{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,23]],"date-time":"2026-09-23T11:32:44Z","timestamp":1790163164768,"version":"4.1.0"},"reference-count":50,"publisher":"MDPI AG","issue":"22","license":[{"start":{"date-parts":[[2025,11,9]],"date-time":"2025-11-09T00:00:00Z","timestamp":1762646400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"seed grant funding","award":["ASG2022053"],"award-info":[{"award-number":["ASG2022053"]}]},{"DOI":"10.13039\/100009526","name":"Amrita Vishwa Vidyapeetham","doi-asserted-by":"crossref","award":["SUR\/2022\/003961"],"award-info":[{"award-number":["SUR\/2022\/003961"]}],"id":[{"id":"10.13039\/100009526","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>Rv1899c, a previously identified HDAC1\u2013ZBTB25-interacting protein of Mycobacterium tuberculosis, plays a crucial role in bacterial adaptation and immune modulation. Recombinant M. smegmatis-expressing Rv1899c (MS_ Rv1899c) showed enhanced survival under acidic and oxidative stress compared to vector controls, along with improved early intracellular growth in THP1-derived macrophages. This was accompanied by reduced reactive oxygen species (ROS), diminished cytokines associated with inflammation and downregulation of autophagy proteins ATG5, Beclin, and LC3, which ultimately skewed the immune response, suppressing the pro-inflammatory M1 macrophage population. Targeting Rv1899c with 3-aminobenzamide (3-AB) impaired intracellular bacterial survival and restored IL-12B expression, while its combination with the HDAC inhibitor C1994 significantly enhanced bacterial clearance. Structural modelling confirmed the high stereochemical quality of the Rv1899c macrodomain, and computational studies identified 3-AB as the strongest ligand (\u22125.75 kcal\/mol), stabilized through hydrogen bonding and hydrophobic interactions with key residues. Molecular dynamics simulations conducted for 200 ns demonstrated stable protein\u2013ligand interactions with consistent parameters, while MM\/GBSA analysis indicated favourable binding energy (\u0394G_bind = \u22126.6 kcal\/mol), largely influenced by van der Waals and electrostatic forces. Together, these findings highlight Rv1899c as a mediator of stress resistance and immune evasion and propose it as a potential therapeutic target against M. tuberculosis.<\/jats:p>","DOI":"10.3390\/ijms262210872","type":"journal-article","created":{"date-parts":[[2025,11,10]],"date-time":"2025-11-10T08:57:55Z","timestamp":1762765075000},"page":"10872","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["Rv1899c, an HDAC1\u2013ZBTB25-Interacting Protein of Mycobacterium tuberculosis, Promotes Stress Resistance and Immune Evasion in Infected Macrophages"],"prefix":"10.3390","volume":"26","author":[{"ORCID":"https:\/\/orcid.org\/0009-0004-2263-0350","authenticated-orcid":false,"given":"Arjun M.","family":"Menon","sequence":"first","affiliation":[{"name":"School of Biotechnology, Amrita Vishwa Vidyapeetham, Amritapuri, Kollam 690525, Kerala, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0001-6652-6326","authenticated-orcid":false,"given":"Boinapalli","family":"Gopichand","sequence":"additional","affiliation":[{"name":"School of Biotechnology, Amrita Vishwa Vidyapeetham, Amritapuri, Kollam 690525, Kerala, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shwetha Susan","family":"Thomas","sequence":"additional","affiliation":[{"name":"School of Biotechnology, Amrita Vishwa Vidyapeetham, Amritapuri, Kollam 690525, Kerala, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-2943-7006","authenticated-orcid":false,"given":"Kuniyil","family":"Abhinand","sequence":"additional","affiliation":[{"name":"School of Biotechnology, Amrita Vishwa Vidyapeetham, Amritapuri, Kollam 690525, Kerala, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bipin G.","family":"Nair","sequence":"additional","affiliation":[{"name":"School of Biotechnology, Amrita Vishwa Vidyapeetham, Amritapuri, Kollam 690525, Kerala, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Geetha B.","family":"Kumar","sequence":"additional","affiliation":[{"name":"School of Biotechnology, Amrita Vishwa Vidyapeetham, Amritapuri, Kollam 690525, Kerala, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0569-6628","authenticated-orcid":false,"given":"Pradeesh","family":"Babu","sequence":"additional","affiliation":[{"name":"School of Biotechnology, Amrita Vishwa Vidyapeetham, Amritapuri, Kollam 690525, Kerala, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8292-5933","authenticated-orcid":false,"given":"KB","family":"Arun","sequence":"additional","affiliation":[{"name":"Department of Life Sciences, CHRIST (Deemed to be University), Bangalore 560029, Karnataka, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2599-7428","authenticated-orcid":false,"given":"Lekshmi K.","family":"Edison","sequence":"additional","affiliation":[{"name":"Department of Comparative, Diagnostic, and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, FL 32608, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aravind","family":"Madhavan","sequence":"additional","affiliation":[{"name":"School of Biotechnology, Amrita Vishwa Vidyapeetham, Amritapuri, Kollam 690525, Kerala, India"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2025,11,9]]},"reference":[{"key":"ref_1","unstructured":"(2025, September 21). Tuberculosis. Available online: https:\/\/www.who.int\/news-room\/fact-sheets\/detail\/tuberculosis."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"167","DOI":"10.1016\/j.jgar.2025.02.014","article-title":"Second-line drug resistance among multidrug-resistant tuberculosis patients in Ethiopia: A laboratory-based surveillance","volume":"42","author":"Diriba","year":"2025","journal-title":"J. Glob. Antimicrob. Resist."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"654","DOI":"10.2105\/AJPH.2010.199505","article-title":"The Social Determinants of Tuberculosis: From Evidence to Action","volume":"101","author":"Hargreaves","year":"2011","journal-title":"Am. J. Public Health"},{"key":"ref_4","doi-asserted-by":"crossref","unstructured":"Frota, C.C., Hunt, D.M., Buxton, R.S., Rickman, L., Hinds, J., Kremer, K., van Soolingen, D., and Colston, M.J. (2004). Genome structure in the vole bacillus, Mycobacterium microti, a member of the Mycobacterium tuberculosis complex with a low virulence for humans. Microbiology, 150.","DOI":"10.1099\/mic.0.26660-0"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"2236","DOI":"10.1110\/ps.051526305","article-title":"Mycobacterium tuberculosis Rv2536 protein implicated in specific binding to human cell lines","volume":"14","author":"Puentes","year":"2005","journal-title":"Protein Sci."},{"key":"ref_6","doi-asserted-by":"crossref","unstructured":"Manjunath, P., Ahmad, J., Samal, J., Sheikh, J.A., Arora, S.K., Khubaib, M., Aggarwal, H., Kumari, I., Luthra, K., and Rahman, S.A. (2021). Mycobacterium tuberculosis Specific Protein Rv1509 Evokes Efficient Innate and Adaptive Immune Response Indicative of Protective Th1 Immune Signature. Front. Immunol., 12.","DOI":"10.3389\/fimmu.2021.706081"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"7729","DOI":"10.1073\/pnas.1120251109","article-title":"Mycobacterium tuberculosis Eis protein initiates suppression of host immune responses by acetylation of DUSP16\/MKP-7","volume":"109","author":"Kim","year":"2012","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_8","doi-asserted-by":"crossref","unstructured":"Shin, D.M., Jeon, B.-Y., Lee, H.-M., Jin, H.S., Yuk, J.-M., Song, C.-H., Lee, S.-H., Lee, Z.-W., Cho, S.-N., and Kim, J.-M. (2010). Mycobacterium tuberculosis Eis Regulates Autophagy, Inflammation, and Cell Death through Redox-dependent Signaling. PLoS Pathog., 6.","DOI":"10.1371\/journal.ppat.1001230"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"19371","DOI":"10.1073\/pnas.1109201108","article-title":"Mycobacterium tuberculosis protein tyrosine phosphatase (PtpA) excludes host vacuolar-H +-ATPase to inhibit phagosome acidification","volume":"108","author":"Wong","year":"2011","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_10","doi-asserted-by":"crossref","unstructured":"Anes, E., Pires, D., Mandal, M., and Azevedo-Pereira, J.M. (2023). ESAT-6 a Major Virulence Factor of Mycobacterium tuberculosis. Biomolecules, 13.","DOI":"10.20944\/preprints202305.0979.v1"},{"key":"ref_11","doi-asserted-by":"crossref","unstructured":"Singh, V., Kaur, C., Chaudhary, V.K., Rao, K.V.S., and Chatterjee, S.M. (2015). tuberculosis Secretory Protein ESAT-6 Induces Metabolic Flux Perturbations to Drive Foamy Macrophage Differentiation. Sci. Rep., 5.","DOI":"10.1038\/srep12906"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"e00036-21","DOI":"10.1128\/mSphere.00036-21","article-title":"Transcription Repressor Protein ZBTB25 Associates with HDAC1-Sin3a Complex in Mycobacterium tuberculosis-Infected Macrophages, and Its Inhibition Clears Pathogen by Autophagy","volume":"6","author":"Madhavan","year":"2021","journal-title":"mSphere"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"4312","DOI":"10.1016\/S0021-9258(18)83741-3","article-title":"Quantitative studies of inhibitors of ADP-ribosylation in vitro and in vivo","volume":"264","author":"Rankin","year":"1989","journal-title":"J. Biol. Chem."},{"key":"ref_14","doi-asserted-by":"crossref","unstructured":"Rastogi, S., Ellinwood, S., Augenstreich, J., Mayer-Barber, K.D., and Briken, V. (2021). Mycobacterium tuberculosis inhibits the NLRP3 inflammasome activation via its phosphokinase PknF. PLoS Pathog., 17.","DOI":"10.1371\/journal.ppat.1009712"},{"key":"ref_15","doi-asserted-by":"crossref","unstructured":"Simeone, R., Bobard, A., Lippmann, J., Bitter, W., Majlessi, L., Brosch, R., and Enninga, J. (2012). Phagosomal Rupture by Mycobacterium tuberculosis Results in Toxicity and Host Cell Death. PLoS Pathog., 8.","DOI":"10.1371\/journal.ppat.1002507"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"3","DOI":"10.4161\/viru.22329","article-title":"Virulence factors of the Mycobacterium tuberculosis complex","volume":"4","author":"Forrellad","year":"2013","journal-title":"Virulence"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"374","DOI":"10.1002\/eji.201141548","article-title":"Activation of the NLRP3 inflammasome by Mycobacterium tuberculosis is uncoupled from susceptibility to active tuberculosis","volume":"42","author":"Dorhoi","year":"2012","journal-title":"Eur. J. Immunol."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"576","DOI":"10.1080\/15548627.2021.1938912","article-title":"M. tuberculosis PknG manipulates host autophagy flux to promote pathogen intracellular survival","volume":"18","author":"Ge","year":"2022","journal-title":"Autophagy"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"4033","DOI":"10.1073\/pnas.0409716102","article-title":"Mechanism of phagolysosome biogenesis block by viable Mycobacterium tuberculosis","volume":"102","author":"Vergne","year":"2005","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"e0054921","DOI":"10.1128\/mSphere.00549-21","article-title":"Mycobacterium tuberculosis PE_PGRS20 and PE_PGRS47 Proteins Inhibit Autophagy by Interaction with Rab1A","volume":"6","author":"Strong","year":"2021","journal-title":"mSphere"},{"key":"ref_21","first-page":"481","article-title":"Mycobacterium tuberculosis Cpn60.2 (GroEL2) blocks macrophage apoptosis via interaction with mitochondrial mortalin","volume":"6","author":"Joseph","year":"2017","journal-title":"Biol. Open"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"293","DOI":"10.1002\/pro.3330","article-title":"MolProbity: More and better reference data for improved all-atom structure validation","volume":"27","author":"Williams","year":"2018","journal-title":"Protein Sci."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"283","DOI":"10.1107\/S0021889892009944","article-title":"PROCHECK: A program to check the stereochemical quality of protein structures","volume":"26","author":"Laskowski","year":"1993","journal-title":"J. Appl. Crystallogr."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"1129","DOI":"10.1016\/j.neuron.2018.08.011","article-title":"Molecular Dynamics Simulation for All","volume":"99","author":"Hollingsworth","year":"2018","journal-title":"Neuron"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"449","DOI":"10.1517\/17460441.2015.1032936","article-title":"The MM\/PBSA and MM\/GBSA methods to estimate ligand-binding affinities","volume":"10","author":"Genheden","year":"2015","journal-title":"Expert Opin. Drug Discov."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"221","DOI":"10.1007\/s10822-013-9644-8","article-title":"Protein and ligand preparation: Parameters, protocols, and influence on virtual screening enrichments","volume":"27","author":"Sastry","year":"2013","journal-title":"J. Comput. Aided Mol. Des."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"583","DOI":"10.1038\/s41586-021-03819-2","article-title":"Highly accurate protein structure prediction with AlphaFold","volume":"596","author":"Jumper","year":"2021","journal-title":"Nature"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"D439","DOI":"10.1093\/nar\/gkab1061","article-title":"AlphaFold Protein Structure Database: Massively expanding the structural coverage of protein-sequence space with high-accuracy models","volume":"50","author":"Varadi","year":"2022","journal-title":"Nucleic Acids Res."},{"key":"ref_29","unstructured":"(The PyMOL Molecular Graphics System, 2015). The PyMOL Molecular Graphics System, Version 1.8."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1107\/S0907444909042073","article-title":"MolProbity: All-atom structure validation for macromolecular crystallography","volume":"66","author":"Chen","year":"2010","journal-title":"Acta Crystallogr. D Biol. Crystallogr."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"D1516","DOI":"10.1093\/nar\/gkae1059","article-title":"PubChem 2025 update","volume":"53","author":"Kim","year":"2025","journal-title":"Nucleic Acids Res."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1186\/1758-2946-3-33","article-title":"Open Babel: An Open chemical toolbox","volume":"3","author":"Banck","year":"2011","journal-title":"J. Cheminform."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"2785","DOI":"10.1002\/jcc.21256","article-title":"AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility","volume":"30","author":"Morris","year":"2009","journal-title":"J. Comput. Chem."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"3891","DOI":"10.1021\/acs.jcim.1c00203","article-title":"AutoDock Vina 1.2.0: New Docking Methods, Expanded Force Field, and Python Bindings","volume":"61","author":"Eberhardt","year":"2021","journal-title":"J. Chem. Inf. Model."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"1701","DOI":"10.1002\/jcc.20291","article-title":"GROMACS: Fast, flexible, and free","volume":"26","author":"Lindahl","year":"2005","journal-title":"J. Comput. Chem."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1016\/j.softx.2015.06.001","article-title":"GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers","volume":"1\u20132","author":"Abraham","year":"2015","journal-title":"SoftwareX"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"3554","DOI":"10.1021\/acs.jctc.1c00254","article-title":"Additive CHARMM36 Force Field for Nonstandard Amino Acids","volume":"17","author":"Croitoru","year":"2021","journal-title":"J. Chem. Theory Comput."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"2135","DOI":"10.1002\/jcc.23354","article-title":"CHARMM36 all-atom additive protein force field: Validation based on comparison to NMR data","volume":"34","author":"Huang","year":"2013","journal-title":"J. Comput. Chem."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"671","DOI":"10.1002\/jcc.21367","article-title":"CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields","volume":"31","author":"Vanommeslaeghe","year":"2010","journal-title":"J. Comput. Chem."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"3144","DOI":"10.1021\/ci300363c","article-title":"Automation of the CHARMM General Force Field (CGenFF) I: Bond perception and atom typing","volume":"52","author":"Vanommeslaeghe","year":"2012","journal-title":"J. Chem. Inf. Model."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"3155","DOI":"10.1021\/ci3003649","article-title":"Automation of the CHARMM General Force Field (CGenFF) II: Assignment of Bonded Parameters and Partial Atomic Charges","volume":"52","author":"Vanommeslaeghe","year":"2012","journal-title":"J. Chem. Inf. Model."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"014101","DOI":"10.1063\/1.2408420","article-title":"Canonical sampling through velocity rescaling","volume":"126","author":"Bussi","year":"2007","journal-title":"J. Chem. Phys."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"124108","DOI":"10.1063\/1.4978807","article-title":"Application of Berendsen barostat in dissipative particle dynamics for nonequilibrium dynamic simulation","volume":"146","author":"Lin","year":"2017","journal-title":"J. Chem. Phys."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"14631472","DOI":"10.1002\/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H","article-title":"LINCS: A Linear Constraint Solver for Molecular Simulations","volume":"18","author":"Hess","year":"1997","journal-title":"J. Comput. Chem."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"10089","DOI":"10.1063\/1.464397","article-title":"Particle mesh Ewald: An N\u22c5log(N) method for Ewald sums in large systems","volume":"98","author":"Darden","year":"1993","journal-title":"J. Chem. Phys."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"184102","DOI":"10.1063\/1.2779878","article-title":"On the calculation of velocity-dependent properties in molecular dynamics simulations using the leapfrog integration algorithm","volume":"127","author":"Cuendet","year":"2007","journal-title":"J. Chem. Phys."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"90","DOI":"10.1109\/MCSE.2007.55","article-title":"Matplotlib: A 2D graphics environment","volume":"9","author":"Hunter","year":"2007","journal-title":"Comput. Sci. Eng."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"3021","DOI":"10.21105\/joss.03021","article-title":"seaborn: Statistical data visualization","volume":"6","author":"Waskom","year":"2021","journal-title":"J. Open Source Softw."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"3314","DOI":"10.1021\/ct300418h","article-title":"MMPBSA.py: An efficient program for end-state free energy calculations","volume":"8","author":"Miller","year":"2012","journal-title":"J. Chem. Theory Comput."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"6281","DOI":"10.1021\/acs.jctc.1c00645","article-title":"Gmx_MMPBSA: A New Tool to Perform End-State Free Energy Calculations with GROMACS","volume":"17","author":"Valiente","year":"2021","journal-title":"J. Chem. Theory Comput."}],"container-title":["International Journal of Molecular Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1422-0067\/26\/22\/10872\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,11,12]],"date-time":"2025-11-12T05:18:22Z","timestamp":1762924702000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1422-0067\/26\/22\/10872"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,11,9]]},"references-count":50,"journal-issue":{"issue":"22","published-online":{"date-parts":[[2025,11]]}},"alternative-id":["ijms262210872"],"URL":"https:\/\/doi.org\/10.3390\/ijms262210872","relation":{},"ISSN":["1422-0067"],"issn-type":[{"value":"1422-0067","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,11,9]]}}}