Rufomycins or Ilamycins: Naming Clarifications and Definitive Structural Assignments

Abstract

Rufomycin and ilamycin are synonymous for the same class of cyclopeptides, currently encompassing 33 structurally characterized isolates and 9 semisynthetic derivatives. Elucidation of new structures prioritized the consolidation of the names and established the structures of four diastereoisomeric rufomycins with a 2-piperidinone, named rufomycins 4-7, including full ¹H/¹³C NMR assignments. The characteristic HSQC cross-peak for the CH-5, the hemiaminal carbon in amino acid #5, allows assignment of the stereocenters C-4 and C-5 within this ring. Semisynthetic derivatives (rufomycinSS 1, 2, and 3) were prepared from a rufomycins 4 and 6 mixture to validate the structural assignments. Based on the X-ray crystal structures of rufomycins 2 and 4, considering the NMR differences of rufomycins 7 vs 4-6 compared to rufomycinSS 1 vs 2 and 3, and taking into account that two major conformers, A and B, occur in both rufomycinSS 2 and 3, structural modeling was pursued. Collectively, this paper discusses the NMR spectroscopic differences of the stereoisomers and their possible 3D conformers and correlates these with the anti-Mycobacterium tuberculosis activity. In addition, a look at the history prioritizes names and numbering schemes for this group of antibiotics and leads to consolidated nomenclature for all currently known members, natural and semisynthetic derivatives, and serves to accommodate future discoveries.

Figure 1.

General structure of the rufomycins with consolidated numbering scheme. Individual amino acids are labeled by their NRPS loading sequence. Within each amino acid, atom labels follow IUPAC schemes.

Figure 2.

ROESY correlations within the 2-piperidinone of rufomycins 4–7 and rufomycinSS 1–3.

Figure 3.

HPLC chromatograms (RP-18; 55% ACN/H₂O, 2.8 mL/min for the anomers and their corresponding ring-opened forms (aldehyde hydrate) of rufomycins 4/5 (A) and rufomycins 6/7 (B).

Figure 4.

Putative mechanisms for the interconversion between the hemiaminal, aldehyde-amide, and (deuterated) hydrate forms of the rufomycins 4–7.

Figure 5.

¹H NMR (A) and HSQC (B) spectra of the three related LC peaks (Figure 3) of the mutarotatory rufomycins 4 and 5.

Figure 6.

¹³C NMR chemical shift differences (Δδ_C) between the anomeric compound pairs of rufomycins 4/5, 4/6, and 4/7 in selected regions. The X- and Y-axes represent the carbon number and the Δδ_C values (in ppm), respectively.

Figure 7.

¹H NMR chemical shift differences (Δδ_H) between the compound pairs of rufomycins 4/5, 4/6, and 4/7 in selected regions. The X- and Y-axes represent the proton number and Δδ_H values (in ppm), respectively.

Figure 8.

Δδ_H and Δδ_C values between conformers A and B of rufomycinSS 2 and 3 in selected regions. The X- and Y-axes represent the nuclei number and Δδ values (left Y-axis for Δδ_H and right Y-axis for Δδ_C in ppm), respectively.

Figure 9.

Plausible 3D structures for conformers A and B of rufomycinSS 2, along with selected ROESY correlations. The conformers were drawn based on reported X-ray crystallographic structures of the rufomycins, and the observed ROESY correlations were fitted into these structures.