Daptomycin, sold under the brand name Cubicin among others, is a lipopeptide antibiotic used in the treatment of systemic and life-threatening infections caused by Gram-positive organisms. The World Health Organization classifies daptomycin as critically important for human medicine.
Medical uses
In the United States, daptomycin is indicated for use in adults for skin and skin structure infections caused by Gram-positive infections, S. aureus bacteremia, and right-sided S. aureus endocarditis. Daptomycin is not recommended for patients younger than one year of age, given the potential for adverse effects on the muscular, neuromuscular, and nervous systems observed in neonatal animal studies.
Adverse effects
Common adverse drug reactions associated with daptomycin therapy include:
- Cardiovascular: low blood pressure, high blood pressure, swelling
- Central nervous system: insomnia
- Dermatological: rash
- Gastrointestinal: diarrhea, abdominal pain
- Hematological: eosinophilia
- Respiratory: dyspnea
- Other: injection site reactions, fever, hypersensitivity
Less common, but serious adverse events reported in the literature include
- Hepatotoxicity: elevated transaminases
- Nephrotoxicity: acute kidney injury from rhabdomyolysis
Also, myopathy and rhabdomyolysis have been reported in patients simultaneously taking statins, but whether this is due entirely to the statin or whether daptomycin potentiates this effect is unknown. Due to the limited data available, the manufacturer recommends that statins be temporarily discontinued while the patient is receiving daptomycin therapy. Creatine kinase levels are usually checked regularly while individuals undergo daptomycin therapy.
In July 2010, the FDA issued a warning that daptomycin could cause life-threatening eosinophilic pneumonia. The FDA said it had identified seven confirmed cases of eosinophilic pneumonia between 2004 and 2010 and an additional 36 possible cases. The seven confirmed cases were all older than 60 and symptoms appeared within two weeks of initiation of therapy.
Pharmacology
Mechanism of action
Daptomycin has a distinct mechanism of action, disrupting multiple aspects of bacterial cell membrane function. It inserts into the cell membrane in a phosphatidylglycerol-dependent fashion, where it then aggregates. The aggregation of daptomycin alters the curvature of the membrane, which creates holes that leak ions. This causes rapid depolarization, resulting in a loss of membrane potential leading to inhibition of protein, DNA, and RNA synthesis, which results in bacterial cell death.
It has been proposed that the formation of spherical micelles by daptomycin may affect the mode of action.
Microbiology
Daptomycin is bactericidal against Gram-positive bacteria only. It has proven in vitro activity against enterococci (including glycopeptide-resistant enterococci (GRE)), staphylococci (including methicillin-resistant Staphylococcus aureus), streptococci, corynebacteria and stationary-phase Borrelia burgdorferi persisters.
Daptomycin's bactericidal activity is concentration-dependent and is preserved against organisms in the stationary phase of growth, distinguishing it from many antibacterials that depend on active cell division for lethal effect. In in vitro studies, the drug also produces a prolonged concentration-dependent post-antibiotic effect, during which bacterial growth remains suppressed after drug exposure ends.
Daptomycin resistance
Daptomycin resistance is still uncommon, but has been increasingly reported in GRE, starting in Korea in 2005, in Europe in 2010, in Taiwan 2011, and in the United States, where nine cases have been reported from 2007 to 2011. Daptomycin resistance emerged in five of the six cases while they were treated. The mechanism of resistance is unknown. A four-million year-old strain of Paenibacillus isolated from soil samples in Lechuguilla Cave was found to be naturally resistant to daptomycin.
It has been suggested that co-administration of daptomycin with at least another active antibiotic might help prevent the emergence of resistance and increase the bactericidal effect. Data from in vitro and in vivo studies suggest that a tailored approach should be used taking into account both the causative agent and the site of infection.
Efficacy
Daptomycin has been shown to be non-inferior to standard therapies (nafcillin, oxacillin, flucloxacillin or vancomycin) in the treatment of bacteraemia and right-sided endocarditis caused by S. aureus. A study in Detroit, Michigan compared 53 patients treated for suspected MRSA skin or soft tissue infection with daptomycin against vancomycin, showing faster recovery (4 versus 7 days) with daptomycin.
A 2022 systematic review and meta-analysis of seven studies enrolling 907 patients with MRSA bacteremia where vancomycin MIC exceeded 1 µg/mL found that daptomycin was associated with significantly lower all-cause mortality compared to vancomycin, with an odds ratio of 0.53 (95% CI 0.29–0.98), as well as higher rates of treatment success, with an odds ratio of 2.20 (95% CI 1.63–2.96).
In Phase III clinical trials, limited data showed daptomycin to be associated with poor outcomes in patients with left-sided endocarditis. Daptomycin has not been studied in patients with prosthetic valve endocarditis or meningitis.
Biosynthesis
thumb|Figures 1–7. Biosynthesis of daptomycin
[[File:nbt1265-F2.png|thumb|Figure 8. Structures of lipopeptide antibiotics
Colors highlight the positions in daptomycin that have been modified by genetic engineering, as well as the origins of modules or subunits from A54145 or calcium-dependent antibiotic (CDA).
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[[File:Nbt1265-F3.png|thumb|Figure 9. Combinatorial biosynthesis of lipopeptide antibiotics related to daptomycin. Position 8, which typically has D-Ala in daptomycin, was modified by module exchanges to contain D-Ser, D-Asn or D-Lys; position 11, which naturally has D-Ser, was modified by module exchanges to consist of D-Ala or D-Asn; position 12, which normally has 3-methyl-L-Glu, was modified by deletion of the methyltransferase gene to possess L-Glu; position 13, which normally has L-kynurenine (L-Kyn), was modified by subunit exchanges to contain L-Trp, L-Ile or L-Val; position 1 usually includes the anteiso-undecanoyl, isododecanoyl and anteiso-tridecanoyl fatty acyl groups. All of these alterations have been combinatorialized.
Daptomycin consists of 13 amino acids, 10 of which are arranged in a cyclic fashion, and three on an exocyclic tail. Two nonproteinogenic amino acids exist in the drug, the unusual amino acid L-kynurenine (Kyn), only known to daptomycin, and L-3-methylglutamic acid (mGlu). The N-terminus of the exocyclic tryptophan residue is coupled to decanoic acid, a medium-chain (C10) fatty acid. Biosynthesis is initiated by the coupling of decanoic acid to the N-terminal tryptophan, followed by the coupling of the remaining amino acids by nonribosomal peptide synthetase (NRPS) mechanisms. Finally, a cyclization event occurs, which is catalyzed by a thioesterase enzyme, and subsequent release of the lipopeptide is granted.
The NRPS responsible for the synthesis of daptomycin is encoded by three overlapping genes, dptA, dptBC and dptD. The dptE and dptF genes, immediately upstream of dptA, are likely to be involved in the initiation of daptomycin biosynthesis by coupling decanoic acid to the N-terminal Trp. These novel genes (dptE, dptF) correspond to products that most likely work in conjunction with a unique condensation domain to acylate the first amino acid (tryptophan). These and other novel genes (dptI, dptJ) are believed to be involved in supplying the nonproteinogenic amino acids L-3-methylglutamic acid and Kyn; they are located next to the NRPS genes. Within each module are catalytic domains that carry out the elongation of the growing peptidyl chain. The growing peptide is covalently tethered to a thiolation domain; here it is termed the peptidyl carrier protein, as it carries the growing peptide from one catalytic domain to the next. Again, the apo-T domain must be primed to the holo-T domain by a PPTase, attaching a flexible phosphopantetheine arm to a conserved serine residue. An adenylation domain selects the amino acid monomer to be incorporated and activates the carboxylate with ATP to make the aminoacyl-AMP. Next, the A domain installs an aminoacyl group on the thiolate of the adjacent T domain. The condensation (C) domain catalyzes the peptide bond forming reaction, which elicits chain elongation. It joins an upstream peptidyl-S-T to the downstream aminoacyl-S-T (Figure 7). Chain elongation by one aminoacyl residue and chain translocation to the next T domain occurs in concert. The order of these domains is C-A-T. In some instances, an epimerization domain is necessary in those modules where L-amino acid monomers are to be incorporated and epimerized to D-amino acids. The domain organization in such modules is C-A-T-E. It is an attractive target for combinatorial biosynthesis for many reasons: second generation derivatives are currently in the clinic for development;
Streptomyces roseosporus, the producer organism of daptomycin, is amenable to genetic manipulation; the daptomycin biosynthetic gene cluster has been cloned, sequenced, and expressed in S. lividans; other lipopeptide gene clusters, both related and unrelated to daptomycin, have been cloned and sequenced, and lastly, efforts in medicinal chemistry are able to further modify these products of molecular engineering. Some of these compounds have in vitro antibacterial activities analogous to daptomycin. Further, one displayed ameliorated activity against an E. coli imp mutant that was defective in its ability to assemble its inherent lipopolysaccharide. A number of these compounds were produced in yields that spanned from 100 to 250 mg/liter; this, of course, opens up the possibility for successful scale-ups by fermentation techniques. Only a small percentage of the possible combinations of amino acids within the peptide core have been investigated thus far.
History
Daptomycin, originally designated as LY 146032, was discovered by researchers at Eli Lilly and Company in the late 1980s from the actinomycete Streptomyces roseosporus. LY 146032 showed promise in phase I/II clinical trials for treatment of infection caused by Gram-positive organisms. Lilly ceased development because high-dose therapy was associated with adverse effects on skeletal muscle, including myalgia.
The rights to LY 146032 were acquired by Cubist Pharmaceuticals in 1997, which following U.S. Food and Drug Administration (FDA) approval in September 2003, for use in people older than 18 years, began marketing the drug under the trade name Cubicin. Cubicin is marketed in the EU and in several other countries by Novartis following its purchase of Chiron Corporation, the previous licensee. In July 2016 the FDA approved a reformulated version of daptomycin, designated Cubicin RF, which is stored at controlled room temperature rather than requiring refrigeration.
In December 2014, Merck & Co. reached an agreement to acquire Cubist Pharmaceuticals for a total transaction value of approximately $9.5 billion, comprising an equity valuation of $8.4 billion at $102 per share in cash and $1.1 billion in assumed net debt, with the transaction expected to close in the first quarter of 2015.