Asymmetric synthesis of BB-3497--a potent peptide deformylase inhibitor

Structural Insights into Antibacterial Payload Release from Gold Nanoparticles Bound to E. coli Peptide Deformylase

The lack of new antibiotics and the rapidly rising number of pathogens resistant to antibiotics pose a serious problem to mankind. In bacteria, the cell membrane provides the first line of defence to antibiotics by preventing them from reaching their molecular target. To overcome this entrance barrier, it has been suggested[1] that small Gold-Nanoparticles (AuNP) could possibly function as drug delivery systems for antibiotic ligands. Using actinonin-based ligands, we provide here proof-of-principle of AuNP functionalisation, the capability to bind and inhibit the target protein of the ligand, and the possibility to selectively release the antimicrobial payload. To this end, we successfully synthesised AuNP coated with thio-functionalised actinonin and a derivative. Interactions between 15N-enriched His-peptide deformylase 1-147 from E. coli (His-ecPDF 1-147) and compound-coated AuNP were investigated via 2D 1H-15N-HSQC NMR spectra proving the direct binding to His-ecPDF 1-147. More importantly by adding dithiothreitol (DTT), we show that the derivative is successfully released from AuNPs while still bound to His-ecPDF 1-147. Our findings indicate that AuNP-conjugated ligands can address and bind intracellular target proteins. The system introduced here presents a new delivery platform for antibiotics and allows for the easy optimisation of ligand coated AuNPs.

Ribosomal Synthesis of Macrocyclic Peptides with β2- and β2,3-Homo-Amino Acids for the Development of Natural Product-Like Combinatorial Libraries

The development of large, natural-product-like, combinatorial macrocyclic peptide libraries is essential in the quest to develop therapeutics for "undruggable" cellular targets. Herein we report the ribosomal synthesis of macrocyclic peptides containing one or more β²-homo-amino acids (β²haa) to enable their incorporation into mRNA display-based selection libraries. We confirmed the compatibility of 14 β²-homo-amino acids, (S)- and (R)-stereochemistry, for single incorporation into a macrocyclic peptide with low to high translation efficiency. Interestingly, N-methylation of the backbone amide of β²haa prevented the incorporation of this amino acid subclass by the ribosome. Additionally, we designed and incorporated several α,β-disubstituted β^2,3-homo-amino acids (β^2,3haa) with different R-groups on the α- and β-carbons of the same amino acid. Incorporation of these β^2,3haa enables increased diversity in a single position of a macrocyclic peptide without significantly increasing the overall molecular weight, which is an important consideration for passive cell permeability. We also successfully incorporated multiple (S)-β²hAla into a single macrocycle with other non-proteinogenic amino acids, confirming that this class of β-amino acid is suitable for development of large scale macrocyclic peptide libraries.

SuperQuat chiral auxiliaries: design, synthesis, and utility

The design, synthesis and outline of some of the most common synthetic applications of the SuperQuat (4-substituted 5,5-dimethyloxazolidine-2-one) family of chiral auxiliaries, developed to address the shortcomings of the Evans (4-substituted oxazolidin-2-one) family of chiral auxiliaries, are presented.

Synthesis and bioactivity of antitubercular peptides and peptidomimetics: an update

This mini-review provides an update on the synthesis and bioactivity of peptides and peptidomimetics that exhibit very potent antitubercular activity.

Highly efficient synthesis of heterocyclic and alicyclic β2-amino acid derivatives by catalytic asymmetric hydrogenation

A valuable class of new heterocyclic and alicyclic prochiral α-aminomethylacrylates has been conveniently synthesized through a three-step transformation involving a Baylis-Hillman reaction, O-acetylation, and a subsequent allylic amination. The corresponding novel β(2)-amino acid derivatives were prepared with excellent enantioselectivities and high yields by catalytic asymmetric hydrogenation using the catalyst rhodium(Et-Duphos) (Et-Duphos = 2',5',2'',5''-tetraethyl-1,2-bis(phospholanyl)benzene)) under mild reaction conditions (up to 99 % ee and S/C = 1000). The influence of the substrate on the enantioselectivity and reactivity is investigated, and the most suitable substrate configuration for the highly efficient enantioselective hydrogenation of β-substituted α-aminomethylacrylates under the Rh-Duphos system is reported. The current protocol provides a very practical, facile, and scalable method for the preparation of heterocyclic and alicyclic β(2)-amino acids and their derivatives.

Peptide deformylase inhibitors of Mycobacterium tuberculosis: synthesis, structural investigations, and biological results

Bacterial peptide deformylase (PDF) belongs to a subfamily of metalloproteases catalyzing the removal of the N-terminal formyl group from newly synthesized proteins. We report the synthesis and biological activity of highly potent inhibitors of Mycobacterium tuberculosis (Mtb) PDF enzyme as well as the first X-ray crystal structure of Mtb PDF. Structure-activity relationship and crystallographic data clarified the structural requirements for high enzyme potency and cell based potency. Activities against single and multi-drug-resistant Mtb strains are also reported.

Enantioselective hydrogenation of alpha-aminomethylacrylates containing a free NH group for the synthesis of beta-amino acid derivatives

We describe highly enantioselective synthesis of beta-amino acid derivatives (1a-c) using asymmetric hydrogenation of alpha-aminomethylacrylates (2a-c), which contain a free basic N H group, as the key step. The alpha-aminomethylacrylates (2a-c) were prepared using the Baylis-Hillman reaction of an appropriate aldehyde with methyl acrylate followed by acetylation of the resulting allylic alcohols (4a-b) and S(N)2'-type amination of the allylic acetates (3a-b).

Asymmetric synthesis of β2-amino acids: 2-substituted-3-aminopropanoic acids from N-acryloyl SuperQuat derivatives

Conjugate addition of lithium dibenzylamide to (S)-N(3)-acryloyl-4-isopropyl-5,5-dimethyloxazolidin-2-one (derived from l-valine) and alkylation of the resultant lithium beta-amino enolate provides, after deprotection, a range of (S)-2-alkyl-3-aminopropanoic acids in good yield and high ee. Alternatively, via a complementary pathway, conjugate addition of a range of secondary lithium amides to (S)-N(3)-(2'-alkylacryloyl)-4-isopropyl-5,5-dimethyloxazolidin-2-ones, diastereoselective protonation with 2-pyridone, and subsequent deprotection furnishes a range of (R)-2-alkyl- and (R)-2-aryl-3-aminopropanoic acids in good yield and high ee. Additionally, the boron-mediated aldol reaction of beta-amino N-acyl oxazolidinones is a highly diastereoselective method for the synthesis of a range of beta-amino-beta'-hydroxy N-acyl oxazolidinones.

Peptide deformylase inhibitors with activity against respiratory tract pathogens

A series of analogues of the peptide deformylase (PDF) inhibitor BB-3497 where the P3' amide bond was replaced with a ketone functionality is described. The in vitro antibacterial profiling of these compounds revealed that they demonstrate activity against pathogens associated with respiratory tract infections.

Structure-activity relationships of the peptide deformylase inhibitor BB-3497: modification of the methylene spacer and the P1' side chain

Structural modifications to the peptide deformylase inhibitor BB-3497 are described. In this paper, we describe the initial SAR around this lead for modifications to the methylene spacer and the P1' side chain. Enzyme inhibition and antibacterial activity data revealed that the optimum distance between the N-formyl hydroxylamine metal binding group and the P1' side chain is one unsubstituted methylene unit. Additionally, lipophilic P1' side chains that closely mimic the methionine residue in the substrate provided compounds with the best microbiological profile.

Structure--activity relationships of the peptide deformylase inhibitor BB-3497: modification of the P2' and P3' side chains

Structural modifications to the peptide deformylase inhibitor BB-3497 are described. In this paper, we describe the initial SAR around this lead for modifications to both the P2' and P3' side chains. Enzyme inhibition and antibacterial activity data revealed that a variety of substituents are tolerated at the P2' and P3' positions of the inhibitor backbone. The data from this study highlights the potential for modification at the P2' and P3' positions to optimise the physicochemical properties.

Structure-activity relationships of the peptide deformylase inhibitor BB-3497: modification of the metal binding group

A series of analogues of the potent peptide deformylase (PDF) inhibitor BB-3497 containing alternative metal binding groups was synthesised. Enzyme inhibition and antibacterial activity data for these compounds revealed that the bidentate hydroxamic acid and N-formyl hydroxylamine structural motifs represent the optimum chelating groups on the pseudopeptidic BB-3497 backbone.