Bottromycin

Bottromycin is a macrocyclic peptide with antibiotic activity. It was first discovered in 1957 as a natural product isolated from Streptomyces bottropensis. It has been shown to inhibit methicillin-resistant Staphylococcus aureus and vancomycin-resistant Enterococci among other Gram-positive bacteria and mycoplasma. Bottromycin is structurally distinct from both vancomycin, a glycopeptide antibiotic, and methicillin, a beta-lactam antibiotic.
Bottromycin binds to the A site of the ribosome and blocks the binding of aminoacyl-tRNA, therefore inhibiting bacterial protein synthesis. Although bottromycin exhibits antibacterial activity in vitro, it has not yet been developed as a clinical antibiotic, potentially due to its poor stability in blood plasma. To increase its stability in vivo, some bottromycin derivatives have been explored.
The structure of bottromycin contains a macrocyclic amidine as well as a thiazole ring. The absolute stereochemistry at several chiral centers has been determined as of 2009. In 2012, a three-dimensional solution structure of bottromycin was published. The solution structure revealed that several methyl groups are on the same face of the structure.
Bottromycin falls within the ribosomally synthesized and post-translationally modified peptide class of natural product.

History

Bottromycin was first isolated from Streptomyces bottropensis in 1957. It has since been identified in at least two other members of the genus Streptomyces; members of Streptomyces are known to be prolific producers of secondary metabolites. Bottromycin has a unique structure, consisting of the macrocyclic amidine linkage and four β-methylated amino acids. Bottromycin blocks aminoacyl tRNA binding to the ribosome by binding to the A site of the 50s subunit. Although bottromycin was discovered over 50 years ago, there was a lack of research following initial studies on bottromycin until recent years. The lack of research is potentially a result of bottromycin's low stability in blood plasma. However, the unique structure and mode of action have recently made bottromycin a more target for drug development, especially given the rise of antibiotic resistance.

Mechanism of action

The mechanism of action of bottromycin was confirmed nearly 20 years following the discovery of bottromycin. Bottromycin functions as an antibiotic through inhibition of protein synthesis. It blocks aminoacyl tRNA binding to the ribosome by binding to the A site of the 50s subunit. This results in release of aminoacyl tRNA from the ribosome and premature termination of protein synthesis. A comparison of other antibiotics known to bind to the A site of the ribosome, including micrococcin, tetracycline, streptomycin, and chloramphenicol, suggested that only bottromycin and chloramphenicol caused release of aminoacyl tRNA from the ribosome. Of those antibiotics, only micrococcin is also a macrocyclic peptide.

Structure determination

Bottromycin is produced naturally as a series of products differing in methylation patterns. All products contain valine and phenylalanine methylation. Bottromycin A2 is singly methylated on proline, bottromycin B lacks methylation on proline, and bottromycin C contains a doubly methylated proline.
A partial structure of bottromycin was reported shortly after the initial discovery of bottromycin. The first structural studies relied on traditional methods of analysis. Its peptide-like structure, including the presence of glycine and valine, was first suggested by a combination of acidic hydrolysis, acetylation, ninhydrin staining, and paper chromatography, among other experiments. The presence of a thiazole ring, along with an adjacent β-methylated phenylalanine, was established by ninhydrin staining, potassium permanganate oxidation, and comparison to synthetic standards. A methyl ester substituent was reported in 1958. The same study also reported that the Kunz hydrolysis product lacking a methyl ester was biologically inactive. Nakamura and colleagues later reported that bottromycin contained tert-leucine and cis-3-methylproline. They also proposed a linear iminohexapeptide structure.
These early structural studies were not followed up until recent years with the renewed interest in bottromycin. The structure was confirmed in the 1980s and 1990s to be a cyclic iminopeptide based on NMR studies, with a linear side chain connected to the macrocycle via an amidine linkage.
Its absolute stereochemistry, however, was not characterized until 2009. Stereochemistry at carbon 18 and 25 was proposed by comparing predicted conformers obtained using molecular dynamics to experimental constraints obtained through NMR experiments. Stereochemistry at carbon 43 was confirmed by comparing ¹H NMR of authentic hydrolysis product to a chemically synthesized sample of the same fragment. Finally, optical rotation, ¹H NMR, and HRMS experiments of chemically synthesized bottromycin matched that of biologically produced bottromycin.
The three-dimensional solution structure of bottromycin A2 was solved by NMR in 2012. The overall structure was obtained with good resolution, with a RMSD of 0.09±0.06 Å for the macrocycle. In this study, it was proposed that the methylated proline residue contributed to the restricted conformation of the macrocycle. The methylated proline and β-OMe alanine residues were found to be on the same face of bottroymycin A2 and it was suggested that this characteristic contributed to binding of bottromycin to the ribosomal A site.

Biosynthesis

The production of bottromycin by S. bottropensis and S. scabies, as well as the production of a bottromycin analog termed bottromycin D, has been studied. It was independently confirmed in 2012 by multiple groups that bottromycin is produced as a ribosomal peptide natural product that it subsequently post-translationally modified. Before this, it was unclear whether bottromycin was produced by nonribosomal peptide synthetase machinery. The presence of amino acids other than the 20 proteinogenic amino acids is often a feature of NRPS products because NRPS machinery can directly incorporate other amino acids, among other chemical building blocks. Ribosomal peptide synthesis, which is the same machinery that produces all proteins found in the cell, is limited to the 20 proteinogenic amino acids. However, bottromycin was found to be a highly modified ribosomal peptide by a combination of genome mining and gene deletion studies.
In ribosomal peptide synthesis, the final product results from modifications to a linear peptide starting material translated by the ribosome from an mRNA transcript. In S. scabies the precursor peptide, termed BtmD, is a 44-amino acid peptide. The precursor peptide is termed BmbC in S. bottropensis. The amino acids forming the bottromycin core are residues 2-9 in BtmD: Gly-Pro-Val-Val-Val-Phe-Asp-Cys. In bottromycin D, the sequence is Gly-Pro-Ala-Val-Val-Phe-Asp-Cys, and the precursor peptide is termed BstA. BstA shares high sequence homology with BtmD in the follower peptide region. Unlike other ribosomal peptide natural products, which are normally synthesized with a leader peptide that is cleaved, bottromycin is synthesized with a follower peptide. The presence of a follower peptide was identified by bioinformatic analysis of the bottromycin biosynthetic cluster.
The complete biosynthetic gene cluster for bottromycin has been identified. It is predicted to contain 13 genes, including the precursor peptide. One of the genes in the cluster, btmL, is proposed to be a transcriptional regulator. Another gene, btmA, is proposed to export bottromycin. The remaining ten genes are expected to modify the precursor peptide btmD from a linear peptide to the final macrocyclic product.

S. scabies	S. bottropensis	WMMB272	Predicted function
btmA	bmbT	bstK	Major facilitator superfamily/transporter
btmB	bmbA	bstB	o-Methyltransferase
btmC	bmbB	bstC	Radical SAM methyltransferase
btmD	bmbC	bstA	Precursor peptide
btmE	bmbD	bstD	YcaO-domain
btmF	bmbE	bstE	YcaO-domain
btmG	bmbF	bstF	Radical SAM methyltransferase
btmH	bmbG	bstG	α/β Hydrolase
btmI	bmbH	bstH	Metallo-dependent hydrolase
btmJ	bmbI	bstI	Cytochrome P450
btmK	bmbJ	bstJ	Radical SAM methyltransferase
btmL	bmbR		Transcriptional regulator
btmM	bmbK		M17 aminopeptidase

A biosynthetic pathway has been hypothesized based on proposed gene functions. btmM, with homology to Zn+2 aminopeptidases, is predicted to cleave the N-terminal methionine residue, which is not present in the bottromycin final product. btmE and btmF both contain YcaO-like domains. It is believed that one Although it is unclear which enzyme is responsible for which step, it is hypothesized that one catalyzes macrocyclic amidine formation while the other catalyzes thiazoline formation. btmJ, encoding an enzyme with cytochrome P450 homology, may oxidize the thiazoline to the thiazole. btmH or btmI both have homology to hydrolytic enzymes may catalyze follower peptide hydrolysis. An alternative proposed role for btmH or btmI is to function as a cyclodehydratase in macrocyclization. Gene deletion studies failed to elucidate the function of other proteins within the cluster.