Adamu A, Li S, Gao F, Xue G (2024) The role of neuroinflammation in neurodegenerative diseases: current understanding and future therapeutic targets. Front Aging Neurosci 16(4):1347987. https://doi.org/10.3389/fnagi.2024.1347987

Article  CAS  PubMed  PubMed Central  Google Scholar 

Akbar S, Ullah M, Raza A, Zou Q, Alghamdi W (2024) DeepAIPs-Pred: predicting anti-inflammatory peptides using local evolutionary transformation images and structural embedding-based optimal descriptors with self-normalized BiTCNs. J Chem Inf Model 64(24):9609–9625. https://doi.org/10.1021/acs.jcim.4c01758

Article  CAS  PubMed  Google Scholar 

Akiba T, Sano S, Yanase T, Ohta T, Koyama M (2019) Optuna: a next-generation hyperparameter optimization framework. ArXiv. https://doi.org/10.48550/arXiv.1907.10902

Alles SRA, Smith PA (2021) Peripheral voltage-gated cation channels in neuropathic pain and their potential as therapeutic targets. Front Pain Res 2(12):750583. https://doi.org/10.3389/fpain.2021.750583

Article  Google Scholar 

Bellver-Sanchis A, Ávila-López P, Tic I, Valle-García D, Ribalta-Vilella M, Griñán-Ferré C et al (2024) Neuroprotective effects of G9a inhibition through modulation of peroxisome-proliferator activator receptor gamma-dependent pathways by miR-128. Neural Regen Res 19(11):2532–2542. https://doi.org/10.4103/1673-5374.393102

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bellver-Sanchis A, Ribalta-Vilella M, Irisarri A, Gehlot P, Choudhary BS, Griñán-Ferré C et al (2025) G9a an epigenetic therapeutic strategy for neurodegenerative conditions: from target discovery to clinical trials. Med Res Rev. https://doi.org/10.1002/med.22096

Article  PubMed  PubMed Central  Google Scholar 

Chen X, Xie L, Sheehy R, Xiong Y, Muneer A et al (2023) Novel brain-penetrant inhibitor of G9a methylase blocks Alzheimer’s disease proteopathology for precision medication. Res Sq. https://doi.org/10.21203/rs.3.rs-2743792/v1

Article  PubMed  PubMed Central  Google Scholar 

Chen YZ, Zhu XM, Lv P, Hou XK, Pan Y, Li A, Du Z, Xuan JF, Guo X, Xing JX, Liu K (2024) Association of histone modification with the development of schizophrenia. Biomed Pharmacother 175(6):116747. https://doi.org/10.1016/j.biopha.2024.116747

Article  CAS  PubMed  Google Scholar 

Cheng T, Zhao Y, Li X, Lin F, Lai L et al (2007) Computation of octanol-water partition coefficients by guiding an additive model with knowledge. J Chem Inf Modell 47(6):2140–2148. https://doi.org/10.1021/ci700257y

Article  CAS  Google Scholar 

Costa AP, Choren R, Pereira DA, Terra AV, Costa IP, Junior CD, Santos MD, Gomes CF, Moreira MÂ (2024) Integrating multicriteria decision making and principal component analysis: a systematic literature review. Cogent Eng 11(1):2374944. https://doi.org/10.1080/23311916.2024.2374944

Article  Google Scholar 

Crews FT, Fisher RP, Qin L, Vetreno RP (2023) HMGB1 neuroimmune signalling and REST-G9a gene repression contribute to ethanol-induced reversible suppression of the cholinergic neuron phenotype. Mol Psychiatry 28(12):5159–5172. https://doi.org/10.1038/s41380-023-02160-6

Article  CAS  PubMed  PubMed Central  Google Scholar 

Ertl P, Rohde B, Selzer P (2000) Fast calculation of molecular polar surface area as a sum of fragment-based contributions and its application to the prediction of drug transport properties. J Med Chem 43(20):3714–3717. https://doi.org/10.1021/jm000942e

Article  CAS  PubMed  Google Scholar 

Ghosh K, Pan HL (2022) Epigenetic mechanisms of neural plasticity in chronic neuropathic pain. ACS Chem Neurosci 13(4):432–441. https://doi.org/10.1021/acschemneuro.1c00841

Article  CAS  PubMed  Google Scholar 

Ghosh K, Huang Y, Jin D, Chen SR, Pan HL (2025) Histone methyltransferase G9a in primary sensory neurons promotes inflammatory pain and transcription of Trpa1 and Trpv1 via bivalent histone modifications. J Neurosci 45(6):e1790242024. https://doi.org/10.1523/jneurosci.1790-24.2024

Article  CAS  PubMed  PubMed Central  Google Scholar 

Hwang JY, Zukin RS (2018) REST, a master transcriptional regulator in neurodegenerative disease. Curr Opin Neurobiol 48:193–200. https://doi.org/10.1016/j.conb.2017.12.008

Article  CAS  PubMed  PubMed Central  Google Scholar 

Imbalanced Learn (2025) RandomOverSampler. https://imbalanced-learn.org/stable/references/generated/imblearn.over_sampling.RandomOverSampler.html. Accessed 20 Feb 2025

IUPAC (2025) Home page. IUPAC. https://iupac.org/. Accessed 20 Feb 2025

Ivanova ML, Russo N, Djaid N, Nikolic K (2024) Application of machine learning for predicting G9a inhibitors. Digit Discov 3(10):2010–2018. https://doi.org/10.1039/D4DD00101J

Article  CAS  Google Scholar 

Ivanova ML, Russo N, Nikolic K (2025a) Predicting novel pharmacological activities of compounds using PubChem IDs and machine learning (CID-SID ML model). ArXiv. https://doi.org/10.48550/arXiv.2501.02154

Ivanova ML, Russo N, Nikolic K (2025b) Leveraging 13C NMR spectrum data derived from SMILES for machine learning-based prediction of a small molecule functionality: a case study on human Dopamine D1 receptor antagonists. ArXiv. https://doi.org/10.48550/arXiv.2501.14044

Ivanova ML, Russo N, Nikolic K (2025c) Hierarchical functional group ranking via IUPAC name analysis for drug discovery: a case study on TDP1 Inhibitors. ArXiv. https://doi.org/10.48550/arXiv.2503.05591

Ivanova ML, Russo N, Nikolic K (2025d) Comparative analysis of computational approaches for predicting Transthyretin transcription activators and human dopamine D1 receptor antagonists. ArXiv. https://doi.org/10.48550/arXiv.2506.01137

Jupyter (2024) Home page. Jupyter. https://jupyter.org/. Accessed 4 Jan 2025

Kim S, Thiessen PA, Bolton EE, Chen J, Fu G, Gindulyte A, Han L, He J, He S et al (2016) PubChem substance and compound databases. Nucleic Acids Res 44:D1202–D1213. https://doi.org/10.1093/nar/gkv951

Article  CAS  PubMed  Google Scholar 

Laumet G, Garriga J, Chen SR, Zhang Y, Li DP, Pan HL et al (2015) G9a is essential for epigenetic silencing of K (+) channel genes in acute-to-chronic pain transition. Nat Neurosci 18(12):1746–1755. https://doi.org/10.1038/nn.4165

Article  CAS  PubMed  PubMed Central  Google Scholar 

Luo Y, Zhang J, Chen L, Chen SR, Chen H, Zhang G, Pan HL (2020) Histone methyltransferase G9a diminishes expression of cannabinoid CB1 receptors in primary sensory neurons in neuropathic pain. J Biol Chem 295(11):3553–3562. https://doi.org/10.1074/jbc.ra119.011053

Article  CAS  PubMed  PubMed Central  Google Scholar 

Muneer A, Wang L, Xie L, Zhang F, Wu B, Mei L, Lenarcic EM, Feng EH et al (2023) Non-canonical function of histone methyltransferase G9a in the translational regulation of chronic inflammation. Cell Chem Biol 30(12):1525-1541.e7. https://doi.org/10.1016/j.chembiol.2023.09.012

Article  CAS  PubMed  PubMed Central  Google Scholar 

Park J, Lee K, Kim K, Yi S-J (2022) The role of histone modifications: from neurodevelopment to neurodiseases. Signal Transduct Target Ther 7:217. https://doi.org/10.1038/s41392-022-01078-9

Article  CAS  PubMed  PubMed Central  Google Scholar 

Pedregosa F, Varoquaux G, Gramfort A, Michel V, Thirion B, Grisel O, Blondel M, Prettenhofer P, Weiss R, Dubourg V, Vanderplas J (2011) Scikit-learn: machine learning in python. J Mach Learn Res 1(12):2825–2830

Google Scholar 

PubChem (2009) Compound summary. National Institutes of Health. https://pubchem.ncbi.nlm.nih.gov/compound/25150857#section=InChIKey. Accessed 20 Feb 2025

PubChem (2010) Aqueous solubility from MLSMR stock solutions. National Institutes of Health. https://pubchem.ncbi.nlm.nih.gov/bioassay/1996. Accessed 20 Feb 2025

PubChem (2011) qHTS assay for inhibitors of histone lysine methyltransferase G9a. National Institutes of Health. https://pubchem.ncbi.nlm.nih.gov/bioassay/504332. Accessed 20 Feb 2025

PubChem (2024) Inhibition of G9a (unknown origin). National Institutes of Health. https://pubchem.ncbi.nlm.nih.gov/bioassay/1938431#section=Data-Table. Accessed 20 Feb 2025

PubChem (2025a) Explore chemistry. National Institutes of Health. https://pubchem.ncbi.nlm.nih.gov/. Accessed 20 Feb 2025

PubChem (2025b) About PubChem. National Institutes of Health. https://pubchem.ncbi.nlm.nih.gov/docs/about. Accessed 20 Feb 2025

PubChem (2025c) Compound summary. National Institutes of Health. https://pubchem.ncbi.nlm.nih.gov/compound/171347753. Accessed 20 Feb 2025

Roopra A, Qazi R, Schoenike B, Daley TJ, Morrison JF (2004) Localized domains of G9a-mediated histone methylation are required for silencing of neuronal genes. Mol Cell 14(6):727–738. https://doi.org/10.1016/j.molcel.2004.05.026

Article  CAS  PubMed  Google Scholar 

Rothammer N, Woo MS, Bauer S, Binkle-Ladisch L, Di Liberto G, Egervari K et al (2022) G9a dictates neuronal vulnerability to inflammatory stress via transcriptional control of ferroptosis. Sci Adv 8(31):5500. https://doi.org/10.1126/sciadv.abm5500

Article  CAS  Google Scholar 

Rukh G, Akbar S, Rehman G, Alarfaj FK, Zou Q (2024) StackedEnC-AOP: prediction of antioxidant proteins using transform evolutionary and sequential features based multi-scale vector with stacked ensemble learning. BMC Bioinf 25:256. https://doi.org/10.1186/s12859-024-05884-6

Article  CAS