Total Synthesis of [Ψ[C(═S)NH]Tpg⁴]Vancomycin Aglycon, [Ψ[C(═NH)NH]Tpg⁴]Vancomycin Aglycon, and Related Key Compounds: Reengineering Vancomycin for Dual d-Ala-d-Ala and d-Ala-d-Lac Binding

Abstract

The total synthesis of [Ψ[C(=S)NH]Tpg4]vancomycin aglycon (8) and its unique AgOAc-promoted single-step conversion to [Ψ[C(=NH)NH]Tpg4]vancomycin aglycon (7), conducted on a fully deprotected substrate, are disclosed. The synthetic approach not only permits access to 7, but it also allows late stage access to related residue 4 derivatives, alternative access to [Ψ[CH2NH]Tpg4]vancomycin aglycon (6) from a common late stage intermediate, and provides authentic residue 4 thioamide and amidine derivatives of the vancomycin aglycon that will facilitate ongoing efforts on their semisynthetic preparation. In addition to early stage residue 4 thioamide introduction, allowing differentiation of one of seven amide bonds central to the vancomycin core structure, the approach relied on two aromatic nucleophilic substitution reactions for formation of the 16-membered diaryl ethers in the CD/DE ring systems, an effective macrolactamization for closure of the 12-membered biaryl AB ring system, and the defined order of CD, AB, and DE ring closures. This order of ring closures follows their increasing ease of thermal atropisomer equilibration, permitting the recycling of any newly generated unnatural atropisomer under progressively milder thermal conditions where the atropoisomer stereochemistry already set is not impacted. Full details of the evaluation of 7 and 8 along with several related key synthetic compounds containing the core residue 4 amidine and thioamide modifications are reported. The binding affinity of compounds containing the residue 4 amidine with the model d-Ala-d-Ala ligand 2 was found to be only 2–3 times less than the vancomycin aglycon (5) and this binding affinity is maintained with the model d-Ala-d-Lac ligand 4, representing a nearly 600-fold increase in affinity relative to the vancomycin aglycon. Importantly, the amidines display effective dual, balanced binding affinity for both ligands (Ka 2/4 = 0.9–1.05) and they exhibit potent antimicrobial activity against VanA resistant bacteria (E. faecalis, VanA VRE) at a level accurately reflecting these binding characteristics (MIC = 0.3–0.6 µg/mL), charting a rational approach forward in the development of antibiotics for the treatment of vancomycin-resistant bacterial infections. In sharp contrast, 8 and related residue 4 thioamides failed to bind either 2 or 4 to any appreciable extent, do not exhibit antimicrobial activity, and serve to further underscore the remarkable behavior of the residue 4 amidines.

Natural Products as Platforms To Overcome Antibiotic Resistance

“…217 Here, a thioamide is introduced via treatment of precursor 260 with Lawesson’s reagent. Due to difficulties in effecting Suzuki coupling, the thioamide must be masked as the methyl thioimidate 281 .…”

Peripheral modifications of [Ψ[CH 2 NH]Tpg 4 ]vancomycin with added synergistic mechanisms of action provide durable and potent antibiotics

“…In a series of studies, we reported the first vancomycin analogs that contain changes at a key single-atom site in its target binding pocket (residue 4 carbonyl O → S, NH, H 2 ), the latter two of which were designed to directly address this underlying molecular basis of resistance to vancomycin ( Fig. 1) (43)(44)(45)(46)(47)(48)(49)(50). These rationally designed binding pocket modifications reinstated binding to the altered target D-Ala-D-Lac and maintained binding affinity for the unaltered target D-Ala-D-Ala.…”

Synthesis of bicyclic tripeptides inspired by the ABC-ring system of vancomycin through ruthenium-based cyclization chemistries

“…To evaluate if this structural resemblance correlates with binding affinity toward Ac-Lys(Ac)-D-Ala-D-Ala-OH and Ac-Lys(Ac)-D-Ala-D-Lac-OH, isothermal microcalorimetry (ITC) was performed, as shown in Table 1. 29,30 Based on these data, mimics 11a and 11b still bind Ac-Lys(Ac)-D-Ala-D-Ala-OH appreciably, considering that a large part of the 'clam' is missing, albeit at least 100-fold less compared to vancomycin. Bicycle 11b is somewhat more active than 11a, while binding toward Ac-Lys(Ac)-D-Ala-D-Lac-OH was comparable for all three receptor molecules.…”