Hydrolytic stability versus ring size in lactams: implications for the development of lactam antibiotics and other serine protease inhibitors

Thiophene-fused γ-lactams inhibit the SARS-CoV-2 main protease via reversible covalent acylation

Enzyme inhibitors working by O-acylation of nucleophilic serine residues are of immense medicinal importance, as exemplified by the β-lactam antibiotics. By contrast, inhibition of nucleophilic cysteine enzymes by S-acylation has not been widely exploited for medicinal applications. The SARS-CoV-2 main protease (Mpro) is a nucleophilic cysteine protease and a validated therapeutic target for COVID-19 treatment using small-molecule inhibitors. The clinically used Mpro inhibitors nirmatrelvir and simnotrelvir work via reversible covalent reaction of their electrophilic nitrile with the Mpro nucleophilic cysteine (Cys145). We report combined structure activity relationship and mass spectrometric studies revealing that appropriately functionalized γ-lactams can potently inhibit Mpro by reversible covalent reaction with Cys145 of Mpro. The results suggest that γ-lactams have potential as electrophilic warheads for development of covalently reacting small-molecule inhibitors of Mpro and, by implication, other nucleophilic cysteine enzymes.

Antibacterial Activity of CdTe/ZnS Quantum Dot-β Lactum Antibiotic Conjugates

β-Lactum antibiotics are broad class of antibiotics which kills bacteria by inhibiting the formation of peptidoglycan that constitutes the bacterial cell wall. The resistance that develops in bacteria for antibiotics led the scientific world to think about the future aspects for modifying the way through which antibiotics are acted on the bacteria and become lethal for them. In this consequence, the potential of latest marketed antibiotics e.g. Amoxiciline (I), ceftazidim (II) have been evaluated after being conjugated with quantum dots. The surface of quantum dots has been conjugated with antibiotics by carbodiimide coupling with the help of 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide (EDC) and N-hydroxysuccinimide (NHS) as conjugating agent between antibiotic and functionalized quantum dots. The antibacterial properties of QD-conjugated antibiotics have been determined by disc diffusion assay. The potency of QD-conjugated antibiotics has been estimated by determining their MIC50 for the selected strain of Gram-negative (Escherichia coli) and Gram-positive (Staphylococcus aureus) bacteria. Minimum inhibitory concentration study, minimum bactericidal concentration and growth pattern analysis revealed that QD-antibiotic conjugates showed slightly more prospective than pure native antibiotics against both Gram-negative (Escherichia coli) and Gram-positive (Staphylococcus aureus) bacteria.

A multiple linear regression approach to the estimation of carboxylic acid ester and lactone alkaline hydrolysis rate constants

Pesticides, pharmaceuticals, and other organic contaminants often undergo hydrolysis when released into the environment; therefore, measured or estimated hydrolysis rates are needed to assess their environmental persistence. An intuitive multiple linear regression (MLR) approach was used to develop robust QSARs for predicting base-catalyzed rate constants of carboxylic acid esters (CAEs) and lactones. We explored various combinations of independent descriptors, resulting in four primary models (two for lactones and two for CAEs), with a total of 15 and 11 parameters included in the CAE and lactone QSAR models, respectively. The most significant descriptors include pKa, electronegativity, charge density, and steric parameters. Model performance is assessed using Drug Theoretics and Cheminformatics Laboratory's DTC-QSAR tool, demonstrating high accuracy for both internal validation (r2 = 0.93 and RMSE = 0.41-0.43 for CAEs; r2 = 0.90-0.93 and RMSE = 0.38-0.46 for lactones) and external validation (r2 = 0.93 and RMSE = 0.43-0.45 for CAEs; r2 = 0.94-0.98 and RMSE = 0.33-0.41 for lactones). The developed models require only low-cost computational resources and have substantially improved performance compared to existing hydrolysis rate prediction models (HYDROWIN and SPARC).

Penicillin Derivatives Inhibit the SARS-CoV-2 Main Protease by Reaction with Its Nucleophilic Cysteine

The SARS-CoV-2 main protease (Mpro) is a medicinal chemistry target for COVID-19 treatment. Given the clinical efficacy of β-lactams as inhibitors of bacterial nucleophilic enzymes, they are of interest as inhibitors of viral nucleophilic serine and cysteine proteases. We describe the synthesis of penicillin derivatives which are potent Mpro inhibitors and investigate their mechanism of inhibition using mass spectrometric and crystallographic analyses. The results suggest that β-lactams have considerable potential as Mpro inhibitors via a mechanism involving reaction with the nucleophilic cysteine to form a stable acyl-enzyme complex as shown by crystallographic analysis. The results highlight the potential for inhibition of viral proteases employing nucleophilic catalysis by β-lactams and related acylating agents.

Dicarboxylic Acid Monoesters in β- and δ-Lactam Synthesis

A N-(2-methoxy-2-oxoethyl)-N-(phenylsulfonyl)glycine monomethyl ester of the respective dicarboxylic acid was involved in a reaction with imines promoted by acetic anhydride at an elevated temperature. Instead of the initially expected δ-lactam products of the Castagnoli–Cushman-type reaction, medicinally important 3-amino-2-azetidinones were obtained as the result of cyclization, involving a methylene group adjacent to an acid moiety. In contrast, replacing alcohol residue with hexafluoroisopropyl in the same substrate made another methylene group (adjacent to the ester moiety) more reactive to furnishing the desired δ-lactam in the Castagnoli–Cushman fashion.

ETX2514 is a broad-spectrum β-lactamase inhibitor for the treatment of drug-resistant Gram-negative bacteria including Acinetobacter baumannii

Multidrug-resistant (MDR) bacterial infections are a serious threat to public health. Among the most alarming resistance trends is the rapid rise in the number and diversity of β-lactamases, enzymes that inactivate β-lactams, a class of antibiotics that has been a therapeutic mainstay for decades. Although several new β-lactamase inhibitors have been approved or are in clinical trials, their spectra of activity do not address MDR pathogens such as Acinetobacter baumannii. This report describes the rational design and characterization of expanded-spectrum serine β-lactamase inhibitors that potently inhibit clinically relevant class A, C and D β-lactamases and penicillin-binding proteins, resulting in intrinsic antibacterial activity against Enterobacteriaceae and restoration of β-lactam activity in a broad range of MDR Gram-negative pathogens. One of the most promising combinations is sulbactam-ETX2514, whose potent antibacterial activity, in vivo efficacy against MDR A. baumannii infections and promising preclinical safety demonstrate its potential to address this significant unmet medical need.

Defeating Bacterial Resistance and Preventing Mammalian Cells Toxicity Through Rational Design of Antibiotic-Functionalized Nanoparticles

The rational synthesis of alternative materials is highly demanding due to the outbreak of infectious diseases and resistance to antibiotics. Herein, we report a tailored nanoantibiotic synthesis protocol where the antibiotic binding was optimized on the silver-silica core-shell nanoparticles surface to maximize biological responses. The obtained silver nanoparticles coated with mesoporous silica functionalized with ampicillin presented remarkable antimicrobial effects against susceptible and antibiotic-resistant Escherichia coli. In addition, these structures were not cell-death inducers and different steps of the mitotic cell cycle (prophase, anaphase and metaphase) were clearly identified. The superior biological results were attributed to a proper and tailored synthesis strategy.

The road to avibactam: the first clinically useful non-β-lactam working somewhat like a β-lactam

Avibactam, which is the first non-β-lactam β-lactamase inhibitor to be introduced for clinical use, is a broad-spectrum serine β-lactamase inhibitor with activity against class A, class C, and, some, class D β-lactamases. We provide an overview of efforts, which extend to the period soon after the discovery of the penicillins, to develop clinically useful non-β-lactam compounds as antibacterials, and, subsequently, penicillin-binding protein and β-lactamase inhibitors. Like the β-lactam inhibitors, avibactam works via a mechanism involving covalent modification of a catalytically important nucleophilic serine residue. However, unlike the β-lactam inhibitors, avibactam reacts reversibly with its β-lactamase targets. We discuss chemical factors that may account for the apparently special nature of β-lactams and related compounds as antibacterials and β-lactamase inhibitors, including with respect to resistance. Avenues for future research including non-β-lactam antibacterials acting similarly to β-lactams are discussed.

Investigations on recyclisation and hydrolysis in avibactam mediated serine β-lactamase inhibition

β-Lactams inhibit penicillin-binding proteins (PBPs) and serine β-lactamases by acylation of a nucleophilic active site serine. Avibactam is approved for clinical use in combination with ceftazidime, and is a breakthrough non β-lactam β-lactamase inhibitor also reacting via serine acylation. Molecular dynamics (MD) and quantum chemical calculations on avibactam-mediated inhibition of a clinically relevant cephalosporinase reveal that recyclisation of the avibactam derived carbamoyl complex is favoured over hydrolysis. In contrast, we show that analogous recyclisation in β-lactam mediated inhibition is disfavoured. Avibactam recyclisation is promoted by a proton shuttle, a 'structural' water protonating the nucleophilic serine, and stabilization of the negative charge developed on aminocarbonyl oxygen. The results imply the potential of calculations for distinguishing between bifurcating pathways during inhibition and in generating hypotheses for predicting resistance. The inability of β-lactams to undergo recyclisation may be an Achilles heel, but one that can be addressed by suitably functionalized reversibly binding inhibitors.

Development of new drugs for an old target: the penicillin binding proteins

The widespread use of β-lactam antibiotics has led to the worldwide appearance of drug-resistant strains. Bacteria have developed resistance to β-lactams by two main mechanisms: the production of β-lactamases, sometimes accompanied by a decrease of outer membrane permeability, and the production of low-affinity, drug resistant Penicillin Binding Proteins (PBPs). PBPs remain attractive targets for developing new antibiotic agents because they catalyse the last steps of the biosynthesis of peptidoglycan, which is unique to bacteria, and lies outside the cytoplasmic membrane. Here we summarize the “current state of the art” of non-β-lactam inhibitors of PBPs, which have being developed in an attempt to counter the emergence of β-lactam resistance. These molecules are not susceptible to hydrolysis by β-lactamases and thus present a real alternative to β-lactams. We present transition state analogs such as boronic acids, which can covalently bind to the active serine residue in the catalytic site. Molecules containing ring structures different from the β-lactam-ring like lactivicin are able to acylate the active serine residue. High throughput screening methods, in combination with virtual screening methods and structure based design, have allowed the development of new molecules. Some of these novel inhibitors are active against major pathogens, including methicillin-resistant Staphylococcus aureus (MRSA) and thus open avenues new for the discovery of novel antibiotics.

Structural basis for the interaction of lactivicins with serine beta-lactamases

Lactivicin (LTV) is a natural non-beta-lactam antibiotic that inhibits penicillin-binding proteins and serine beta-lactamases. A crystal structure of a BS3-LTV complex reveals that, as for its reaction with PBPs, LTV reacts with the nucleophilic serine and that cycloserine and lactone rings of LTV are opened. This structure, together with reported structures of PBP1b with lactivicins, provides a basis for developing improved lactivicin-based gamma-lactam antibiotics.

Ring opening at N1-C2 bond of azetidin-2-ones by a molybdenum hydroxo-carbonyl complex: evidence from a computational study

Computations on the reaction of azetidin-2-one, N-sulfonate azetidin-2-one, and 3-formylamine-N-sulfonate azetidin-2-one with [Mo(OH)(eta3-C3H5)(CO)2(N2C2H4)] were performed at the B3LYP/6-31+G(d,p) (LANL2DZ for Mo augmented by f polarization functions with exponents 1.043) taking into account solvent effects by means of the PCM-UAHF model. According to our calculations, the rate-determining energy barrier for the azetidin-2-one case, 38.0 kcal mol(-1), becomes 28.8 and 26.1 kcal mol(-1) for the N-sulfonate azetidin-2-one and 3-formylamine-N-sulfonate azetidin-2-one ones, respectively. The presence of the sulfonate group is crucial to cleave the beta-lactam N1-C2 bond by the Mo complex thanks to the interaction of the sulfonate group with the hydroxyl and bidentate ligands of the complex. This could be of interest for the synthesis of beta-amino acids and their derivatives from beta-lactams in mild conditions and low polarity solvents promoted by organometallic complexes.

Structural and mechanistic basis of penicillin-binding protein inhibition by lactivicins

Beta-lactam antibiotics, including penicillins and cephalosporins, inhibit penicillin-binding proteins (PBPs), which are essential for bacterial cell wall biogenesis. Pathogenic bacteria have evolved efficient antibiotic resistance mechanisms that, in Gram-positive bacteria, include mutations to PBPs that enable them to avoid beta-lactam inhibition. Lactivicin (LTV; 1) contains separate cycloserine and gamma-lactone rings and is the only known natural PBP inhibitor that does not contain a beta-lactam. Here we show that LTV and a more potent analog, phenoxyacetyl-LTV (PLTV; 2), are active against clinically isolated, penicillin-resistant Streptococcus pneumoniae strains. Crystallographic analyses of S. pneumoniae PBP1b reveal that LTV and PLTV inhibition involves opening of both monocyclic cycloserine and gamma-lactone rings. In PBP1b complexes, the ring-derived atoms from LTV and PLTV show a notable structural convergence with those derived from a complexed cephalosporin (cefotaxime; 3). The structures imply that derivatives of LTV will be useful in the search for new antibiotics with activity against beta-lactam-resistant bacteria.

Synthesis of Urea-Tethered Disaccharides in Water

A new method for the synthesis of urea-linked disaccharides in aqueous media has been developed. The key feature of our approach is two strained Steyermark-type gluco- and galactopyranosyl oxazolidinones. Each oxazolidinone is attached to a pyranose ring in a di-equatorial trans-annulation framework. Reaction of these oxazolidinones with 4-aminohexopyranose in water proceeded smoothly to afford the urea-tethered cellobiose and lactose analogues. The galactose-type oxazolidinone proved to be more reactive than the glucose-type, which is explained by the presence of an axial hydroxy group at C4 in the former.

Synthesis and evaluation of delta-lactams (piperazones) as elastase inhibitors

A series of monocyclic delta-lactams (piperazones) was prepared and analysed as inhibitors of porcine pancreatic elastase and human neutrophil elastase.

Design and synthesis of a novel class of constrained tricyclic pyrrolizidinone carboxylic acids as carbapenem mimics

A series of tricyclic pyrrolizidinone carboxylic acids harboring an angular methano group were synthesized as mimics of carbapenems and carbapenams. A key reaction involved a novel intramolecular cyclopropanation mediated by a trimethylstannylmethyl group and an adjacent iminium ion. Enolate chemistry on a tricyclic lactam ring unit allowed the introduction of various substituents. Further elaboration afforded tricyclic pyrrolidinone carboxylic acids, which were found to be inactive as inhibitors against a panel of bacterial strains. However, the antibacterial activity of ceftazidine was enhanced in the presence of the tricyclic analogues.

Hydrolysis in pharmaceutical formulations

This literature review presents hydrolysis of active pharmaceutical ingredients as well as the effects on dosage form stability due to hydrolysis of excipients. Mechanisms and measurement methods are discussed and recommendations for formulation stabilization are listed.

Is there stereoelectronic control in formation and cleavage of tetrahedral intermediates?

Deslongchamps' hypothesis of stereoelectronic control states that preferential cleavage of a tetrahedral intermediate occurs when a leaving group is antiperiplanar to two lone pairs. It is argued that the evidence supporting the hypothesis is suspect. An alternative explanation is that product stabilities bias the results. A more suitable test is hydrolysis of cyclic amidines and related species. Product studies show substantial cleavage of the bond that is antiperiplanar to only one lone pair and syn to the other, especially in five- and seven-membered rings. Even in the most favorable cases, six-membered rings, antiperiplanar lone pairs provide <2 kcal/mol of transition-state stabilization.