Evaluation of novel compounds as anti-bacterial or anti-virulence agents

Antimicrobial resistance is a global threat, leading to an alarming increase in the prevalence of bacterial infections that can no longer be treated with available antibiotics. The World Health Organization estimates that by 2050 up to 10 million deaths per year could be associated with antimicrobial resistance, which would equal the annual number of cancer deaths worldwide. To overcome this emerging crisis, novel anti-bacterial compounds are urgently needed. There are two possible approaches in the fight against bacterial infections: a) targeting structures within bacterial cells, similar to existing antibiotics; and/or b) targeting virulence factors rather than bacterial growth. Here, for the first time, we provide a comprehensive overview of the key steps in the evaluation of potential new anti-bacterial and/or anti-virulence compounds. The methods described in this review include: a) in silico methods for the evaluation of novel compounds; b) anti-bacterial assays (MIC, MBC, Time-kill); b) anti-virulence assays (anti-biofilm, anti-quorum sensing, anti-adhesion); and c) evaluation of safety aspects (cytotoxicity assay and Ames test). Overall, we provide a detailed description of the methods that are an essential tool for chemists, computational chemists, microbiologists, and toxicologists in the evaluation of potential novel antimicrobial compounds. These methods are cost-effective and have high predictive value. They are widely used in preclinical studies to identify new molecular candidates, for further investigation in animal and human trials

In silico identification, synthesis and biological evaluation of novel tetrazole inhibitors of MurB

In the context of antibacterial drug discovery resurgence, novel therapeutic targets and new compounds with alternative mechanisms of action are of paramount importance. We focused on UDP-N- acetylenolpyruvylglucosamine reductase (i.e. MurB), an underexploited target enzyme that is involved in early steps of bacterial peptidoglycan biosynthesis. On the basis of the recently reported crystal structure of MurB in complex with NADP+ , a pharmacopohore model was generated and used in a virtual screening campaign with combined structure-based and ligand-based approaches. In order to explore chemical space around hit compounds, further similarity search and organic synthesis was employed to obtain several compounds with micromolar IC50 values on MurB. The best inhibitors in the reported series of 5-substituted tetrazol-2-yl acetamides were compounds 13, 26 and 30 with IC50 values of 34, 28 and 25 µM, respectively. None of the reported compounds possessed in vitro antimicrobial activity against S. aureus and E. coli

Amide containing NBTI antibacterials with reduced hERG inhibition, retained antimicrobial activity against gram-positive bacteria and in vivo efficacy

Novel bacterial topoisomerase inhibitors (NBTIs) are new promising antimicrobials for the treatment of multidrug-resistant bacterial infections. In recent years, many new NBTIs have been discovered, however most of them struggle with the same issue - the balance between antibacterial activity and hERG-related toxicity. We started a new campaign by optimizing the previous series of NBTIs, followed by the design and synthesis of a new, amide-containing focused NBTI library to reduce hERG inhibition and maintain antibacterial activity against Gram-positive bacteria, including methicillin-resistant Staphylococcus aureus (MRSA). This optimization strategy yielded the lead compound 12 that exhibits potent antibacterial activity against Gram-positive bacteria, reduced hERG inhibition, no cardiotoxicity in zebrafish model, and a favorable in vivo efficacy in a neutropenic murine thigh infection model of MRSA infection

Development of benzodioxane-benzamides inhibitors of FtsZ as potent broad-spectrum antimicrobial agents

1 p.-1 graph. abst.Antimicrobial resistance is a serious worldwide health threat. The identification of novel potential antibiotic targets is one of the ways to slow down its worsening. FtsZ, one of the bacterial cell division machinery proteins, emerged in the last decade for its crucial role in bacterial replication and viability [1]. Benzamide compounds are the most studied and promising FtsZ inhibitors developed so far, due to their high anti-staphylococcal activity, their low cytotoxicity and the interesting results obtained in association with other antibiotic classes [2]. Along these lines, here we report our recent findings on a class of FtsZ inhibitors, containing a 2,6-difluoro-benzamide scaffold linked to a hydrophobically substituted 1,4-benzodioxane ring [3-6]. We firstly validated a robust computational model, which drove us to identify the structural features the 1,4-benzodioxane moiety and the alkoxy linker should possess, in order to perfectly fit the FtsZ binding pocket. We thus developed several interesting compounds, having submicromolar antibacterial activities and showing comparable inhibitory activities towards both Gram-positive (Staphylococcus aureus and Bacillus subtilis) [3,5] and Gram-negative (Escherichia coli) FtsZ. Nevertheless, these derivatives proved to be substrates of E. coli efflux pump AcrAB, thus affecting their potencies [4]. These surprising and novel results confirmed how a single molecule can target both species while maintaining potent antimicrobial activity. We set-up and performed different assays, to firstly validate FtsZ as the target of our class of compounds. Morphometric analysis and fluorescence microscopy let us evaluate the typical alterations of cell division and FtsZ inhibition, as well as the effects on FtsZ localization [6].Moreover, we took advantages of fluorescence anisotropy to investigate and assess the impact of our derivatives on the kinetics of disassembly of the GTP triggered FtsZ polymers. Furthermore, we used confocal microscopy, to evaluate the shape and the dimension of FtsZ polymers, when in presence or in absence of our compounds in solutions containing crowding agents mimicking the crowded environment in the cytoplasm.Peer reviewe

Design and Preparation of Antimicrobial Agents

Improper use and misuse of antibacterial agents have led to the emergence of (multi)resistant bacterial strains, which are 1 of the top-10 public-health threats, according to the WHO [...

Application of the N-dibenzyl protective group in the preparation of β-lactam pseudopeptides

Despite the great importance of β-lactam antibiotics, there is still a limited number of synthetic approaches for the formation of β-lactam containing dipeptides. In this study, we report upon the stereoselective preparation of β-lactam-containing pseudopeptides, where different reaction conditions and NH$_2$ protective groups were tested to obtain compounds that contain 3-amino-azetidin-2-one. We demonstrate that the protective group is essential for the outcome of the reaction. Successful implementation of dibenzyl-protected serine-containing dipeptides through the Mitsunobu reaction can provide the desired products at high yields and stereoselectivity

Inhibition of MurA Enzyme from Escherichia coli by Flavonoids and Their Synthetic Analogues

MurA catalyzes the first step of peptidoglycan (PG) biosynthesis and is a validated target for the development of new antimicrobial agents. In this study, a library of 49 plant flavonoids and their synthetic derivatives were evaluated for their inhibitory properties against MurA from Escherichia coli. The compounds were tested with and without preincubation and with the addition of DTT to understand the mechanism of inhibition. Thirteen compounds were identified as reversible, time-dependent inhibitors, with inhibition levels ranging from 480 nM to 57 μM, and ampelopsin as the most potent compound. To investigate the major pharmacophore elements responsible for the activity, 2D-QSAR and docking analyzes were performed. The results showed that the catechol moiety and an additional aromatic system were the most important features contributing to the activity of the compounds. However, most of the compounds did not show antibacterial activity against E. coli and Staphylococcus aureus strains, suggesting that their inhibitory activity against MurA may not be strong enough to induce antibacterial effects. Nevertheless, our results suggest that flavonoids are a promising starting point to develop new inhibitors of MurA and show great potential for further steps in drug development

Application of the <i>N</i>-Dibenzyl Protective Group in the Preparation of β-Lactam Pseudopeptides

Despite the great importance of &#946;-lactam antibiotics, there is still a limited number of synthetic approaches for the formation of &#946;-lactam&#8211;containing dipeptides. In this study, we report upon the stereoselective preparation of &#946;-lactam&#8211;containing pseudopeptides, where different reaction conditions and NH2 protective groups were tested to obtain compounds that contain 3-amino-azetidin-2-one. We demonstrate that the protective group is essential for the outcome of the reaction. Successful implementation of dibenzyl-protected serine-containing dipeptides through the Mitsunobu reaction can provide the desired products at high yields and stereoselectivity

Screening of big pharma’s library against various in-house biological targets

Open innovation initiatives provide opportunities for collaboration and sharing of knowledge and experience between industry, academia, and government institutions. Through open innovation, Merck is offering a Mini Library of 80 carefully selected compounds from previous research and development projects to a broader scientific community for testing in academic drug discovery projects. These compounds are predominantly drug-like and cover a broad range of molecular targets. They could potentially interact with other enzymes, receptors, transporters, and ion channels of interest. The Mini Library was tested on seven in-house enzymes (bacterial MurA, MurC ligase, and DdlB enzyme, human MAO-A/B, human BChE, and murine AChE), and several hits were identified. A follow-up series of structural analogues provided by Merck gave a more detailed insight into the accessibility and the quality of the hit compounds. For example, sartan derivatives were moderate inhibitors of MurC, whereas bisarylureas were potent, selective, nanomolar inhibitors of hMAO-B. Importantly, 3-n-butyl-substituted indoles were identified as low nanomolar selective inhibitors of hBChE. All in all, the hit derivatives provide new starting points for the further exploration of the chemical space of high-quality enzyme inhibitors

The synthesis of (2R)-aziridine-2-carboxylic acid containing dipeptides

Optimized conditions for the synthesis of fully deprotected (2R)-aziridine containing dipeptides are described. Preparation of fully protected N- and C- terminal aziridine containing dipeptides was found to be straightforward and high yielding for the majority of compounds, whereas their full deprotection was possible only for C-terminal analogs. Deprotection of N-terminal derivatives using standard procedures of peptide chemistry was found difficult providing only mixtures of unidentifiable products. The described molecules have potential as building blocks in synthetic chemistry, in the chemical biology arena, as covalent modifiers, and as biomarkers.V prispevku so opisani optimizirani pogoji za sintezo dipeptidov, ki vsebujejo popolnoma odščiten (2R)-aziridin. Priprava popolnoma zaščitenih N- in C- terminalnih dipeptidov, ki vsebujejo aziridin, je enostavna in poteka z visokim izkoristkom za večino spojin, medtem ko je njihova popolna odščita možna le za C-terminalne analoge. Odstranjevanje zaščite z N-terminalnih derivatov z uporabo standardnih postopkov peptidne kemije se je izkazalo kot težko, saj vodi do mešanice nedoločljivih produktov. Opisane molekule imajo velik potencial kot gradniki v sintezni kemiji, na področju kemijske biologije, kot kovalentni modifikatorji in kot biomarkerji