Sialic Acid Derivatives Inhibit SiaT Transporters and Delay Bacterial Growth

Abstract

Antibiotic resistance is a major worldwide concern, and new drugs with mechanistically novel modes of action are urgently needed. Here, we report the structure-based drug design, synthesis, and evaluation in vitro and in cellular systems of sialic acid derivatives able to inhibit the bacterial sialic acid symporter SiaT. We designed and synthesized 21 sialic acid derivatives and screened their affinity for SiaT by a thermal shift assay and elucidated the inhibitory mechanism through binding thermodynamics, computational methods, and inhibitory kinetic studies. The most potent compounds, which have a 180-fold higher affinity compared to the natural substrate, were tested in bacterial growth assays and indicate bacterial growth delay in methicillin-resistant Staphylococcus aureus . This study represents the first example and a promising lead in developing sialic acid uptake inhibitors as novel antibacterial agents.

Sialic Acid 4‐N‐Piperazine and Piperidine Derivatives Bind with High Affinity to the P. mirabilis Sialic Acid Sodium Solute Symporter

“…From a thermodynamic perspective, the affinity increase seems to be driven by an increase in the entropic component. We have previously observed a similar trend and we believe that the large entropic gain is indicative of an entropy‐enthalpy transduction (EET) [7,28] …”

“…The complex for the simulations was constructed by placing 6 c with its Neu5Ac part identically positioned as Neu5Ac in the x‐ray structure of Neu5Ac in complex with the outward open Pm SiaT (pdb id 5NV9). The molecular dynamic simulation was performed as described [7] . B) Overlay of the MD simulation 90 ns snapshots of compound 6 c and the previously published 3,5‐dibromobenyl ether [7] .…”

“…Thus, molecular mimicry favours bacterial growth and infectivity [6] . We have recently developed the first example of bacterial sialic acid uptake inhibition by targeting the SiaT sodium solute symporter (SSS) from Proteus mirabilis ( Pm SiaT) and Staphylococcus aureus ( Sa SiaT) [7] . Neu5Ac 4‐ O ‐benzyl derivatives with nanomolar affinity were capable of blocking the SiaT from the two different bacterial strains in a competitive mode, as shown by a proteoliposome uptake assay.…”

“… [23] We anticipated this procedure to be efficient at introducing cyclic secondary amines, specifically piperidine and piperazine at C4 of sialic acid. Piperidines and piperazines possess rigid structures that could restrain the position of the scaffold at C4 and possibly increase interactions with the hydrophobic residues of the so called hydrophobic gate, formed, among others, by Phe78, Phe243, Phe458 and Phe459 (Figure 1b) [7,24] …”

“…[19][20] H. ducreyi is a pathogenic bacterium associated with chancroid, a sexually transmitted disease in developing countries. [21] Based on the discovery that 4-O-benzyl ethers of sialic acid inhibit PmSiaT and SaSiaT, [7] investigations of novel structural scaffolds at C4 of sialic acid emerged as an attractive strategy. A procedure described by Ye et al, and further developed by us, [22] enables the introduction of cyclic secondary amines at C4 in a single step from commonly employed intermediate 1 (Scheme 1).…”