Optimization of pyridylpiperazine-based inhibitors of the Escherichia coli AcrAB-TolC efflux pump

Multidrug-resistant Escherichia coli is a continuously growing worldwide public health problem, in which the well-known AcrAB-TolC tripartite RND efflux pump is a critical driver. We have previously described pyridylpiperazines as a novel class of allosteric inhibitors of E. coli AcrB which bind to a unique site in the protein transmembrane domain, allowing for the potentiation of antibiotic activity. Here, we show a rational optimization of pyridylpiperazines by modifying three specific derivatization points of the pyridine core to improve the potency and the pharmacokinetic properties of this chemical series. In particular, this work found that the introduction of a primary amine to the pyridine through ester (29, BDM91270) or oxadiazole (44, BDM91514) based linkers allowed for analogues with improved antibiotic boosting potency through AcrB inhibition. In vitro studies, using genetically engineered mutants, showed that this improvement in potency is mediated through novel interactions with distal acidic residues of the AcrB binding pocket. Of the two leads, compound 44 was found to have favorable physico-chemical properties and suitable plasma and microsomal stability. Together, this work expands the current structure-activity relationship data on pyridylpiperazine efflux pump inhibitors, and provides a promising step towards future in vivo proof of concept of pyridylpiperazines as antibiotic potentiators.

Antibiotics with novel mode of action as new weapons to fight antimicrobial resistance

Antimicrobial resistance (AMR) is a major public health issue, causing 5 million deaths per year. Without any action plan, AMR will be in a near future the leading cause of death ahead of cancer. AMR comes from the ability of bacteria to rapidly develop and share resistance mechanisms towards current antibiotics, rendering them less effective. To circumvent this issue and avoid the phenomenon of cross-resistance, new antibiotics acting on novel targets or with new modes of action are required. Today, the pipeline of potential new treatments with these characteristics includes promising compounds such as gepotidacin, zoliflodacin, ibezapolstat, MGB-BP-3, CRS-3123, afabicin and TXA-709, which are currently in clinical trials, and lefamulin, which has been recently approved by FDA and EMA. In this review, we report the chemical synthesis, mode of action, structure-activity relationships, in vitro and in vivo activities as well as clinical data of these eight small molecules listed above.

Tricyclic SpiroLactams Kill Mycobacteria In Vitro and In Vivo by Inhibiting Type II NADH Dehydrogenases

It is critical that novel classes of antituberculosis drugs are developed to combat the increasing burden of infections by multidrug-resistant strains. To identify such a novel class of antibiotics, a chemical library of unique 3-D bioinspired molecules was explored revealing a promising, mycobacterium specific Tricyclic SpiroLactam (TriSLa) hit. Chemical optimization of the TriSLa scaffold delivered potent analogues with nanomolar activity against replicating and nonreplicating Mycobacterium tuberculosis. Characterization of isolated TriSLa-resistant mutants, and biochemical studies, found TriSLas to act as allosteric inhibitors of type II NADH dehydrogenases (Ndh-2 of the electron transport chain), resulting in an increase in bacterial NADH/NAD⁺ ratios and decreased ATP levels. TriSLas are chemically distinct from other inhibitors of Ndh-2 but share a dependence for fatty acids for activity. Finally, in vivo proof-of-concept studies showed TriSLas to protect zebrafish larvae from Mycobacterium marinum infection, suggesting a vulnerability of Ndh-2 inhibition in mycobacterial infections.

Discovery of the First Selective Nanomolar Inhibitors of ERAP2 by Kinetic Target-Guided Synthesis

Endoplasmic reticulum aminopeptidase 2 (ERAP2) is a key enzyme involved in the trimming of antigenic peptides presented by Major Histocompatibility Complex class I. It is a target of growing interest for the treatment of autoimmune diseases and in cancer immunotherapy. However, the discovery of potent and selective ERAP2 inhibitors is highly challenging. Herein, we have used kinetic target-guided synthesis (KTGS) to identify such inhibitors. Co-crystallization experiments revealed the binding mode of three different inhibitors with increasing potency and selectivity over related enzymes. Selected analogues engage ERAP2 in cells and inhibit antigen presentation in a cellular context. 4 d (BDM88951) displays favorable in vitro ADME properties and in vivo exposure. In summary, KTGS allowed the discovery of the first nanomolar and selective highly promising ERAP2 inhibitors that pave the way of the exploration of the biological roles of this enzyme and provide lead compounds for drug discovery efforts.

Sox9 Determines Translational Capacity During Early Chondrogenic Differentiation of ATDC5 Cells by Regulating Expression of Ribosome Biogenesis Factors and Ribosomal Proteins

Introduction

In addition to the well-known cartilage extracellular matrix-related expression of Sox9, we demonstrated that chondrogenic differentiation of progenitor cells is driven by a sharply defined bi-phasic expression of Sox9: an immediate early and a late (extracellular matrix associated) phase expression. In this study, we aimed to determine what biological processes are driven by Sox9 during this early phase of chondrogenic differentiation.

Materials

Sox9 expression in ATDC5 cells was knocked down by siRNA transfection at the day before chondrogenic differentiation or at day 6 of differentiation. Samples were harvested at 2 h and 7 days of differentiation. The transcriptomes (RNA-seq approach) and proteomes (Label-free proteomics approach) were compared using pathway and network analyses. Total protein translational capacity was evaluated with the SuNSET assay, active ribosomes were evaluated with polysome profiling, and ribosome modus was evaluated with bicistronic reporter assays.

Results

Early Sox9 knockdown severely inhibited chondrogenic differentiation weeks later. Sox9 expression during the immediate early phase of ATDC5 chondrogenic differentiation regulated the expression of ribosome biogenesis factors and ribosomal protein subunits. This was accompanied by decreased translational capacity following Sox9 knockdown, and this correlated to lower amounts of active mono- and polysomes. Moreover, cap- versus IRES-mediated translation was altered by Sox9 knockdown. Sox9 overexpression was able to induce reciprocal effects to the Sox9 knockdown.

Conclusion

Here, we identified an essential new function for Sox9 during early chondrogenic differentiation. A role for Sox9 in regulation of ribosome amount, activity, and/or composition may be crucial in preparation for the demanding proliferative phase and subsequent cartilage extracellular matrix production of chondroprogenitors in the growth plate in vivo.

Comparative label-free proteomic analysis of equine osteochondrotic chondrocytes

Osteochondrosis is a developmental orthopedic disease affecting growing cartilage in young horses. In this study we compared the proteomes of equine chondrocytes obtained from healthy and osteochondrotic cartilage using a label-free mass spectrometry approach. Quantitative changes of some proteins selected for their involvement in different functional pathways highlighted by the bioinformatics analysis, were validated by western blotting, while biochemical alterations of extracellular matrix were confirmed via Raman spectroscopy analysis. In total 1637 proteins were identified, of which 59 were differentially abundant. Overall, the results highlighted differentially represented proteins involved in metabolic and functional pathways that may be related to the failure of the endochondral ossification process occurring in osteochondrosis. In particular, we identified proteins involved in extracellular matrix degradation and organization, vitamin metabolism, osteoblast differentiation, apoptosis, protein folding and localization, signalling and gene expression modulation and lysosomal activities. These results provide valuable new insights to elucidate the underlying molecular mechanisms associated with the development and progression of osteochondrosis. SIGNIFICANCE: Osteochondrosis is a common articular disorder in young horses mainly due to defects in endochondral ossification. The pathogenesis of osteochondrosis is still poorly understood and only a limited number of proteomic studies have been conducted. This study provides a comprehensive characterization of proteomic alterations occurring in equine osteochondrotic chondrocytes, the only resident cell type that modulates differentiation and maturation of articular cartilage. The results evidenced alterations in abundance of proteins involved in functional and metabolic pathways and in extracellular matrix remodelling. These findings could help clarify some molecular aspects of osteochondrosis and open new fields of research for elucidating the pathogenesis of this disease.

OP0240 A MULTIMODAL MASS SPECTROMETRY APPROACH REVEALS SPECIFIC CARTILAGE MOLECULAR PROFILES ASSOCIATED TO TYPE 2 DIABETIC PATIENTS

Background:

Osteoarthritis (OA) is mainly characterized by the progressive deterioration of articular cartilage. Recent studies support that type 2 diabetes (TD2) is a risk factor to develop OA [1, 2]. However, the molecular cartilage profile of patients combining these two diseases remains unclear, and a better understanding of the different OA phenotypes should be considered for the development of personalized medicine.

Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI) is used to investigate the bimolecular distribution of proteins, lipids or metabolites through thein-situanalysis of tissue sections. Bottom-up proteomics focuses on the relative quantification of proteins. The combination of both technologies could be considered to reveal specific molecular profiles and help for patient classification.

Objectives:

The main goal of this study is to apply a multimodal mass spectrometry approach on cartilage to reveal specific lipidomic and proteomic profiles associated to TD2 patients.

Methods:

Human cartilages from OA (na=10) and OA/TD2 human patients (nb=10) were obtained from donors undergoing total knee joint replacement. Cartilage punches of 8*8mm were sectioned at 12 µm thickness for MALDI-MSI and bottom-up proteomics.

For MALDI-MSI experiments (na=6; nb=6), norharmane matrix was sprayed over the samples for the detection of lipids. Experiments were then performed in positive ion polarity at 50 µm of lateral resolution using a RapifleX MALDI Tissue-typer instrument. LipostarMSI and in-house ChemomeTricks toolbox for MATLAB software were used for data processing and analysis.

For bottom-up proteomics experiment (na=10; nb=10), proteins were extracted, separated using SDS-PAGE and digested prior to liquid chromatography separation coupled to an orbitrap MS Q-Exactive HF mass spectrometer. Proteome Discoverer, enrichR and Reactome software were used for data processing and analysis.

Results:

MALDI-MSI showed overall differences between OA and OA/TD2 patients based on their specific lipidomic profiles. In particular, sphingomyelin and phosphatidylcholine species were significantly more abundant in OA patients whereas lysolipids such as lysophosphatidylcholine species were mainly present in OA/TD2 patients, providing therefore phenotype-specific OA molecular panels. Additionally, we observed that phosphatidylcholine and sphingomyelin species were more present in the superficial layer of the cartilage whereas lysophosphatidylcholine species were more abundant in the deep layer (Fig. 1A, B).

Proteomics experiments applied on cartilage enables the quantification of 114 proteins. Among those, 73 were overexpressed in OA samples whereas 41 were overexpressed in OA/TD2 patients. Among the differentially regulated proteins (Fig. 1C), phospholipase A2 was increased in the diabetic cohort, in line with the elevated level of lysolipids found in the imaging data. Our results also involved the fatty acid omega oxidation and the fatty acid biosynthesis pathways as relevant to explain this deregulation of the lipid metabolism.

Conclusion:

MALDI–MSI combined with proteomics experiments showed different profiles between OA and OA/TD2 patients and could be employed for patient classification.

References:

[1]Louati, K., et al., Association between diabetes mellitus and osteoarthritis: systematic literature review and meta-analysis. RMD Open, 2015.1(1): p. e000077.

[2]Williams, M.F., et al.,Type 2 diabetes and osteoarthritis: a systematic review and meta-analysis.J Diabetes Complications, 2016.30(5): p. 944-50.

Acknowledgments:

The Dutch Province of Limburg and MUMC institutional grant.

Disclosure of Interests:

Maxime Eveque: None declared, Pieter Emans Shareholder of: Shareholder and cofounder start-up company Chondropeptix, Grant/research support from: Institution received grants from STW, ReumaNederland, InSciTE, Consultant of: Consultancy to Kiomed, Speakers bureau: Payment for lectures by Kiomed, Episurf, Britt Claes: None declared, Freek Bouwman: None declared, Ron M A Heeren: None declared, Berta Cillero-Pastor: None declared