Discovery of a Novel Natural Allosteric Inhibitor That Targets NDM-1 Against Escherichia coli

Elucidation of critical chemical moieties of metallo-β-lactamase inhibitors and prioritisation of target metallo-β-lactamases

The urgent demand for effective countermeasures against metallo-β-lactamases (MBLs) necessitates development of novel metallo-β-lactamase inhibitors (MBLIs). This study is dedicated to identifying critical chemical moieties within previously developed MBLIs, and critical MBLs should serve as the target in MBLI evaluations. Using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA), a systematic literature analysis was conducted, and the NCBI RefSeq genome database was exploited to access the abundance profile and taxonomic distribution of MBLs and their variant types. Through the implementation of two distinct systematic approaches, we elucidated critical chemical moieties of MBLIs, providing pivotal information for rational drug design. We also prioritised MBLs and their variant types, highlighting the imperative need for comprehensive testing to ensure the potency and efficacy of the newly developed MBLIs. This approach contributes valuable information to advance the field of antimicrobial drug discovery.

Role of β-Lactamase Inhibitors as Potentiators in Antimicrobial Chemotherapy Targeting Gram-Negative Bacteria

Since the discovery of penicillin, β-lactam antibiotics have commonly been used to treat bacterial infections. Unfortunately, at the same time, pathogens can develop resistance to β-lactam antibiotics such as penicillins, cephalosporins, monobactams, and carbapenems by producing β-lactamases. Therefore, a combination of β-lactam antibiotics with β-lactamase inhibitors has been a promising approach to controlling β-lactam-resistant bacteria. The discovery of novel β-lactamase inhibitors (BLIs) is essential for effectively treating antibiotic-resistant bacterial infections. Therefore, this review discusses the development of innovative inhibitors meant to enhance the activity of β-lactam antibiotics. Specifically, this review describes the classification and characteristics of different classes of β-lactamases and the synergistic mechanisms of β-lactams and BLIs. In addition, we introduce potential sources of compounds for use as novel BLIs. This provides insights into overcoming current challenges in β-lactamase-producing bacteria and designing effective treatment options in combination with BLIs.

Comprehensive screening of marine metabolites against class B1 metallo-β-lactamases of Klebsiella pneumoniae using two-pronged in silico approach

The emergence of antibiotic resistance is one of the major global threats in healthcare. Metallo-β-Lactamases (MBL) are a class of enzymes in bacteria that cleave β-lactam antibiotics and confer resistance. MBLs are further divided into subclasses B1, B2 and B3. Of these, subclasses B1-MBLs (including NDM-1, VIM-2 and IMP-1) constitute the clinically prevalent lactamases conferring resistance. To date, no effective drugs are available clinically against MBLs. In this work, we aim to identify potent inhibitors for the B1 subclass of MBL from available marine metabolites in Comprehensive Marine Natural Product database through integrated in silico approaches. We have used two methods, namely, the high-throughput strategy and the pharmacophore-based strategy to identify potential inhibitors from marine metabolites. High-throughput virtual screening identified N-methyl mycosporine-Ser, which had the highest binding affinity to NDM-1. The pharmacophore-based approach based on co-crystallized ligands identified makaluvic acid and didymellamide with higher binding affinity across B1-MBLs. Taking into account of the advantage of a pharmacophore model-based approach with higher binding affinity, we conclude that both makaluvic acid and didymellamide show potential broad-spectrum effects by binding to all three B1-MBL receptors. The study also indicates the need to take multiple in silico approaches to screen and identify novel inhibitors. Together, our study reveals promising inhibitors that can be identified from marine systems.Communicated by Ramaswamy H. Sarma.

Discovering NDM-1 inhibitors using molecular substructure embeddings representations

NDM-1 (New-Delhi-Metallo-β-lactamase-1) is an enzyme developed by bacteria that is implicated in bacteria resistance to almost all known antibiotics. In this study, we deliver a new, curated NDM-1 bioactivities database, along with a set of unifying rules for managing different activity properties and inconsistencies. We define the activity classification problem in terms of Multiple Instance Learning, employing embeddings corresponding to molecular substructures and present an ensemble ranking and classification framework, relaying on a k-fold Cross Validation method employing a per fold hyper-parameter optimization procedure, showing promising generalization ability. The MIL paradigm displayed an improvement up to 45.7 %, in terms of Balanced Accuracy, in comparison to the classical Machine Learning paradigm. Moreover, we investigate different compact molecular representations, based on atomic or bi-atomic substructures. Finally, we scanned the Drugbank for strongly active compounds and we present the top-15 ranked compounds.

Small-molecule inhibitors of bacterial-producing metallo-β-lactamases: insights into their resistance mechanisms and biochemical analyses of their activities

Antibiotic resistance (AR) remains one of the major threats to the global healthcare system, which is associated with alarming morbidity and mortality rates. The defence mechanisms of Enterobacteriaceae to antibiotics occur through several pathways including the production of metallo-β-lactamases (MBLs). The carbapenemases, notably, New Delhi MBL (NDM), imipenemase (IMP), and Verona integron-encoded MBL (VIM), represent the critical MBLs implicated in AR pathogenesis and are responsible for the worst AR-related clinical conditions, but there are no approved inhibitors to date, which needs to be urgently addressed. Presently, the available antibiotics including the most active β-lactam-types are subjected to deactivation and degradation by the notorious superbug-produced enzymes. Progressively, scientists have devoted their efforts to curbing this global menace, and consequently a systematic overview on this topic can aid the timely development of effective therapeutics. In this review, diagnostic strategies for MBL strains and biochemical analyses of potent small-molecule inhibitors from experimental reports (2020-date) are overviewed. Notably, N1 and N2 from natural sources, S3-S7, S9 and S10 and S13-S16 from synthetic routes displayed the most potent broad-spectrum inhibition with ideal safety profiles. Their mechanisms of action include metal sequestration from and multi-dimensional binding to the MBL active pockets. Presently, some β-lactamase (BL)/MBL inhibitors have reached the clinical trial stage. This synopsis represents a model for future translational studies towards the discovery of effective therapeutics to overcome the challenges of AR.

β-Lactam potentiators to re-sensitize resistant pathogens: Discovery, development, clinical use and the way forward

β-lactam antibiotics are one of the most widely used and diverse classes of antimicrobial agents for treating both Gram-negative and Gram-positive bacterial infections. The β-lactam antibiotics, which include penicillins, cephalosporins, monobactams and carbapenems, exert their antibacterial activity by inhibiting the bacterial cell wall synthesis and have a global positive impact in treating serious bacterial infections. Today, β-lactam antibiotics are the most frequently prescribed antimicrobial across the globe. However, due to the widespread use and misapplication of β-lactam antibiotics in fields such as human medicine and animal agriculture, resistance to this superlative drug class has emerged in the majority of clinically important bacterial pathogens. This heightened antibiotic resistance prompted researchers to explore novel strategies to restore the activity of β-lactam antibiotics, which led to the discovery of β-lactamase inhibitors (BLIs) and other β-lactam potentiators. Although there are several successful β-lactam-β-lactamase inhibitor combinations in use, the emergence of novel resistance mechanisms and variants of β-lactamases have put the quest of new β-lactam potentiators beyond precedence. This review summarizes the success stories of β-lactamase inhibitors in use, prospective β-lactam potentiators in various phases of clinical trials and the different strategies used to identify novel β-lactam potentiators. Furthermore, this review discusses the various challenges in taking these β-lactam potentiators from bench to bedside and expounds other mechanisms that could be investigated to reduce the global antimicrobial resistance (AMR) burden.

In vitro and in silico β-lactamase inhibitory properties and phytochemical profile of Ocimum basilicum cultivated in central delta of Egypt

CONTEXT

Some studies reported the chemical content and antimicrobial properties of Ocimum basilicum L. (Lamiaceae), relevant to the ecological variations in some areas of Egypt and other countries, yet no research was conducted on the plant cultivated in the central delta region of Egypt. Also, no previous data reported on inhibition of β-lactamases by O. basilicum.

OBJECTIVE

To assess β-lactamases inhibition by O. basilicum extracts and the individual constituents.

MATERIALS AND METHODS

Dried aerial parts of O. basilicum were extracted by hydrodistillation for preparation of essential oil and by methanol for non-volatile constituents. Essential oil content and the methanol extract were analysed by GC-MS and UPLC-PDA-MS/MS, respectively. Methyl cinnamate was isolated and analysed by NMR. Broth microdilution method was used to investigate the antimicrobial against resistant clinical isolates of Escherichia coli identified by double disc synergy, combination disc tests and PCR. The most active oil content was further tested with a nitrocefin kit for β-lactamase inhibition and investigated by docking.

RESULTS

O. basilicum was found to contain methyl cinnamate as the major content of the essential oil. More interestingly, methyl cinnamate inhibited ESBL β-lactamases of the type CTX-M. The in vitro IC₅₀ using nitrocefin kit was 11.6 µg/mL vs. 8.1 µg/mL for clavulanic acid as a standard β-lactamase inhibitor.

DISCUSSION AND CONCLUSIONS

This is the first study to report the inhibitory activity of O. basilicum oil and methyl cinnamate against β-lactamase-producing bacteria. The results indicate that methyl cinnamate could be a potential alternative for β-lactamase inhibition.

Towards combating antibiotic resistance by exploring the quantitative structure-activity relationship of NDM-1 inhibitors

The emergence of New Delhi metallo-beta-lactamase-1 (NDM-1) has conferred enteric bacteria resistance to almost all beta-lactam antibiotics. Its capability of horizontal transfer through plasmids, amongst humans, animal reservoirs and the environment, has added up to the totality of antimicrobial resistance control, animal husbandry and food safety. Thus far, there have been no effective drugs for neutralizing NDM-1. This study explores the structure-activity relationship of NDM-1 inhibitors. IC₅₀ values of NDM-1 inhibitors were compiled from both the ChEMBL database and literature. After curation, a final set of 686 inhibitors were used for machine learning model building using the random forest algorithm against 12 sets of molecular fingerprints. Benchmark results indicated that the KlekotaRothCount fingerprint provided the best overall performance with an accuracy of 0.978 and 0.778 for the training and testing set, respectively. Model interpretation revealed that nitrogen-containing features (KRFPC 4080, KRFPC 3882, KRFPC 677, KRFPC 3608, KRFPC 3750, KRFPC 4287 and KRFPC 3943), sulfur-containing substructures (KRFPC 2855 and KRFPC 4843), aromatic features (KRFPC 1566, KRFPC 1564, KRFPC 1642, KRFPC 3608, KRFPC 4287 and KRFPC 3943), carbonyl features (KRFPC 1193 and KRFPC 3025), aliphatic features (KRFPC 2975, KRFPC 297, KRFPC 3224 and KRFPC 669) are features contributing to NDM-1 inhibitory activity. It is anticipated that findings from this study would help facilitate the drug discovery of NDM-1 inhibitors by providing guidelines for further lead optimization.

The Synthesis of Triazolium Salts as Antifungal Agents: A Biological and In Silico Evaluation

The control of fungal pathogens is increasingly difficult due to the limited number of effective drugs available for antifungal therapy. In addition, both humans and fungi are eukaryotic organisms; antifungal drugs may have significant toxicity due to the inhibition of related human targets. Furthermore, another problem is increased incidents of fungal resistance to azoles, such as fluconazole, ketoconazole, voriconazole, etc. Thus, the interest in developing new azoles with an extended spectrum of activity still attracts the interest of the scientific community. Herein, we report the synthesis of a series of triazolium salts, an evaluation of their antifungal activity, and docking studies. Ketoconazole and bifonazole were used as reference drugs. All compounds showed good antifungal activity with MIC/MFC in the range of 0.0003 to 0.2/0.0006–0.4 mg/mL. Compound 19 exhibited the best activity among all tested with MIC/MFC in the range of 0.009 to 0.037 mg/mL and 0.0125–0.05 mg/mL, respectively. All compounds appeared to be more potent than both reference drugs. The docking studies are in accordance with experimental results.

Discovery of an Effective Small-Molecule Allosteric Inhibitor of New Delhi Metallo-β-lactamase (NDM)

To identify novel inhibitors of the carbapenemase New Delhi metallo-β-lactamase (NDM) as possible therapeutic compounds, we conducted a high-throughput screen of a 43,358-compound library. One of these compounds, a 2-quinazolinone linked through a diacylhydrazine to a phenyl ring (QDP-1) (IC₅₀ = 7.9 ± 0.5 μM), was characterized as a slow-binding reversible inhibitor (K_i^app = 4 ± 2 μM) with a noncompetitive mode of inhibition in which substrate and inhibitor enhance each other's binding affinity. These studies, along with differential scanning fluorimetry, zinc quantitation, and selectivity studies, support an allosteric mechanism of inhibition. Cotreatment with QDP-1 effectively lowers minimum inhibitory concentrations of carbapenems for a panel of resistant Escherichia coli and Klebsiella pneumoniae clinical isolates expressing NDM-1 but not for those expressing only serine carbapenemases. QDP-1 represents a novel allosteric approach for NDM drug development for potential use alone or with other NDM inhibitors to counter carbapenem resistance in enterobacterales.

Mulberrin inhibits Botrytis cinerea for strawberry storage by interfering with the bioactivity of 14α-demethylase (CYP51)

Currently, chemical agents hold great promise in preventing and combating Botrytis cinerea. However, the antifungal mechanism of some agents for B. cinerea remains rather vague, imposing restrictions on the research and development of novel antifungal inhibitors. In this work, we discovered that mulberrin (MBN), a natural compound from the root bark of Ramulus Mori, with an IC₅₀ of 1.38 μM together, demonstrated marked anti-14α-demethylase (CYP51) activity through high throughput virtual screening and in vitro bioactivity assay. The computational biology results demonstrated that MBN and its derivatives were bound to the catalytic activity region of CYP51, but only MBN could form a strong π-cation interaction with the Fe ion of heme in CYP51 via the 2-methylpent-2-ene moiety at atom C9. MBN had a stronger binding free energy than the other three compounds with CYP51, implying that the 2-methylpent-2-ene moiety at atom C9 is a critical pharmacophore for CYP51 inhibitors. Subsequently, through an antifungal test, MBN demonstrated excellent anti-B. cinerea activity by inhibiting CYP51 activity. The EC₅₀ values of MBN toward hyphal growth and spore germination in B. cinerea were 17.27 and 9.56 μg mL^-1, respectively. The bioactivity loss of CYP51 by direct interaction with MBN induced the increase of cell membrane permeability, membrane destruction, and cell death. Meanwhile, in the B. cinerea infection model, MBN significantly prolonged the preservation of strawberries by preventing B. cinerea from infecting strawberries and could be used as a potential natural preserving agent for storing fruits.