Chemical Biology

In their ongoing quest for new therapies against pathogens, scientists are focusing primarily on chemical and biological agents. These can function as antibiotics or stimulate the immune system. Discovering new drugs, characterising their functionality and optimising their properties are the three main goals of the department “Chemical Biology” at the HZI.  

Leader

1. Screening for novel anti infectives

The HZI S3-facility offers the opportunity to investigate the properties of pathogenic viruses and bacteria. One task addressed by the Department of Chemical Biology is the screening of (natural-) compound libraries for new anti-viral-agents. This is accomplished by an automated pipetting robot which can be operated under S3-safety conditions. In an ongoing project, the malignant hepatoma cell-line Huh-7 is cultivated in 96-wells and subjected to Dengue Virus. After addition of compounds and viral infection, cells are fixed and immunostained for viral epitopes. Finally, the percentage of infected cells is determined by automated fluorescence microscopy.

By applying different modifications to this high-content screening approach, our group intends to identify new anti-viral compounds blocking virus/host-interactions or interfering with viral replication and viral maturation.

2. Characterization of Biofilm-formation

The control of chronic bacterial infections is significantly affected by the formation of biofilms. In the human body, such structures enable pathogens to display an array of different adaption strategies and an increase in their resistance to drug therapies. Biofilms provide a physical barrier to the immune system and to the penetration of antibiotics. In addition, bacteria in biofilms display an altered metabolism compared to planktonic growth. In a biofilm, bacteria are embedded in a self-produced matrix of extracellular polymeric substances (EPS), which consist of DNA, proteins and polysaccharides. Since bacteria in biofilms are much less susceptible towards antibiotics, antimicrobial treatment in the presence of biofilms is often inefficient.

In our group, we are addressing biofilm formation in particular with two clinically very relevant pathogensPseudomonas aeruginosa, which is a Gram-negative bacterium, and Staphylococcus aureus, a Gram-positive pathogen. A new method based on impedance spectroscopy is being developed that aims at the real-time determination of biofilm growth dynamics. Pseudomonas aeruginosa was taken a first model strain. Other ESKAPE microorganisms will also be addressed (Figure A). This opens up the opportunity for further miniaturization of the method with the goal to develop a microchip based diagnostic tool, which can be used as a high-throughput assay system for drug research, the stratification of clinical bacterial isolates as well as the optimization of individualized medical treatments.

For Staphyloccocus aureus we are trying to identify compounds that (i) prevent the formation of biofilms or (ii) that are able to kill the bacteria inside of established biofilms. In collaboration with a major pharmaceutical company we have investigated approximately 20,000 natural compounds in a primary screening assay for their effect on biofilm formation. Primary actives were further characterized by laser-scanning fluorescence microscopy at the Twincore in Hannover (Prof. S. Häußler). In an example that is shown in Figure B (below) the bacteria have been visualized by fluorescent dyes that stain living bacteria green and dead ones red following compound treatment. Compound 1 killed bacteria at increasing concentrations and also caused a reduction of the amount of biofilm (left panel). Compound 2 left the bacteria alive, but reduced the amount of biofilm (right panel). Especially the profile of compound 2 is desirable as part of a pathoblocker concept.

(A) Changes in the standardized impedance during biofilm growth of Pseudomonas aeruginosa. (B) Laser scanning fluorescence microscopy of biofilm forming Staphylococcus aureus. After fluorescence staining living bacteria appear green and dead bacteria red.

3. Biological profiling and mode of action studies

The characterization of the mode of action of a bioactive compound is an essential prerequisite for its application as a therapeutic. The mode of action manifests itself in terms of direct binding partners, functional perturbations as a consequence of binding, and induced downstream effects on a cellular, tissue and whole organism level. We tackle the challenge of mode of action analysis through a variety of orthogonal approaches:

Biological profiling

High content analysis

For compounds with an unknown mode of action, we apply two high content profiling methods to obtain information about their influence on distinct cellular pathways. The first method is based on impedance spectroscopy. Under treatment time-dependent cellular response profiles (TCRP, A) of epithelial cells are captured and mathematically described by fitting parameters. Workflow for a typical analysis is shown in B. The compound specific fitting parameters are then compared to those of a reference library of 64 compounds in a clustering analysis (C). Compounds with similar effects will group close to each other and reveal the potential mode of action. Within the second approach phenotypic changes of mammalian cells are visualized by immunofluorescent staining and evaluated by high content microscopy in comparison to the same reference set of compounds.

Such biological profiling by high-content assays has been successfully applied for evaluation of paleo-soraphens and jerantinine e:

  • Synthesis and biological evaluation of paleo-soraphens. Lu HH, Raja A, Franke R, Landsberg D, Sasse F, Kalesse M. Angew Chem Int Ed Engl. 2013 Dec 16;52(51):13549-52.
  • Total synthesis and biological evaluation of jerantinine e. Frei R, Staedler D, Raja A, Franke R, Sasse F, Gerber-Lemaire S, Waser J., Angew Chem Int Ed Engl. 2013 Dec 9;52(50):13373-6.
Impedance profiling

Profiling of small-molecules by application to a panel of organisms

For external and internal partners: CBIO offers to characterize the growth inhibitory effects of small molecules on a panel of microorganisms and eukaryotic cells using standardized protocols.

The so-called ESKAPE panel of bacteria comprises the clinically relevant gram-positive species Enteroccocus faecium and Staphylococcus aureus and the gram-negative species Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacteriaceae, such as Escherichia coli and Enterobacter cloacae. The range of tested microorganisms is completed by yeasts and fungi, such as Saccharomyces cerevisiae and Candida albicans. In the first instance growth inhibitory properties are evaluated by incubating the strains in either defined minimal media or in complex media to promote sufficient growth rates in (96 well or 384 well, A) microtiter plates.

In addition a range of standard mammalian cell lines, e.g. L929, MCF-7, KB 3.1, is treated with the compounds under investigation to evaluate cytotoxic effects. Cytotoxicity is determined via tetrazolium-dye based assays, such as the MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) or the WST (water soluble tetrazolium) assay. In these assays the substrate turnover by NAD(P)H-dependent cellular oxidoreductases reflects, under defined conditions, the number of viable cells present. The exposure times of the cells with the compounds vary from 24 h for the estimation of acute cytotoxicity to 5 days for the detection of general cytotoxic effects. In subsequent assays, effects on DNA synthesis (using BrdU) or the mitochondrial membrane potential ΔΨm are probed (C,D).

Generally all biological activities are characterized by the compound concentrations leading to either a reduction of the growth or the viability by 50% (IC50) or to complete growth inhibition (minimal inhibitory concentration MIC, B).

Target identification

Whole genome sequencing of resistant cells

A recently introduced method for target identification is whole genome sequencing (WGS) of resistant cell lines. For this approach bacteria or eukaryotic cells are cultivated under increasing concentrations of the compound of interest. Resistant clones are selected and subjected to WGS. By comparison to the wildtype genome, mutations in protein encoding sequences are identified that hint to the potential target of a given compound. For further confirmation mutant proteins are recombinantly expressed in the respective wildtype strains. Resulting resistance identifies the compound target. Verification can alternatively be done by reversing the genomic mutation. This strategy has been successfully applied for identifying the osmosensitive K+-channel sensor histidine kinase as a target of the antimicrobially active inhibitor vz0825 of Vibrio cholera.

  • High-throughput screening and whole genome sequencing identifies an antimicrobially active inhibitor of Vibrio cholerae. Sergeev G, Roy S, Jarek M, Zapolskii V, Kaufmann DE, Nandy RK1, Tegge W. BMC Microbiol. 2014 Feb 26;14:49.

Drug affinity responsive target stability (DARTS)

With the DARTS method, direct binding of a compound to a cellular target can be monitored (Lomenick 2009). DARTS is based on the fact that a protein can be protected to a certain degree from degradation by proteases by binding of small molecules. Protected protein bands can be identified by PAGE and MS. The method was successfully applied to identify the target of the bioactive small molecules myriaporone 3/4 (Murhukumar 2013) and tellurium containing naphthoquinones (Schneider 2012).

  • Lomenick, B., Hao, R., Jonai, N., Chin, R.M., Aghajan, M., Warburton, S., Wang, J., Wu, R.P., Gomez, F., Loo, J.A., Wohlschlegel, J.A., Vondriska, T.M., Pelletier, J., Herschman, H.R., Clardy, J., Clarke, C.F., Huang, J. (2009) Target identification using drug affinity responsive target stability (DARTS). Proc Natl Acad Sci U S A. 106, 21984-9. 
  • Schneider, T., Muthukumar, Y., Hinkelmann, B., Franke, R., Döring, M., Jacob, C., Sasse, F. (2012) Deciphering intracellular targets of organochalcogen based redox catalysts. MedChemComm 3, 784-787. 
  • Muthukumar, Y., Roy, M., Raja, A., Taylor, R.E., Sasse, F. (2013) The marine polyketide myriaporone 3/4 stalls translation by targeting the elongation phase. ChemBioChem 14, 1439-7633. 

Target fishing

Protein targets of a chemical compound can be identified by a so-called target fishing approach. For this the chemical compound has to be modified by the introduction of a functional affinity tag (i.e. biotin). The resulting conjugate consisting of affinity tag, linker and ligand is called a fishing probe. The affinity tag enables purification of compound-protein complexes that formed during incubation with cells or cell lysates. Compound binding proteins obtained from this chemical pull down are then identified by PAGE and MS.

4. Diagnostic peptide arrays

An innovative method for the generation of peptide arrays on cellulose membranes has been developed in our group (Dr. R. Frank, former head of department), which is internationally applied and known as the SPOT method. The arrays have been used in a multitude of different biological investigations like e.g. epitope mapping, enzymatic transformations, development of antimicrobial compounds and many more. The SPOT method has been extended in our department to the generation of miniaturized arrays, where up to 10,000 different peptides can be accommodated on a microscope slide and used in biological tests (SC2 method). The SC2 method allows the printing of several thousand copies of a microarray from one single SPOT membrane. Current projects focus on the characterization of the immune response to different viral infections in monkeys and humans.

5. Metabolome analysis (Metabolomics)

The overall aim of Metabolomics is to obtain a qualitative and quantitative overview of the whole metabolome by analysing all metabolic intermediate in a given scenario. Amongst other omics-techniques, Metabolomics comprises the highest diversity of analytes, is closest to phenotype and is very dynamic.

Recent studies have demonstrated the potential of Metabolomics to decipher the mode of action of bioactive compounds (e.g. Kitagawa, Chem Biol 2010; Zlitni, Nat Chem Biol 2013), to detect metabolite switches upon induction of resistance (e.g. Derewacz, PNAS2013), or to simply discover novel metabolites even in well-known organisms (e.g. Srinivasan, Nature 2008; Globisch, PNAS2013). In our group, Metabolomics is mainly applied to capture the dynamics of small molecule metabolite networks in response to antibiotics, microbes and other perturbations. By this, we will be able to understand the mechanisms of action of novel antibiotics, and to improve their functionality.

To cope with the analytical challenges of the dynamic metabolism and the high diversity of metabolites, we use state-of the art instruments in untargeted and targeted approaches via LC/MS and GC/MS. We use chemical standards and available spectral libraries for identification. In addition to that we use high resolution TOF mass spectrometry and preparative LC(MS) coupled to NMR to elucidate the structure of unknown but significant compounds.

The obtained metabolite patterns will be combined with transcriptome and proteome information, to provide a system wide view of the adaptation of bacteria to drug Treatment.

(A) UPLC-ESI-Q-TOF-MS: Ultimate 3000 (Dionex) coupled to Maxis HD mass spectrometer (Bruker Daltonic). This LC/MS system is used for non-targeted analysis for polar and non-polar metabolites. The mass spectrometry can also be coupled with gas chromatography via an APCI source.

(B) UPLC-ESI-QQQ-MS: 1290 Infinity (Agilent) coupled to QTrap 6500 (ABSciex). This LC/MS system is used for high-throughput screening analysis for selected metabolites and compound classes.

(C) GC-EI-iontrap-MS: Trace GC Ultra coupled to ITQ900 MS (Thermo Fisher Scientific). This GC/MS system is mainly used for analysis of polar compounds of primary metabolism

6. Improving and quantifying bacterial penetration

Antimicrobial resistance of Gram-negative bacteria has become a major issue for public health, and there is acute medical need for novel antibiotics. Especially the complex structure of the Gram-negative cell wall limits uptake of bioactive compounds. To accomplish this we are developing carrier-conjugates that facilitate and improve compound penetration into bacteria. Applied carriers are synthetic molecules that are designed based on natural templates like nutrients. The carriers will specifically mediate uptake of the conjugates through distinct outer membrane receptors in a Trojan horse strategy. For quantifying uptake of the carrier-conjugates we apply the two following approaches.

Measuring uptake by LCMS

In order to quantify the intracellular accumulation of small molecules without relying on fluorescent or radioactive labels we are currently implementing a broadly applicable, LCMS-based technique combined with subcellular fractionation. Within this approach, bacteria are incubated with the compound of interest and are then subjected to a fractionation workflow for separating periplasmic, cytoplasmic and membrane contents. Upon compound extraction out of the lysates their identity and concentration is measured by highly sensitive mass spectrometric analysis.

Monitoring compound uptake by conjugation to fluorogenic dyes

In order to visualize the internalization and intracellular localization of uptake mediating carriers, we make use of a conjugation-based approach. The carrier of interest is conjugated to a fluorogenic dye that only obtains fluorescent properties upon binding to a specific dye activator protein. Genetically modified bacteria that express this dye activator protein are treated with the fluorogen-conjugates. Upon uptake and intracellular binding the resulting fluorescent signal can be monitored by fluorescence microscopy, flow cytometry or fluorescence reader. By directed expression of the dye activator protein in either cytoplasm or periplasm, detailed information about the intracellular localization of a given carrier-conjugate can be obtained.

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