Daptomycin
Encyclopedia
Daptomycin is a novel lipopeptide
antibiotic
used in the treatment of certain infections caused by Gram-positive
organisms. It is a naturally occurring compound found in the soil saprotroph Streptomyces roseosporus
. Its distinct mechanism of action means that it may be useful in treating infections caused by multi-resistant bacteria. It is marketed in the United States under the trade name Cubicin (Cubist Pharmaceuticals
).
in the late 1980s.
LY 146032 showed promise in Phase I/II clinical trial
s 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
and potential myositis
. 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 began marketing the drug under the trade name CUBICIN . Cubicin is marketed in the EU and several other countries by Novartis
following its purchase of Chiron Corporation
, previous licensee.
function. It appears to bind to the membrane and cause rapid depolarization
, resulting in a loss of membrane potential leading to inhibition of protein
, DNA
and RNA
synthesis, which results in bacterial cell death.
(including glycopeptide
-resistant Enterococci (GRE)), staphylococci
(including methicillin-resistant Staphylococcus aureus
), streptococci
and corynebacteria
.
s caused by Gram-positive
infections, Staphylococcus aureus
bacteraemia and right-sided S. aureus endocarditis
. It binds avidly to pulmonary surfactant
, and therefore cannot be used in the treatment of pneumonia. There seems to be a difference in working daptomycin on hematogenous pneumonia.
, flucloxacillin
or vancomycin
) in the treatment of bacteraemia and right-sided endocarditis
caused by Staphylococcus aureus. A study in Detroit, Michigan
compared 53 patients treated suspected MRSA skin or soft tissue infection with daptomycin against vancomycin
, has been shown to result in faster recovery from skin and soft tissue infections (4 days versus 7 days). The main problems with this study were that vancomycin controls were historical (which means that the improved outcomes observed in the daptomycin treated patients could be due to improvements in practice over time that were unrelated to daptomycin use), and the target drug levels were low (lower limit 5 mg/dl, compared to the 10 mg/dl or 15 mg/dl currently recommended).
In Phase III clinical trials, limited data showed that daptomycin was associated with poor outcomes in patients with left-sided endocarditis. It is inactivated by pulmonary surfactant
s and is not indicated for the treatment of pneumonia
. Daptomycin has not been studied in patients with prosthetic valve endocarditis or meningitis
.
Daptomycin is given every 48 hours in patients with renal impairment, clearance < 30 ml/min. There is no information available on dosing in people less than 18 years of age.
Daptomycin is supplied as a sterile preservative-free pale yellow to light brown lyophilised 500 mg and 350 mg cake that must be reconstituted with 0.9% saline prior to use.
Daptomycin is applicable as 30-min-infusion or 2-min-injection.
There are also reports of myopathy
and rhabdomyolysis
occurring in patients simultaneously taking statin
s 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.
In July 2010, the FDA issued a warning that Daptomycin could cause life-threatening eosinophilic pneumonia. The FDA said that 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.
Daptomycin is a cyclic lipopeptide antibiotic produced by the organism Streptomyces roseosporus. Daptomycin consists of thirteen amino acids, ten of which are arranged in a cyclic fashion, and three that adorn an exocyclic tail. Two non-proteinogenic 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 non-ribosomal peptide synthetase (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 non-proteinogenic 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). Posttranslational 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 now provide a thiol on which the substrate and acyl chains are covalently tethered 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 (KR) domain, followed by dehydration to the olefin catalyzed by a dehydratase (DH) domain, and finally reduction to the methylene catalyzed by an enoylreductase (ER) 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 a non-ribosomal peptide synthetase (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, there are catalytic domains that carry out the elongation of the growing peptidyl chain. The growing peptide is covalently tethered to a thiolation (T) domain; here it is termed the peptidyl carrier protein (PCP), 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 via a PPTase, attaching a flexible phosphopantetheine arm to a conserved serine residue. An adenylation (A) 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 (PCP). 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 (E) 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-aspartate, 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 non-proteinogenic amino acids, L-3-methylglutamic acid (mGlu) and the unusual amino acid L-kynurenine (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 (TE) domain catalyzes chain termination and release of the mature lipopeptide.
With the recent advances in molecular engineering over the past 25 years, new approaches in the production of novel antibiotics have emerged. Innovations in cloning and the subsequent analysis of antibiotic gene clusters, the engineering of biosynthetic pathways in Escherichia coli, the transfer of engineered pathways from E. coli into Streptomyces expression hosts, and finally the stable maintenance and expression of cloned genes are all processes that have streamlined the process. More comprehensive understanding and knowledge of the mechanisms, as well as the substrate specificities during their assembly by polyketide synthases, nonribosomal peptide synthetases, glycosyltransferases and other enzymes have made molecular engineering design and outcomes more predictable.
The molecular engineering of Daptomycin, the only marketed acidic lipopeptide antibiotic up 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 a 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 (CDA) pathways to create molecules containing Trp13, Ile13, or Val13. Dpt D is responsible for incorporating the penultimate amino acid, 3-methyl-glutamic acid (3mGlu12), and the last amino acid, kynurenine (Kyn13), into the growing chain. This exchange was achieved without engineering the interpeptide dockingsites. These whole-subunit exchanges have been coupled combinatorially 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 seventy 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 means of fermentation techniques. Only a small percentage of the possible combinations of amino acids within the peptide core have been investigated thus far.
Thus, the biosynthetic genes for daptomycin, a calcium-dependent antibiotic, have been cloned, sequenced, analyzed bioinformatically, genetically, and biochemically. The resultant information on the organization and expression of NRPS genes, among others, has been exploited and utilized to create combinatorial libraries of hybrid lipopeptide antibiotics related to daptomycin that have proven as effective antibiotics thus far in clinical trials .
Lipopeptide
A lipopeptide is a molecule consisting of a lipid connected to a peptide. Bacteria express these molecules. They are bound by TLR 1, and other, Toll-like receptors.Certain lipopeptides are used as antibiotics....
antibiotic
Antibiotic
An antibacterial is a compound or substance that kills or slows down the growth of bacteria.The term is often used synonymously with the term antibiotic; today, however, with increased knowledge of the causative agents of various infectious diseases, antibiotic has come to denote a broader range of...
used in the treatment of certain infections caused by Gram-positive
Gram-positive
Gram-positive bacteria are those that are stained dark blue or violet by Gram staining. This is in contrast to Gram-negative bacteria, which cannot retain the crystal violet stain, instead taking up the counterstain and appearing red or pink...
organisms. It is a naturally occurring compound found in the soil saprotroph Streptomyces roseosporus
Streptomyces roseosporus
Streptomyces roseosporus is a species of actinobacteria. It produces the novel antibiotic daptomycin ....
. Its distinct mechanism of action means that it may be useful in treating infections caused by multi-resistant bacteria. It is marketed in the United States under the trade name Cubicin (Cubist Pharmaceuticals
Cubist Pharmaceuticals
Cubist Pharmaceuticals is a biopharmaceutical company with activities spanning from research and development to commercialization of pharmaceutical products. Its main products address unmet medical needs in acute care, specifically pathogens like MRSA...
).
History
The compound LY 146032 was discovered by researchers at Eli Lilly and CompanyEli Lilly and Company
Eli Lilly and Company is a global pharmaceutical company. Eli Lilly's global headquarters is located in Indianapolis, Indiana, in the United States...
in the late 1980s.
LY 146032 showed promise in Phase I/II clinical trial
Clinical trial
Clinical trials are a set of procedures in medical research and drug development that are conducted to allow safety and efficacy data to be collected for health interventions...
s for treatment of infection caused by Gram-positive
Gram-positive
Gram-positive bacteria are those that are stained dark blue or violet by Gram staining. This is in contrast to Gram-negative bacteria, which cannot retain the crystal violet stain, instead taking up the counterstain and appearing red or pink...
organisms. Lilly ceased development because high dose therapy was associated with adverse effects on skeletal muscle, including myalgia
Myalgia
Myalgia means "muscle pain" and is a symptom of many diseases and disorders. The most common causes are the overuse or over-stretching of a muscle or group of muscles. Myalgia without a traumatic history is often due to viral infections...
and potential myositis
Myositis
Myositis is a general term for inflammation of the muscles. Many such conditions are considered likely to be caused by autoimmune conditions, rather than directly due to infection It is also a documented side effect of the lipid-lowering drugs statins and fibrates.Elevation of creatine kinase in...
. The rights to LY 146032 were acquired by Cubist Pharmaceuticals
Cubist Pharmaceuticals
Cubist Pharmaceuticals is a biopharmaceutical company with activities spanning from research and development to commercialization of pharmaceutical products. Its main products address unmet medical needs in acute care, specifically pathogens like MRSA...
in 1997, which following U.S. Food and Drug Administration
Food and Drug Administration
The Food and Drug Administration is an agency of the United States Department of Health and Human Services, one of the United States federal executive departments...
(FDA) approval in September 2003 began marketing the drug under the trade name CUBICIN . Cubicin is marketed in the EU and several other countries by Novartis
Novartis
Novartis International AG is a multinational pharmaceutical company based in Basel, Switzerland, ranking number three in sales among the world-wide industry...
following its purchase of Chiron Corporation
Chiron Corporation
Chiron Corporation was a multinational biotechnology firm based in Emeryville, California that was acquired by Novartis International AG on April 20, 2006. It had offices and facilities in eighteen countries on five continents. Chiron's business and research was in three main areas:...
, previous licensee.
Mechanism of action
Daptomycin has a distinct mechanism of action, disrupting multiple aspects of bacterial cell membraneCell membrane
The cell membrane or plasma membrane is a biological membrane that separates the interior of all cells from the outside environment. The cell membrane is selectively permeable to ions and organic molecules and controls the movement of substances in and out of cells. It basically protects the cell...
function. It appears to bind to the membrane and cause rapid depolarization
Depolarization
In biology, depolarization is a change in a cell's membrane potential, making it more positive, or less negative. In neurons and some other cells, a large enough depolarization may result in an action potential...
, resulting in a loss of membrane potential leading to inhibition of protein
Protein
Proteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form, facilitating a biological function. A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of...
, DNA
DNA
Deoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms . The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in...
and RNA
RNA
Ribonucleic acid , or RNA, is one of the three major macromolecules that are essential for all known forms of life....
synthesis, which results in bacterial cell death.
Microbiology
Daptomycin is active against Gram-positive bacteria only. It has proven in vitro activity against enterococciEnterococcus
Enterococcus is a genus of lactic acid bacteria of the phylum Firmicutes. Enterococci are Gram-positive cocci that often occur in pairs or short chains, and are difficult to distinguish from streptococci on physical characteristics alone. Two species are common commensal organisms in the...
(including glycopeptide
Glycopeptide
Glycopeptides are peptides that contain carbohydrate moieties covalently attached to the side chains of the amino acid residues that constitute the peptide. Over the past few decades it has been recognised that glycans on cell surface and those bound to proteins play a critical role in biology...
-resistant Enterococci (GRE)), staphylococci
Staphylococcus
Staphylococcus is a genus of Gram-positive bacteria. Under the microscope they appear round , and form in grape-like clusters....
(including methicillin-resistant Staphylococcus aureus
Methicillin-resistant Staphylococcus aureus
Methicillin-resistant Staphylococcus aureus is a bacterium responsible for several difficult-to-treat infections in humans. It is also called multidrug-resistant Staphylococcus aureus and oxacillin-resistant Staphylococcus aureus...
), streptococci
Streptococcus
Streptococcus is a genus of spherical Gram-positive bacteria belonging to the phylum Firmicutes and the lactic acid bacteria group. Cellular division occurs along a single axis in these bacteria, and thus they grow in chains or pairs, hence the name — from Greek στρεπτος streptos, meaning...
and corynebacteria
Corynebacterium
Corynebacterium is a genus of Gram-positive rod-shaped bacteria. They are widely distributed in nature and are mostly innocuous. Some are useful in industrial settings such as C. glutamicum. Others can cause human disease. C...
.
Indications
Daptomycin is approved in the United States for skin and skin structure infectionSkin and skin structure infection
A skin and skin structure infection is a bacterial infection of skin and associated tissues. It often requires treatment by antibiotics.It is/was divided into two types, complicated skin and skin structure infection and...
s caused by Gram-positive
Gram-positive
Gram-positive bacteria are those that are stained dark blue or violet by Gram staining. This is in contrast to Gram-negative bacteria, which cannot retain the crystal violet stain, instead taking up the counterstain and appearing red or pink...
infections, Staphylococcus aureus
Staphylococcus aureus
Staphylococcus aureus is a facultative anaerobic Gram-positive coccal bacterium. It is frequently found as part of the normal skin flora on the skin and nasal passages. It is estimated that 20% of the human population are long-term carriers of S. aureus. S. aureus is the most common species of...
bacteraemia and right-sided S. aureus endocarditis
Endocarditis
Endocarditis is an inflammation of the inner layer of the heart, the endocardium. It usually involves the heart valves . Other structures that may be involved include the interventricular septum, the chordae tendineae, the mural endocardium, or even on intracardiac devices...
. It binds avidly to pulmonary surfactant
Pulmonary surfactant
Pulmonary surfactant is a surface-active lipoprotein complex formed by type II alveolar cells. The proteins and lipids that surfactant comprises have both a hydrophilic region and a hydrophobic region...
, and therefore 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 not inferior to standard therapies (nafcillin, oxacillinOxacillin
Oxacillin sodium is a narrow spectrum beta-lactam antibiotic of the penicillin class.It was developed by Beecham.-Uses:...
, flucloxacillin
Flucloxacillin
Flucloxacillin or floxacillin is a narrow-spectrum beta-lactam antibiotic of the penicillin class. It is used to treat infections caused by susceptible Gram-positive bacteria. Unlike other penicillins, flucloxacillin has activity against beta-lactamase-producing organisms such as Staphylococcus...
or vancomycin
Vancomycin
Vancomycin INN is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. It has traditionally been reserved as a drug of "last resort", used only after treatment with other antibiotics had failed, although the emergence of...
) in the treatment of bacteraemia and right-sided endocarditis
Endocarditis
Endocarditis is an inflammation of the inner layer of the heart, the endocardium. It usually involves the heart valves . Other structures that may be involved include the interventricular septum, the chordae tendineae, the mural endocardium, or even on intracardiac devices...
caused by Staphylococcus aureus. A study in Detroit, Michigan
Detroit, Michigan
Detroit is the major city among the primary cultural, financial, and transportation centers in the Metro Detroit area, a region of 5.2 million people. As the seat of Wayne County, the city of Detroit is the largest city in the U.S. state of Michigan and serves as a major port on the Detroit River...
compared 53 patients treated suspected MRSA skin or soft tissue infection with daptomycin against vancomycin
Vancomycin
Vancomycin INN is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. It has traditionally been reserved as a drug of "last resort", used only after treatment with other antibiotics had failed, although the emergence of...
, has been shown to result in faster recovery from skin and soft tissue infections (4 days versus 7 days). The main problems with this study were that vancomycin controls were historical (which means that the improved outcomes observed in the daptomycin treated patients could be due to improvements in practice over time that were unrelated to daptomycin use), and the target drug levels were low (lower limit 5 mg/dl, compared to the 10 mg/dl or 15 mg/dl currently recommended).
In Phase III clinical trials, limited data showed that daptomycin was associated with poor outcomes in patients with left-sided endocarditis. It is inactivated by pulmonary surfactant
Surfactant
Surfactants are compounds that lower the surface tension of a liquid, the interfacial tension between two liquids, or that between a liquid and a solid...
s and is not indicated for the treatment of pneumonia
Pneumonia
Pneumonia is an inflammatory condition of the lung—especially affecting the microscopic air sacs —associated with fever, chest symptoms, and a lack of air space on a chest X-ray. Pneumonia is typically caused by an infection but there are a number of other causes...
. Daptomycin has not been studied in patients with prosthetic valve endocarditis or meningitis
Meningitis
Meningitis is inflammation of the protective membranes covering the brain and spinal cord, known collectively as the meninges. The inflammation may be caused by infection with viruses, bacteria, or other microorganisms, and less commonly by certain drugs...
.
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 given every 48 hours in patients with renal impairment, clearance < 30 ml/min. There is no information available on dosing in people less than 18 years of age.
Daptomycin is supplied as a sterile preservative-free pale yellow to light brown lyophilised 500 mg and 350 mg cake that must be reconstituted with 0.9% saline prior to use.
Daptomycin is applicable as 30-min-infusion or 2-min-injection.
Adverse effects
Adverse drug reactions associated with daptomycin therapy include:- Cardiovascular: hypotensionHypotensionIn physiology and medicine, hypotension is abnormally low blood pressure, especially in the arteries of the systemic circulation. It is best understood as a physiologic state, rather than a disease. It is often associated with shock, though not necessarily indicative of it. Hypotension is the...
(2.4%), hypertensionHypertensionHypertension or high blood pressure is a cardiac chronic medical condition in which the systemic arterial blood pressure is elevated. What that means is that the heart is having to work harder than it should to pump the blood around the body. Blood pressure involves two measurements, systolic and...
(1.1%), edemaEdemaEdema or oedema ; both words from the Greek , oídēma "swelling"), formerly known as dropsy or hydropsy, is an abnormal accumulation of fluid beneath the skin or in one or more cavities of the body that produces swelling...
, cardiac failure, supraventricular tachycardiaSupraventricular tachycardiaSupraventricular tachycardia is a general term that refers to any rapid heart rhythm originating above the ventricular tissue. Supraventricular tachycardias can be contrasted to the potentially more dangerous ventricular tachycardias - rapid rhythms that originate within the ventricular... - Central nervous system: headache (5.4%), insomnia (4.5%), dizziness (2.2%), anxiety, confusion, vertigoVertigo (medical)Vertigo is a type of dizziness, where there is a feeling of motion when one is stationary. The symptoms are due to a dysfunction of the vestibular system in the inner ear...
, paraesthesia - Dermatological: rash (4.3%), pruritus (2.8%), eczemaEczemaEczema is a form of dermatitis, or inflammation of the epidermis . In England, an estimated 5.7 million or about one in every nine people have been diagnosed with the disease by a clinician at some point in their lives.The term eczema is broadly applied to a range of persistent skin conditions...
- Endocrine: hypokalaemia, hyperglycemiaHyperglycemiaHyperglycemia or Hyperglycæmia, or high blood sugar, is a condition in which an excessive amount of glucose circulates in the blood plasma. This is generally a glucose level higher than 13.5mmol/l , but symptoms may not start to become noticeable until even higher values such as 15-20 mmol/l...
, hypomagnesemiaHypomagnesemiaHypomagnesemia is an electrolyte disturbance in which there is an abnormally low level of magnesium in the blood. Usually a serum level less than 0.7 mmol/L is used as reference. The prefix hypo- means low . The middle 'magnes' refers to magnesium...
, increased serum bicarbonateBicarbonateIn inorganic chemistry, bicarbonate is an intermediate form in the deprotonation of carbonic acid...
, other electrolyteElectrolyteIn chemistry, an electrolyte is any substance containing free ions that make the substance electrically conductive. The most typical electrolyte is an ionic solution, but molten electrolytes and solid electrolytes are also possible....
disturbances - Gastrointestinal: constipation (6.2%), nausea (5.8%), diarrhea (5.2%), vomiting (3.2%), dyspepsia (0.9%), abdominal pain, decreased appetite, stomatitisStomatitisStomatitis is an inflammation of the mucous lining of any of the structures in the mouth, which may involve the cheeks, gums, tongue, lips, throat, and roof or floor of the mouth...
, flatulence - Hematological: anemiaAnemiaAnemia is a decrease in number of red blood cells or less than the normal quantity of hemoglobin in the blood. However, it can include decreased oxygen-binding ability of each hemoglobin molecule due to deformity or lack in numerical development as in some other types of hemoglobin...
(2.1%), leukocytosisLeukocytosisLeukocytosis is a raised white blood cell count above the normal range in the blood. It is frequently a sign of an inflammatory response, most commonly the result of infection, and is observed in certain parasitic infections...
, thrombocytopeniaThrombocytopeniaThrombocytopenia is a relative decrease of platelets in blood.A normal human platelet count ranges from 150,000 to 450,000 platelets per microliter of blood. These limits are determined by the 2.5th lower and upper percentile, so values outside this range do not necessarily indicate disease...
, thrombocytosisThrombocytosisThrombocytosis is the presence of high platelet counts in the blood, and can be either primary or reactive...
, eosinophiliaEosinophiliaEosinophilia is a condition in which the eosinophil count in the peripheral blood exceeds 0.45×109/L . A marked increase in non-blood tissue eosinophil count noticed upon histopathologic examination is diagnostic for tissue eosinophilia. Several causes are known, with the most common being...
, increased international normalised ratio (INR) - Hepatic: abnormal liver function tests (3%) (including alkaline phosphataseAlkaline phosphataseAlkaline phosphatase is a hydrolase enzyme responsible for removing phosphate groups from many types of molecules, including nucleotides, proteins, and alkaloids. The process of removing the phosphate group is called dephosphorylation...
and lactate dehydrogenaseLactate dehydrogenaseLactate dehydrogenase is an enzyme present in a wide variety of organisms, including plants and animals.Lactate dehydrogenases exist in four distinct enzyme classes. Two of them are cytochrome c-dependent enzymes, each acting on either D-lactate or L-lactate...
), jaundiceJaundiceJaundice is a yellowish pigmentation of the skin, the conjunctival membranes over the sclerae , and other mucous membranes caused by hyperbilirubinemia . This hyperbilirubinemia subsequently causes increased levels of bilirubin in the extracellular fluid... - Musculoskeletal: elevated creatine kinaseCreatine kinaseCreatine kinase , also known as creatine phosphokinase or phospho-creatine kinase , is an enzyme expressed by various tissues and cell types. CK catalyses the conversion of creatine and consumes adenosine triphosphate to create phosphocreatine and adenosine diphosphate...
(CK) levels (2.8–10.5%), limb pain (1.5%), arthralgiaArthralgiaArthralgia literally means joint pain; it is a symptom of injury, infection, illnesses or an allergic reaction to medication....
(0.9%), myalgiaMyalgiaMyalgia means "muscle pain" and is a symptom of many diseases and disorders. The most common causes are the overuse or over-stretching of a muscle or group of muscles. Myalgia without a traumatic history is often due to viral infections...
, muscle cramps, muscle weakness, osteomyelitisOsteomyelitisOsteomyelitis simply means an infection of the bone or bone marrow... - Renal: acute renal failureRenal failureRenal failure or kidney failure describes a medical condition in which the kidneys fail to adequately filter toxins and waste products from the blood...
(2.2%) - Respiratory: dyspneaDyspneaDyspnea , shortness of breath , or air hunger, is the subjective symptom of breathlessness.It is a normal symptom of heavy exertion but becomes pathological if it occurs in unexpected situations...
(2.1%) - Other: injection site reactions (5.8%), fever (1.9%), hypersensitivityHypersensitivityHypersensitivity refers to undesirable reactions produced by the normal immune system, including allergies and autoimmunity. These reactions may be damaging, uncomfortable, or occasionally fatal. Hypersensitivity reactions require a pre-sensitized state of the host. The four-group classification...
There are also reports of myopathy
Myopathy
In medicine, a myopathy is a muscular disease in which the muscle fibers do not function for any one of many reasons, resulting in muscular weakness. "Myopathy" simply means muscle disease...
and rhabdomyolysis
Rhabdomyolysis
Rhabdomyolysis is a condition in which damaged skeletal muscle tissue breaks down rapidly. Breakdown products of damaged muscle cells are released into the bloodstream; some of these, such as the protein myoglobin, are harmful to the kidneys and may lead to kidney failure...
occurring in patients simultaneously taking statin
Statin
Statins are a class of drugs used to lower cholesterol levels by inhibiting the enzyme HMG-CoA reductase, which plays a central role in the production of cholesterol in the liver. Increased cholesterol levels have been associated with cardiovascular diseases, and statins are therefore used in the...
s 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.
In July 2010, the FDA issued a warning that Daptomycin could cause life-threatening eosinophilic pneumonia. The FDA said that 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
Daptomycin is a cyclic lipopeptide antibiotic produced by the organism Streptomyces roseosporus. Daptomycin consists of thirteen amino acids, ten of which are arranged in a cyclic fashion, and three that adorn an exocyclic tail. Two non-proteinogenic 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
Tryptophan
Tryptophan is one of the 20 standard amino acids, as well as an essential amino acid in the human diet. It is encoded in the standard genetic code as the codon UGG...
, 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 non-ribosomal peptide synthetase (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
Condensation domain
In molecular biology, the condensation domain is a protein domain found in many multi-domain enzymes which synthesise peptide antibiotics. This domain catalyses a condensation reaction to form peptide bonds in non-ribosomal peptide biosynthesis. It is usually found to the carboxy side of a...
to acylate the first amino acid (tryptophan). These and other novel genes (dptI, dptJ) are believed to be involved in supplying the non-proteinogenic 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). Posttranslational 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 now provide a thiol on which the substrate and acyl chains are covalently tethered 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 (KR) domain, followed by dehydration to the olefin catalyzed by a dehydratase (DH) domain, and finally reduction to the methylene catalyzed by an enoylreductase (ER) 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 a non-ribosomal peptide synthetase (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, there are catalytic domains that carry out the elongation of the growing peptidyl chain. The growing peptide is covalently tethered to a thiolation (T) domain; here it is termed the peptidyl carrier protein (PCP), 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 via a PPTase, attaching a flexible phosphopantetheine arm to a conserved serine residue. An adenylation (A) 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 (PCP). 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 (E) 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-aspartate, 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 non-proteinogenic amino acids, L-3-methylglutamic acid (mGlu) and the unusual amino acid L-kynurenine (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 (TE) domain catalyzes chain termination and release of the mature lipopeptide.
With the recent advances in molecular engineering over the past 25 years, new approaches in the production of novel antibiotics have emerged. Innovations in cloning and the subsequent analysis of antibiotic gene clusters, the engineering of biosynthetic pathways in Escherichia coli, the transfer of engineered pathways from E. coli into Streptomyces expression hosts, and finally the stable maintenance and expression of cloned genes are all processes that have streamlined the process. More comprehensive understanding and knowledge of the mechanisms, as well as the substrate specificities during their assembly by polyketide synthases, nonribosomal peptide synthetases, glycosyltransferases and other enzymes have made molecular engineering design and outcomes more predictable.
The molecular engineering of Daptomycin, the only marketed acidic lipopeptide antibiotic up 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 a 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 (CDA) pathways to create molecules containing Trp13, Ile13, or Val13. Dpt D is responsible for incorporating the penultimate amino acid, 3-methyl-glutamic acid (3mGlu12), and the last amino acid, kynurenine (Kyn13), into the growing chain. This exchange was achieved without engineering the interpeptide dockingsites. These whole-subunit exchanges have been coupled combinatorially 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 seventy 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 means of fermentation techniques. Only a small percentage of the possible combinations of amino acids within the peptide core have been investigated thus far.
Thus, the biosynthetic genes for daptomycin, a calcium-dependent antibiotic, have been cloned, sequenced, analyzed bioinformatically, genetically, and biochemically. The resultant information on the organization and expression of NRPS genes, among others, has been exploited and utilized to create combinatorial libraries of hybrid lipopeptide antibiotics related to daptomycin that have proven as effective antibiotics thus far in clinical trials .
External links
- PubChem Substance ID
- New ATC Codes (from WHOWhoWho may refer to:* Who , an English-language pronoun* who , a Unix command* Who?, one of the Five Ws in journalism- Art and entertainment :* Who? , a 1958 novel by Algis Budrys...
) - Orientations of daptomycin and tsushimycin in membrane