Discovery and optimization of a new class of pyruvate kinase inhibitors as potential therapeutics for the treatment of methicillin-resistant Staphylococcus aureus infections

Abstract

A novel series of bis-indoles derived from naturally occurring marine alkaloid 4 were synthesized and evaluated as inhibitors of methicillin-resistant Staphylococcus aureus (MRSA) pyruvate kinase (PK). PK is not only critical for bacterial survival which would make it a target for development of novel antibiotics, but it is reported to be one of the most highly connected ‘hub proteins’ in MRSA, and thus should be very sensitive to mutations and making it difficult for the bacteria to develop resistance. From the co-crystal structure of cis-3–4-dihydrohamacanthin B (4) bound to S. aureus PK we were able to identify the pharmacophore needed for activity. Consequently, we prepared simple direct linked bis-indoles such as 10b that have similar anti-MRSA activity as compound 4. Structure–activity relationship (SAR) studies were carried out on 10b and led us to discover more potent compounds such as 10c, 10d, 10k and 10m with enzyme inhibiting activities in the low nanomolar range that effectively inhibited the bacteria growth in culture with minimum inhibitory concentrations (MIC) for MRSA as low as 0.5 μg/ml. Some potent PK inhibitors, such as 10b, exhibited attenuated antibacterial activity and were found to be substrates for an efflux mechanism in S. aureus. Studies comparing a wild type S. aureus with a construct (S. aureus LAC Δpyk::ErmR) that lacks PK activity confirmed that bactericidal activity of 10d was PK-dependant.

The Manganese-Dependent Pyruvate Kinase PykM Is Required for Wild-Type Glucose Utilization by Brucella abortus 2308 and Its Virulence in C57BL/6 Mice

“…These findings also support the proposition put forth by Zúñiga-Ripa et al (27) that Brucella strains rely on the simultaneous catabolism of carbohydrates (e.g., glucose) and amino acids (e.g., gluconeogenic substrates) to support their intracellular replication in mammalian hosts. From a practical perspective, the independent roles that PykM and PpdK play in the virulence of B. abortus 2308 make them both attractive targets for the development of chemotherapeutic agents, and in fact, preliminary studies have shown that some of the bis-indole class of synthetic pyruvate kinase inhibitors (37) To the authors' knowledge, the Bradyrhizobium and Brucella PykM proteins are the only members of this class of pyruvate kinases that have been examined. However, the observation that neither of these enzymes is allosterically regulated by fructose-1,6bisphosphate (FBP) or AMP is notable.…”

Alkaloids: An overview of their antibacterial, antibiotic-enhancing and antivirulence activities

“…Efforts to improve alkaloid activity through synthetic modifications have been successful when using indole, isoquinoline, pyrrole, and thiazole alkaloids as scaffolds. In the indole class, a β-carboline dimer (NCD9; Supplementary Table 1) and simple indole dimer (5,6,6'-tribromo-1H,1'H-2,2'-biindole) have been synthesised with respective MICs of 0.1-4.0 µg/mL [83] and 0.5 µg/mL [84] against Grampositive pathogens. Also, a manzamine A derivative has been produced (8-n-hexamidomanzamine A)…”

Synthesis and MRSA PK inhibitory activity of thiazole containing deoxytopsentin analogues

“…We shed new light on known syntheses of -bromo-1-(1H-indol-3-yl)-ethanones (15)(16)(17)(18) and indolyl-3-carbonylnitriles (27)(28)(29)(30) and in the process have gained new mechanistic insight into these useful transformations. Finally, we have confirmed the pivotal contribution of the piperazine-2-one and imidazole rings to the MRSA PK inhibition of cis-3,4-dihydrohamacanthin B and bromodeoxytopsentin respectively.…”

“…11 Recently a series of novel halogenated bisindoles were found to potently inhibit MRSA PK highlighting the importance of the bisindole scaffold to the pharmacophore. 15 X-ray analysis of 1 bound to MRSA PK indicated that this compound was located in a symmetrical hydrophobic binding pocket located at the small interface of the MRSA PK homotetramer, wedged between two prominent aromatic histidine (HIS365) residues (Figure 1). 11 From the potent inhibition (16 and 60 nM) of MRSA PK observed for both the piperazine-2-none and imidazole containing bisindoles 1 and 2 respectively, 11 we decided to extend the structure activity relationship study of these bisindole alkaloids, through bioisoteric replacement of the imidazole ring of 2 with a thiazole ring, in which a hydrogen bond accepting sulfur atom replaced the hydrogen bond donor (NH) present in both the imidazole and piperazine rings.…”