ダプトマイシン

ダプトマイシン(Daptomycin, DPT)はリポペプチド系の抗菌薬のひとつ。 ほとんどの抗菌薬が効かないMRSA感染による皮膚軟部組識感染や敗血症、感染性心内膜炎などの治療薬として利用される。

ダプトマイシン

IUPAC命名法による物質名
IUPAC名 N-Decanoyl-L-tryptophyl-L-asparaginyl-L-aspartyl-L-threonylglycyl-L-ornithyl-L-aspartyl-D-alanyl-L-aspartylglycyl-D-seryl-threo-3-methyl-L-glutamyl-3-anthraniloyl-L-alanine[egr]1-lactone
臨床データ
販売名	キュビシン, Cubicin
Drugs.com	monograph
ライセンス	EMA:リンク
胎児危険度分類	US: B
法的規制	JP: 処方箋医薬品 US: ℞-only
投与経路	静脈投与
薬物動態データ
生物学的利用能	n/a
血漿タンパク結合	90–95%
代謝	Renal (speculative)
半減期	7–11 hours (up to 28 hours in renal impairment)
排泄	Renal (78%; primarily as unchanged drug); faeces (5.7%)
識別
CAS番号	103060-53-3
ATCコード	J01XX09 (WHO)
PubChem	CID: 16129629
DrugBank	DB00080
ChemSpider	10482098
UNII	NWQ5N31VKK
KEGG	D01080
ChEBI	CHEBI:600103
ChEMBL	CHEMBL508162
化学的データ
化学式	C72H101N17O26
分子量	1619.7086 g/mol

ダプトマイシン
1. Daptomycin binds and inserts into the cell membrane. 2. It aggregates in the membrane. 3. It alters the shape of the membrane to form a hole, allowing ions in and out of the cell easily.
識別子
略号	N/A
TCDB	1.D.15
OPM superfamily	163
OPM protein	1t5n

歴史

ダプトマイシンは放線菌 Streptomyces roseosporus が生成する物質より発見された。 1980年代にイーライリリー社が発見した(LY146032)が、臨床試験で高用量投与時に筋炎などの副作用が発症したため、試験中止となっていた。

その後LY 146032の開発権利は1997年、Cubist Pharmaceuticalsに引き継がれ、2003年に18歳以上の患者に対しての適応がFDAで承認。アメリカ国内で販売された。その後キュビシン(Cubicin)という商品名でEUなどでも利用されている。 日本では2011年よりMSD（旧万有製薬）が販売している。

作用機序

• ダプトマイシンはグラム陽性菌の細胞膜にカルシウムイオン濃度依存的に結合し、細胞膜中で多量体（オリゴマー）を形成し、膜電位の脱分極を引き起こし、カリウムイオンを流出させる。その結果、蛋白質、DNA及びRNAの合成を阻害し、細胞融解を引き起こすことなく細菌を死滅させる。

耐性

• 耐性をもたらす伝達性因子は知られていない。また他の抗生物質・抗菌薬に対する交差耐性はみられていない。

効能効果

• ＜適応菌種＞
  • ダプトマイシンに感性のメチシリン耐性黄色ブドウ球菌（MRSA）
• ＜適応症＞
  • 敗血症、感染性心内膜炎、深在性皮膚感染症、外傷・熱傷及び手術創等の二次感染、びらん・潰瘍の二次感染

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.

ダプトマイシン耐性

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 USA, 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.

Indications

Daptomycin is approved for use in adults in the United States for skin and skin structure infections caused by Gram-positive infections, S. aureus bacteraemia, and right-sided S. aureus endocarditis. It binds avidly to pulmonary surfactant, so cannot be used in the treatment of pneumonia. There seems to be a difference in working daptomycin on hematogenous pneumonia.

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.

In phase III clinical trials, limited data showed daptomycin to be associated with poor outcomes in patients with left-sided endocarditis. It is inactivated by pulmonary surfactants and is not indicated for the treatment of pneumonia. Daptomycin has not been studied in patients with prosthetic valve endocarditis or meningitis.

Dosage and presentation

In skin and soft tissue infections, 4 mg/kg daptomycin is given intravenously once daily. For S. aureus bacteraemia or right-sided endocarditis, the approved dose is 6 mg/kg given intravenously once daily.

Daptomycin is supplied as a sterile, preservative-free, pale yellow to light brown, lyophilised 500- or 350-mg cake that must be reconstituted with normal saline prior to use.

Daptomycin is applicable as 30-min infusion or 2-min injection.

Adverse effects

Common adverse drug reactions associated with daptomycin therapy include:

• Cardiovascular: hypotension, hypertension, edema
• Central nervous system: insomnia
• Dermatological: rash
• Gastrointestinal: diarrhea, abdominal pain
• Hematological: eosinophilia
• Respiratory: dyspnea
• Other: injection site reactions, fever, hypersensitivity

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 victims were all older than 60 and symptoms appeared within two weeks of initiation of therapy.

Biosynthesis

Figures 1-7. Biosynthesis of daptomycin

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).

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 is a cyclic lipopeptide antibiotic produced by Streptomyces roseosporus. 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 lipopeptide, 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.

The decanoic acid portion of daptomycin is synthesized by fatty acid synthase machinery (Figure 2). Post-translational modification of the apo-acyl carrier protein (ACP, thiolation, or T domain) by a phosphopantetheinyltransferase (PPTase) enzyme catalyzes the transfer of a flexible phosphopantetheine arm from coenzyme A to a conserved serine in the ACP domain through a phosphodiester linkage. The holo-ACP can provide a thiol on which the substrate and acyl chains are covalently bound during chain elongations. The two core catalytic domains are an acyltransferase (AT) and a ketosynthase (KS). The AT acts upon a malonyl-CoA substrate and transfers an acyl group to the thiol of the ACP domain. This net transthiolation is an energy-neutral step. Next, the acyl-S-ACP gets transthiolated to a conserved cysteine on the KS; the KS decarboxylates the downstream malonyl-S-ACP and forms a β-ketoacyl-S-ACP. This serves as the substrate for the next cycle of elongation. Before the next cycle begins, however, the β-keto group undergoes reduction to the corresponding alcohol catalyzed by a ketoreductase domain, followed by dehydration to the olefin catalyzed by a dehydratase domain, and finally reduction to the methylene catalyzed by an enoylreductase domain. Each KS catalytic cycle results in the net addition of two carbons. After three more iterations of elongation, a thioesterase enzyme catalyzes the hydrolysis, and thus release, of the free C-10 fatty acid.

To synthesize the peptide portion of daptomycin, the mechanism of an NRPS is employed. The biosynthetic machinery of an NRPS system is composed of multimodular enzymatic assembly lines that contain one module for each amino acid monomer incorporated. 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.

The first module has a three-domain C-A-T organization; these often occur in assembly lines that make N-acylated peptides. The first C domain catalyzes N-acylation of the initiating amino acid (tryptophan) while it is installed on T. An adenylating enzyme (Ad) catalyzes the condensation of decanoic acid and the N-terminal tryptophan, which incorporates decanoic acid into the growing peptide (Figure 3). The genes responsible for this coupling event are dptE and dptF, which are located upstream of dptA, the first gene of the Daptomycin NRPS biosynthetic gene cluster. Once the coupling of decanoic acid to the N-terminal tryptophan residue occurs, the condensation of amino acids begins, catalyzed by the NRPS.

The first five modules of the NRPS are encoded by the dptA gene and catalyze the condensation of L-tryptophan, D-asparagine, L-aspartate, L-threonine, and glycine, respectively (Figure 4). Modules 6-11, which catalyze the condensation of L-ornithine, L-aspartate, D-alanine, L-aspartate, glycine, and D-serine are encoded for the dptBC gene (Figure 5). dptD catalyzes the incorporation of two nonproteinogenic amino acids, L-3-methylglutamic acid (mGlu) and Kyn, which is only known thus far to daptomycin, into the growing peptide (Figure 6). Elongation by these NRPS modules ultimately leads to macrocyclization and release in which an α-amino group, namely threonine, acts as an internal nucleophile during cyclization to yield the 10-amino-acid ring (Figure 6). The termination module in the NRPS assembly line has a C-A-T-TE organization. The thioesterase domain catalyzes chain termination and release of the mature lipopeptide.

The molecular engineering of daptomycin, the only marketed acidic lipopeptide antibiotic to date (Figure 8), has seen many advances since its inception into clinical medicine in 2003. 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; the lipopeptide biosynthetic machinery has the potential to be interrupted by variations of natural precursors, as well as precursor-directed biosynthesis, gene deletion, genetic exchange, and module exchange; the molecular engineering tools have been developed to facilitate the expression of the three individual NRPS genes from three different sites in the chromosome, using ermEp* for expression of two genes from ectopic loci; other lipopeptide gene clusters, both related and unrelated to daptomycin, have been cloned and sequenced, thus providing genes and modules to allow the generation of hybrid molecules; derivatives can be afforded via chemoenzymatic synthesis; and lastly, efforts in medicinal chemistry are able to further modify these products of molecular engineering.

New derivatives of daptomycin (Figure 9) were originally generated by exchanging the third NRPS subunit (dptD) with the terminal subunits from the A54145 (Factor B1) or calcium-dependent antibiotic pathways to create molecules containing Trp13, Ile13, or Val13. dptD is responsible for incorporating the penultimate amino acid, 3-methyl-glutamic acid (3mGlu12), and the last amino acid, Kyn13, into the chain. This exchange was achieved without engineering the interpeptide docking sites. These whole-subunit exchanges have been coupled with the deletion of the Glu12-methyltransferase gene, with module exchanges at intradomain linker sites at Ala8 and Ser11, and with variations of natural fatty-acid side chains to generate over 70 novel lipopeptides in significant quantities; most of these resultant lipopeptides have potent antibacterial activities. 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.