Hepatitis C
Hepatitis C virus (HCV) is a positive strand RNA virus, and infection is a leading cause of post-transfusional hepatitis.  HCV is the most common chronic blood borne infection, and the leading cause of death from liver disease in United States.  The World Health Organization estimates that there are more than 170 million chronic carriers of HCV infection, which is about 3% of the world population.  Among the un-treated HCV-infected patients, about 70%-85% develop chronic HCV infection, and are therefore at high risk to develop liver cirrhosis and hepatocellular carcinoma.  In developed countries, 50-76% of all cases of liver cancer and two-thirds of all liver transplants are due to chronic HCV infection (Manns et al, 2007). 
In addition to liver diseases, chronically infected patients may also develop other chronic HCV-related diseases, and serve as a source of transmission to others.  HCV infection causes non-liver complications such as arthralgias (joint pain), skin rash, and internal organ damage predominantly to the kidney.  HCV infection represents an important global health-care burden, and currently there is no vaccine available for hepatitis C (Strader et al.,  2004; Jacobson et al.  2007; Manns et al.,  2007 Pawlotsky, 2005; Zeuzem & Hermann, 2002). 
Treatment of HCV
The current standard of care (SoC) is subcutaneous injections of pegylated interferon-α (plFNα) and oral dosing of the antiviral drug ribavirin for a period of 24-48 weeks.  Success in treatment is defined by sustained virologic response (SVR), which is defined by absence of HCV RNA in serum at the end of treatment period and 6 months later.  Overall response rates to SoC depend mainly on genotype and pretreatment HCV RNA levels.  Patients with genotype 2 and 3 are more likely to respond to SoC than patients infected with genotype 1 (Melnikova, 2008; Jacobson et al.,  2007). 
A significant number of HCV patients do not respond adequately to the SoC treatment, or cannot tolerate the therapy due to side effects, leading to frequent issues with completion of the full course.  The overall clinical SVR rate of SoC is only around 50% (Melnikova, 2008).  Development of resistance is another underlying factor for failure of treatment (Jacobson et al.  et al.  2007).  SoC is also contraindicated in some patients who are not considered candidates for treatment, such as patients with past significant episodes of depression or cardiac disease.  Side effects of the SoC, which frequently lead to discontinuation of treatment include a flu-like illness, fever, fatigue, haematological disease, anaemia, leucopaenia, thrombocytopaenia, alopecia and depression (Manns et al.,  2007). 
Considering the side effects associated with the lengthy treatments using SoC, development of resistance, and suboptimum overall rate of success, more efficacious and safer new treatments are urgently needed for treatment of HCV infection.  The objectives of new treatments include improved potency, improved toxicity profile, improved resistance profile, improved quality of life and the resulting improvement in patient compliance.  HCV has a short life cycle and therefore development of drug resistance during drug therapy is common. 
Novel, specifically targeted antiviral therapy for hepatitis C (STAT-C), also known as direct acting antiviral (DAA) drugs are being developed that target viral proteins such as viral RNA polymerase NS5B or viral protease NS3 (Jacobson et al, 2007; Parfieniuk et al.,  2007).  In addition, novel compounds also are being developed that target human proteins (e.g. cyclophilins) rather than viral targets, which might be expected to lead to a reduction in incidence of resistance during drug therapy (Manns et al.,  2007; Pockros, 2008; Pawlotsky J-M, 2005). 
Cyclophilin Inhibitors
Cyclophilins (CyP) are a family of cellular proteins that display peptidyl-prolyl cis-trans isomerase activity facilitating protein conformation changes and folding.  CyPs are involved in cellular processes such as transcriptional regulation, immune response, protein secretion, and mitochondrial function.  HCV virus recruits CyPs for its life cycle during human infection.  Originally, it was thought that CyPs stimulate the RNA binding activity of the HCV non-structural protein NS5B RNA polymerase that promotes RNA replication, although several alternative hypotheses have been proposed including a requirement for CyP PPlase activity.  Various isoforms of CyPs, including A and B, are believed to be involved in the HCV life cycle (Yang et al.,  2008; Appel et al.,  2006; Chatterji et al.,  2009; Gaither et al.,  2010).  The ability to generate knockouts in mice (Colgan et al.,  2000) and human T cells (Braaten and Luban, 2001) indicates that CyPA is optional for cell growth and survival.  Similar results have been observed with disruption of CyPA homologues in bacteria (Herrler et al.,  1994), Neurospora (Tropschug et al.,  1989) and Saccharomyces cerevisiae (Dolinski et al.  1997).  Therefore, inhibiting CyPs represents a novel and attractive host target for treating HCV infection, and a new potential addition to current SoC or STAT-C/DAA drugs, with the aim of increasing SVR, preventing emergence of resistance and lowering treatment side effects. 

Cyclosporine A (Inoue et al.  2003) (“CsA”) and its closely structurally related non-immunosuppressive clinical analogues DEBIO-025 (Paeshuyse et al.  2006; Flisiak et al.  2008), NIM811 (Mathy et al.  2008) and SCY-635 (Hopkins et al.,  2009) are known to bind to cyclophilins, and as cyclophilin inhibitors have shown in vitro and clinical efficacy in the treatment of HCV infection (Crabbe et al.,  2009; Flisiak et al.  2008; Mathy et al.  2008; Inoue et al.,  2007; Ishii et al.,  2006; Paeshuyse et al.,  2006).  Although earlier resistance studies on CsA showed mutations in HCV NS5B RNA polymerase and suggested that only cyclophilin B would be involved in the HCV replication process (Robida et al.,  2007), recent studies have suggested an essential role for cyclophilin A in HCV replication (Chatterji et al.  2009; Yang et al.,  2008).  Considering that mutations in NS5A viral protein are also associated with CsA resistance and that NS5A interacts with both CyPA and CypB for their specific peptidyl-prolyl cis/trans isomerase (PPlase) activity, a role for both cyclophilins in viral life cycle is further suggested (Hanoulle et al.,  2009). 
The anti-HCV effect of cyclosporine analogues is independent of the immunosuppressive property, which is dependent on calcineurin.  This indicated that the essential requirement for HCV activity is CyP binding and calcineurin binding is not needed.  DEBIO-025, the most clinically advanced cyclophilin inhibitor for the treatment of HCV, has shown in vitro and in vivo potency against the four most prevalent HCV genotypes (genotypes 1, 2, 3, and 4).  Resistance studies showed that mutations conferring resistance to DEBIO-025 were different from those reported for polymerase and protease inhibitors, and that there was no cross resistance with STAT-C/DAA resistant viral replicons.  More importantly, DEBIO-025 also prevented the development of escape mutations that confer resistance to both protease and polymerase inhibitors (Crabbe et al.,  2009). 
However, the CsA-based cyclophilin inhibitors in clinical development have a number of issues, which are thought to be related to their shared structural class, including: certain adverse events that can lead to a withdrawal of therapy and have limited the clinical dose levels; variable pharmacokinetics that can lead to variable efficacy; and an increased risk of drug-drug interactions that can lead to dosing issues. 
The most frequently occurring adverse events (AEs) in patients who received DEBIO-025 included jaundice, abdominal pain, vomiting, fatigue, and pyrexia.  The most clinically important AEs were hyperbilirubinemia and reduction in platelet count (thrombocytopaenia).  Peg-IFN can cause profound thrombocytopaenia and combination with DEBIO-025 could represent a significant clinical problem.  Both an increase in bilirubin and decrease in platelets have also been described in early clinical studies with NIM-811 (Ke et al.,  2009).  Although the hyperbilirubinemia observed during DEBIO-025 clinical studies was reversed after treatment cessation, it was the cause for discontinuation of treatment in 4 out of 16 patients, and a reduction in dose levels for future trials.  As the anti-viral effect of cyclophilin inhibitors in HCV is dose related, a reduction in dose has led to a reduction in anti-viral effect, and a number of later trials with CsA-based cyclophilin inhibitors have shown no or poor reductions in HCV viral load when dosed as a monotherapy (Lawitz et al.,  2009; Hopkins et al.,  2009; Nelson et al.,  2009).  DEBIO-025 and cyclosporine A are known to be inhibitors of biliary transporters such as bile salt export pumps and other hepatic transporters (especially MRP2/cMOAT/ABCC2) (Crabbe et al.,  2009).  It has been suggested that the interaction with biliary transporters, in particular MRP2, may be the cause of the hyperbilirubinaemia seen at high dose levels of DEBIO-025 (Nelson et al.,  2009, Wring et al.,  2010).  CsA class-related drug-drug interactions (DDIs) via inhibition of other drug transporters such as OAT1B1 and OAT1B3 (Konig et al.,  2010) may also be a concern, potentially limiting certain combinations and use in some patients undergoing treatment for co-infections such as HIV (Seden et al.,  2010). 
Moreover, DEBIO-025 and cyclosporine A are substrates for metabolism by cytochrome P450 (especially CYP3A4), and are known to be substrates and inhibitors of human P-glycoprotein (MDR1) (Crabbe et al.,  2009).  Cyclosporine A has also been shown to be an inhibitor of CYP3A4 in vitro (Niwa et al.,  2007).  This indicates that there could be an increased risk of drug-drug interactions with other drugs that are CYP3A4 substrates, inducers or inhibitors such as for example ketoconazole, cimetidine and rifampicin.  In addition, interactions are also expected with drugs that are subject to transport by P-glycoprotein (e.g. digoxin), which could cause severe drug-drug interactions in HCV patients receiving medical treatments for other concomitant diseases (Crabbe et al.  2009).  CsA is also known to have highly variable pharmacokinetics, with early formulations showing oral bioavailability from 1-89% (Kapurtzak et al.,  2004).  Without expensive monitoring of patient blood levels, this can lead to increased prevalence of side effects due to increased plasma levels, or reduced clinical response due to lowered plasma levels. 
Considering that inhibition of cyclophilins represent a promising new approach for treatment of HCV, there is a need for discovery and development of more potent and safer CyP inhibitors for use in combination therapy against HCV infection. 
Sanglifehrins
Sanglifehrin A (SfA) and its natural congeners belong to a class of mixed non-ribosomal peptide/polyketides, produced by Streptomyces sp.  A92-308110 (also known as DSM 9954) (see WO 97/02285), which were originally discovered on the basis of their high affinity to cyclophilin A (CyPA).  SfA is the most abundant component in fermentation broths and exhibits approximately 20-fold higher affinity for CyPA compared to CsA. This has led to the suggestion that sanglifehrins could be useful for the treatment of HCV (WO2006/138507).  Sanglifehrins have also been shown to exhibit a lower immunosuppressive activity than CsA when tested in vitro (Sanglier et al.,  1999; Fehr et al.,  1999).  SfA binds with high affinity to the CsA binding site of CyPA (Kallen et al.,  2005). 
Biosynthesis of Sanglifehrins
Sanglifehrins are biosynthesised by a mixed polyketide synthase (PKS)/Non-ribosomal peptide synthetase (NRPS) (see WO2010/034243, Qu et al.,  2011).  The 22-membered macrolide backbone consists of a polyketide carbon chain and a tripeptide chain.  The peptide chain consists of one natural amino acid, valine, and two non-natural amino acids: (S)-meta-tyrosine and (S)-piperazic acid, linked by an amide bond.  Hydroxylation of phenylalanine (either in situ on the NRPS or prior to biosynthesis) to generate (S)-meta-tyrosine is thought to occur via the gene product of sfaA.
Immunosuppressive action of Sanglifehrins
The immunosuppressive mechanism of action of SfA is different to that of other known immunophilin-binding immunosuppressive drugs such as CsA, FK506 and rapamycin.  SfA does not inhibit the phosphatase activity of calcineurin, the target of CsA (Zenke et al.  2001), instead its immunosuppressive activity has been attributed to the inhibition of interleukin-6 (Hartel et al.,  2005), interleukin-12 (Steinschulte et al.,  2003) and inhibition of interleukin-2-dependent T cell proliferation (Zhang & Liu, 2001).  However, the molecular target and mechanism through which SfA exerts its immunosuppressive effect is hitherto unknown. 
The molecular structure of SfA is complex and its interaction with CyPA is thought to be mediated largely by the macrocyclic portion of the molecule.  In fact, a macrocyclic compound (hydroxymacrocycle) derived from oxidative cleavage of SfA has shown strong affinity for CyPA (Sedrani et al.,  2003).  X-ray crystal structure data has shown that the hydroxymacrocycle binds to the same active site of CyPA as CsA. Analogues based on the macrocycle moiety of SfA have also previously been shown to be devoid of immunosuppressive properties (Sedrani et al.,  2003), providing opportunity for design of non-immunosuppressive CyP inhibitors for potential use in HCV therapy. 
Converse to this, there is also an opportunity to develop immunosuppressive agents with low toxicity for use in such areas as prophylaxis of transplant rejection, autoimmune, inflammatory and respiratory disorders, including, but not limited to, Crohn's disease, Behcet syndrome, uveitis, psoriasis, atopic dermatitis, rheumatoid arthritis, nephritic syndrome, aplastic anaemia, biliary cirrhosis, asthma, pulmonary fibrosis, chronic obstructive pulmonary disease (COPD) and celiac disease.  Sanglifehrins have been shown to have a novel mechanism of immunosuppressive activity (Zenke et al.,  2001), potentially acting through dendritic cell chemokines (Immecke et al.,  2011) and there is therefore an opportunity to develop agents with a mechanism of action different to current clinical agents, such as cyclosporine A, rapamycin and FK506. 
Other Therapeutic Uses of Cyclophilin Inhibitors
Human Immunodeficiency Virus (HIV)
Cyclophilin inhibitors, such as CsA and DEBIO-025 have also shown potential utility in inhibition of HIV replication.  The cyclophilin inhibitors are thought to interfere with function of CyPA during progression/completion of HIV reverse transcription (Ptak et al.,  2008).  However, when tested clinically, DEBIO-025 only reduced HIV-1 RNA levels ≧0.5 and >1 log 10 copies/mL in nine and two patients respectively, whilst 27 of the treated patients showed no reduction in HIV-1 RNA levels (Steyn et al.,  2006).  Following this, DEBIO-025 was trialed in HCV/HIV coinfected patients, and showed better efficacy against HCV, and the HIV clinical trials were discontinued (see Watashi et al.,  2010). 
Treatment of HIV
More than 30 million people are infected by HIV-1 worldwide, with 3 million new cases each year.  Treatment options have improved dramatically with the introduction of highly active antiretroviral therapy (HAART) (Schopman et al.,  2010), By 2008, nearly 25 antiretroviral drugs had been licensed for treatment of HIV-1, including nine nucleoside reverse transcriptase inhibitors (NRTI), four non-nucleoside reverse transcriptase inhibitors (NNRTI), nine protease inhibitors (PI), one fusion inhibitor, one CCR5 inhibitor and one integrase inhibitor (Shafer and Schapiro, 2008).  However, none of these current regimens leads to complete viral clearance, they can lead to severe side effects and antiviral resistance is still a major concern.  Therefore, there still remains a need for new antiviral therapies, especially in mechanism of action classes where there are no approved drugs, such as is the case for cyclophilin inhibitors. 
Hepatitis B Virus
Hepatitis B is a DNA virus of the family hepadnaviridae, and is the causative agent of Hepatitis B. As opposed to the cases with HCV and HIV, there have been very few published accounts of activity of cyclophilin inhibitors against Hepatitis B virus.  Ptak et al.  2008 have described weak activity of Debio-025 against HBV (IC50 of 4.1 μM), whilst Xie et al.,  2007 described some activity of CsA against HBV (IC50 >1.3 μg/mL).  This is in contrast to HIV and HCV, where there are numerous reports of nanomolar antiviral activity of cyclophilin inhibitors. 
Treatment of HBV
HBV infects up to 400 million people worldwide and is a major cause of chronic viral hepatitis and hepatocellular carcinoma.  As of 2008, there were six drugs licensed for the treatment of HBV; interferon alpha and pegylated interferon alpha, three nucleoside analogues (lamivudine, entecavir and telbivudine) and one nucleotide analogue (adefovir dipivoxil).  However, due to high rates of resistance, poor tolerability and possible side effects, new therapeutic options are needed (Ferir et al.,  2008). 
Inhibition of the Mitochondrial Permeability Transition Pore (mPTP)
Opening of the high conductance permeability transition pores in mitochondria initiates onset of the mitochondrial permeability transition (MPT).  This is a causative event, leading to necrosis and apoptosis in hepatocytes after oxidative stress, Ca2+ toxicity, and ischaemia/reperfusion.  Inhibition of Cyclophilin D (also known as Cyclophilin F) by cyclophilin inhibitors has been shown to block opening of permeability transition pores and protects cell death after these stresses.  Cyclophilin D inhibitors may therefore be useful in indications where the mPTP opening has been implicated, such as muscular dystrophy, in particular Ullrich congenital muscular dystrophy and Bethlem myopathy (Millay et al.,  2008, WO2008/084368, Palma et al.,  2009), multiple sclerosis (Forte et al.,  2009), diabetes (Fujimoto et al.,  2010), amyotrophic lateral sclerosis (Martin 2009), bipolar disorder (Kubota et al.,  2010), Alzheimer's disease (Du and Yan, 2010), Huntington's disease (Perry et al.,  2010), recovery after myocardial infarction (Gomez et al.,  2007) and chronic alchohol consumption (King et al.,  2010). 
Further Therapeutic Uses
Cyclophilin inhibitors have potential activity against and therefore in the treatment of infections of other viruses, such as Varicella-zoster virus (Ptak et al.,  2008), Influenza A virus (Liu et al.,  2009), Severe acute respiratory syndrome coronavirus and other human and feline coronaviruses (Chen et al.,  2005, Ptak et al.,  2008), Dengue virus (Kaul et al.,  2009), Yellow fever virus (Qing et al.,  2009), West Nile virus (Qing et al.,  2009), Western equine encephalitis virus (Qing et al.,  2009), Cytomegalovirus (Kawasaki et al.,  2007) and Vaccinia virus (Castro et al.,  2003). 
There are also reports of utility of cyclophilin inhibitors and cyclophilin inhibition in other therapeutic areas, such as in cancer (Han et al.,  2009). 
General Comments on Sanglifehrins
One of the issues in drug development of compounds such as sanglifehrins is rapid metabolism and glucuronidation, leading to low oral bioavailability.  This can lead to an increased chance of food effect, more frequent incomplete release from the dosage form and higher interpatient variability. 
Therefore there remains a need to identify novel cyclophilin inhibitors and anti-inflammatory agents, which may have utility, particularly in the treatment of HCV infection and anti-inflammatory conditions, but also in the treatment of other disease areas where inhibition of cyclophilins may be useful, such as HIV infection, Muscular Dystrophy or aiding recovery after myocardial infarction or where immunosuppression is useful.  Preferably, such cyclophilin inhibitors have improved properties over the currently available cyclophilin inhibitors, including one or more of the following properties: longer half-life or increased oral bioavailability, possibly via reduced P450 metabolism and/or reduced glucuronidation, improved water solubility, improved potency against HCV, reduced toxicity (including hepatotoxicity), improved pharmacological profile, such as high exposure to target organ (e.g. liver in the case of HCV) and/or long half life (enabling less frequent dosing), reduced drug-drug interactions, such as via reduced levels of CYP3A4 metabolism and inhibition and reduced (Pgp) inhibition (enabling easier multi-drug combinations) and improved side-effect profile, such as low binding to MRP2, leading to a reduced chance of hyperbilirubinaemia, lower immunosuppressive effect, improved activity against resistant virus species, in particular CsA and CsA analogue (e.g DEBIO-025) resistant virus species and higher therapeutic (and/or selectivity) index.  The present invention discloses novel sanglifehrin analogues which may have one or more of the above properties.  In particular, the present invention discloses novel mutasynthetic sanglifehrin analogues which, in at least some embodiments, have reduced metabolism via P450 or glucuronidation, for example as shown by increased microsome half-life and/or improved potency against HCV, for example as shown by a low replicon EC50 and/or increased selectivity index. 
There is also a need to develop novel immunosuppressive agents, which may have utility in the prophylaxis of transplant rejection, or in the treatment of autoimmune, inflammatory and respiratory disorders.  Preferably, such immunosuppressants have improved properties over the known natural sanglifehrins, including one or more of the following properties: longer half-life or increased oral bioavailability, possibly via reduced P450 metabolism and/or reduced glucuronidation, improved water solubility, improved potency in immunosuppressive activity, such as might be seen in t-cell proliferation assays, reduced toxicity (including hepatotoxicity), improved pharmacological profile, such as high exposure to target organ and/or long half-life (enabling less frequent dosing), reduced drug-drug interactions, such as via reduced levels of CYP3A4 metabolism and inhibition and reduced (Pgp) inhibition (enabling easier multi-drug combinations) and improved side-effect profile.  The present invention discloses novel sanglifehrin analogues which may have one or more of the above properties.  In particular, the present invention discloses novel sanglifehrin analogues which, in at least some embodiments, have reduced metabolism via P450 or glucuronidation, for example as shown by increased microsome half-life and may have improved immunosuppressive potency, for example as shown by a low t-cell proliferation IC50.