring higher efficacy levels is also generated. FIGS.
  • RNAseH inhibitors act strongly synergistically with an approved nucleos(t)ide analog drug against HBV. This demonstrates feasibility for employing RNAseH inhibitors in combination therapy with the nucleos(t)ide analogs during HBV treatment.
  • RNAseH Inhibitor Sensitivity is Insensitive to High Genetic Variation
  • RNAseH inhibitors #1 [2-hydroxyisoquinoline-1,3(2H,4H)-dione], an HID, and #46 (P3-thujaplicinol), an ⁇ -hydroxytropolone, for the ability to inhibit variant RNAseHs. Twelve purified, patient-derived RNAseH enzymes (4 from each genotypes B, C and D) were tested with the compounds at their respective IC 50 values in a biochemical RNAseH assay.
  • compositions and methods disclosed and claimed herein can be made and executed without undue experimentation in light of the present disclosure. While the compositions and methods of this disclosure have been described in terms of preferred embodiments, it will be apparent to those of skill in the art that variations may be applied to the compositions and methods, and in the steps or in the sequence of steps of the methods described herein without departing from the concept, spirit and scope of the disclosure. More specifically, it will be apparent that certain agents which are both chemically and physiologically related may be substituted for the agents described herein while the same or similar results would be achieved. All such similar substitutes and modifications apparent to those skilled in the art are deemed to be within the spirit, scope and concept of the disclosure as defined by the appended claims.

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Abstract

The present disclosure relates to identification of inhibitors of hepatitis and herpesvirus replication including compounds of the formula: wherein the variables are as defined herein. Also provided are methods of treatment using agents so identified.
Figure US20180169083A1-20180621-C00001

Description

  • The present application claims benefit of priority to U.S. Provisional Application Ser. No. 62/174,385, filed Jun. 11, 2015, and U.S. Provisional Application Ser. No. 62/309,303, filed Mar. 16, 2016, the entire contents of which are hereby incorporated by reference.
  • The invention was made with government support under Grant No. Grants No. R01 AI104494, U01 DK082871, and R03 AI109460 awarded by the National Institutes of Health.
  • The government has certain rights in the invention.
    • BACKGROUND I. Field
  • The disclosure relates to the fields of pathology, virology, molecular biology and pharmaceuticals. More specifically, the disclosure relates to the identification of candidate inhibitors for the treatment and prevention of herpesvirus and hepatitis B diseases. Also provided are compounds having such activity.
    • II. Related Art
  • Herpesviridae is a large family of DNA viruses that cause diseases in vertebrates, including humans. These viruses are significant pathogens and, in addition to primary infections, cause latent, recurring infections. At least six species of Herpesviridae—herpes simplex virus 1 (HSV-1) and HSV-2 (both of which can cause orolabial herpes and genital herpes), Varicella-zoster virus (which causes chickenpox and shingles), Epstein-Barr virus (which causes mononucleosis), Cytomegalovirus (which causes mental retardation and deafness in neonates), and Human herpesvirus 6B (which causes roseola infantum and febrile seizures)—are extremely widespread among humans. More than 90% of adults have been infected with at least one of these, and a latent form of the virus remains in most people. Other viruses with human tropism include human herpesvirus 6A, human herpesvirus 7 and Kaposi's sarcoma-associated herpesvirus. There are more than 130 herpesviruses, including those that infect non-human mammals, birds, fish, reptiles, amphibians, and mollusks.
  • The drugs, acyclovir and ganciclovir, are considered the standard treatments and prophylactic agents for infections caused by HSV, VZV and CMV. Until a decade ago, the impact of acyclovir on the control of severe and life-threatening herpesvirus infections was unprecedented. Recently, approval of new drugs (i.e., penciclovir and the oral prodrugs, valaciclovir, famciclovir, cidofovir, fomivirsen, and foscamet) has increased the number of therapeutic options for medical practitioners. Newer agents, such as brivudin and benzimidavir, are in ongoing clinical development, while others have been suspended because of safety concerns. Regardless, new anti-herpes agents are needed to face clinical issues such as drug resistance, increased use of anti-herpes prophylaxis, and safety concerns in small children or pregnant women.
  • Similarly, hepatitis B virus (HBV) is a hepatotropic DNA virus that replicates by reverse transcription (Hostomsky et al., 1993). It chronically infects >350 million people world-wide and kills up to 1.2 million patients annually by inducing liver failure and liver cancer (Steitz, 1995; Katayanagi et al., 1990; Yang et al., 1990; Lai et al., 2000). Reverse transcription is catalyzed by a virally-encoded polymerase that has two enzymatic activities: a DNA polymerase that synthesizes new DNA and a ribonuclease H (RNAseH) that destroys the viral RNA after it has been copied into DNA (Hostomsky et al., 1993; Rice et al., 2001; Hickman et al., 1994; Ariyoshi et al., 1994). Both activities are essential for viral replication.
  • HBV infections are treated with interferon α or one of five nucleos(t)ide analogs (Parker et al., 2004; Song et al., 2004; Lima et al., 2001). Interferon α leads to sustained clinical improvement in 20-30% of patients, but the infection is very rarely cleared (Hostomsky et al., 1993; Katayanagi et al., 1990; Braunshofer-Reiter et al., 1998). The nucleos(t)ide analogs are used more frequently than interferon. They inhibit DNA synthesis and suppress viral replication by 4-5 log10 in up to 70-90% patients, often to below the standard clinical detection limit of 300-400 copies/ml (Braunshofer-Reiter et al., 1998; Nowotny et al., 2005; Klumpp et al., 2003. However, treatment eradicates the infection as measured by loss of the viral surface antigen (HBsAg) from the serum in only 3-6% of patients even after years of therapy (Braunshofer-Reiter et al., 1998; Nowotny et al., 2005; Klumpp et al., 2003; Nowotny et al., 2006). Antiviral resistance was a major problem with the earlier nucleos(t)ide analogs, but resistance to the newer drugs entecavir and tenofovir is very low (Parker et al., 2004; Keck et al., 1998; Goedken et al., 2001; Li et al., 1995). This has converted HBV from a steadily worsening disease into a controllable condition for most individuals (McClure, 1993). The cost of this control is indefinite administration of the drugs (probably life-long; (Song et al., 2004), with ongoing expenses of $400-600/month (Poch et al., 1989; Hu et al. 1996; Hu et al., 1997) and unpredictable adverse effects associated with decades-long exposure to the drugs.
  • As such, there remains a need to develop new therapeutic options for these diseases.
    • SUMMARY
  • Thus, in accordance with the present disclosure, there is provided a method of inhibiting a cellular or herpesvirus nucleic acid metabolism enzyme comprising contacting said enzyme with a compound having the formula:
  • Figure US20180169083A1-20180621-C00002
  • or a compound of the formula:
  • Figure US20180169083A1-20180621-C00003
  • wherein:
      • R4 is alkyl(C≤12), aryl(C≤12), aralkyl(C≤12), heteroaryl(C≤12), or a substituted version of any of these groups;
      • R5 and R8 are each independently hydrogen, alkyl(C≤8), or substituted alkyl(C≤8);
      • R6 is hydrogen, hydroxy, alkyl(C≤8), or substituted alkyl(C≤8); and
      • R7 is aryl(C≤12), aralkyl(C≤12), heteroaryl(C≤12), or a substituted version of any of these groups; or
        a compound of the formula:
  • Figure US20180169083A1-20180621-C00004
  • wherein:
      • R9 is alkyl(C≤12), aryl(C≤12), aralkyl(C≤12), heteroaryl(C≤12), or a substituted version of any of these groups;
      • R10 is hydrogen, alkyl(C≤8), or substituted alkyl(C≤8); and
      • R11 is hydrogen or Y1—O—X1—OR12; wherein:
        • Y1 is alkanediyl(C≤8) or substituted alkanediyl(C≤8);
        • X1 is arenediyl(C≤12), heteroarenediyl(C≤12), or a substituted version of either of these groups;
      • R12 is aryl(C≤12), aralkyl(C≤12), heteroaryl(C≤12), or a substituted version of any of these groups;
        or a pharmaceutically acceptable salt or tautomer thereof.
  • In some embodiments, the compound is further defined as:
  • Figure US20180169083A1-20180621-C00005
  • wherein:
      • R4 is alkyl(C≤12), aryl(C≤12), aralkyl(C≤12), heteroaryl(C≤12), or a substituted version of any of these groups;
      • R5 and R8 are each independently hydrogen, alkyl(C≤8), or substituted alkyl(C≤8);
      • R6 is hydrogen, hydroxy, alkyl(C≤8), or substituted alkyl(C≤8); and
      • R7 is aryl(C≤12), aralkyl(C≤12), heteroaryl(C≤12), or a substituted version of any of these groups; or
        or a pharmaceutically acceptable salt or tautomer thereof. In other embodiments, the compound is further defined as:
  • Figure US20180169083A1-20180621-C00006
  • wherein:
      • R9 is alkyl(C≤12), aryl(C≤12), aralkyl(C≤12), heteroaryl(C≤12), or a substituted version of any of these groups;
      • R10 is hydrogen, alkyl(C≤8), or substituted alkyl(C≤8); and
      • R11 is hydrogen or Y1—O—X1—OR12; wherein:
        • Y1 is alkanediyl(C≤8) or substituted alkanediyl(C≤8);
        • X1 is arenediyl(C≤12), heteroarenediyl(C≤12), or a substituted version of either of these groups;
        • R12 is aryl(C≤12), aralkyl(C≤12), heteroaryl(C≤12), or a substituted version of any of these groups;
          or a pharmaceutically acceptable salt or tautomer thereof.
  • In other embodiments, the compound is further defined as:
  • Figure US20180169083A1-20180621-C00007
  • or a pharmaceutically acceptable salt or tautomer thereof. In other embodiments, the compound is further defined as:
  • Figure US20180169083A1-20180621-C00008
  • or a pharmaceutically acceptable salt or tautomer thereof.
  • The salt maybe an ethanolamine salt. The method may further comprise contacting said enzyme with a second inhibitor of said enzyme, or further comprise contacting said enzyme with said compound a second time. The enzyme may be located in a cell, which cell may be located in vitro or located in a living subject. The subject may be a vertebrate infected with a herpesvirus. The compound may be administered intravenously, intraarterially, ocularly, orally, buccally, nasally, rectally, vaginally, topically, intramuscularly, intradermally, cutaneously or subcutaneously. The subject may be further administered a second anti-herpesvirus therapy distinct from the compound. The second anti-herpesvirus therapy may be foscarnet or a nucleoside analog, such as acyclovir, famciclovir, valaciclovir, penciclovir, or ganciclovir. The second anti-herpesvirus therapy may be administered to the subject before or after said compound. The second anti-herpesvirus therapy may be administered to said subject at the same time as said compound.
  • The subject may have previously received a first-line anti-herpesvirus therapy, and further may have developed resistance to said first-line anti-herpesvirus therapy. The herpevirus may be selected from a human alpha herpesvirus, a human beta herpesvirus or a human gamma herpesvirus. The human alpha herpesvirus may be selected from herpes simplex virus 1 (HSV-1), herpes simplex virus 2 (HSV-2), and Varicella-Zoster virus (VZV). The human beta herpesvirus may be selected from human cytomegalovirus (HCMV), human herpesvirus 6A, (HHV-6A), human herpesvirus 6B (HHV-6B), and human herpesvirus 7 (HHV-7). The human gamma herpesvirus may be selected from Epstein-Barr virus (EBV) and Kaposi's sarcoma herpesvirus (KSHV). The herpesvirus may be a non-human herpesvirus, such as Marek's disease virus, equine herpesviruses, Bovine herpeviruses, or pseudorabies virus.
  • In another aspect, the present disclosure provides a pharmaceutical composition comprising a compound of the formula:
  • Figure US20180169083A1-20180621-C00009
  • or a pharmaceutically acceptable salt or tautomer thereof. The salt may be an ethanolamine salt. In some embodiments, the compound is dispersed in a pharmaceutically acceptable buffer, diluent, excipient or carrier. In some embodiments, the pharmaceutical composition is formulated for administration: orally, nasally, ocularly, buccally, corneally, rectally, vaginally, or topically. In other embodiments, the pharmaceutical composition formulated for administration via injection. In some embodiments, the injection is formulated for administration: intradermally, cutaneously, subcutaneously, intramuscularly, intraperitoneally, intraarterially, or intravenously.
  • In still another aspect, the present disclosure provides compounds of the formula:
  • Figure US20180169083A1-20180621-C00010
  • wherein:
      • R1 is aryl(C≤12), aralkyl(C≤18), heteroaryl(C≤12), alkylamino(C≤12), dialkylamino(C≤12), arylamino(C≤12), diarylamino(C≤12), aralkylamino(C≤18), diaralkylamino(C≤18), or a substituted version of any of these groups;
      • R2 is hydrogen, alkyl(C≤8), or substituted alkyl(C≤8); and
      • R3 is hydrogen, amino, carboxyl, cyano, halo, hydroxy, nitro, hydroxysulfonyl, or sulfonylamine; or
        • alkyl(C≤8), aryl(C≤8), acyl(C≤8), alkoxy(C≤8), acyloxy(C≤8), amido(C≤8), or substituted version of any of these groups;
      • X2 is hydrogen or —C(O)Ra, wherein: Ra is hydroxy, alkoxy(C≤8), or substituted alkoxy(C≤8); or
        compounds of the formula:
  • Figure US20180169083A1-20180621-C00011
  • wherein:
      • R4 is alkyl(C≤12), aryl(C≤12), aralkyl(C≤12), heteroaryl(C≤12), or a substituted version of any of these groups;
      • R5 and R8 are each independently hydrogen, alkyl(C≤8), or substituted alkyl(C≤8);
      • R6 is hydrogen, hydroxy, alkyl(C≤8), or substituted alkyl(C≤8); and
      • R7 is aryl(C≤12), aralkyl(C≤12), heteroaryl(C≤12), or a substituted version of any of these groups; or
        compounds of the formula:
  • Figure US20180169083A1-20180621-C00012
  • wherein:
      • R9 is alkyl(C≤12), aryl(C≤12), aralkyl(C≤12), heteroaryl(C≤12), or a substituted version of any of these groups;
      • R10 is hydrogen, alkyl(C≤8), or substituted alkyl(C≤8); and
      • R11 is hydrogen or Y1—O—X1—OR12; wherein:
        • Y1 is alkanediyl(C≤8) or substituted alkanediyl(C≤8);
        • X1 is arenediyl(C≤12), heteroarenediyl(C≤12), or a substituted version of either of these groups;
        • R12 is aryl(C≤12), aralkyl(C≤12), heteroaryl(C≤12), or a substituted version of any of these groups;
          or a pharmaceutically acceptable salt thereof. In some embodiments, the compounds are further defined as:
  • Figure US20180169083A1-20180621-C00013
  • wherein:
      • R1 is aryl(C≤12), aralkyl(C≤8), heteroaryl(C≤12), alkylamino(C≤12), dialkylamino(C≤12), arylamino(C≤12), diarylamino(C≤12), aralkylamino(C≤8), diaralkylamino(C≤8), or a substituted version of any of these groups; and
      • R2 is hydrogen, alkyl(C≤8), or substituted alkyl(C≤8);
      • X2 is hydrogen or —C(O)Ra, wherein: Ra is hydroxy, alkoxy(C≤8), or substituted alkoxy(C≤8);
        or a pharmaceutically acceptable salt thereof. In other embodiments, the compounds are further defined as:
  • Figure US20180169083A1-20180621-C00014
  • wherein:
      • R5 is hydrogen, alkyl(C≤8), or substituted alkyl(C≤8);
      • R6 is hydrogen, hydroxy, alkyl(C≤8), or substituted alkyl(C≤8); and
      • R7 is aryl(C≤12), aralkyl(C≤12), heteroaryl(C≤12), or a substituted version of any of these groups;
        or a pharmaceutically acceptable salt thereof. In other embodiments, the compounds are further defined as:
  • Figure US20180169083A1-20180621-C00015
  • wherein:
      • R10 is hydrogen, alkyl(C≤8), or substituted alkyl(C≤8); and
      • R11 is hydrogen or Y1—O—X1—OR12; wherein:
        • Y1 is alkanediyl(C≤8) or substituted alkanediyl(C≤8);
        • X1 is arenediyl(C≤12), heteroarenediyl(C≤12), or a substituted version of either of these groups;
        • R12 is aryl(C≤12), aralkyl(C≤12), heteroaryl(C≤12), or a substituted version of any of these groups;
          or a pharmaceutically acceptable salt thereof.
  • In some embodiments, R2, R5, or R10 is hydrogen. In some embodiments, R2, R5, and R10 are hydrogen. In some embodiments, R1 is aralky(C≤18), aralkylamino(C≤18), or a substituted version of either group. In some embodiments, R6 is hydroxy. In some embodiments, R7 is aryl(C≤12). In some embodiments, R11 is Y1—O—X1—OR12; wherein:
  • Y1 is alkanediyl(C≤8);
  • X1 is arenediyl(C≤12), or a substituted version of either of these groups;
  • R12 is aryl(C≤12) or substituted aryl(C≤12).
  • In some embodiments, the compounds are further defined as:
  • Figure US20180169083A1-20180621-C00016
  • or a pharmaceutically acceptable salt thereof.
  • In still yet another aspect, the present disclosure provides a compound of the formula:
  • Figure US20180169083A1-20180621-C00017
  • or a pharmaceutically acceptable salt thereof.
  • In still yet another aspect, the present disclosure provides pharmaceutical compositions comprising:
  • (A) a compound described herein; and
  • (B) an excipient.
  • In some embodiments, the pharmaceutical composition is formulated for administration: orally, nasally, buccally, corneally, rectally, vaginally, topically, intradermally, cutaneously, ocularly, subcutaneously, intramuscularly, intraperitoneally, intraarterially, or intravenously. In some embodiments, the pharmaceutical composition is formulated as a unit dose.
  • In yet another aspect, the present disclosure provides methods of inhibiting a hepatitis B virus RNaseH comprising administering an effective amount of a compound or composition described herein. In some embodiments, the method is performed in vitro. In other embodiments, the method is performed in vivo. In other embodiments, the method is performed ex vivo. In some embodiments, the methods are sufficient to inhibit viral replication.
  • In still yet another aspect, the present disclosure provides methods of inhibiting replication of a hepatitis B virus comprising contacting the virus with an effective amount of a compound or composition described herein. In some embodiments, the method is performed in vitro. In other embodiments, the method is performed in vivo. In other embodiments, the method is performed ex vivo. In some embodiments, the methods are sufficient to treat an infection of a hepatitis B virus.
  • In another aspect, the present disclosure provides methods of treating an infection of a hepatitis B virus in a patient comprising administering a therapeutically effective amount of a compound or composition described herein. In some embodiments, the method further comprises a second antiviral treatment. In some embodiments, the second antiviral therapy is interferon alfa-2b, lamivudine, adefovir, telbivudine, entercavir, or tenofovir. In some embodiments, the patient is a mammal such as a human.
  • The use of the word “a” or “an,” when used in conjunction with the term “comprising” in the claims and/or the specification may mean “one,” but it is also consistent with the meaning of “one or more,” “at least one,” and “one or more than one.”
  • Throughout this application, the term “about” is used to indicate that a value includes the inherent variation of error for the device, the method being employed to determine the value, or the variation that exists among the study subjects, or +/−5% of the stated value.
  • Other objects, features and advantages of the present disclosure will become apparent from the following detailed description. It should be understood, however, that the detailed description and the specific examples, while indicating preferred embodiments of the disclosure, are given by way of illustration only, since various changes and modifications within the spirit and scope of the disclosure will become apparent to those skilled in the art from this detailed description.
    • BRIEF DESCRIPTION OF THE DRAWINGS
  • The following drawings form part of the present specification and are included to further demonstrate certain aspects of the present disclosure. The disclosure may be better understood by reference to one or more of these drawings in combination with the detailed description of specific embodiments presented herein.
  • FIG. 1. Structure of Piroctone Olamine.
  • FIG. 2. Compound #191 inhibits replication of HSV-2 primary clinical isolates. Vero cell monolayers were infected with the indicated patient isolates at moi of 0.1 in the presence of piroctone olamine (#191) or DMSO control at 5 μM. Cultures were collected 24 hours post-infection and infectious virus titers were determined by plaque assay. Titers in #191-treated samples were subtracted from DMSO-treated samples. Values are the averages of duplicate cultures.
  • FIG. 3. Sensitivity of thymidine kinase-deficient HSV-2 to piroctone olamine. Vero cell monolayers were infected with the indicated wild-type or mutant HSV-1 or HSV-2 strains at moi of 0.1 in the presence of DMSO control or piroctone olamine at 5 μM. Duplicate cultures were collected 24 hours post-infection and infectious virus titers were determined by plaque assay. Titers in compound-treated samples were subtracted from DMSO-treated samples. Values are the averages±one standard error of the mean.
  • FIGS. 4A & 4B. RNAseH inhibitors work synergistically with Lamivudine against HBV replication. Chou-Talaly combination indexes for compounds #1 (FIG. 4A) and #46 (FIG. 4B) together with Lamivudine. Additive interactions are shown with the red line, synergistic interactions below the line, and antagonistic interactions are above the line.
  • FIGS. 5A & 5B. HBV's genetic variation is unlikely to present a barrier to RNAseH drug development. Four variant patient-derived RNAseH enzymes were expressed as recombinant enzymes, purified, and tested in an RNAseH assay with compounds #1 (FIG. 5A) and #46 (FIG. 5B) at their respective IC50s.
    •  DETAILED DESCRIPTION
  • The inventors have previously demonstrated that inhibitors of nucleotidyl-transferase superfamily (NTS) enzymes can come from multiple different chemical classes. The compounds described herein may be used from a variety of different viral infections including herpesvirus and hepatitis B virus. Inhibitors of NTS enzymes like this compound may well have a high barrier to development of antiviral resistance, and its unique mode of action suggests that it should be a good candidate for combination therapy with the existing antiviral drugs to improve overall efficacy of antiviral therapy. These and other aspects of the disclosure are discussed in detail below.
    • A. HERPESVIRUS
  • Herpesviruses are a diverse group of enveloped viruses having a large, double-stranded DNA genome enclosed in an icosahedral capsid (Pellet & Roizman 2013). The herpesviruses rely on the host cell RNA polymerase II for transcription, but encode all of the enzymes needed for replication of their genomes, including DNA polymerase, helicase, primase, terminase, ribonucleotide reductase, and thymidine kinase. All herpesviruses share the capacity to establish latency in host cells, allowing them to maintain the infection for the life of the host. Periodic reactivation from latency in response to cues in the cellular environment leads to lytic replication at mucosal surfaces, causing recurrent disease and providing the opportunity for transmission to uninfected individuals.
  • The herpesviruses are divided into three subclasses based primarily on their cellular tropism and characteristics of the latent infection. The human alpha herpesviruses herpes simplex virus 1 (HSV-1) (Roizman et al., 2013), herpes simplex virus 2 (HSV-2) (Roizman et al., 2013) and Varicella-Zoster virus (VZV) (Arvin & Gilden 2013) establish latency in sensory neurons where they may remain quiescent for long periods of time. HSV-1 and HSV-2 are similar viruses with colinear genomes and 83% nucleotide sequence identity in protein coding regions (Dolan et al., 1998); VZV contains a smaller, less homologous genome. The human beta herpesviruses human cytomegalovirus (HCMV), human herpesvirus 6A (HHV-6A), human herpesvirus 6B (HHV-6B) and human herpesvirus 7 (HHV-7) (Yamanishi et al., 2013) establish latency predominantly in mononuclear cells. The human gamma herpesviruses Epstein-Barr virus (EBV) (Longnecker et al., 2013) and Kaposi's sarcoma herpesvirus (KSHV) (Damania & Cesarman 2013) stimulate cellular proliferation upon infection. EBV infects B lymphocytes, where it establishes latency, and also epithelial cells. By contrast, endothelial cells harbor the latent reservoir of KSHV, although the virus infects numerous other cell types as well. The genomes of latent beta and gamma herpesviruses are replicated as the host cell divides in order to maintain latent infection.
  • Herpesviruses related the human alpha, beta and gamma herpesviruses infect numerous animal species, including several of significant economic importance. Key among these are pseudorabies virus which infects pigs, Marek's disease virus which infects chickens, bovine herpesvirus, equine herpesvirus, and salmonid and related herpesviruses that infect game fish.
    • 1. Pathology
  • Primary infections with herpesviruses produce a broad spectrum of disease. HSV-1 causes numerous maladies (Roizman et al., 2013): gingivostomatitis; eczema herpeticum; herpes gladiatorum; less common but frequently fatal encephalitis; and an increasing proportion of ulcerative anogential lesions (Gilbert et al., 2011; Horowitz et al., 2011; Pena et al., 2010; Smith & Roberts 2009). Nearly two-thirds of the U.S. population has been exposed to HSV-1 (Xu et al., 2006). HSV-2 infects approximately 17% of Americans (Xu et al., 2006) and up to 75% of some demographics world-wide (Obasi et al., 1999 and Kamali et al., 1999), with an estimated global disease burden of more than half a billion people (Looker, et al., 2008). HSV-2 is the primary cause of ulcerative anogenital lesions. In addition, HSV-1 and HSV-2 may be transmitted from a pregnant woman to her child during birth, often causing potentially fatal disseminated disease in the newborn (Kimberlin 2007). HCMV is the most common in utero virus infection (Manicklal et al., 2013), and approximately 8,000 HCMV-infected infants born each year in the U.S. suffer sensorineural deafness, chorioretinitis, and/or mental retardation (James et al., 2009). In immunocompromised individuals, HCMV can cause mononucleosis, retinitis, colitis, pneumonitis, and esophagitis. These serious HCMV infections are associated with increased morbidity and mortality (Komatsu et al., 2014). EBV causes the vast majority of infectious mononucleosis, which strikes nearly half of young adults (Luzuriaga & Sullivan 2010). Notably, of the eight human herpesviruses, a vaccine is available only for VZV.
  • The novel capacity of herpesviruses to establish and reactivate from latency is also associated with numerous pathologies. HSV-1 causes recurrent cold sores; a significant proportion of devastating viral encephalitis; and corneal scarring known as herpetic stromal keratitis which is the most frequent infectious cause of blindness, afflicting nearly 400,000 persons annually in the U.S. (Roizman et al., 2013). HSV-2 frequently reactivates to cause genital ulcers and prior HSV-2 infection is associated with an increased risk of human immunodeficiency virus (HIV) acquisition (Roizman et al., 2013). Infants who survive HSV-1 or HSV-2 infections often experience life-long sequellae and periodic recurrent lesions (Kimberlin 2007 and James et al., 2009). VZV reactivates in up to half of older adults (Cohen 2013), and pain associated with the classic Zoster (shingles) rash and post-rash neuralgia can be excruciating. HCMV reactivation is associated with increased incidence of restenosis after angioplasty (Popovic et al., 2012), and also causes significant morbidity and mortality in recipients of bone marrow and solid organ transplants (Snydman 2008). Latent EBV infection is associated with a variety of cancers including Burkitt's lymphoma, two types of Hodgkin's lymphoma, non-Hodgkin's lymphoma, nasopharyngeal carcinoma, and post-transplant lymphoproliferative disease. Latent KSHV infection can lead to three types of cancer: Kaposi's sarcoma, pleural effusion lymphoma, and Castleman's disease (Damania & Cesarman 2013).
  • Veterinary herpesviruses also take a significant toll on livestock. Marek's disease is highly contagious, spreading rapidly through flocks of chickens that have not been vaccinated. It causes T cell lymphoma with infiltration of nerves and somatic organs, leading to paralysis and death in up to 80% of infected birds (Hirari, 2001). In addition, vaccine efficacy has declined with a concomitant increase in Marek's virus virulence (Gimeno, 2008). Pseudorabies (PRV) is the second most economically important viral disease of swine. Although PRV does not cause illness in adult swine, infection of pregnant sows results in a high incidence of abortion or resorption (Smith, 1997). Piglets infected with PRV suffer coughing, sneezing, fever, constipation, and a variety of neurologic symptoms. Mortality in piglets less than one month of age is close to 100%, but declines rapidly with age (Nauwynck et al., 2007). Ruminants and dogs and cats are also susceptible to lethal PRV infection (Fenner et al., 1993). In cattle, symptoms include intense itching followed by neurological signs and death. In dogs, intense itching is accompanied by jaw and pharyngeal paralysis and subsequent death (Decaro et al., 2008). In cats, usually no symptoms are observed because the disease is so rapidly fatal (Gaskell et al., 2007). Bovine herpesviruses (BHV) cause a variety of illnesses in young cattle, and can also cause abortion. Although the illnesses caused by BHV's are mostly not life-threatening, they cause important diseases because infection may trigger a decline in meat and milk production and affect trade restrictions (Nandi et al., 2009). Equine herpesviruses typically cause respiratory disease, but certain species also cause myeloencephalopathy in horses, abortion and occasionally neonatal mortality due to pneumonia (Fortier et al., 2010). The herpesviruses of various fish species can cause significant mortality in aquaculture settings, particularly at the fingerling stage (Hanson et al., 2011). Importantly, all of these viruses share the same basic genomic replication mechanisms, so if the presumed mechanism by which the NTS enzymes inhibit HSV-1 and HSV-2 is correct, most of the other herpesvirus pathogens should also be highly sensitive to NTS inhibitors. Development of NTS inhibitors into anti-herpesvirus drugs would be particularly valuable in cases like HCMV, where current antiviral therapies frequently drive resistance and are plagued by toxicity issues (Weller and Kuchta, 2013). Finally, NTS inhibitors may be promising candidates for pan anti-herpesvirus drug development due to similarities in replication mechanisms of all the herpesviruses.
  • 2. Infection and Latency
  • Enveloped herpesvirus particles fuse with the plasma membrane of a cell, releasing viral regulatory proteins and the viral capsid containing the linear double-stranded DNA genome into the cytoplasm. The capsids deliver the viral genome to the nucleus via release through nuclear pores, whereupon the genome circularizes and becomes transcriptionally active. Viral infection at this point can proceed by two patterns, lytic or latent. In the lytic cycle, coordinated phases of viral transcription lead to expression of the viral regulatory proteins, viral enzymes, and concurrently with the onset of DNA replication, the viral structural proteins. Nascent viral capsids assemble in the nucleus and then bud through the nuclear membranes to acquire their envelope (Mettenleiter et al., 2009). Release from the cells is primarily lytic, resulting in the death of the cell. Alternatively, the virus may enter a latent state, where transcription is limited to a few viral regulatory loci and viral DNA replication is strictly limited. Upon recognition of appropriate cellular stimuli, viral transcription reverts to the lytic pattern and productive viral replication occurs.
  • Initial infections with alpha herpesviruses are lytic, resulting in dispersion of the virus to other cells and organs. These viruses establish latency in the unique environment of the neuron, and also in satellite cells in the case of VZV. During latency, replication of alpha herpesvirus DNA may occur at a low level because latently infected neurons contain multiple copies of the genome (Chen et al., 2002; Wang et al., 2005). Once latency is established, DNA replication increases markedly only during a reactivation event. Initial infections with beta herpesviruses are typically non-lytic but may cause cell-cell fusion. The gamma herpesviruses stimulate proliferation of infected cells, replicating their DNA along with cellular DNA replication to transmit copies of the viral genome to daughter cells (Longnecker et al., 2013). All the herpesviruses cause episodic lytic infection of at least some cell types, allowing them to be shed from mucosal surfaces to facilitate transmission to uninfected individuals.
  • 3. Genomic Replication
  • Circularization of the linear double-stranded herpesvirus DNA occurs in the nucleus shortly after viral uncoating, presumably through a recombination-mediated event. Replication of the viral DNA occurs in the nucleus within three-dimensional domains termed replication compartments (Quinlan et al., 1984). DNA replication is thought to employ a double-stranded rolling circle mechanism [reviewed in (Weller & Coen 2012; Lehman & Boehmer 1999)]. In preparation for viral DNA replication, virus-encoded transcriptional activators upregulate expression of proteins involved in nucleic acid metabolism. DNA replication then initiates at one of three viral origins of DNA replication and is mediated through action of the viral ICP6 origin binding protein. (All viral gene names in this section are for HSV-1). DNA synthesis is primed by the viral helicase/primase complex (pUL5, pUL8, and pUL52). DNA elongation occurs by coupled leading- and lagging-strand DNA synthesis through formation of a replication fork that is grossly similar to the forks that replicate cellular DNA. DNA synthesis is catalyzed by the pUL30 DNA polymerase/UL42 processivity protein complex that also possesses 5′-3′ exonuclease, 3′-5′ exonuclease, and RNase H activities. Helical torsion is relieved by the viral helicase/primase complex, and proper replication fork initiation, architecture and dynamics are promoted by the ICP8 single-stranded DNA binding protein. The initial product of DNA replication is a head-to-tail concatamer, but later in the replication cycle complex branched concatamers accumulate through recombination and/or re-initiation mechanisms. The concatamer is cleaved to unit length by the terminase complex (pUL15, pUL28, and pUL33) (Selvarajan et al., 2013) during encapsidation of the viral genome into pre-formed viral capsids. Without wishing to be bound by any theory, it is believed that some of the compounds described herein inhibit the activity of pUL15 terminase.
  • 4. Therapeutic Targets in the Herpesvirus Genome
  • Possible targets for nucleotidyl transferase superfamily inhibitors in the herpesvirus genomes. The inhibitors screened here function against HIV by binding to the viral RNase H or integrase active sites and chelating the essential divalent cations within the active site (Fuji et al., 2009; Su et al., 2010; Chung et al., 2011; Billamboz et al., 2011; Himmel et al., 2009; Kirschberg et al., 2009). Other compounds screened here are chemically related to inhibitors of the HIV RNase H and integrase. Therefore, their presumed mechanism of action is to inhibit one or more of the viral and/or cellular NTS enzymes essential for herpesviral genomic replication. This mechanism has not yet been tested.
  • For the herpes simplex viruses, candidate genes include the RNase H activity of the pUL30 DNA polymerase (Liu et al., 2006), the 3′-5′ exonuclease activity of pUL30 (Coen 1996), the strand transfer activity of ICP8 (Bortner et al., 1993; Nimonkar & Boehmer, 2003), or the 5′-3′ exonuclease activity of the pUL12 polymerase accessory protein (Schumacher et al., 2012) that are directly involved in virus replication (Weller & Coen 2012). The pUL15 terminase protein that cleaves the concatameric viral DNA produced by DNA replication into the mature linear monomers is also a prime candidate (Selvarajan et al., 2013).
  • Other herpesviruses encode proteins with functions consistent with NTS enzymes that could be plausible targets. For example, pUL98 is the HCMV ortholog of HSV pUL12 and is functionally conserved, as demonstrated by trans-complementation experiments (Gao et al., 1998). At least two of the seven HCMV proteins involved in encapsidation form an essential terminase complex which likely functions as both an endonuclease and a DNA translocase during DNA cleavage and packaging (Bogner, 2002; Hwang & Bogner, 2002; Scheffczik et al., 2002; Scholz et al., 2003). These genes are conserved throughout the herpesvirus family (Alba et al., 2001) and deletion of any of the seven results in accumulation of empty capsids in the nucleus. The human cytomegalovirus (HCMV) terminase subunits pUL56 and pUL89, encoded by the UL56 and UL89 genes, have been extensively studied. Both gene products form toroidal structures, bind DNA, and have nuclease activity (Bogner et al., 1998; Scheffczik et al., 2002). While pUL56 mediates the specific binding to pac sequences on DNA concatamers and provides energy and structural assistance for DNA translocation into the procapsids, pUL89 cleaves the DNA concatomers (Bogner, 2002). These are the orthologs of HSV terminase subunits pUL15 and pUL28.
  • Cellular proteins are also plausible targets for the action of the NTS inhibitors, especially because DNA recombination events appear to be important during productive replication (Weller & Coen 2012). These proteins include the human RNase H1 that could assist in removal of RNA primers for DNA synthesis. Other candidates include the Fen1 endonuclease that may assist in removal of primers (Zhu et al., 2010), and the double-stranded break repair enzymes Mre11, Rad50, NBS1, Rad51 (Weizman & Weller 2011), and Rad52 (Schumacher et al., 2012). The base-excision repair enzymes SSH2 and MLH1 which form complexes that are recruited to viral replication sites and contribute to HSV genomic replication (Mohni et al., 2011) are also plausible targets.
  • 5. Treatments
  • Herpesvirus DNA polymerase inhibitors (nucleoside analogs), including acyclovir, famciclovir, valaciclovir, penciclovir, and ganciclovir are the most common forms of treatment. A pyrophosphate analog, foscarnet, also inhibits the herpesvirus DNA polymerases. A DNA helicase-primase inhibitor, AIC316 (pritelivir), was shown to reduce HSV-2 shedding and number of days without lesions in a phase 2 clinical trial (Wald et al., 2014). However, a subsequent double-blind trial by the same group was terminated by the sponsor because of concurrent findings of toxicity in monkeys (De et al., 2015). Similarly, the helicase-primase inhibitor Amenamevir (ASP2151) is active against HSV-1 and HSV-2 in culture (Chono et al., 2010) and significantly reduced the median time to lesion healing in a phase II clinical trial (Tyring et al., 2012), but a subsequent trial was terminated due to adverse effects (De et al., 2015). CMX001 (brincidofovir), an orally bioavailable lipid conjugate of cidofovir, potentiates the antiviral effect of acyclovir in mice inoculated intranasally with HSV-1 or HSV-2 (Prichard et al., 2011). N-Methanocarbathymidine (N-MCT) reduces lethality in a mouse model of HSV-2 infection (Quenelle et al., 2011) and a guinea pig model of neonatal herpes (Bernstein et al., 2011). N-MCT also reduces acute and recurrent disease caused by HSV-2 in an adult guinea pig model. The monoamine oxidase inhibitor tranylcypromine (TCP), which also blocks the activity of histone demethylase LSD1, reduces HSV-1 infection of the cornea, trigeminal ganglia and brain of mice, corneal disease, and percentage of mice shedding virus upon induced reactivation (Yao et al., 2014). TCP has also been tested in a rabbit eye model of recurrent infection with HSV-1 and the mouse and guinea pig models of HSV-2 genital infection. An acyclic nucleoside phosphonate, PMEO-DAPym, inhibits HSV replication in a variety of cultured cell types by targeting the viral DNA polymerase (Balzarini et al., 2013). The HIV integrase inhibitor, Raltegravir, has a small amount of inhibitory activity against replication of several herpesviruses in cultured cells (Zhou et al., 2014; Yan et al., 2014) and appears to target the polymerase processivity factor UL42 (Zhou et al., 2014). Two other integrase inhibitors, XZ15 and XZ45, reduce replication of HSV-1 in cell culture by approximately 800- to 8000-fold, respectively (Yan et al., 2014). XZ45 also inhibits HCMV replication and KSHV gene expression (Yan et al., 2014).
  • Therapy based on existing drugs such as acyclovir is incompletely effective (Johnston et al., 2012), and viral resistance to current nucleos(t)ide analog therapies is relatively common. Acyclovir resistant variants are particularly prevalent among children, the immunocompromised, and patients with herpetic stromal keratitis (Duan et al., 2008; Wang et al., 2011; Field & Vere Hodge, 2013; Morfin & Thouvenot, 2003; Andrei & Snoeck, 2013). Ganciclovir-resistant variants occur in the naturally circulating viral population (Drew et al., 1993) and can be selected in patients over time (Marfori et al., 2007; Imai et al., 2004; Drew et al., 2001; Drew et al., 1999).
    • B. HEPATITIS B VIRUS
  • 1. Biology
  • Hepatitis B virus, abbreviated HBV, is a species of the genus Orthohepadnavirus, which is likewise a part of the Hepadnaviridae family of viruses. This virus causes the disease hepatitis B. In addition to causing hepatitis B, infection with HBV can lead to hepatic fibrosis, cirrhosis and hepatocellular carcinoma. It has also been suggested that it may increase the risk of pancreatic cancer.
  • The hepatitis B virus is classified as the type species of the Orthohepadnavirus, which contains at least five other species: the pomona roundleaf bat hepatitis virus, long-fingered bat hepatitis virus, the Ground squirrel hepatitis virus, Woodchuck hepatitis virus, and the Woolly monkey hepatitis B virus. The genus is classified as part of the Hepadnaviridae family along with Avihepadnavirus. This family of viruses have not been assigned to a viral order. Viruses similar to hepatitis B have been found in all the Old World apes (orangutan, gibbons, gorillas and chimpanzees) and from a New World woolly monkey suggesting an ancient origin for this virus in primates.
  • The virus is divided into four major serotypes (adr, adw, ayr, ayw) based on antigenic epitopes present on its envelope proteins, and into eight genotypes (A-H) according to overall nucleotide sequence variation of the genome. The genotypes have a distinct geographical distribution and are used in tracing the evolution and transmission of the virus. Differences between genotypes affect the disease severity, course and likelihood of complications, and response to treatment and possibly vaccination.
  • The virus particle (virion) consists of an outer lipid envelope and an icosahedral nucleocapsid core composed of protein. The nucleocapsid encloses the viral DNA and a DNA polymerase that has reverse transcriptase activity similar to retroviruses. The outer envelope contains embedded proteins which are involved in viral binding of, and entry into, susceptible cells. The virus is one of the smallest enveloped animal viruses with a virion diameter of 42 nm, but pleomorphic forms exist, including filamentous and spherical bodies that both lack a core. These particles are not infectious and are composed of the lipid and protein that forms part of the surface of the virion, which is called the surface antigen (HBsAg), and are produced in excess during the life cycle of the virus. The HBV virus itself is called a Dane particle and consists of HBsAg, a lipid envelope, the core protein (HBcAg), the viral genome, and the Hepatitis B virus DNA polymerase. The functions of the small regulatory protein (HBx) are not yet well known but may be related to interfering with transcription, signal transduction, signal transduction, cell cycle progress, protein degradation, apoptosis, or chromosomal stability. The virus also produces a secreted protein called HBeAg that is an amino-terminal extension of HBcAg initiating from an upstream start codon that is involved in suppressing antiviral immune responses.
  • The genome of HBV is made of circular DNA, but it is unusual because the DNA is not fully double-stranded in the virion. One end of the full length strand is linked to the viral DNA polymerase. The genome is 3020-3320 nucleotides long (for the full length strand) and 1700-2800 nucleotides long (for the short length strand). The negative-sense, (non-coding), strand is the complete strand and it is complementary to the viral mRNA. The viral DNA is found in the nucleus soon after infection of the cell. The partially double-stranded DNA is rendered fully double-stranded shortly after infection of a cell by completion of the (+) sense strand and removal of a protein molecule from the (−) sense strand and a short sequence of RNA from the (+) sense strand. A short terminal duplication of are removed from the ends of the (−) sense strand and the ends are rejoined. The mature nuclear form of the genome is called the “cccDNA.” The cccDNA is the template for transcription of all of the viral mRNAs.
  • There are four known genes encoded by the genome called C, X, P, and S. The core protein (HBcAg) is coded for by gene C, and its start codon is preceded by an upstream in-frame AUG start codon from which the pre-core protein is produced. HBeAg is produced by proteolytic processing of the pre-core protein. The DNA polymerase is encoded by gene P. Gene S is the gene that codes for the surface antigens (HBsAg). The HBsAg gene is one long open reading frame but contains three in frame “start” (ATG) codons that divide the gene into three sections, pre-S1, pre-S2, and S. Because of the multiple start codons, polypeptides of three different sizes called large, middle, and small (pre-S1+pre-S2+S, pre-S2+S, or S) are produced. The function of the protein coded for by gene X is not fully understood, but it has pleiotropic regulatory functions in both the cytoplasm and nucleus.
  • There are at least eight known genotypes labeled A through H. A possible new “I” genotype has been described, but acceptance of this notation is not universal. Different genotypes may respond to treatment in different ways. The genotypes differ by at least 8% of the sequence and have distinct geographical distributions and this has been associated with anthropological history. Type F which diverges from the other genomes by 14% is the most divergent type known. Type A is prevalent in Europe, Africa and South-east Asia, including the Philippines. Type B and C are predominant in Asia; type D is common in the Mediterranean area, the Middle East and India; type E is localized in sub-Saharan Africa; type F (or H) is restricted to Central and South America. Type G has been found in France and Germany. Genotypes A, D and F are predominant in Brazil and all genotypes occur in the United States with frequencies dependent on ethnicity. The E and F strains appear to have originated in aboriginal populations of Africa and the New World, respectively. Within these genotypes, 24 subtypes have been described which differ by 4-8% of the genome:
      • Type A has two subtypes: Aa (A1) in Africa/Asia and the Philippines and Ae (A2) in Europe/United States.
      • Type B has two distinct geographical distributions: Bj/B1 (‘j’—Japan) and Ba/B2 (‘a’—Asia). Type Ba has been further subdivided into four clades (B2-B4).
      • Type C has two geographically subtypes: Cs (C1) in South-east Asia and Ce (C2) in East Asia. The C subtypes have been divided into five clades (C1-C5). A sixth clade (C6) has been described in the Philippines but only in one isolate to date. Type C1 is associated with Vietnam, Myanmar and Thailand; type C2 with Japan, Korea and China; type C3 with New Caledonia and Polynesia; C4 with Australia; and C5 with the Philippines. A further subtype has been described in Papua, Indonesia.
      • Type D has been divided into 7 subtypes (D1-D7).
      • Type F has been subdivided into 4 subtypes (F1-F4). F1 has been further divided in to 1a and 1b. In Venezuela subtypes F1, F2, and F3 are found in East and West Amerindians. Among South Amerindians only F3 was found. Subtypes Ia, III, and IV exhibit a restricted geographic distribution (Central America, the North and the South of South America respectively) while clades Ib and II are found in all the Americas except in the Northern South America and North America respectively.
  • The life cycle of hepatitis B virus is complex. Hepatitis B is one of a few known non-retroviral viruses which use reverse transcription as a part of its replication process:
      • Attachment—The virus gains entry into the cell by binding to a receptor on the surface of the cell and enters it by endocytosis.
      • Penetration—The virus membrane then fuses with the host cell's membrane releasing the DNA and core proteins into the cytoplasm.
      • Uncoating—Because the virus multiplies via RNA made by a host enzyme, the viral genomic DNA has to be transferred to the cell nucleus by host proteins. The core proteins dissociate from the partially double-stranded viral DNA is then made fully double-stranded and transformed into covalently closed circular DNA (cccDNA) that serves as a template for transcription of four viral mRNAs.
      • Replication—The cccDNA is the transcriptional template for all of HBV's RNAs. The largest of the mRNAs is called the pre-core mRNA that encodes HBeAg. A slightly shorter mRNA is called the pregenomic RNA that encodes the HBcAg and the viral DNA polymerase. Both the precore and pregenomic RNAs are longer than the viral genome, but only the pregenomic RNA is packaged into nascent core particles along with the viral polymerase. Reverse transcription within the capsids is catalyzed by the coordinate activity of the viral DNA polymerase's reverse transcriptase and ribonuclease H activities and results in the partially double-stranded viral DNA found within HBV virions.
      • Assembly and Release—Progeny virions are formed budding of the viral capsid particles containing the viral DNA into endoplasmic-reticulum-derived membranes, where they pick up their envelope and HBsAgs are released from the cell by non-cytolytic secretion or are returned to the nucleus and re-cycled to produce even more copies of the nuclear cccDNA.
  • 2. Treatment
  • Currently, there are seven FDA approved drugs in the U.S. to treat chronic HBV: Intron A® (Interferon Alpha), Pegasys® (Pegylated Interferon), Epivir HBV® (Lamivudine), Hepsera® (Adefovir), Baraclude® (Entecavir), Tyzeka® (Telbivudine), and Viread® (Tenofovir).
  • Adefovir, previously called bis-POM PMEA, with trade names Preveon® and Hepsera®, is an orally-administered nucleotide analog reverse transcriptase inhibitor (ntRTI). It can be formulated as the pivoxil prodrug adefovir dipivoxil. Adefovir works by blocking reverse transcriptase, the enzyme that is crucial for the hepatitis B virus (HBV) to reproduce in the body because it synthesizes the viral DNA. It is approved for the treatment of chronic hepatitis B in adults with evidence of active viral replication and either evidence of persistent elevations in serum aminotransferases (primarily ALT) or histologically active disease. The main benefit of adefovir over drugs like lamivudine (below) is that it takes a much longer period of time before the virus develops resistance to it. Adefovir dipivoxil contains two pivaloyloxymethyl units, making it a prodrug form of adefovir.
  • Lamivudine (2′,3′-dideoxy-3′-thiacytidine, commonly called 3TC) is a potent nucleoside analog reverse transcriptase inhibitor (nRTI). It is marketed by GlaxoSmithKline with the brand names Zeffix®, Heptovir®, Epivir®, and Epivir-HBV®. Lamivudine has been used for treatment of chronic hepatitis B at a lower dose than for treatment of HIV. It improves the seroconversion of HBeAg positive hepatitis B and also improves histology staging of the liver. Long term use of lamivudine unfortunately leads to emergence of a resistant hepatitis B virus mutants with alterations to the key YMDD motif in the reverse transcriptase active site. Despite this, lamivudine is still used widely as it is well tolerated and as it is less expensive than the newer drugs and is the only anti-HBV drug many people in emerging economies can afford.
  • Lamivudine is an analogue of cytidine. It can inhibit both types (1 and 2) of HIV reverse transcriptase and also the reverse transcriptase of hepatitis B. It is phosphorylated to active metabolites that compete for incorporation into viral DNA. It inhibits the HIV reverse transcriptase enzyme competitively and acts as a chain terminator of DNA synthesis. The lack of a 3′—OH group in the incorporated nucleoside analogue prevents the formation of the 5′ to 3′ phosphodiester linkage essential for DNA chain elongation, and therefore, the viral DNA growth is terminated. Lamivudine is administered orally, and it is rapidly absorbed with a bio-availability of over 80%. Some research suggests that lamivudine can cross the blood-brain barrier.
  • Entecavir, abbreviated ETV, is an oral antiviral drug used in the treatment of hepatitis B infection. It is marketed under the trade names Baraclude® (BMS) and Entaliv® (DRL). Entecavir is a nucleoside analog (more specifically, a guanosine analogue) that inhibits reverse transcription and DNA replication thus preventing transcription in the viral replication process. The drug's manufacturer claims that entecavir is more efficacious than previous agents used to treat hepatitis B (lamivudine and adefovir). Entecavir was approved by the U.S. FDA in March 2005 and is used to treat chronic hepatitis B. It also helps prevent the hepatitis B virus from multiplying and infecting new liver cells. Entecavir is also indicated for the treatment of chronic hepatitis B in adults with HIV/AIDS infection. However, entecavir is not active against HIV.
  • Telbivudine is an antiviral drug used in the treatment of hepatitis B infection. It is marketed by Swiss pharmaceutical company Novartis under the trade names Sebivo® (Europe) and Tyzeka® (United States). Clinical trials have shown it to be significantly more effective than lamivudine or adefovir, and less likely to cause resistance. Telbivudine is a synthetic thymidine nucleoside analogue; it is the L-isomer of thymidine. It is taken once daily.
  • Tenofovir disoproxil fumarate (TDF or PMPA), marketed by Gilead Sciences under the trade name Viread®, it is also a nucleotide analogue reverse transcriptase inhibitor (nRTIs) which blocks the HBV reverse transcriptase, an enzyme crucial to viral production. Tenofovir disoproxil fumarate is a prodrug form of tenofovir. Tenofovir is indicated in combination with other antiretroviral agents for the treatment of HIV-1 infection in adults. This indication is based on analyses of plasma HIV-1 RNA levels and CD4 cell counts in controlled studies of tenofovir in treatment-naive and treatment-experienced adults. There are no study results demonstrating the effect of tenofovir on the clinical progression of HIV. It also has activity against wild-type and lamivudine-resistant HBV.
    • C. NUCLEOTIDYL TRANSFERASE SUPERFAMILY ENZYMES
  • The inhibitors screened in this project were selected for their ability to inhibit the HIV RNAse H and/or integrase enzymes (or to be close chemical analogs of known inhibitors). The RNAse H and integrase are members of the nucleotidyl transferase superfamily (NTS) whose members share a similar protein fold and enzymatic mechanisms (Yang 1995). Therefore, the presumed targets of the anti-herpesvirus compounds claimed here are viral and/or cellular NTS enzymes. RNAse H enzymes (Hostomsky et al., 1993a; 1993b; 1993c) digest RNA when it is hybridized to DNA. Their physiological roles include removal of RNA primers during DNA synthesis, removal of abortive transcription products, and removal of RNA strands following reverse transcription by viruses or retrotransposons. Integrase enzymes cleave DNA strands and catalyze the covalent insertion of another DNA strand at the cleavage site. Consequently, the presumed mechanism of action for the herpesvirus inhibitors is through suppression of one or more of the nucleolytic or recombination-related activities essential for replication of the herpesvirus DNA.
  • The NTS family of enzymes includes E. coli RNase H I and II (Katayanagi et al., 1990, Yang et al., 1990 and Lai et al., 2000); human RNase H 1 and 2 (Lima et al., 2001, Frank et al., 1998 and Frank et al., 1998); the RuvC Holiday junction resolvase (Ariyoshi et al., 1994); and the Argonaute RNAse (Parker et al., 2004 and Song et al., 2004); retroviral RNase H enzymes including the HIV enzyme (Nowotny 2009); retroviral integrases including the HIV integrase (Dyda et al., 1994); and the hepatitis B virus (HBV) RNase H (Tavis et al., 2013). These enzymes function in a wide range of nucleic acid metabolic events, including RNA and DNA digestion, DNA recombination, DNA integration, DNA excision, replication fork repair, DNA repair, miRNA maturation, and miRNA-directed RNA cleavage. The canonical RNase H structure contains about 100 amino acids that fold into a 5-stranded β-sheet overlaid with 3 α-helices arranged like an “H”. Within the active site are four conserved carboxylates (the “DEDD” motif) that coordinate two divalent cations (Nowotny et al., 2005).
  • The RNase H enzymatic mechanism is believed to involve both divalent cations (Klumpp et al., 2003; Yang and Steitz, 1995), although a 1-ion mechanism has been proposed (Goedken and Marqusee, 2001; Keck et al., 1998). There are 3 classes of RNAse Hs distinguished by how they bind to their substrates. RNA binding by the “stand-alone” class typified by E. coli RNAse H I is promoted by a basic “handle” region (Hostomsky et al., 1993; Kwun et al., 2001). Eukaryotic RNase Hs typically contain a “RHBD” domain that influences nucleic acid binding. Finally, substrate binding by the retroviral enzymes can either be a property of the RNase H domain itself (e.g., Moloney murine leukemia virus) or may require the reverse transcriptase domain to provide sufficient affinity for the nucleic acid substrate (e.g., HIV) (Hostomsky et al., 1993; Smith et al., 1994).
  • The HBV RNase H is a NTS enzyme. Mutational analysis of the HBV RNase H revealed the DEDD active site residues to be D702, E731, D750, and D790 (numbering for HBV strain adw2) (Gerelsaikhan et al., 1996; Tavis et al., 2013). Data obtained with the HBV RNase H will be used as an example to establish how anti-RNase H drug discovery can be conducted and to establish utility of the claimed compounds against HBV replication.
  • HIV reverse transcription requires a virally encoded RNase H activity to remove the viral RNA after it has been copied into DNA (Freed and Martin, 2007). Consequently, the HIV RNase H activity has attracted much attention as a drug target (Billamboz et al., 2011; Bokesch et al., 2008; Budihas et al., 2005; Chung et al., 2011; Chung et al., 2010; Di et al., 2010; Didierjean et al., 2005; Fuji et al., 2009; Himmel et al., 2009; Himmel et al., 2006; Kirschberg et al., 2009; Klarmann et al., 2002; Klumpp et al., 2003; Klumpp and Mirzadegan, 2006; Shaw-Reid et al., 2003; Su et al., 2010; Takada et al., 2007; Wendeler et al., 2008; Williams et al., 2010). Over 100 anti-HIV RNase H compounds, based on a wide variety of chemical scaffolds, have been reported (Chung et al., 2011; Klumpp and Mirzadegan, 2006). They typically have inhibitory concentration-50% (IC50) values in the low M range. The large majority of these compounds inhibit the RNase H by chelating divalent cations in the active site (Billamboz et al., 2011; Chung et al., 2011; Fuji et al., 2009; Himmel et al., 2009; Kirschberg et al., 2009; Su et al., 2010), but compounds that alter the enzyme's conformation or its interaction with nucleic acids have also been reported (Himmel et al., 2006; Wendeler et al., 2008). The inhibitors typically have EC50 values ˜10× higher than the IC50 values, and they often cause modest cytotoxicity, leading to therapeutic indexes (TI) that are usually <10. Second-generation inhibitors with substantially improved efficacy have been reported, (Billamboz et al., 2011; Chung et al., 2011; Williams et al., 2010), and compounds with efficacy and TI values appropriate for a human drug exist (Himmel et al., 2006; Williams et al., 2010).
  • None of the anti-HIV RNase H compounds have entered clinical trials yet. This is due in part to their relatively low TI values but also to the large number of approved and developmental anti-HIV drugs, raising doubts about the marketability of anti-HIV RNase H compounds. Despite these challenges, the HIV RNase H remains a target of intensive ongoing drug development, as is evidenced by the large number of groups working in the field (Billamboz et al., 2011; Bokesch et al., 2008; Budihas et al., 2005; Chung et al., 2011; Chung et al., 2010; Di et al., 2010; Didierjean et al., 2005; Fuji et al., 2009; Himmel et al., 2009; Himmel et al., 2006; Kirschberg et al., 2009; Klarmann et al., 2002; Klumpp et al., 2003; Klumpp and Mirzadegan, 2006; Shaw-Reid et al., 2003; Su et al., 2010; Takada et al., 2007; Wendeler et al., 2008; Williams et al., 2010).
  • Because both the RNase H and integrase are NTS enzymes, some anti-RNase H compounds can inhibit the HIV integrase, and some anti-integrase compounds can inhibit the RNase H (Klarmann et al., 2002, Williams et al., 2010 and Billamboz et al., 2011). Despite this cross-inhibitory potential, resistance mutations to HIV DNA polymerase or integrase drugs have not led to cross-resistance to RNase H inhibitors (Billamboz et al., 2011 and Himmel et al., 2006).
  • HBV reverse transcription requires two viral enzymatic activities that are both located on the viral reverse transcriptase protein. The DNA polymerase activity synthesizes new DNA and is targeted by the nucleos(t)ide analogs. The RNase H destroys the viral RNA after it has been copied into DNA. Inhibiting the RNAse H would block DNA synthesis and consequently halt viral replication, but anti-HBV RNase H drugs have not been developed because enzyme suitable for drug screening could not be readily made. One of the inventors recently produced active recombinant HBV RNase H and identified 35 inhibitors of the RNase H (Table 1; Tavis et al., 2013; Hu et al., 2013; Tavis and Lomonosova, 2015; Lu, et al., 2015; and Cai, et al., 2014).
  • These examples of cross-inhibition of NTS enzymes by RNase H and integrase inhibitors provide the precedent upon which the studies with the herpesviruses rest.
    • D. CHEMICAL ENTITY
  • The compound of the present disclosure appears to inhibit a different enzymatic activity than the existing anti-hepatitis or anti-herpesvirus drugs, and does so with a striking capacity to suppress virus replication at very low toxicity to uninfected cells. This implies that it will be effective against viral isolates resistant to the existing drugs and suggests that these drugs could be combined effectively with the existing drugs to both increase efficacy and to reduce the rate of resistance development to either drug. Furthermore, the compound was more effective against HSV-2 than a currently accepted first line therapy, acyclovir, indicating that it may be more effective than the existing drugs when formulated for pharmaceutical delivery. In other embodiments, the present compounds may be used to treat infections of hepatitis B virus or used in combination with other hepatitis B virus therapies.
  • The compound of the present disclosure is represented by the formula below:
  • Figure US20180169083A1-20180621-C00018
  • wherein:
      • R1 is aryl(C≤12), aralkyl(C≤18), heteroaryl(C≤12), alkylamino(C≤12), dialkylamino(C≤12), arylamino(C≤12), diarylamino(C≤12), aralkylamino(C≤18), diaralkylamino(C≤18), or a substituted version of any of these groups;
      • R2 is hydrogen, alkyl(C≤8), or substituted alkyl(C≤8); and
      • R3 is hydrogen, amino, carboxyl, cyano, halo, hydroxy, nitro, hydroxysulfonyl, or sulfonylamine; or
        • alkyl(C≤8), aryl(C≤8), acyl(C≤8), alkoxy(C≤8), acyloxy(C≤8), amido(C≤8), or substituted version of any of these groups;
      • X2 is hydrogen or —C(O)Ra, wherein: Ra is hydroxy, alkoxy(C≤8), or substituted alkoxy(C≤8); or
  • a compound of the formula:
  • Figure US20180169083A1-20180621-C00019
  • wherein:
      • R4 is alkyl(C≤12), aryl(C≤12), aralkyl(C≤12), heteroaryl(C≤12), or a substituted version of any of these groups;
      • R5 and R8 are each independently hydrogen, alkyl(C≤8), or substituted alkyl(C≤8);
      • R6 is hydrogen, hydroxy, alkyl(C≤8), or substituted alkyl(C≤8); and
      • R7 is aryl(C≤12), aralkyl(C≤12), heteroaryl(C≤12), or a substituted version of any of these groups;
  • a compound of the formula:
  • Figure US20180169083A1-20180621-C00020
  • wherein:
      • R9 is alkyl(C≤12), aryl(C≤12), aralkyl(C≤12), heteroaryl(C≤12), or a substituted version of any of these groups;
      • R10 is hydrogen, alkyl(C≤8), or substituted alkyl(C≤8); and
      • R11 is hydrogen or Y1—O—X1—OR12; wherein:
        • Y1 is alkanediyl(C≤8) or substituted alkanediyl(C≤8);
        • X1 is arenediyl(C≤12), heteroarenediyl(C≤12), or a substituted version of either of these groups;
        • R12 is aryl(C≤12), aralkyl(C≤12), heteroaryl(C≤12), or a substituted version of any of these groups; or
  • Figure US20180169083A1-20180621-C00021
  • or a pharmaceutically acceptable salt or tautomer thereof.
  • TABLE 1
    Non-Limiting Examples of Compounds
    Com-
    pound
    ID Structure
    #41
    Figure US20180169083A1-20180621-C00022
    #49
    Figure US20180169083A1-20180621-C00023
    #150
    Figure US20180169083A1-20180621-C00024
    #151
    Figure US20180169083A1-20180621-C00025
    #191
    Figure US20180169083A1-20180621-C00026
    #208
    Figure US20180169083A1-20180621-C00027
    #210
    Figure US20180169083A1-20180621-C00028
    #211
    Figure US20180169083A1-20180621-C00029
  • The compound of the disclosure contains one or more asymmetrically-substituted carbon or nitrogen atoms, and may be isolated in optically active or racemic form. Thus, all chiral, diastereomeric, racemic form, epimeric form, and all geometric isomeric forms of the chemical formula are intended, unless the specific stereochemistry or isomeric form is specifically indicated. The compound may occur as a racemate and racemic mixtures, single enantiomers, diastereomeric mixtures and individual diastereomers. In some embodiments, a single enantiomer or diastereomer is obtained. The chiral centers of the compound of the present disclosure can have the S or the R configuration.
  • Chemical formulas used to represent the compound of the disclosure will typically only show one of possibly several different tautomers. For example, many types of ketone groups are known to exist in equilibrium with corresponding enol groups. Regardless of which tautomer is depicted for a given compound, and regardless of which one is most prevalent, all tautomers of a given chemical formula are intended.
  • The compound of the disclosure may also have the advantage of being more efficacious than, be less toxic than, be longer acting than, be more potent than, produce fewer side effects than, be more easily absorbed than, and/or have a better pharmacokinetic profile (e.g., higher oral bioavailability and/or lower clearance) than, and/or have other useful pharmacological, physical, or chemical properties over, compounds known in the prior art, whether for use in the indications stated herein or otherwise.
  • In addition, atoms making up the compound of the present disclosure are intended to include all isotopic forms of such atoms. Isotopes, as used herein, include those atoms having the same atomic number but different mass numbers. By way of general example and without limitation, isotopes of hydrogen include tritium and deuterium, and isotopes of carbon include 13C and 14C. Similarly, it is contemplated that one or more carbon atom(s) of a compound of the present disclosure may be replaced by a silicon atom(s). Furthermore, it is contemplated that one or more oxygen atom(s) of a compound of the present disclosure may be replaced by a sulfur or selenium atom(s).
  • The compound of the present disclosure may also exist in prodrug form. Since prodrugs are known to enhance numerous desirable qualities of pharmaceuticals (e.g., solubility, bioavailability, manufacturing, etc.), the compound employed in some methods of the disclosure may, if desired, be delivered in prodrug form. Thus, the disclosure contemplates prodrugs of the compound of the present disclosure as well as methods of delivering prodrugs. Prodrugs of the compound employed in the disclosure may be prepared by modifying functional groups present in the compound in such a way that the modifications are cleaved, either in routine manipulation or in vivo, to the parent compound. Accordingly, prodrugs include, for example, compounds described herein in which a hydroxy group is bonded to any group that, when the prodrug is administered to a subject, cleaves to form a hydroxy group.
  • It should be recognized that the particular anion or cation forming a part of any salt of this disclosure is not critical, so long as the salt, as a whole, is pharmacologically acceptable. Additional examples of pharmaceutically acceptable salts and their methods of preparation and use are presented in Handbook of Pharmaceutical Salts: Properties, and Use (2002), which is incorporated herein by reference.
    • 2. Definitions
  • When used in the context of a chemical group: “hydrogen” means —H; “hydroxy” means —OH; “oxo” means ═O; “carbonyl” means —C(═O)—; “carboxy” means —C(═O)OH (also written as —COOH or —CO2H); “halo” means independently —F, —Cl, —Br or —I; “amino” means —NH2; “hydroxyamino” means —NHOH; “nitro” means —NO2; imino means ═NH; “cyano” means —CN; “isocyanate” means —N═C═O; “azido” means —N3; in a monovalent context “phosphate” means —OP(O)(OH)2 or a deprotonated form thereof; in a divalent context “phosphate” means —OP(O)(OH)O— or a deprotonated form thereof; “mercapto” means —SH; and “thio” means=S; “sulfonyl” means —S(O)2—; and “sulfinyl” means —S(O)—.
  • In the context of chemical formulas, the symbol “—” means a single bond, “=” means a double bond, and “
    Figure US20180169083A1-20180621-P00001
    ” means triple bond. The symbol “
    Figure US20180169083A1-20180621-P00002
    ” represents an optional bond, which if present is either single or double. The symbol “
    Figure US20180169083A1-20180621-P00003
    ” represents a single bond or a double bond. Thus, the formula
  • Figure US20180169083A1-20180621-C00030
  • covers, for example,
  • Figure US20180169083A1-20180621-C00031
  • And it is understood that no one such ring atom forms part of more than one double bond. Furthermore, it is noted that the covalent bond symbol “—”, when connecting one or two stereogenic atoms, does not indicate any preferred stereochemistry. Instead, it covers all stereoisomers as well as mixtures thereof. The symbol “
    Figure US20180169083A1-20180621-P00004
    ”, when drawn perpendicularly across a bond (e.g.,
  • Figure US20180169083A1-20180621-C00032
  • for methyl) indicates a point of attachment of the group. It is noted that the point of attachment is typically only identified in this manner for larger groups in order to assist the reader in unambiguously identifying a point of attachment. The symbol “
    Figure US20180169083A1-20180621-P00005
    ” means a single bond where the group attached to the thick end of the wedge is “out of the page.” The symbol “
    Figure US20180169083A1-20180621-P00006
    ” means a single bond where the group attached to the thick end of the wedge is “into the page”. The symbol “
    Figure US20180169083A1-20180621-P00007
    ” means a single bond where the geometry around a double bond (e.g., either E or Z) is undefined. Both options, as well as combinations thereof are therefore intended. Any undefined valency on an atom of a structure shown in this application implicitly represents a hydrogen atom bonded to that atom. A bold dot on a carbon atom indicates that the hydrogen attached to that carbon is oriented out of the plane of the paper.
  • When a group “R” is depicted as a “floating group” on a ring system, for example, in the formula:
  • Figure US20180169083A1-20180621-C00033
  • then R may replace any hydrogen atom attached to any of the ring atoms, including a depicted, implied, or expressly defined hydrogen, so long as a stable structure is formed. When a group “R” is depicted as a “floating group” on a fused ring system, as for example in the formula:
  • Figure US20180169083A1-20180621-C00034
  • then R may replace any hydrogen attached to any of the ring atoms of either of the fused rings unless specified otherwise. Replaceable hydrogens include depicted hydrogens (e.g., the hydrogen attached to the nitrogen in the formula above), implied hydrogens (e.g., a hydrogen of the formula above that is not shown but understood to be present), expressly defined hydrogens, and optional hydrogens whose presence depends on the identity of a ring atom (e.g., a hydrogen attached to group X, when X equals —CH—), so long as a stable structure is formed. In the example depicted, R may reside on either the 5-membered or the 6-membered ring of the fused ring system. In the formula above, the subscript letter “y” immediately following the group “R” enclosed in parentheses, represents a numeric variable. Unless specified otherwise, this variable can be 0, 1, 2, or any integer greater than 2, only limited by the maximum number of replaceable hydrogen atoms of the ring or ring system.
  • For the chemical groups and compound classes, the number of carbon atoms in the group or class is as indicated as follows: “Cn” defines the exact number (n) of carbon atoms in the group/class. “C≤n” defines the maximum number (n) of carbon atoms that can be in the group/class, with the minimum number as small as possible for the group/class in question, e.g., it is understood that the minimum number of carbon atoms in the group “alkenyl(C≤8)” or the class “alkene(C≤8)” is two. Compare with “alkoxy(C≤10)”, which designates alkoxy groups having from 1 to 10 carbon atoms. “Cn-n′” defines both the minimum (n) and maximum number (n′) of carbon atoms in the group. Thus, “alkyl(C≤10)” designates those alkyl groups having from 2 to 10 carbon atoms. These carbon number indicators may precede or follow the chemical groups or class it modifies and it may or may not be enclosed in parenthesis, without signifying any change in meaning. Thus, the terms “C5 olefin”, “C5-olefin”, “olefin(C5)”, and “olefinC5” are all synonymous. When any of the chemical groups or compound classes defined herein is modified by the term “substituted”, any carbon atom(s) in a moiety replacing a hydrogen atom is not counted. Thus methoxyhexyl, which has a total of seven carbon atoms, is an example of a substituted alkyl(C1-6).
  • The term “saturated” when used to modify a compound or chemical group means the compound or chemical group has no carbon-carbon double and no carbon-carbon triple bonds, except as noted below. When the term is used to modify an atom, it means that the atom is not part of any double or triple bond. In the case of substituted versions of saturated groups, one or more carbon oxygen double bond or a carbon nitrogen double bond may be present. And when such a bond is present, then carbon-carbon double bonds that may occur as part of keto-enol tautomerism or imine/enamine tautomerism are not precluded. When the term “saturated” is used to modify a solution of a substance, it means that no more of that substance can dissolve in that solution.
  • The term “aliphatic” when used without the “substituted” modifier signifies that the compound or chemical group so modified is an acyclic or cyclic, but non-aromatic hydrocarbon compound or group. In aliphatic compounds/groups, the carbon atoms can be joined together in straight chains, branched chains, or non-aromatic rings (alicyclic). Aliphatic compounds/groups can be saturated, that is joined by single carbon-carbon bonds (alkanes/alkyl), or unsaturated, with one or more carbon-carbon double bonds (alkenes/alkenyl) or with one or more carbon-carbon triple bonds (alkynes/alkynyl).
  • The term “aromatic” when used to modify a compound or a chemical group refers to a planar unsaturated ring of atoms with 4n+2 electrons in a fully conjugated cyclic it system.
  • The term “alkyl” when used without the “substituted” modifier refers to a monovalent saturated aliphatic group with a carbon atom as the point of attachment, a linear or branched acyclic structure, and no atoms other than carbon and hydrogen. The groups —CH3 (Me), —CH2CH3 (Et), —CH2CH2CH3 (n-Pr or propyl), —CH(CH3)2 (i-Pr, iPr or isopropyl), —CH2CH2CH2CH3 (n-Bu), —CH(CH3)CH2CH3 (sec-butyl), —CH2CH(CH3)2 (isobutyl), —C(CH3)3 (tert-butyl, t-butyl, t-Bu or tBu), and —CH2C(CH3)3 (neo-pentyl) are non-limiting examples of alkyl groups. The term “alkanediyl” when used without the “substituted” modifier refers to a divalent saturated aliphatic group, with one or two saturated carbon atom(s) as the point(s) of attachment, a linear or branched acyclic structure, no carbon-carbon double or triple bonds, and no atoms other than carbon and hydrogen. The groups —CH2-(methylene), —CH2CH2—, —CH2C(CH3)2CH2—, and —CH2CH2CH2— are non-limiting examples of alkanediyl groups. The term “alkylidene” when used without the “substituted” modifier refers to the divalent group ═CRR′ in which R and R′ are independently hydrogen or alkyl. Non-limiting examples of alkylidene groups include: ═CH2, ═CH(CH2CH3), and ═C(CH3)2. An “alkane” refers to the class of compounds having the formula H—R, wherein R is alkyl as this term is defined above. When any of these terms is used with the “substituted” modifier one or more hydrogen atom has been independently replaced by —OH, —F, —Cl, —Br, —I, —NH2, —NO2, —CO2H, —CO2CH3, —CN, —SH, —OCH3, —OCH2CH3, —C(O)CH3, —NHCH3, —NHCH2CH3, —N(CH3)2, —C(O)NH2, —C(O)NHCH3, —C(O)N(CH3)2, —OC(O)CH3, —NHC(O)CH3, —S(O)2OH, or —S(O)2NH2. The following groups are non-limiting examples of substituted alkyl groups: —CH2OH, —CH2Cl, —CF3, —CH2CN, —CH2C(O)OH, —CH2C(O)OCH3, —CH2C(O)NH2, —CH2C(O)CH3, —CH2OCH3, —CH2OC(O)CH3, —CH2NH2, —CH2N(CH3)2, and —CH2CH2Cl.
  • The term “aryl” when used without the “substituted” modifier refers to a monovalent unsaturated aromatic group with an aromatic carbon atom as the point of attachment, said carbon atom forming part of a one or more six-membered aromatic ring structure, wherein the ring atoms are all carbon, and wherein the group consists of no atoms other than carbon and hydrogen. If more than one ring is present, the rings may be fused or unfused. As used herein, the term does not preclude the presence of one or more alkyl or aralkyl groups (carbon number limitation permitting) attached to the first aromatic ring or any additional aromatic ring present. Non-limiting examples of aryl groups include phenyl (Ph), methylphenyl, (dimethyl)phenyl, —C6H4CH2CH3 (ethylphenyl), naphthyl, and a monovalent group derived from biphenyl. The term “arenediyl” when used without the “substituted” modifier refers to a divalent aromatic group with two aromatic carbon atoms as points of attachment, said carbon atoms forming part of one or more six-membered aromatic ring structure(s) wherein the ring atoms are all carbon, and wherein the monovalent group consists of no atoms other than carbon and hydrogen. As used herein, the term does not preclude the presence of one or more alkyl, aryl or aralkyl groups (carbon number limitation permitting) attached to the first aromatic ring or any additional aromatic ring present. If more than one ring is present, the rings may be fused or unfused. Unfused rings may be connected via one or more of the following: a covalent bond, alkanediyl, or alkenediyl groups (carbon number limitation permitting). Non-limiting examples of arenediyl groups include:
  • Figure US20180169083A1-20180621-C00035
  • An “arene” refers to the class of compounds having the formula H—R, wherein R is aryl as that term is defined above. Benzene and toluene are non-limiting examples of arenes. When any of these terms are used with the “substituted” modifier one or more hydrogen atom has been independently replaced by —OH, —F, —Cl, —Br, —I, —NH2, —NO2, —CO2H, —CO2CH3, —CN, —SH, —OCH3, —OCH2CH3, —C(O)CH3, —NHCH3, —NHCH2CH3, —N(CH3)2, —C(O)NH2, —C(O)NHCH3, —C(O)N(CH3)2, —OC(O)CH3, —NHC(O)CH3, —S(O)2OH, or —S(O)2NH2.
  • The term “aralkyl” when used without the “substituted” modifier refers to the monovalent group -alkanediyl-aryl, in which the terms alkanediyl and aryl are each used in a manner consistent with the definitions provided above. Non-limiting examples are: phenylmethyl (benzyl, Bn) and 2-phenyl-ethyl. When the term aralkyl is used with the “substituted” modifier one or more hydrogen atom from the alkanediyl and/or the aryl group has been independently replaced by —OH, —F, —Cl, —Br, —I, —NH2, —NO2, —CO2H, —CO2CH3, —CN, —SH, —OCH3, —OCH2CH3, —C(O)CH3, —NHCH3, —NHCH2CH3, —N(CH3)2, —C(O)NH2, —C(O)NHCH3, —C(O)N(CH3)2, —OC(O)CH3, —NHC(O)CH3, —S(O)2OH, or —S(O)2NH2. Non-limiting examples of substituted aralkyls are: (3-chlorophenyl)-methyl, and 2-chloro-2-phenyl-eth-1-yl.
  • The term “heteroaryl” when used without the “substituted” modifier refers to a monovalent aromatic group with an aromatic carbon atom or nitrogen atom as the point of attachment, said carbon atom or nitrogen atom forming part of one or more aromatic ring structures wherein at least one of the ring atoms is nitrogen, oxygen or sulfur, and wherein the heteroaryl group consists of no atoms other than carbon, hydrogen, aromatic nitrogen, aromatic oxygen and aromatic sulfur. If more than one ring is present, the rings may be fused or unfused. As used herein, the term does not preclude the presence of one or more alkyl, aryl, and/or aralkyl groups (carbon number limitation permitting) attached to the aromatic ring or aromatic ring system. Non-limiting examples of heteroaryl groups include furanyl, imidazolyl, indolyl, indazolyl (Im), isoxazolyl, methylpyridinyl, oxazolyl, phenylpyridinyl, pyridinyl (pyridyl), pyrrolyl, pyrimidinyl, pyrazinyl, quinolyl, quinazolyl, quinoxalinyl, triazinyl, tetrazolyl, thiazolyl, thienyl, and triazolyl. The term “N-heteroaryl” refers to a heteroaryl group with a nitrogen atom as the point of attachment. A “heteroarene” refers to the class of compounds having the formula H—R, wherein R is heteroaryl. Pyridine and quinoline are non-limiting examples of heteroarenes. When these terms are used with the “substituted” modifier one or more hydrogen atom has been independently replaced by —OH, —F, —Cl, —Br, —I, —NH2, —NO2, —CO2H, —CO2CH3, —CN, —SH, —OCH3, —OCH2CH3, —C(O)CH3, —NHCH3, —NHCH2CH3, —N(CH3)2, —C(O)NH2, —C(O)NHCH3, —C(O)N(CH3)2, —OC(O)CH3, —NHC(O)CH3, —S(O)2OH, or —S(O)2NH2.
  • The term “acyl” when used without the “substituted” modifier refers to the group —C(O)R, in which R is a hydrogen, alkyl, cycloalkyl, or aryl as those terms are defined above. The groups, —CHO, —C(O)CH3 (acetyl, Ac), —C(O)CH2CH3, —C(O)CH(CH3)2, —C(O)CH(CH2)2, —C(O)C6H5, and —C(O)C6H4CH3 are non-limiting examples of acyl groups. A “thioacyl” is defined in an analogous manner, except that the oxygen atom of the group —C(O)R has been replaced with a sulfur atom, —C(S)R. The term “aldehyde” corresponds to an alkyl group, as defined above, attached to a —CHO group. When any of these terms are used with the “substituted” modifier one or more hydrogen atom (including a hydrogen atom directly attached to the carbon atom of the carbonyl or thiocarbonyl group, if any) has been independently replaced by —OH, —F, —Cl, —Br, —I, —NH2, —NO2, —CO2H, —CO2CH3, —CN, —SH, —OCH3, —OCH2CH3, —C(O)CH3, —NHCH3, —NHCH2CH3, —N(CH3)2, —C(O)NH2, —C(O)NHCH3, —C(O)N(CH3)2, —OC(O)CH3, —NHC(O)CH3, —S(O)2OH, or —S(O)2NH2. The groups, —C(O)CH2CF3, —CO2H (carboxyl), —CO2CH3 (methylcarboxyl), —CO2CH2CH3, —C(O)NH2 (carbamoyl), and —CON(CH3)2, are non-limiting examples of substituted acyl groups.
  • The term “alkoxy” when used without the “substituted” modifier refers to the group —OR, in which R is an alkyl, as that term is defined above. Non-limiting examples include: —OCH3 (methoxy), —OCH2CH3 (ethoxy), —OCH2CH2CH3, —OCH(CH3)2 (isopropoxy), —OC(CH3)3 (tert-butoxy), —OCH(CH2)2, —O-cyclopentyl, and —O-cyclohexyl. The terms “cycloalkoxy”, “alkenyloxy”, “alkynyloxy”, “aryloxy”, “aralkoxy”, “heteroaryloxy”, “heterocycloalkoxy”, and “acyloxy”, when used without the “substituted” modifier, refers to groups, defined as —OR, in which R is cycloalkyl, alkenyl, alkynyl, aryl, aralkyl, heteroaryl, heterocycloalkyl, and acyl, respectively. The term “alkylthio” and “acylthio” when used without the “substituted” modifier refers to the group —SR, in which R is an alkyl and acyl, respectively. The term “alcohol” corresponds to an alkane, as defined above, wherein at least one of the hydrogen atoms has been replaced with a hydroxy group. The term “ether” corresponds to an alkane, as defined above, wherein at least one of the hydrogen atoms has been replaced with an alkoxy group. When any of these terms is used with the “substituted” modifier one or more hydrogen atom has been independently replaced by —OH, —F, —Cl, —Br, —I, —NH2, —NO2, —CO2H, —CO2CH3, —CN, —SH, —OCH3, —OCH2CH3, —C(O)CH3, —NHCH3, —NHCH2CH3, —N(CH3)2, —C(O)NH2, —C(O)NHCH3, —C(O)N(CH3)2, —OC(O)CH3, —NHC(O)CH3, —S(O)2OH, or —S(O)2NH2.
  • The term “alkylamino” when used without the “substituted” modifier refers to the group —NHR, in which R is an alkyl, as that term is defined above. Non-limiting examples include: —NHCH3 and —NHCH2CH3. The term “dialkylamino” when used without the “substituted” modifier refers to the group —NRR′, in which R and R′ can be the same or different alkyl groups, or R and R′ can be taken together to represent an alkanediyl. Non-limiting examples of dialkylamino groups include: —N(CH3)2 and —N(CH3)(CH2CH3). The terms “cycloalkylamino”, “alkenylamino”, “alkynylamino”, “arylamino”, “aralkylamino”, “heteroarylamino”, “heterocycloalkylamino”, “alkoxyamino”, and “alkylsulfonylamino” when used without the “substituted” modifier, refers to groups, defined as —NHR, in which R is cycloalkyl, alkenyl, alkynyl, aryl, aralkyl, heteroaryl, heterocycloalkyl, alkoxy, and alkylsulfonyl, respectively. A non-limiting example of an arylamino group is —NHC6H5. The term “amido” (acylamino), when used without the “substituted” modifier, refers to the group —NHR, in which R is acyl, as that term is defined above. A non-limiting example of an amido group is —NHC(O)CH3. The term “alkylimino” when used without the “substituted” modifier refers to the divalent group ═NR, in which R is an alkyl, as that term is defined above. When any of these terms is used with the “substituted” modifier one or more hydrogen atom attached to a carbon atom has been independently replaced by —OH, —F, —Cl, —Br, —I, —NH2, —NO2, —CO2H, —CO2CH3, —CN, —SH, —OCH3, —OCH2CH3, —C(O)CH3, —NHCH3, —NHCH2CH3, —N(CH3)2, —C(O)NH2, —C(O)NHCH3, —C(O)N(CH3)2, —OC(O)CH3, —NHC(O)CH3, —S(O)2OH, or —S(O)2NH2. The groups —NHC(O)OCH3 and —NHC(O)NHCH3 are non-limiting examples of substituted amido groups.
  • The use of the word “a” or “an,” when used in conjunction with the term “comprising” in the claims and/or the specification may mean “one,” but it is also consistent with the meaning of “one or more,” “at least one,” and “one or more than one.”
  • Throughout this application, the term “about” is used to indicate that a value includes the inherent variation of error for the device, the method being employed to determine the value, or the variation that exists among the study subjects, or +/−5% of the stated value.
  • The terms “comprise,” “have” and “include” are open-ended linking verbs. Any forms or tenses of one or more of these verbs, such as “comprises,” “comprising,” “has,” “having,” “includes” and “including,” are also open-ended. For example, any method that “comprises,” “has” or “includes” one or more steps is not limited to possessing only those one or more steps and also covers other unlisted steps.
  • The term “effective,” as that term is used in the specification and/or claims, means adequate to accomplish a desired, expected, or intended result. “Effective amount,” “Therapeutically effective amount” or “pharmaceutically effective amount” when used in the context of treating a patient or subject with a compound means that amount of the compound which, when administered to a subject or patient for treating a disease, is sufficient to effect such treatment for the disease.
  • As used herein, the term “IC50” refers to an inhibitory dose which is 50% of the maximum response obtained. This quantitative measure indicates how much of a particular drug or other substance (inhibitor) is needed to inhibit a given biological, biochemical or chemical process (or component of a process, i.e. an enzyme, cell, cell receptor or microorganism) by half.
  • An “isomer” of a first compound is a separate compound in which each molecule contains the same constituent atoms as the first compound, but where the configuration of those atoms in three dimensions differs.
  • As used herein, the term “patient” or “subject” refers to a living vertebrate organism, such as a human, monkey, cow, sheep, goat, dog, cat, mouse, rat, guinea pig, bird, fish or transgenic species thereof. In certain embodiments, the patient or subject is a primate. Non-limiting examples of human subjects are adults, juveniles, infants and fetuses.
  • As generally used herein, “pharmaceutically acceptable” refers to those compounds, materials, compositions, and/or dosage forms which are, within the scope of sound medical judgment, suitable for use in contact with the tissues, organs, and/or bodily fluids of human beings and animals without excessive toxicity, irritation, allergic response, or other problems or complications commensurate with a reasonable benefit/risk ratio.
  • “Pharmaceutically acceptable salts” means salts of the compound of the present disclosure which are pharmaceutically acceptable, as defined above, and which possess the desired pharmacological activity. Such salts include acid addition salts formed with inorganic acids such as hydrochloric acid, hydrobromic acid, sulfuric acid, nitric acid, phosphoric acid, and the like; or with organic acids such as 1,2-ethanedisulfonic acid, 2-hydroxyethanesulfonic acid, 2-naphthalenesulfonic acid, 3-phenylpropionic acid, 4,4′-methylenebis(3-hydroxy-2-ene-1-carboxylic acid), 4-methylbicyclo[2.2.2]oct-2-ene-1-carboxylic acid, acetic acid, aliphatic mono- and dicarboxylic acids, aliphatic sulfuric acids, aromatic sulfuric acids, benzenesulfonic acid, benzoic acid, camphorsulfonic acid, carbonic acid, cinnamic acid, citric acid, cyclopentanepropionic acid, ethanesulfonic acid, fumaric acid, glucoheptonic acid, gluconic acid, glutamic acid, glycolic acid, heptanoic acid, hexanoic acid, hydroxynaphthoic acid, lactic acid, laurylsulfuric acid, maleic acid, malic acid, malonic acid, mandelic acid, methanesulfonic acid, muconic acid, o-(4-hydroxybenzoyl)benzoic acid, oxalic acid, p-chlorobenzenesulfonic acid, phenyl-substituted alkanoic acids, propionic acid, p-toluenesulfonic acid, pyruvic acid, salicylic acid, stearic acid, succinic acid, tartaric acid, tertiarybutylacetic acid, trimethylacetic acid, and the like. Pharmaceutically acceptable salts also include base addition salts which may be formed when acidic protons present are capable of reacting with inorganic or organic bases. Acceptable inorganic bases include sodium hydroxide, sodium carbonate, potassium hydroxide, aluminum hydroxide and calcium hydroxide. Acceptable organic bases include ethanolamine, diethanolamine, triethanolamine, tromethamine, N-methylglucamine and the like. It should be recognized that the particular anion or cation forming a part of any salt of this disclosure is not critical, so long as the salt, as a whole, is pharmacologically acceptable. Additional examples of pharmaceutically acceptable salts and their methods of preparation and use are presented in Handbook of Pharmaceutical Salts: Properties, and Use (2002).
  • “Prevention” or “preventing” includes: (1) inhibiting the onset of a disease in a subject or patient which may be at risk and/or predisposed to the disease but does not yet experience or display any or all of the pathology or symptomatology of the disease, and/or (2) slowing the onset of the pathology or symptomatology of a disease in a subject or patient which may be at risk and/or predisposed to the disease but does not yet experience or display any or all of the pathology or symptomatology of the disease, including reactivation.
  • “Prodrug” means a compound that is convertible in vivo metabolically into an inhibitor according to the present disclosure. The prodrug itself may or may not also have activity with respect to a given target protein. For example, a compound comprising a hydroxy group may be administered as an ester that is converted by hydrolysis in vivo to the hydroxy compound. Suitable esters that may be converted in vivo into hydroxy compounds include acetates, citrates, lactates, phosphates, tartrates, malonates, oxalates, salicylates, propionates, succinates, fumarates, maleates, methylene-bis-β-hydroxynaphthoate, gentisates, isethionates, di-p-toluoyltartrates, methanesulfonates, ethanesulfonates, benzenesulfonates, p-toluenesulfonates, cyclohexylsulfamates, quinates, esters of amino acids, and the like. Similarly, a compound comprising an amine group may be administered as an amide that is converted by hydrolysis in vivo to the amine compound.
  • A “stereoisomer” or “optical isomer” is an isomer of a given compound in which the same atoms are bonded to the same other atoms, but where the configuration of those atoms in three dimensions differs. “Enantiomers” are stereoisomers of a given compound that are mirror images of each other, like left and right hands. “Diastereomers” are stereoisomers of a given compound that are not enantiomers. Chiral molecules contain a chiral center, also referred to as a stereocenter or stereogenic center, which is any point, though not necessarily an atom, in a molecule bearing groups such that an interchanging of any two groups leads to a stereoisomer. In organic compounds, the chiral center is typically a carbon, phosphorus or sulfur atom, though it is also possible for other atoms to be stereocenters in organic and inorganic compounds. A molecule can have multiple stereocenters, giving it many stereoisomers. In compounds whose stereoisomerism is due to tetrahedral stereogenic centers (e.g., tetrahedral carbon), the total number of hypothetically possible stereoisomers will not exceed 2n, where n is the number of tetrahedral stereocenters. Molecules with symmetry frequently have fewer than the maximum possible number of stereoisomers. A 50:50 mixture of enantiomers is referred to as a racemic mixture. Alternatively, a mixture of enantiomers can be enantiomerically enriched so that one enantiomer is present in an amount greater than 50%. Typically, enantiomers and/or diasteromers can be resolved or separated using techniques known in the art. It is contemplated that for any stereocenter or axis of chirality for which stereochemistry has not been defined, that stereocenter or axis of chirality can be present in its R form, S form, or as a mixture of the R and S forms, including racemic and non-racemic mixtures. As used herein, the phrase “substantially free from other stereoisomers” means that the composition contains ≤15%, more preferably ≤10%, even more preferably ≤5%, or most preferably ≤1% of another stereoisomer(s).
  • “Effective amount,” “therapeutically effective amount” or “pharmaceutically effective amount” means that amount which, when administered to a subject or patient for treating a disease, is sufficient to effect such treatment for the disease.
  • “Treatment” or “treating” includes (1) inhibiting a disease in a subject or patient experiencing or displaying the pathology or symptomatology of the disease (e.g., arresting further development of the pathology and/or symptomatology), (2) ameliorating a disease in a subject or patient that is experiencing or displaying the pathology or symptomatology of the disease (e.g., reversing the pathology and/or symptomatology), and/or (3) effecting any measurable decrease in a disease in a subject or patient that is experiencing or displaying the pathology or symptomatology of the disease. In some embodiments, treatment of a patient afflicted with one of the pathological conditions described herein comprises administering to such a patient an amount of compound described herein which is therapeutically effective in controlling the condition or in prolonging the survivability of the patient beyond that expected in the absence of such treatment. As used herein, the term “inhibition” of the condition also refers to slowing, interrupting, arresting or stopping the condition and does not necessarily indicate a total elimination of the condition. It is believed that prolonging the survivability of a patient, beyond being a significant advantageous effect in and of itself, also indicates that the condition is beneficially controlled to some extent.
  • The above definitions supersede any conflicting definition in any reference that is incorporated by reference herein. The fact that certain terms are defined, however, should not be considered as indicative that any term that is undefined is indefinite. Rather, all terms used are believed to describe the disclosure in terms such that one of ordinary skill can appreciate the scope and practice the present disclosure.
    • E. THERAPEUTIC METHODS
  • 1. Pharmaceutical Formulations
  • In particular embodiments, where clinical application of an active ingredient is undertaken, it will be necessary to prepare a pharmaceutical composition appropriate for the intended application. Generally, this will entail preparing a pharmaceutical composition that is essentially free of pyrogens, as well as any other impurities or contaminants that could be harmful to humans or animals. One also will generally desire to employ appropriate buffers to render the complex stable and allow for uptake by target cells.
  • Aqueous compositions of the present disclosure comprise an effective amount of the active compound, as discussed above, further dispersed in pharmaceutically acceptable carrier or aqueous medium. Such compositions also are referred to as inocula. The phrase “pharmaceutically or pharmacologically acceptable” refers to compositions that do not produce an adverse, allergic or other untoward reaction when administered to an animal, or a human, as appropriate, as well as the requisite sterility for in vivo uses.
  • As used herein, “pharmaceutically acceptable carrier” includes any and all solvents, dispersion media, coatings, antibacterial and antifungal agents, isotonic and absorption delaying agents and the like. The use of such media and agents for pharmaceutically active substances is well known in the art. Except insofar as any conventional media or agent is incompatible with the active ingredient, its use in the therapeutic compositions is contemplated. Supplementary active ingredients also can be incorporated into the compositions.
  • Solutions of therapeutic compositions can be prepared in water suitably mixed with a surfactant, such as hydroxypropylcellulose. Dispersions also can be prepared in glycerol, liquid polyethylene glycols, mixtures thereof and in oils. Under ordinary conditions of storage and use, these preparations contain a preservative to prevent the growth of microorganisms.
  • The therapeutic compositions of the present disclosure are advantageously administered in the form of injectable compositions either as liquid solutions or suspensions; solid forms suitable for solution in, or suspension in, liquid prior to injection may also be prepared. These preparations also may be emulsified. A typical composition for such purpose comprises a pharmaceutically acceptable carrier. For instance, the composition may contain 10 mg, 25 mg, 50 mg or up to about 100 mg of human serum albumin per milliliter of phosphate buffered saline. Other pharmaceutically acceptable carriers include aqueous solutions, non-toxic excipients, including salts, preservatives, buffers and the like.
  • Examples of non-aqueous solvents are propylene glycol, polyethylene glycol, vegetable oil and injectable organic esters such as ethyloleate. Aqueous carriers include water, alcoholic/aqueous solutions, saline solutions, parenteral vehicles such as sodium chloride, Ringer's dextrose, etc. Intravenous vehicles include fluid and nutrient replenishers. Preservatives include antimicrobial agents, anti-oxidants, chelating agents and inert gases. The pH and exact concentration of the various components the pharmaceutical composition are adjusted according to well-known parameters.
  • Additional formulations are suitable for oral administration. Oral formulations include such typical excipients as, for example, pharmaceutical grades of mannitol, lactose, starch, magnesium stearate, sodium saccharine, cellulose, magnesium carbonate and the like. The compositions take the form of solutions, suspensions, tablets, pills, capsules, sustained release formulations or powders. When the route is topical, the form may be a cream, ointment, a controlled release patch, salve or spray. In some embodiments, the topical formulation by used for administration to the skin, to mucosa membranes such as the eye, eye lids, the genitals, the anus, or the inside of the mouth or nose, and in particular to the cornea.
  • An effective amount of the therapeutic composition is determined based on the intended goal. The term “unit dose” or “dosage” refers to physically discrete units suitable for use in a subject, each unit containing a predetermined quantity of the therapeutic composition calculated to produce the desired responses, discussed above, in association with its administration, i.e., the appropriate route and treatment regimen. The quantity to be administered, both according to number of treatments and unit dose, depends on the protection desired.
  • Precise amounts of the therapeutic composition also depend on the judgment of the practitioner and are peculiar to each individual. Factors affecting dose include physical and clinical state of the patient, the route of administration, the intended goal of treatment and the potency, stability and toxicity of the particular therapeutic substance.
  • 2. Routes of Administration
  • Formulations of the present disclosure are suitable for oral administration. However, the therapeutic compositions of the present disclosure may be administered via any common route so long as the target tissue is available via that route. This includes nasal, buccal, corneal, ocularly, rectal, vaginal, or topical administration, and intradermal, subcutaneous, intramuscular, intraperitoneal or intravenous injection. As such, compositions would be formulated pharmaceutically in route-acceptable compositions that include physiologically acceptable carriers, buffers or other excipients.
  • As with dosing amounts, the timing of delivery (including intervals and total number of doses) depends on the judgment of the practitioner and are peculiar to each individual. Factors affecting dose include physical and clinical state of the patient, the route of administration, the intended goal of treatment and the potency, stability and toxicity of the particular therapeutic substance.
  • 3. Combination Therapy
  • In many clinical situations, it is advisable to use a combination of distinct therapies. Thus, it is envisioned that, in addition to the therapies described above, one would also wish to provide to the patient more “traditional” pharmaceutical hepatitis or herpesvirus therapies. Examples of standard therapies are described above. Combinations may be achieved by administering a single composition or pharmacological formulation that includes both agents, or with two distinct compositions or formulations, at the same time, wherein one composition includes the agents of the present disclosure and the other includes the standard therapy. Alternatively, standard therapy may precede or follow the present agent treatment by intervals ranging from minutes to weeks to months. In embodiments where the treatments are applied separately, one would generally ensure that a significant period of time did not expire between the time of each delivery, such that the agents would still be able to exert an advantageously combined effect on the subject. In such instances, it is contemplated that one would administer both modalities within about 12-24 hours of each other and, more preferably, within about 6-12 hours of each other, with a delay time of only about 12 hours being most preferred. In some situations, it may be desirable to extend the time period for treatment significantly, however, where several days (2, 3, 4, 5, 6 or 7) to several weeks (1, 2, 3, 4, 5, 6, 7 or 8) lapse between the respective administrations.
  • It also is conceivable that more than one administration of either the agent of the present disclosure, or the standard therapy will be desired. Various combinations may be employed, where the present disclosure compound is “A” and the standard therapy is “B,” as exemplified below:
  •
    A/B/A B/A/B B/B/A A/A/B B/A/A A/B/B
    B/B/B/A B/B/A/B A/A/B/B A/B/A/B A/B/B/A B/B/A/A
    B/A/B/A B/A/A/B B/B/B/A A/A/A/B B/A/A/A A/B/A/A
    A/A/B/A A/B/B/B B/A/B/B B/B/A/B
  • Other combinations are contemplated as well. Drugs suitable for such combinations are described above and include, but are not limited to, DNA polymerase inhibitors (nucleoside analogs), including acyclovir, famciclovir, valaciclovir, penciclovir, and ganciclovir. Additionally, it is contemplated that other antiviral agents such as a pegylated interferon, interferon alfa-2b, lamivudine, adefovir, telbivudine, entercavir, or tenofovir may be used in combination with the compounds described herein.
    • E. EXAMPLES
  • The following examples are included to further illustrate various aspects of the disclosure. It should be appreciated by those of skill in the art that the techniques disclosed in the examples which follow represent techniques and/or compositions discovered by the inventors to function well in the practice of the disclosure, and thus can be considered to constitute preferred modes for its practice. However, those of skill in the art should, in light of the present disclosure, appreciate that many changes can be made in the specific embodiments which are disclosed and still obtain a like or similar result without departing from the spirit and scope of the disclosure.
  • 1. Materials and Methods
  • Cells and Viruses.
  • Vero cells were maintained in Dulbecco's modified Eagle's medium (DMEM) containing 3% newborn calf serum, 3% bovine growth serum, 2 mM L-glutamine and 100 IU/mL penicillin and 0.1 mg/mL streptomycin (P/S). HSV-1 #6 and HSV-2 #1 are de-identified clinical isolates from the Saint Louis University Hospital. Stocks were prepared after a single passage in cell culture and were titered by standard plaque assay (Knipe and Spang, 1982). Wild-type HSV-2 used in FIG. 3 was laboratory strain 333. The TK-deficient mutant of HSV-2 strain 333, ΔTK−, contains a 180-bp KpnI-KpnI deletion in the UL23 open reading frame that abrogates TK activity (McDermott, et al, 1984). ΔTK− was the generous gift of Jim Smiley. Virus stocks were grown and titered on Vero cells (Morrison and Knipe, 1996).
  • Compound Selection Strategy.
  • The compound was selected for evaluation of its ability to inhibit HSV replication based on one or more of the following criteria:
      • close chemical relatives of compounds that inhibit the HIV RNase H, the HIV integrase, or the HBV RNase H
      • availability from commercial sources and/or through the NCI compound repository.
  • Anti-HSV-1 and -HSV-2 Replication Assay.
  • Compounds to be screened were diluted in PBS supplemented to contain 2% newborn calf serum and 1% glutamine, and added in 100 μL volume to confluent cell monolayers in 24-well cluster plates. Immediately thereafter HSV-1 and HSV-2, diluted in the supplemented PBS medium, were added to the wells in 50 μl volume such that the final concentration of compound was 50 μM, 5 μM and 1 μM and the multiplicity of infection was 0.1. The plates were incubated at 37° C. for 1 hour and then virus-containing inoculum was removed and the wells were washed once in PBS. Compound, diluted to 50 μM, 5 μM and 1 μM in DMEM supplemented to contain 2% newborn calf serum and 1% each penicillin/streptomycin, was added at 0.5 mL/well. Plates were incubated at 37° C. an additional 23 hours, and then the plates were visually inspected through a phase contrast microscope for cytopathic effect, and for toxic effect. The entire contents of each well were collected by scraping. Samples were frozen at −80° C., and then subsequently thawed, sonicated, and infectious virus titer was determined by standard plaque assay on Vero cell monolayers. Because the compounds were dissolved at 10 mM in 100% DMSO, equivalent dilutions of DMSO were added to additional wells as a control for effects of the diluent. Each experiment was repeated once. EC50 values were determined as above except that serial dilutions of the compound to be tested were prepared starting at 50 μM. The inhibitory values were calculated by non-linear curve-fitting in GraphPad Prism.
  • Toxicity Assays.
  • Qualitative assessments of cytotoxicity were done visually by inspecting the cells in the primary screening assays. For the quantitative assays, cells were plated in 96-well plates at 1.0×104 per well. The next day the compounds were added at 0.78 to 100 μM in a final concentration of 1% (v/v) DMSO, and the cells were incubated for 24 hours under conditions identical to those employed for the viral replication inhibition assays. Mitochondrial toxicity was measured by incubating the cells with 0.25 mg/mL thiazolyl blue tetrazolium bromide (MTT, SigmaAldrich Chemical Co.), the cultures were incubated for 60 min, metabolites were solubilized in acidic isopropanol, and absorbance was read at 570 nm. CC50 values were calculated by non-linear curve fitting using GraphPad Prism.
  • Mouse Liver Microsome Assays.
  • Microsomal incubations are run at a final P450 concentration of 0.25 μM. The microsomal mixture is composed of 0.1M potassium phosphate containing 3.3 mM MgCl and 1 μM compound (final concentration). The mixture is prewarmed for 5 min at 37° C. To initiate the reaction a 12 mM stock of NAPDH (1.2 mM, final concentration) is added to the warmed microsomal mixture and aliquots are removed at 0, 5, 10, 20 and 30 min. Samples are quenched with ice cold acetonitrile containing internal standard and either 1.8 mM EDTA or EGTA (final concentration). Samples are vortexed and spun down at 3200 rpm for 5 min. The supernant is transferred to 96-deep well plates and run on LC/MS/MS.
  • RNaseH Expression and Purification.
  • Recombinant HBV RNaseH and human RNaseH1 were expressed in E. coli and partially purified by nickel-affinity chromatography as previously described in Tavis, et al. (2013). The enriched extracts were dialyzed into 50 mM HEPES pH 7.3, 300 mM NaCl, 20% glycerol, and 5 mM DTT and stored in liquid nitrogen.
  • Oligonucleotide-Directed RNA Cleavage Assay.
  • RNaseH activity was measured using an oligonucleotide-directed RNA cleavage assay as previously described in Hu, et al., Tavis, et al., and Cai, et al. (2013; 2013; and 2014, respectfully). Briefly, 6 μL protein extract was mixed on ice with an internally 32P-labeled 264 nt RNA derived from the Duck Hepatitis B Virus genome (DRF+ RNA) plus 3 μg oligonucleotide D2507- or its inverse-complement oligonucleotide D2526+ as a negative control. This mixture was incubated with test compounds in 50 mM Tris pH 8.0, 190 mM NaCl, 5 mM MgCl2, 3.5 mM DTT, 0.05% NP40, 6% glycerol, and 1% DMSO at 42° C. for 90 minutes. Cleavage products were resolved by denaturing polyacrylamide gel electrophoresis, detected by autoradiography, and quantified using ImageJ. Non-specific background values were determined from the incorrect oligonucleotide negative control lane and subtracted from all experimental values. IC50 values were then calculated with GraphPad Prism using three-parameter log(inhibitor) vs. response non-linear curve fitting with the curve minimum set to zero to reflect background subtraction.
  • HBV Replication Assay.
  • Inhibition of HBV replication was measured in HepDES19 cells as previously described in Cai, et al. (2014). Cells were seeded into 6-well plates and incubated in DMEM/F12, 10% fetal bovine serum (FBS), 1% penicillin/streptomycin (P/S) with 1 μg/mL tetracycline. Tetracycline was withdrawn after 24 hours. The test compound was applied to duplicate wells 48 hours later in medium containing a final DMSO concentration of 1%, and medium containing the compound was refreshed daily for the following two days. Cells were harvested and non-encapsidated nucleic acids were digested with micrococcal nuclease (New England Biolabs). HBV DNA was purified from capsids using QIAamp Cador Pathogen Mini Kit (Qiagen) with proteinase K incubation overnight at 37° C. TaqMan PCR was performed for 40 cycles at an annealing temperature of 60° C. Primers and probe (IDT Inc.) for the plus-polarity strand were: 5′CATGAACAAGAGATGATTAGGCAGAG3′; 5′GGAGGCTGTAGGCATAAATTGG3′; 5′/56-FAM/CTGCGCACC/ZEN/AGCACCATGCA/3IABkFQ. Primers and probe for the minus-polarity strand were: 5′ GCAGATGAGAAGGCACAGA3′; 5′CTTCTCCGTCTGCCGTT3′; 5′/56-FAM/AGTCCGCGT/ZEN/AAAGAGAGGTGCG/3IABkFQ.
  • MTT Cytotoxicity Assays.
  • 1.0×104 HepDES19 cells per well were seeded in 96-well plates and incubated in DMEM with 10% FBS plus 1% P/S, 1% non-essential amino acids, and 1% glutamine. Compounds were diluted in medium to the indicated concentrations plus 1% DMSO and added to cells 24 hours after plating, with each concentration tested in triplicate. Medium containing the compound was refreshed daily for the next two days. Thiazolyl blue tetrazolium bromide (MTT, Sigma-Aldrich) was added to 0.25 mg/mL, the cultures were incubated for 60 minutes, metabolites were solubilized in acidic isopropanol, and absorbance was read at 570 nM.
  • 2. Results
  • Compound Selection Strategy.
  • This compound was selected based on its structural similarity to polyoxygenated heterocycle compounds with anti-microbial activity. Piroctone olamine (octopirox; #191) is an approved antifungal in Europe. Its structure is shown in FIG. 1. Nine napthyridinones were tested for capacity to inhibit the nuclease activity of pUL15C (Masaoka et al., 2016). Seven of these inhibited nuclease activity with IC50 values ≤2 μM, and two of the seven compounds (#151 and 155) strongly suppressed HSV-1 and HSV-2 replication in cell culture at 5 μM or less (Table 2).
  • Primary Screening for Inhibition of HSV-1 and HSV-2 Replication.
  • Efficacy of this compound against both HSV-1 and HSV-2 was initially assessed at 50, 5 and 1 μM in a semi-quantitative replication inhibition assay. Inhibition was categorized as negligible (<1 log10 at 50 μM relative to the DMSO-treated control), intermediate (1 to 3 log10 suppression, which equals 10- to 1,000-fold reduction), or strong (3 to 6 log10 suppression, or 1,000- to 1,000,000-fold reduction). Compound #191 (piroctone olamine or octopirox) showed strong inhibitory activity at 50 and 5 μM against HSV-1 and HSV-2 (Table 2). Compound #191 maintained intermediate inhibition of HSV-1 and HSV-2 even at 1 μM (Table 2). Thus, it inhibited HSV-1 by 3.61 log10 (4,074-fold) and HSV-2 by 4.59 log10 (39,000-fold) at 5 μM. For comparison, the approved anti-HSV drug acyclovir inhibited HSV-1 replication in this assay by 4.22 log10 (16,600-fold) and HSV-2 by only 3.6 log10 (3,980-fold) at 5 μM. Therefore, this polyoxygenated heterocycle compound inhibits both HSV-1 and HSV-2 replication as well as or better than acyclovir.
  • TABLE 2
    HSV-1 HSV-2
    Compound Number and Log10 suppression Log10 suppression Anti-human
    Reference
    50 μM 5 μM 1 μM EC 50 50 μM 5 μM 1 μM EC50 RNase H1 CC50
    #191 (Piroctone olamine) 3.85 3.53 2.71 1.57 μM 4.25 4.53 1.70 1.53 μM — >100
    #208 2.63 0.15 0.26 0.11
    #211 1.6 0.08 1.81 0.04
    Acyclovir 5.39 3.61 nd 0.16 μM 5.25 3.91 nd 1.44 μM nd >100
    nd, not determined.
  • Compound Toxicity.
  • Visual inspection of the infected cells at the end of the 24 hour infection window through a phase-contrast microscope revealed substantially less cytopathic effect (CPE) than the DMSO-treated control wells without appearance of apoptosis or necrosis.
  • A quantitative toxicity measurement was conducted. Toxicity was assessed by measuring release of intracellular proteases into the culture medium due to cellular lysis. Cells were plated in 96-well plates at 1.0×104 per well. The next day compound was added in concentrations ranging from 0.78 to 100 μM in a final concentration of 1% (v/v) DMSO. The cells were incubated for 24 hours under conditions identical to those employed for the viral replication inhibition assays, and then mitochondrial activity was measured with the MTT assay (Sigma Aldrich) according to the manufacturer's instructions. Percent viability was determined for each compound concentration from the luminosity data, and then 50% cytotoxic concentration (CC50) value was calculated by non-linear curve fitting using GraphPad Prism. Consistent with the subjective assessments of toxicity, #191 had a CC50 value >100 μM under these conditions (Table 1). #191 did not inhibit the activity of human RNaseH1 (Table 1), another indicator of low toxicity.
  • Quantitative HSV-1 and HSV-2 Replication Inhibition Assays.
  • To obtain a more quantitative evaluation of the inhibitory potential of compound #191, EC50 values were determined against HSV-1 and HSV-2. For HSV-1, the EC50 value was 0.27 μM. For HSV-2, the value was 0.60 μM. For comparison, acyclovir had an EC50 of 0.16 and 1.44 μM versus HSV-1 and HSV-2, respectively (Table 1). Overall, these quantitative data confirmed the highly effective inhibition of HSV-1 and HSV-2 by compound #191 in the semi-quantitative assay. They also reinforce the observation that this compound can efficiently inhibit both HSV-1 and HSV-2, and they strengthen the conclusion that the strong inhibitor identified here has equivalent or superior activity against the herpes simplex viruses than the approved drug acyclovir.
  • Compound #191 suppressed replication of three primary clinical isolates of HSV-2 by >4.7 log10 at 5 μM (FIG. 2), indicating that it is active against a range of clinically relevant virus strains.
  • Inhibition of an Acyclovir-Resistant HSV-2 Mutant.
  • ACV is a nucleoside analog prodrug that must be phosphorylated by the viral thymidine kinase (TK) for it to become a substrate for the viral DNA polymerase (Elion, et al., 1977). HSV TK-deficient mutants are therefore insensitive to ACV. Because viral resistance to ACV and other nucleoside analogs is a significant medical problem (Field and Biron, 1994; Coen, 1991; Wang, et al, 2011; Duan, et al., 2009; Duan, et al., 2008; Pelosi, et al., 1992), especially in immunocompromised patients (Reyes, et al., 2013; Levin, et al., 2004; Gilbert, et al., 2002; Schmit and Boivin, 1999), the inventors considered whether defined TK-deficient mutants of HSV-2 would be sensitive to other compounds such as compound #191. Vero cells were infected with a laboratory strain of HSV-2 and an engineered TK-deficient mutant of the same strain. The cells were treated with 5 μM ACV or compound #191 as was done in the primary screening assays, and viral yields 24 hours post-infection were measured by plaque assay. ACV 5 μM inhibited wild-type HSV-2 replication 100-fold, but it had little effect on the TK− mutant (FIG. 3). In marked contrast, compound #191 efficiently inhibited the wild-type HSV-2 and the TK− mutant strain. Therefore, this compound does not require phosphorylation by the viral TK gene to be active, confirming that compound #191 suppress HSV-2 replication in a different manner than ACV. These data also demonstrate that compound #191 are stronger inhibitors of HSV-2 than ACV at 5 μM.
  • Therapeutic Implications.
  • The high suppressive activities against the herpesviruses observed with this compound (as much as 4.59 log10 at 5 μM) and its minimal short-term toxicity implies that it may be suitable for use as an anti-viral drug. This is especially true for the acute and/or topical therapies most commonly employed for the herpes simplex viruses. The structure of this compound and its already proven drugability implies that further improvements in the inhibitory potential against the herpesviruses should be attainable by standard medicinal chemistry approaches.
  • Elimination in Mouse Liver Microsomes.
  • Table 3 below shows the elimination profile of compounds #191, #41, and #208. The table shows the half life, the intrinsic clearance, the hepatic clearance, extraction ratio, and methods of turnover. Several compounds tested in mouse liver microsomes had long half-lives, low extraction ratios, and no evidence of non-P450 turnover (Table 3), suggesting their capacity to resist rapid degradation and elimination by the liver.
  • TABLE 3
    Polyoxygen heterocyclic compounds show favorable resistance
    to elimination in mouse liver microsomes.
    t ½ CL'int CL 'hep Non-P450
    Compound (min) (mL/min/kg) (mL/min/kg) ER turn-over
    208 >120 −201 163 <0.1 No
    41 >120 17 14 0.16 No
    191 >120 9 8 0.09 No
  • Summary.
  • The inventors here demonstrate that a polyoxygenated heterocycle compound profoundly suppresses replication of HSV-1 and HSV-2 with no measurable toxicity in a short-term cell culture assay. Inhibition by this primary screening hit is equal or superior to the approved anti-herpesvirus drug acyclovir, particularly against HSV-2. Thus, the existing compound may already be superior to the drugs that are used for HSV-2 infection, and improved efficacy can readily be envisioned through standard medicinal chemistry approaches. Its structural dissimilarity to the nucleoside analogs implies a novel mode of action, suggesting it would be a good candidate for combination therapy with the existing anti-herpesvirus drugs to improve efficacy of antiviral therapy.
  • 3. HBV Activity
  • HBV activity of some of the compounds described herein is shown in Table 4 below.
  • TABLE 4
    HBV Activity
    Com- Qualitative HBV
    pound EC50 CC50 replication
    Number Compound (μM) (μM) inhibition assay
    151
    Figure US20180169083A1-20180621-C00036
         		4.7 15 **
    153
    Figure US20180169083A1-20180621-C00037
         		4.1 10 **
    210
    Figure US20180169083A1-20180621-C00038
         		1.5 71 **
    208
    Figure US20180169083A1-20180621-C00039
         		0.69 15 **
    211
    Figure US20180169083A1-20180621-C00040
         		13 30 **
    49
    Figure US20180169083A1-20180621-C00041
         		ND  9 —
    ** + DNA suppression <25% and − DNA suppression >60%
    *+ DNA suppression <50% of − DNA suppression
    ND - not determined
  • 4. Synergistic Activity of HBV RNAseH with Nucleoside Analog Drug
  • Current nucleos(t)ide analog therapy for HBV has converted hepatitis type B from an implacably progressing illness to a controllable disease. However, patients are only very rarely cured, in part due to the incomplete inhibition of HBV replication. The inventors hypothesized that the novel RNaseH inhibitors would work synergistically with the existing nucleos(t)ide analogs because the two classes of drugs target physically distinct active sites on the viral polymerase protein. Therefore, potential synergy between the RNAseH inhibitors and the nucleoside analog Lamivudine was analyzed using the Chou-Talalay method (Chou 2010). RNAseH inhibitors from two different chemical classes were employed, compound #1 [2-hydroxyisoquinoline-1,3(2H,4H)-dione], an HID, and #46 (β-thujaplicinol), an α-hydroxytropolone, were tested. Chou-Talaly analysis yields a combination index (CI). CI values <1.0 indicate synergy, CIs of approximately 1.0 indicate additive interactions, and CI values >1.0 indicate antagonism. CI values are calculated at various efficacy levels (EC50, EC75, EC90, and EC95), and a weighted CI value favoring higher efficacy levels is also generated. FIGS. 4A & 4B show the results of four experiments employing compound #1 and three with compound #46. All experiments revealed synergistic interactions between the RNAseH inhibitors and Lamivudine, and the weighted CI values were 0.70±0.1 for the HID compound #1 and 0.44±0.3 for the α-hydroxytropolone #46. Therefore, RNAseH inhibitors act strongly synergistically with an approved nucleos(t)ide analog drug against HBV. This demonstrates feasibility for employing RNAseH inhibitors in combination therapy with the nucleos(t)ide analogs during HBV treatment.
  • 5. RNAseH Inhibitor Sensitivity is Insensitive to High Genetic Variation
  • HBV has 8 genotypes differing in sequence by 8%. Genetic diversity in the RNAseH domain is about 6%, which is easily high enough to modulate viral sensitivity to RNAseH inhibitors. Therefore, the inventors tested the RNAseH inhibitors #1 [2-hydroxyisoquinoline-1,3(2H,4H)-dione], an HID, and #46 (P3-thujaplicinol), an α-hydroxytropolone, for the ability to inhibit variant RNAseHs. Twelve purified, patient-derived RNAseH enzymes (4 from each genotypes B, C and D) were tested with the compounds at their respective IC50 values in a biochemical RNAseH assay. FIGS. 5A & 5B demonstrate that the four genotype D enzymes each inhibited the HBV RNAseH by about 50% at the compounds IC50 values as expected. Equivalent results were obtained for all 12 enzymes against compounds #1 and #46. Therefore, HBV's high genetic variation is unlikely to present a substantial barrier to drug development.
  • All of the compositions and methods disclosed and claimed herein can be made and executed without undue experimentation in light of the present disclosure. While the compositions and methods of this disclosure have been described in terms of preferred embodiments, it will be apparent to those of skill in the art that variations may be applied to the compositions and methods, and in the steps or in the sequence of steps of the methods described herein without departing from the concept, spirit and scope of the disclosure. More specifically, it will be apparent that certain agents which are both chemically and physiologically related may be substituted for the agents described herein while the same or similar results would be achieved. All such similar substitutes and modifications apparent to those skilled in the art are deemed to be within the spirit, scope and concept of the disclosure as defined by the appended claims.
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Claims (59)

What is claimed:
1. A method of inhibiting a cellular or herpesvirus nucleic acid metabolism enzyme comprising contacting said enzyme with a compound having the formula:
Figure US20180169083A1-20180621-C00042
or a compound of the formula:
Figure US20180169083A1-20180621-C00043
wherein:
R4 is alkyl(C≤12), aryl(C≤12), aralkyl(C≤12), heteroaryl(C≤12), or a substituted version of any of these groups;
R5 and R8 are each independently hydrogen, alkyl(C≤8), or substituted alkyl(C≤8);
R6 is hydrogen, hydroxy, alkyl(C≤8), or substituted alkyl(C≤8); and
R7 is aryl(C≤12), aralkyl(C≤12), heteroaryl(C≤12), or a substituted version of any of these groups; or
a compound of the formula:
Figure US20180169083A1-20180621-C00044
wherein:
R9 is alkyl(C≤12), aryl(C≤12), aralkyl(C≤12), heteroaryl(C≤12), or a substituted version of any of these groups;
R10 is hydrogen, alkyl(C≤8), or substituted alkyl(C≤8); and
R11 is hydrogen or Y1—O—X1—OR12; wherein:
Y1 is alkanediyl(C≤8) or substituted alkanediyl(C≤8);
X1 is arenediyl(C≤12), heteroarenediyl(C≤12), or a substituted version of either of these groups;
R12 is aryl(C≤12), aralkyl(C≤12), heteroaryl(C≤12), or a substituted version of any of these groups;
or a pharmaceutically acceptable salt or tautomer thereof.
2. The method of claim 1, wherein the compound is further defined as:
Figure US20180169083A1-20180621-C00045
wherein:
R4 is alkyl(C≤12), aryl(C≤12), aralkyl(C≤12), heteroaryl(c≤12), or a substituted version of any of these groups;
R5 and R8 are each independently hydrogen, alkyl(C≤8), or substituted alkyl(C≤8);
R6 is hydrogen, hydroxy, alkyl(C≤8), or substituted alkyl(C≤8); and
R7 is aryl(C≤12), aralkyl(C≤12), heteroaryl(C≤12), or a substituted version of any of these groups; or
or a pharmaceutically acceptable salt or tautomer thereof.
3. The method of claim 1, wherein the compound is further defined as:
Figure US20180169083A1-20180621-C00046
wherein:
R9 is alkyl(C≤12), aryl(C≤12), aralkyl(C≤12), heteroaryl(C≤12), or a substituted version of any of these groups;
R10 is hydrogen, alkyl(C≤8), or substituted alkyl(C≤8); and
R11 is hydrogen or Y1—O—X1—OR12; wherein:
Y1 is alkanediyl(C≤8) or substituted alkanediyl(C≤8);
X1 is arenediyl(C≤12), heteroarenediyl(C≤12), or a substituted version of either of these groups;
R12 is aryl(C≤12), aralkyl(C≤12), heteroaryl(C≤12), or a substituted version of any of these groups;
or a pharmaceutically acceptable salt or tautomer thereof.
4. The method of claim 1, wherein the compound is further defined as:
Figure US20180169083A1-20180621-C00047
or a pharmaceutically acceptable salt or tautomer thereof.
5. The method of claim 1, wherein the compound is further defined as:
Figure US20180169083A1-20180621-C00048
or a pharmaceutically acceptable salt or tautomer thereof.
6. The method of claim 4, wherein the salt is an ethanolamine salt.
7. The method of claim 1, further comprising contacting said enzyme with a second inhibitor of said enzyme.
8. The method of claim 7, further comprising contacting said enzyme with said compound a second time.
9. The method of claim 7, wherein said enzyme is located in a cell.
10. The method of claim 9, wherein said cell is located in vitro.
11. The method of claim 9, wherein said cell is located in a living subject.
12. The method of claim 11, wherein said subject is a vertebrate infected with a herpesvirus.
13. The method of claim 12, wherein said compound is administered intravenously, intraarterially, orally, buccally, nasally, ocularly, rectally, vaginally, topically, intramuscularly, intradermally, cutaneously or subcutaneously.
14. The method of claim 12, wherein said subject is further administered a second anti-herpesvirus therapy.
15. The method of claim 14, wherein said second anti-herpesvirus therapy is foscarnet or a nucleoside analog.
16. The method of claim 15, wherein said nucleoside analog is acyclovir, famciclovir, valaciclovir, penciclovir, or ganciclovir.
17. The method of claim 15, wherein said second anti-herpesvirus therapy is administered to said subject before or after said compound.
18. The method of claim 15, wherein said second anti-herpesvirus therapy is administered to said subject at the same time as said compound.
19. The method of claim 1, wherein said subject has previously received a first-line anti-herpesvirus therapy.
20. The method of claim 19, wherein said herpesvirus has developed resistance to said first-line anti-herpesvirus therapy.
21. The method of claim 1, wherein said herpevirus is selected from a human alpha herpesvirus, a human beta herpesvirus or a human gamma herpesvirus.
22. The method of claim 21, wherein the human alpha herpesvirus is selected from herpes simplex virus 1 (HSV-1), herpes simplex virus 2 (HSV-2), and Varicella-Zoster virus (VZV).
23. The method of claim 21, wherein the human beta herpesvirus is selected from human cytomegalovirus (HCMV), human herpesvirus 6A (HHV-6A), human herpesvirus 6B (HHV-6B), and human herpesvirus 7 (HHV-7).
24. The method of claim 21, wherein the human gamma herpesvirus is selected from Epstein-Barr virus (EBV) and Kaposi's sarcoma herpesvirus (KSHV).
25. The method of claim 1, wherein the herpesvirus is a non-human herpesvirus.
26. The method of claim 25, wherein the herpesvirus is Marek's disease virus, equine herpesviruses, Bovine herpeviruses, or pseudorabies virus.
27. A pharmaceutical composition comprising a compound having the formula:
Figure US20180169083A1-20180621-C00049
or a pharmaceutically acceptable salt or tautomer thereof, dispersed in a pharmaceutically acceptable buffer, diluent, excipient or carrier.
28. The pharmaceutical composition of claim 27, wherein the pharmaceutical composition is formulated for administration: orally, nasally, buccally, corneally, rectally, vaginally, or topically.
29. The pharmaceutical composition of claim 27, wherein the pharmaceutical composition formulated for administration via injection.
30. The pharmaceutical composition of claim 29, wherein the injection is formulated for administration: intradermally, cutaneously, ocularly, subcutaneously, intramuscularly, intraperitoneally, intraarterially, or intravenously.
31. The pharmaceutical composition of claim 27, wherein the pharmaceutically acceptable salt is an ethanolamine salt.
32. A compound of the formula:
Figure US20180169083A1-20180621-C00050
wherein:
R1 is aryl(C≤12), aralkyl(C≤8), heteroaryl(C≤12), alkylamino(C≤12), dialkylamino(C≤12), arylamino(C≤12), diarylamino(C≤12), aralkylamino(C≤18), diaralkylamino(C≤8), or a substituted version of any of these groups;
R2 is hydrogen, alkyl(C≤8), or substituted alkyl(C≤8); and
R3 is hydrogen, amino, carboxyl, cyano, halo, hydroxy, nitro, hydroxysulfonyl, or sulfonylamine; or
alkyl(C≤8), aryl(C≤8), acyl(C≤8), alkoxy(C≤8), acyloxy(C≤8), amido(C≤8), or substituted version of any of these groups;
X2 is hydrogen or —C(O)Ra, wherein: Ra is hydroxy, alkoxy(C≤8), or substituted alkoxy(C≤8); or
a compound of the formula:
Figure US20180169083A1-20180621-C00051
wherein:
R4 is alkyl(C≤12), aryl(C≤12), aralkyl(C≤12), heteroaryl(C≤12), or a substituted version of any of these groups;
R5 and R8 are each independently hydrogen, alkyl(C≤8), or substituted alkyl(C≤8);
R6 is hydrogen, hydroxy, alkyl(C≤8), or substituted alkyl(C≤8); and
R7 is aryl(C≤12), aralkyl(C≤12), heteroaryl(C≤12), or a substituted version of any of these groups; or
a compound of the formula:
Figure US20180169083A1-20180621-C00052
wherein:
R9 is alkyl(C≤12), aryl(C12), aralkyl(C≤12), heteroaryl(C≤12), or a substituted version of any of these groups;
R10 is hydrogen, alkyl(C≤8), or substituted alkyl(C≤8); and
R11 is hydrogen or Y1—O—X1—OR12; wherein:
Y1 is alkanediyl(C≤8) or substituted alkanediyl(C≤8);
X1 is arenediyl(C≤12), heteroarenediyl(C≤12), or a substituted version of either of these groups;
R12 is aryl(C≤12), aralkyl(C≤12), heteroaryl(C≤12), or a substituted version of any of these groups;
or a pharmaceutically acceptable salt thereof.
33. The compound of claim 32 further defined as:
Figure US20180169083A1-20180621-C00053
wherein:
R1 is aryl(C≤12), aralkyl(C≤18), heteroaryl(C≤12), alkylamino(C≤12), dialkylamino(C≤12), arylamino(C≤12), diarylamino(C≤12), aralkylamino(C≤18), diaralkylamino(C≤18), or a substituted version of any of these groups;
R2 is hydrogen, alkyl(C≤8), or substituted alkyl(C≤8); and
X2 is hydrogen or —C(O)Ra, wherein: Ra is hydroxy, alkoxy(C≤8), or substituted alkoxy(C≤8);
or a pharmaceutically acceptable salt thereof.
34. The compound of claim 32 further defined as:
Figure US20180169083A1-20180621-C00054
wherein:
R5 is hydrogen, alkyl(C≤8), or substituted alkyl(C≤8);
R6 is hydrogen, hydroxy, alkyl(C≤8), or substituted alkyl(C≤8); and
R7 is aryl(C≤12), aralkyl(C≤12), heteroaryl(C≤12), or a substituted version of any of these groups;
or a pharmaceutically acceptable salt thereof.
35. The compound of claim 32 further defined as:
Figure US20180169083A1-20180621-C00055
wherein:
R10 is hydrogen, alkyl(C≤8), or substituted alkyl(C≤8); and
R11 is hydrogen or Y1—O—X1—OR12; wherein:
Y1 is alkanediyl(C≤8) or substituted alkanediyl(C≤8);
X1 is arenediyl(C≤12), heteroarenediyl(C≤12), or a substituted version of either of these groups;
R12 is aryl(C≤12), aralkyl(C≤12), heteroaryl(C≤12), or a substituted version of any of these groups;
or a pharmaceutically acceptable salt thereof.
36. The compound of claim 32, wherein R2, R5, or R10 is hydrogen.
37. The compound of claim 36, wherein R2, R5, and R10 are hydrogen.
38. The compound of claim 33, wherein R1 is aralky(C≤18), aralkylamino(C≤18), or a substituted version of either group.
39. The compound of claim 34, wherein R6 is hydroxy.
40. The compound of claim 34, wherein R7 is aryl(C≤12).
41. The compound of claim 35, wherein R11 is Y1—O—X1—OR12; wherein:
Y1 is alkanediyl(C≤8);
X1 is arenediyl(C≤12), or a substituted version of either of these groups;
R12 is aryl(C≤12) or substituted aryl(C≤12).
42. The compound according to any one of claims 32-35, wherein the compound is further defined as:
Figure US20180169083A1-20180621-C00056
or a pharmaceutically acceptable salt thereof.
43. A compound of the formula:
Figure US20180169083A1-20180621-C00057
or a pharmaceutically acceptable salt thereof.
44. A pharmaceutical composition comprising:
(A) a compound according to any one of claims 32-43; and
(B) an excipient.
45. The pharmaceutical composition of claim 44, wherein the pharmaceutical composition is formulated for administration: orally, nasally, buccally, corneally, rectally, vaginally, topically, intradermally, cutaneously, ocularly, subcutaneously, intramuscularly, intraperitoneally, intraarterially, or intravenously.
46. The pharmaceutical composition of claim 44, wherein the pharmaceutical composition is formulated as a unit dose.
47. A method of inhibiting a hepatitis B virus RNaseH comprising administering an effective amount of a compound or composition according to any one of claims 32-46.
48. The method of claim 47, wherein the method is performed in vitro.
49. The method of claim 47, wherein the method is performed in vivo.
50. The method of claim 47, wherein the method is performed ex vivo.
51. The method of claim 47, wherein the method is sufficient to inhibit viral replication.
52. A method of inhibiting replication of a hepatitis B virus comprising contacting the virus with an effective amount of a compound or composition according to any one of claims 32-46.
53. The method of claim 52, wherein the method is performed in vitro.
54. The method of claim 52, wherein the method is performed in vivo.
55. The method of claim 52, wherein the method is performed ex vivo.
56. The method of claim 52, wherein the method is sufficient to treat an infection of a hepatitis B virus.
57. A method of treating an infection of a hepatitis B virus in a patient comprising administering a therapeutically effective amount of a compound or composition according to any one of claims 32-46.
58. The method of claim 57, wherein the method further comprises a second antiviral treatment.
59. The method of claim 58, wherein the second antiviral therapy is interferon alfa-2b, lamivudine, adefovir, telbivudine, entercavir, or tenofovir.
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