Optimization of LpxC Inhibitor Lead Compounds Focusing on Efficacy and Formulation for High Dose Intravenous Administration

Unrealized targets in the discovery of antibiotics for Gram-negative bacterial infections

Advances in areas that include genomics, systems biology, protein structure determination and artificial intelligence provide new opportunities for target-based antibacterial drug discovery. The selection of a 'good' new target for direct-acting antibacterial compounds is the first decision, for which multiple criteria must be explored, integrated and re-evaluated as drug discovery programmes progress. Criteria include essentiality of the target for bacterial survival, its conservation across different strains of the same species, bacterial species and growth conditions (which determines the spectrum of activity of a potential antibiotic) and the level of homology with human genes (which influences the potential for selective inhibition). Additionally, a bacterial target should have the potential to bind to drug-like molecules, and its subcellular location will govern the need for inhibitors to penetrate one or two bacterial membranes, which is a key challenge in targeting Gram-negative bacteria. The risk of the emergence of target-based drug resistance for drugs with single targets also requires consideration. This Review describes promising but as-yet-unrealized targets for antibacterial drugs against Gram-negative bacteria and examples of cognate inhibitors, and highlights lessons learned from past drug discovery programmes.

Bacterial Zinc Metalloenzyme Inhibitors: Recent Advances and Future Perspectives

Human deaths caused by Gram-negative bacteria keep rising due to the multidrug resistance (MDR) phenomenon. Therefore, it is a priority to develop novel antibiotics with different mechanisms of action. Several bacterial zinc metalloenzymes are becoming attractive targets since they do not show any similarities with the human endogenous zinc-metalloproteinases. In the last decades, there has been an increasing interest from both industry and academia in developing new inhibitors against those enzymes involved in lipid A biosynthesis, and bacteria nutrition and sporulation, e.g., UDP-[3-O-(R)-3-hydroxymyristoyl]-N-acetylglucosamine deacetylase (LpxC), thermolysin (TLN), and pseudolysin (PLN). Nevertheless, targeting these bacterial enzymes is harder than expected and the lack of good clinical candidates suggests that more effort is needed. This review gives an overview of bacterial zinc metalloenzyme inhibitors that have been synthesized so far, highlighting the structural features essential for inhibitory activity and the structure-activity relationships. Our discussion may stimulate and help further studies on bacterial zinc metalloenzyme inhibitors as possible novel antibacterial drugs.

LpxC (UDP-3-O-(R-3-hydroxymyristoyl)-N-acetylglucosamine deacetylase) inhibitors: A long path explored for potent drug design

Microbial infections are becoming resistant to traditional antibiotics. As novel resistance mechanisms are developed and disseminated across the world, our ability to treat the most common infectious diseases is becoming increasingly compromised. As existing antibiotics are losing their effectiveness, especially treatment of bacterial infections, is difficult. In order to combat this issue, it is of utmost importance to identify novel pharmacological targets or antibiotics. LpxC, a zinc-dependent metalloamidase that catalyzes the committed step in the biosynthesis of lipid A (endotoxin) in bacteria, is a prime candidate for drug/therapeutic target. So far, the rate-limiting metallo-amidase LpxC has been the most-targeted macromolecule in the Raetz pathway. This is because it is important for the growth of these bacterial infections. This review showcases on the research done to develop efficient drugs in this area before and after the 2015.

Small molecule LpxC inhibitors against gram-negative bacteria: Advances and future perspectives

Uridine diphosphate-3-O-(hydroxymyristoyl)-N-acetylglucosamine deacetylase (LpxC) is a metalloenzyme with zinc ions as cofactors and is a key enzyme in the essential structural outer membrane lipid A synthesis commitment step of gram-negative bacteria. As LpxC is extremely homologous among different Gram-negative bacteria, it is conserved in almost all gram-negative bacteria, which makes LpxC a promising target. LpxC inhibitors have been reported extensively in recent years, such as PF-5081090 and CHIR-090 were found to have broad-spectrum antibiotic activity against P. aeruginosa and E. coli. They are mainly classified into hydroxamate inhibitors and non-hydroxamate inhibitors based on their structure, but no LpxC inhibitors have been marketed due to safety and activity issues. This review, therefore, focuses on small molecule inhibitors of LpxC against gram-negative pathogenic bacteria and covers recent advances in LpxC inhibitors, focusing on their structural optimization process, structure-activity relationships, and future directions, with the aim of providing ideas for the development of LpxC inhibitors and clinical research.

Targeting LPS biosynthesis and transport in gram-negative bacteria in the era of multi-drug resistance

Gram-negative bacteria pose a major threat to human health in an era fraught with multi-drug resistant bacterial infections. Despite extensive drug discovery campaigns over the past decades, no new antibiotic target class effective against gram-negative bacteria has become available to patients since the advent of the carbapenems in 1985. Antibiotic discovery efforts against gram-negative bacteria have been hampered by limited intracellular accumulation of xenobiotics, in large part due to the impermeable cell envelope comprising lipopolysaccharide (LPS) in the outer leaflet of the outer membrane, as well as a panoply of efflux pumps. The biosynthesis and transport of LPS are essential to the viability and virulence of most gram-negative bacteria. Thus, both LPS biosynthesis and transport are attractive pathways to target therapeutically. In this review, we summarize the LPS biosynthesis and transport pathways and discuss efforts to find small molecule inhibitors against targets within these pathways.

α-Tertiary Propargylamine Synthesis via KA2-Type Coupling Reactions under Solvent-Free CuI-Zeolite Catalysis

The potential of copper(I)-zeolite catalysis was evaluated in the three-component KA²-coupling mediated synthesis of α-tertiary propargylamines. Our archetypal copper(I)-doped zeolite Cu^I-USY proved to be efficient under ligand- and solvent-free conditions at 80 °C. Usable up to four times, this catalytic material enables the coupling of diverse ketones, alkynes, and amines with a broad functional group tolerance. A decarboxylative and a desilylative version, respectively, involving an alkynoic acid and trimethylsilylacetylene as alkyne surrogates, was also set up to bypass selectivity issues and/or to access α-tertiary propargylamines that are unattainable under standard KA² conditions. Interestingly, the KA²-type coupling reactions were successfully linked to other Cu^I-catalyzed reactions, thus resulting in sequential one-pot processes under full Cu^I-USY catalysis.

Diastereoselective Synthesis of Terminal Bromo-Substituted Propargylamines via Generation of Lithium Bromoacetylide and Addition to Chiral N-tert-Butanesulfinyl Aldimines

The stereoselective synthesis of terminal bromo-substituted propargylamines via in situ generation of lithium bromoacetylide from 1,2-dibromoethene and addition to Ellman chiral N-tert-butanesulfinyl aldimines is reported. Modest to good yields (43-85%) and diastereoselectivity (dr = 3:1 to >20:1) were achieved for a range of aryl, heteroaryl, alkyl, and α,β-unsaturated substrates. Terminal bromo-substituted propargylamines prepared via this method can be directly used in the frequently employed Cadiot-Chodkiewicz coupling to produce functionalized diynes. The method reported here increases the structural diversity of chiral terminal bromo-substituted propargylamines that can be readily synthesized as previous methods for the stereoselective synthesis of these compounds rely on amino acid precursors from the chiral pool.

Lipophilicity trends upon fluorination of isopropyl, cyclopropyl and 3-oxetanyl groups

A systematic comparison of lipophilicity modulations upon fluorination of isopropyl, cyclopropyl and 3-oxetanyl substituents, at a single carbon atom, is provided using directly comparable, and easily accessible model compounds. In addition, comparison with relevant linear chain derivatives is provided, as well as lipophilicity changes occurring upon chain extension of acyclic precursors to give cyclopropyl containing compounds. For the compounds investigated, fluorination of the isopropyl substituent led to larger lipophilicity modulation compared to fluorination of the cyclopropyl substituent.

Discovery of Novel Inhibitors of LpxC Displaying Potent in Vitro Activity against Gram-Negative Bacteria

UDP-3-O-((R)-3-hydroxymyristoyl)-N-glucosamine deacetylase (LpxC) is as an attractive target for the discovery and development of novel antibacterial drugs to address the critical medical need created by multidrug resistant Gram-negative bacteria. By using a scaffold hopping approach on a known family of methylsulfone hydroxamate LpxC inhibitors, several hit series eliciting potent antibacterial activities against Enterobacteriaceae and Pseudomonas aeruginosa were identified. Subsequent hit-to-lead optimization, using cocrystal structures of inhibitors bound to Pseudomonas aeruginosa LpxC as guides, resulted in the discovery of multiple chemical series based on (i) isoindolin-1-ones, (ii) 4,5-dihydro-6H-thieno[2,3-c]pyrrol-6-ones, and (iii) 1,2-dihydro-3H-pyrrolo[1,2-c]imidazole-3-ones. Synthetic methods, antibacterial activities and relative binding affinities, as well as physicochemical properties that allowed compound prioritization are presented. Finally, in vivo properties of lead molecules which belong to the most promising pyrrolo-imidazolone series, such as 18d, are discussed.