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BachData-dependent acquisitionMass SpectrometryBottom-up proteomicsBacterial Infectious DiseaseBacterial GastritisHelicobacter pyloriFull proteomeLc-ms/msSecretomeNitroimidazolesAbppMode of actionhttps://www.ebi.ac.uk/pride/archive/projects/PXD051773Labeling and Lysis in H. pylori H. pylori bacterial cultures (4 × 250 mL) were grown to stationary phase (OD600 ≈ 1.0, 90 h). Cells were harvested (6000 × g, 10 min, 4 °C) and washed with PBS once (15 mL, 6000 × g, 10 min, 4 °C). The pellets were resuspended in PBS to obtain a bacterial culture of OD600 ≈ 40. To 1 mL of OD600 ≈ 40 culture, 10 µL probe (Metro-P1, Metro-P2 or Metro-P3, 100 × stock in DMSO, final conc. 1 µM) or 1 % (v/v) DMSO were added and incubated at 37 °C (140 rpm, microaerophilic conditions) for 2 h and subsequently harvested by centrifugation (6000 × g, 10 min, 4 °C). The supernatant was removed, and cell pellet washed twice with 1 mL PBS prior to resuspension in 1 mL 0.4 % SDS in PBS. Cells were lysed by sonication (4 × 20 s, 75 % intensity) with cooling breaks on ice and clarified by centrifugation (20 000 × g, 30 min, r.t.). For competitive labeling experiments, 1 mL of OD600 ≈ 40 H. pylori 26695 culture was pre-incubated with 100 µM Metronidazole (100 x excess, 100 x stock in DMSO) at 37 °C (140 rpm, microaerophilic conditions) for 2 h before probes (1 µM) were added. Protein concentration of each sample was determined by BCA assay. Click Reaction and Protein Washing Click conditions: 100 µM biotin-N3, 500 µM BTTAA, 1 mM CuSO4, 2 mM NaAsc The samples were subjected to Click reaction by adding 5 µL biotin azide (final: 100 µM), 25 µL BTTAA (final: 500 µM), 10 µL CuSO4 (final: 1 mM) and 10 µL NaAsc (final: 2 mM) to a total volume of 500 µL and incubated for 1 h at room temperature. Click reaction was quenched by adding 2 mL cold acetone (−80 °C), vortexed and stored overnight at −80 °C. Precipitated proteins were pelletized (SLA3000, 10 000 × g, 15 min, 4 °C), and supernatant was discarded. Protein pellet was washed with 0.5 mL cold methanol (−80 °C) and centrifuged (21 000 × g, 10 min, 4 °C) twice. Finally, protein pellets were resuspended in 500 µL 0.4 % SDS-PBS by sonication (10 s, 10 % intensity). Avidin Bead Enrichment and On Bead Digest All aqueous solutions were prepared using MS-grade water. Avidin beads (avidin-agarose from egg white, 1.1 mg/mL in aq. glycerol suspension, Sigma Aldrich) were carefully resuspended by inversion on an Eppendorf tube wheel at 4 °C and transferred to an Eppendorf tube. The beads were washed with 0.4 % SDS in PBS (3 × 1 mL), centrifuged (400 × g, 3 min, r.t.) and filled to the original level with 0.4 % SDS in PBS. 50 µL of bead suspension were added to each 500 µL sample and incubated for 1 h at r.t. under continuous mixing. The samples were transferred quantitatively onto spin columns (BioEcho) and washed as follows: 0.4 % SDS in PBS (3 × 700 µL), 6 M urea in ddH2O (2 × 700 µL) and PBS (3 × 700 µL) and transferred into new 1.5 mL LoBind tubes (Eppendorf) with 2 × 100 µL X buffer (7 M urea, 2 M thiourea in 20 mM HEPES, pH = 7.5). Proteins on beads were subsequently reduced with TCEP (final: 5 mM) for 1 h (37 °C, 600 rpm) and alkylated with iodoacetamide (final con. 10 mM) for 30 min (r.t., 600 rpm). The reaction was quenched via addition of dithreithiol (DTT, final con. 10 mM) for 30 min (r.t., 600 rpm). 50 mM Triethylammonium bicarbonate (TEAB, 600 µL) was added and the pH value was checked to be ≥ 8.0. Trypsin (1.5 µL, 0.5 µg/µL in 50 mM acetic acid, Promega) was added to digest the samples for 16 h (37 °C, 600 rpm) and quenched the next day by acidifying with formic acid (10 µL, final pH ≤ 3.0). The digested samples were centrifuged (13 000 × g, 3 min, r.t.) before proceeding to the desalting step. Desalting and Filtration Desalting was performed using SepPak® C18 cartridges Samples were evaporated using a speed vac (Concentrator Plus, Eppendorf). The dried peptides were dissolved in 40 µL 1 % FA in ddH20, vortexed and sonicated (3 × 5 min). PVDF filters (0.22 µM, Merck Millipore) were washed with 300 µL 1 % FA in ddH20 (13 000 × g, 1 min, r.t.). Samples were filtered by centrifugation (13 000 rpm, 1 min, r.t.) and transferred into MS vials (Thermo Fisher).PrideSamples were analyzed via HPLC-MS/MS using an UltiMate 3000 nano HPLC system (Dionex) equipped with Acclaim C18 PepMap100 trap column (75 µm ID × 2 cm, Acclaim, ThermoFisher) and Aurora UltimateTM (1st generation, 20 cm nanoflow UHPLC compatible, ionopticks) separation columns coupled to a Q Exactive Plus Orbitrap Mass Spectrometer (Thermo Fisher Scientific) constantly heated to 40 °C. Samples were loaded onto the trap column and washed with TFA (0.1% in ddH2O). The subsequent separation was carried out with a flow rate of 400 nL/min using buffer A (0.1% FA in ddH20) and buffer B (0.1% FA in acetonitrile). The separation column was heated to 40 °C. The analysis started with washing for 7 min with 5% buffer B for desalting followed by a gradient from 5% to 22% buffer B over 105 min, a second gradient from 22% B to 32% B within 10 min, and a final increase to 90% B in 10 min. Isocratic washing with 90% B was performed for 10 min, then decreased to 5% in 0.1 min and held at 5% for additional 9.9 min for re-equilibration. The Q Exactive Plus mass spectrometer was run in a TOP10 data-dependent mode. In the orbitrap, full MS scans were collected in a scan range of 300-1500 m/z at a resolution of 140 000 and an AGC target of 3e6 with 80 ms maximum injection time. The TOP12 peaks were selected for MS2 scan with a minimum AGC target of 1e3 and isotope exclusion and dynamic exclusion (exclusion duration: 60 s) enabled. Peaks with unassigned charges or a charge of +1 were excluded. Peptide match was “preferred”. MS2 spectra were collected at a resolution of 17 500 aiming at an AGC target of 1e5 with a maximum injection time of 100 ms. Isolation was conducted in the quadrupole using a window of 1.6 m/z. Fragments were generated using higher-energy collision-induced dissociation (HCD, normalized collision energy: 27%) and finally detected in the orbitrap. The lock-mass ion 445.12002 from ambient air was used for real-time mass calibration on the Q Exactive Plus Data was acquired using Xcalibur software version 3.1 sp3 and proteomics raw data were analysed using MaxQuant12 (ver. 1.6.2.10) which uses the Andromeda search engine.13 Settings were default except for LFQ-quantification and match between runs, which were activated during search.The parameters can be found attached in the appendix. Perseus 2.0.10.0 was used for analysis.14 Data was filtered as following: Potential contaminants’ were removed as well as ‘reverse peptides’ and ‘only identified by site’. LFQ intensities were log2 transformed. Rows were annotated in groups – DMSO (control) and different probe treatments. Rows were filtered for 2 valid values in at least one group. Missing values were imputed from normal distribution. Annotations derived from data banks (Uniprot15) were added. Each condition was performed in biological triplicates (n = 3) and volcano plots were created based on two-sided two sample Student‘s t-tests.ProteomicsStephan Axel SieberTechnical University of Munich (TUM), TUM School of Natural Sciences, Department Bioscience, Chair of Organic Chemistry II, Center for Functional Protein Assemblies (CPA), Ernst-Otto-Fischer Str. 8, Garching 85748, GermanyPARTIALHelicobacter Pylori 2669541851492 Fiedler MK, Pandler MSI, Gong R, Fuchs S, Rox K, Friedrich V, Pfeiffer D, Singh D, Reinhardt T, Mibus C, Huber M, Hess CR, Mejías-Luque R, Gerhard M, Groll M, Sieber SA. Metronidazole and ether derivatives target Helicobacter pylori via simultaneous stress induction and inhibition. Nat Microbiol. 2026 11(4):1049-1063 10.1038/s41564-026-02291-wnina.bach@tum.deTU MünchenGermanyMetronidazole is a front-line drug for the treatment of Helicobacter pylori infections. However, its mode of action and cellular targets are poorly defined, and higher dosing and combination therapies are required to overcome resistance. Here we performed activity-based protein profiling with tailored metronidazole probes and identified chaperonin HpGroEL and thiol peroxidase HpTpx as prominent targets, the latter being essential for H. pylori survival under oxidative stress. Alkynylated ether probes exhibited enhanced antibacterial potency compared with the parent drug in vitro, including activity against resistant strains. Biological assays, chemical proteomics and co-crystallization studies confirmed target engagement, with enhanced binding of ether derivatives to HpTpx. Refined ether analogues exhibited favourable pharmacological profiles without cytotoxicity. The in vivo activity of ether analogues using an H. pylori mouse model demonstrated full bacterial eradication at low dosing of 0.3 mg kg^-1 day^-1. Our findings reveal that stress induction and simultaneous inhibition of the stress response represent a mechanism of this compound class.Metronidazole and ether derivatives target Helicobacter pylori via simultaneous stress induction and inhibition.Fiedler Michaela K MK, Pandler Marianne S I MSI, Gong Ruolan R, Fuchs Sonja S, Rox Katharina K, Friedrich Verena V, Pfeiffer Dietmar D, Singh Dharmesh D, Reinhardt Till T, Mibus Cora C, Huber Matthias M, Hess Corinna R CR, Mejías-Luque Raquel R, Gerhard Markus M, Groll Michael M, Sieber Stephan A SAfalse5-Nitroimidazole ethers boost anti-Helicobacter pylori activity via a dual mode of action and effectively eradicate infections in vivoMetronidazole (Metro) represents the front line-drug against Helicobacter pylori infections, but despite its crucial role as an antibiotic, little is known about its exact mode of action (MoA). To unravel cellular protein targets, we here performed activity-based protein profiling (ABPP) with tailored Metro probes. Surprisingly, an alkynylated ether probe (Metro-P3) exhibited a 60-fold enhanced potency against H. pylori, suggesting that this moiety represents a crucial, yet undiscovered switch for the activity profile. ABPP in living H. pylori uncovered two major protein targets, chaperonin HpGroEL and thiol peroxidase HpTpx, which are both part of the oxidative stress response and essential for H. pylori to survive under gastric oxidative stress. Tailored biological assays validated the inhibition of both targets by covalent modification of cysteines. Strikingly, the binding of Metro-P3 to HpTpx was much more pronounced compared to the parent drug. This diverging interaction of both molecules was corroborated by co-crystallization studies with Metro and Metro-P3 identifying the propargyl ether moiety to be essential for a prominent helix-dipole interaction in HpTpx. Metro-P3 along with several refined ether analogs exhibited no human cell toxicity up to 1 mM, favorable pharmacological profiles, and sufficient plasma stability. Satisfyingly, the activity boost translated to in vivo H. pylori mouse infection models where the most potent ether analog showed full eradication of bacteria at 50-fold reduced dosing compared to regular metronidazole standard triple therapy. Overall, our results highlight ether modifications of 5-nitroimidazole alcohols as unprecedented path towards dual MoA antibiotics which induce oxidative stress and simultaneously inhibit the stress response eventually leading to bacterial cell death2026-04-132024-04-26PXD051773NEWT:3555NEWT:71647NEWT:35554NEWT:32046NEWT:544496NEWT:2042546NEWT:32049NEWT:1392696NEWT:259447NEWT:45351NEWT:445974NEWT:43179NEWT:180454NEWT:5722NCBITaxon:1280NEWT:1129NEWT:309807NEWT:55153NEWT:309800NEWT:281395NEWT:1211601NEWT:876138NEWT:44271NEWT:10036NEWT:1590NEWT:498019NEWT:1351NEWT:1438992NEWT:1352NEWT:2649997NEWT:1147161NEWT:224326NEWT:1333499NCBITaxon:79857NEWT:1096976NEWT:95648NEWT:1589NEWT:135622NEWT:1349NEWT:96731NEWT:383379NEWT:10029NEWT:913645NEWT:44491NEWT:556484NEWT:317447NEWT:4688NEWT:7955NEWT:7959NEWT:2261NEWT:31156NEWT:3112NEWT:4442NEWT:192875NEWT:12637NEWT:59729NEWT:2164133NEWT:108061NEWT:1316931NEWT:224308NEWT:3347NEWT:511145NEWT:931281NEWT:658457NEWT:1310161NEWT:77133NEWT:295358NEWT:145481NCBITaxon:79824NCBITaxon:4563NEWT:5755NEWT:44689NEWT:44447NEWT:5759NEWT:1736231NEWT:5518NEWT:1392NEWT:498217NEWT:2242NEWT:11320NEWT:286NEWT:391619NEWT:246196NEWT:287NEWT:246197NEWT:633149NEWT:10239NEWT:44685NEWT:161934NEWT:1148NEWT:5508NEWT:5507NEWT:410661NEWT:55571NEWT:35500NEWT:1140NCBITaxon:2157NEWT:1143NEWT:4896NEWT:1390NEWT:11557NEWT:1094343NEWT:1336795NEWT:644042NEWT:294NEWT:1773NEWT:1182590NEWT:3712NEWT:82380NEWT:935293NEWT:375146NEWT:118698NEWT:263NEWT:118696NEWT:52283NEWT:284812NEWT:8175NEWT:43330NEWT:1603293NEWT:408169NEWT:44664NEWT:47946NEWT:3702NEWT:243277NEWT:7067NEWT:118694NEWT:2850NEWT:118691NEWT:33548NEWT:274NEWT:408172NEWT:408170NEWT:3708NEWT:332648NEWT:44670NEWT:536231NEWT:376219NEWT:1436733NEWT:460519NEWT:572307NEWT:1432138NEWT:1424507NEWT:1194599NEWT:272844NEWT:9483NEWT:333760NEWT:1513458NCBITaxon:40559NEWT:84588NEWT:1679718NEWT:480NEWT:67767NEWT:46835NEWT:109757NEWT:582580NEWT:300852NEWT:1502NEWT:376686NEWT:95486NEWT:508771NEWT:1883446NEWT:253NCBITaxon:2759NEWT:1233435NEWT:93061NEWT:93062NCBITaxon:4932NEWT:644223NEWT:235443NEWT:108458NEWT:272623NEWT:272624NEWT:320637NEWT:983964NEWT:118499NEWT:32644NEWT:527796NEWT:499175NEWT:109779NEWT:3745NEWT:1715989NCBITaxon:4751NEWT:476272NEWT:3747NEWT:195051NEWT:3988NEWT:1255228NEWT:649908NEWT:410289NEWT:373153NEWT:352472NEWT:1071661NEWT:360094NEWT:470NEWT:41364NEWT:1313NEWT:39491NCBITaxon:5811NEWT:29491NEWT:2014887NEWT:33952NEWT:261756NEWT:571256NEWT:40483NEWT:272634NEWT:9031NEWT:1872122NEWT:7091NEWT:141262NEWT:108931NEWT:1055524NEWT:4087NEWT:9778NEWT:306NEWT:150475NEWT:303NEWT:267872NEWT:7111NEWT:347515NEWT:9534NEWT:5180NEWT:256737NEWT:4090NEWT:4092NEWT:9541NEWT:4093NEWT:4096NEWT:185579NEWT:941442NEWT:13076NEWT:7108NEWT:40479NEWT:4076NEWT:317NEWT:1006581NEWT:885318NEWT:39488NEWT:550NEWT:4081NEWT:273068NEWT:554NEWT:98334NEWT:451516NEWT:36185NEWT:1225786NEWT:7574NEWT:1715256NEWT:30640NEWT:575412NEWT:929793NEWT:29204NEWT:28112NEWT:114155NEWT:6494NEWT:6491NEWT:507601NEWT:643680NEWT:214092NCBITaxon:6157NEWT:6239NEWT:162425NEWT:216257NEWT:102169NEWT:9986NEWT:4054NEWT:1268063NEWT:1263854NEWT:118503NEWT:2059687NEWT:160488NEWT:28104NEWT:407821NCBITaxon:2NEWT:985076NEWT:1215323NEWT:986NEWT:52641NEWT:7159NEWT:28532NEWT:353152NEWT:8496NEWT:27448NEWT:40674NEWT:1194669NEWT:243230NEWT:1080772NEWT:519NEWT:8479NEWT:8485NEWT:6063NEWT:49240NEWT:104395NEWT:6289NEWT:6287NEWT:300641NEWT:727NEWT:9796NEWT:725NEWT:469008NEWT:256318NEWT:9321NEWT:206411NCBITaxon:6191NEWT:596153NEWT:229533NEWT:1836NEWT:80863NEWT:105231NEWT:52638NEWT:57075NEWT:4097NEWT:884204NEWT:9785NEWT:6279NEWT:1123869NEWT:9544NEWT:7370NEWT:83906NCBITaxon:780NCBITaxon:1502NEWT:6282NEWT:1134506NEWT:38783NEWT:4006NEWT:6426NCBITaxon:5476NEWT:6669NEWT:9935NEWT:89453NEWT:287889NEWT:51515NEWT:588596NEWT:51511NEWT:8845NEWT:92867NEWT:92866NEWT:5334NEWT:51750NEWT:202950NEWT:382352NEWT:413071NEWT:632957NEWT:9925NEWT:89462NCBITaxon:9606NEWT:8839NEWT:90690NEWT:4232NEWT:2758385NEWT:11298NEWT:171101NEWT:714NEWT:421932NEWT:312017NEWT:196627NEWT:200308NEWT:200302NEWT:870435NEWT:284593NEWT:100392NEWT:5315NEWT:9913NEWT:265872NEWT:105841NEWT:337330NEWT:2666255NEWT:2285NEWT:999810NCBITaxon:5693NEWT:1392998NEWT:380394NEWT:981087NEWT:180066NEWT:226900NEWT:231490NEWT:430615NEWT:326423NEWT:452467NEWT:198822NEWT:36111NEWT:326424NEWT:1416333NEWT:1678078NEWT:749906NEWT:418985NEWT:1817808NEWT:749907NEWT:145263NEWT:694569NEWT:27606NEWT:9739NEWT:59202NEWT:9975NEWT:51953NEWT:3197NEWT:860688NEWT:13443NEWT:36329NEWT:62615NCBITaxon:3044782NEWT:160235NEWT:72407NEWT:349741NEWT:157295NEWT:2096NEWT:192222NEWT:9721NEWT:137221NEWT:9963NEWT:1617910NEWT:565050NEWT:2785785NEWT:411901NEWT:105884NCBITaxon:9615NEWT:58334NEWT:1193501NEWT:58331NEWT:6689NEWT:298315NEWT:70448NEWT:698936NEWT:9940NEWT:3168NEWT:521001NEWT:192011NEWT:1813887NEWT:118702NEWT:118700NEWT:224911NEWT:118705NCBITaxon:11552NEWT:6945NEWT:184922NEWT:6703NEWT:2104NEWT:2NEWT:157546NEWT:474186NEWT:38942NEWT:307972NEWT:1496NEWT:2102NEWT:45474NEWT:1590841NEWT:4513NEWT:1247NEWT:70667NEWT:6938NCBITaxon:10407NEWT:1736309NEWT:4751NEWT:10360NEWT:47664NEWT:317548NEWT:15819NEWT:3654NEWT:237561NEWT:5833NEWT:6928NEWT:1239NEWT:36745NEWT:272563NEWT:82688NEWT:3885NEWT:3888NEWT:5821NEWT:44139NCBITaxon:4896NEWT:6915NEWT:3649NEWT:101510NEWT:28903NEWT:3880NEWT:272559N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