bims-toxgon 2026-09-06 papers

bims-toxgon

Biomed News

on Toxoplasma gondii metabolism

Issue of 2026–09–06
25 papers selected by
Lakesh Kumar, BITS Pilani

The live attenuated DGAT1-knockout whole-cell Toxoplasma vaccine confers protective immunity against acute and chronic toxoplasmosis.
Recombinant Toxoplasma gondii expressing FIPV spike protein S1 subunit: A proof-of-concept approach against toxoplasmosis and feline infectious peritonitis.
Methodological approach to investigate peroxiredoxin 1 deacetylation by histone deacetylase 6.
Experimental approaches for investigating sirtuin-mediated mitochondrial function, cellular metabolism, and epigenetic regulation.
Evaluation of lysine modified peptides and their cell penetrating peptide conjugates with sirtuin activity inhibition properties and intracellular delivery.
Research progress on lysine acetylation (Review).
In Silico design and evaluation of a multi-epitope vaccine candidate against Toxoplasma gondii for humans.
Histone deacetylases: From acetylation homeostasis to oncogenic and neurodegenerative disorders.
SIRT1 deacetylates GAPDH to drive microglial glycolysis and neuroinflammation.
The mitochondrial deacetylase SIRT3 is nonessential for cyclophilin D-dependent procoagulant platelet formation in mice.
General Strategy for Controlling Functional Lysine Acetylation via Induced Proximity.
Crosstalk between cysteine and lysine modifications: Integrating redox and metabolic regulation.
HDAC inhibition via suberoylanilide hydroxamic acid ameliorates doxorubicin-induced cardiotoxicity.
Histone deacetylases in cancer metabolic reprogramming.
The extracellular Zinc-finger ubiquitin-binding domain of histone Deacetylase 6 enhances podosome formation in neuronal cells.
Multicomplex Integrative Structural Modeling of a Human Histone Deacetylase Interactome.
Ribosomal architecture and rRNA modification landscape in the tick-borne parasite Babesia divergens.
Recombinant Production and Characterization of Human Enzymes Responsible for Collagen Lysine Post-translational Modifications.
Mechanistic insights on HDAC6 ZnF UBP-Tau interaction through biophysical and computational approaches.
Machine Learning and Molecular Modeling Reveal HDAC6 as a Key Target of Tanshinone IIA in Multiple Myeloma.
Critical structural features of HDAC11 inhibitors.
Molecular mechanism of pore formation by Plasmodium Perforin-like Protein 2.
TCA cycle-related lactate and malate dehydrogenases differentially modulate fungal development, immune evasion and pathogenicity in the entomopathogen Beauveria bassiana.
Methods to Study CCT Expression and Impact on Cytoskeleton.
Experimental approaches to study histone deacetylation in Caenorhabditis elegans.

Res Sq. 2026 Aug 27. pii: rs.3.rs-10755545. [Epub ahead of print]

The live attenuated DGAT1-knockout whole-cell Toxoplasma vaccine confers protective immunity against acute and chronic toxoplasmosis.

Isabelle Coppens, Shahbaz Khan, Yevel Flores-Garcia, Jiro Sakai, Mustafa Akkoyunlu, Julia Romano, Karen Ehrenman, Viviana Pszenny, Michael Grigg, Krishna Manuguri, Yue Zhao, Duanpei Wang, Fidel Zavala.

The intravacuolar parasite Toxoplasma gondii scavenges fatty acids from host mammalian cells and stores excess in lipid droplets. To investigate the physiological relevance of neutral lipid storage in Toxoplasma , we generated a mutant lacking DGAT1 , an ER-localized enzyme that synthesizes triacylglycerols, from the virulent type I RH strain of T. gondii . Compared to WT, RH ∆DGAT1 parasites grow poorly in mammalian cells, form few LD, suffer from lipotoxicity, and do not cause disease or lethality in immunocompetent and immunodeficient mice. Importantly, mice immunized with RH ∆DGAT1 parasites mount strong, long-term immune responses involving both cellular and humoral components, with higher levels of T . gondii -specific IgG antibodies, effector memory T cells, and both pro-inflammatory and anti-inflammatory cytokines, indicating a mixed Th1/Th2 response with Th1 predominance. This immunity provides complete, long-lasting protection (up to 6 months) against rechallenge from homologous type I (acute infection) and heterologous cyst-forming type II (chronic infection) T . gondii strains. Additional analyses reveal that IFN-γ, CD8 + T cells, as well as B cells are crucial for defending against type I T . gondii in immunized mice. Overall, our live-attenuated RH ∆DGAT1 strain is a promising vaccine candidate and a model for studying immune responses that control T . gondii infections.

DOI: https://doi.org/10.21203/rs.3.rs-10755545/v1
Acta Trop. 2026 Aug 30. pii: S0001-706X(26)00330-X. [Epub ahead of print]282 108297

Recombinant Toxoplasma gondii expressing FIPV spike protein S1 subunit: A proof-of-concept approach against toxoplasmosis and feline infectious peritonitis.

Fujie Xie, Xinyu Jiang, Yilin Yang, Yuehua Xie, Chenxi Zhao, Jingxia Suo, Zhenzhao Zhang, Chaoyue Wang, Xinming Tang, Xun Suo, Xianyong Liu.

  Feline infectious peritonitis virus (FIPV) is a lethal feline pathogen with no widely effective prophylactic vaccine available. To address this unmet need, we explored the feasibility of using Toxoplasma gondii (whose definitive host is felids) as a live delivery platform to develop a bivalent vector vaccine. We generated a transgenic T. gondii strain engineered to express and secrete the FIPV spike protein S1 subunit into the parasitophorous vacuole. Immunization in mice confirmed the immunogenicity of this recombinant parasite, which induced specific antibody responses targeting both the T. gondii vector and the FIPV S1 antigen. In vitro neutralization assays revealed limited FIPV-neutralizing capacity in immune sera, with only low-level inhibitory activity observed at the lowest serum dilution, which was markedly inferior to the neutralization potency induced by recombinant S1 protein vaccination. Collectively, these data preliminarily verify the potential of T. gondii as a multivalent antigen delivery vector. This work provides a proof-of-concept framework for a dual-target vaccination strategy intended to mitigate the epidemiological burden of both FIPV and T. gondii in cats, and underpins integrated One Health-oriented disease prevention and control efforts.

Keywords:  Feline infectious peritonitis virus; S1 protein; Toxoplasma gondii; Vector vaccine

DOI:  https://doi.org/10.1016/j.actatropica.2026.108297
Methods Enzymol. 2026 ;pii: S0076-6879(26)00168-0. [Epub ahead of print]734 381-392

Methodological approach to investigate peroxiredoxin 1 deacetylation by histone deacetylase 6.

Sonali Kumar, Ozasvi R Shanker, Jyotirmoy Banerjee, Aparna Banerjee Dixit.

  Post-translational acetylation of cytoplasmic proteins has emerged as a critical regulatory mechanism in neurological disease. Peroxiredoxin 1 (Prdx1), a key antioxidant enzyme, undergoes reversible lysine acetylation that modulates its enzymatic activity. Histone Deacetylase 6 (HDAC6), a predominantly cytoplasmic deacetylase, has been identified as a regulator of Prdx1 acetylation, linking deacetylase activity to redox homeostasis. Accurate detection of Prdx1 deacetylation requires methodological strategies capable of preserving endogenous acetylation states and selectively enriching acetylated protein fractions. This chapter describes a reproducible workflow for assessing HDAC6-mediated Prdx1 deacetylation in cortical tissue which integrates optimized protein extraction under acetylation-preserving conditions, acetyl-lysine-based co-immunoprecipitation, and immunoblot detection of Prdx1. Parallel assessment of total Prdx1 and established HDAC6 substrates enables normalization and validation of deacetylase activity. Quantitative densitometric analysis provides comparative evaluation of acetylation levels across experimental conditions. This methodology offers a practical and translationally applicable approach for investigating non-histone deacetylation mechanisms and can be adapted to other HDAC6-regulated substrates in neurodegenerative research.

Keywords:  Acetylation; Deacetylation; Histone deacetylase 6; Peroxiredoxin

DOI:  https://doi.org/10.1016/bs.mie.2026.05.040
Methods Enzymol. 2026 ;pii: S0076-6879(26)00237-5. [Epub ahead of print]734 29-53

Experimental approaches for investigating sirtuin-mediated mitochondrial function, cellular metabolism, and epigenetic regulation.

Karthick Chennakesavan, Thangavel Samikkannu.

  Cellular pathways for experimental discovery provide a comprehensive overview of sirtuin biology and its critical involvement in HIV-associated neurocognitive disorders (HAND) and related neurodegenerative diseases, highlighting the translational potential of sirtuin-targeted therapeutic strategies. As NAD+-dependent deacetylases and ADP-ribosyl transferases, sirtuins regulate diverse cellular processes, including stem cell maintenance, cellular proliferation, metabolic homeostasis, apoptosis, autophagy, oxidative stress responses, and genomic stability, all of which contribute to neuronal dysfunction and disease progression. This chapter focuses on key mammalian sirtuins, including SIRT1 and SIRT2, which are primarily localized within the nucleus and cytosol; mitochondrial sirtuins SIRT3, SIRT4, and SIRT5; and nuclear/nucleolar sirtuins SIRT6 and SIRT7. Here, a method with a detailed protocol to isolate compartment-specific sirtuin expression and activity was used: subcellular fractionation was performed using a subcellular fractionation kit to obtain cytosolic and nuclear fractions, while mitochondrial isolation was carried out using Tom20 antibody-conjugated magnetic microbeads. These approaches were applied to brain tissues from HIV-positive individuals, as well as to HIV-Tat-treated human microglial (HMC3) cells and astrocytes. This experimental framework enables accurate assessment of compartment-resolved sirtuin regulation in disease-relevant models. Collectively, the chapter highlights the protective roles of sirtuins in mitigating key pathogenic mechanisms underlying HAND and related neurodegenerative diseases. These findings support the emerging concept that sirtuins represent promising pharmacological targets for the development of novel therapeutic interventions in neurodegeneration and HIV-associated brain disorders.

Keywords:  Epigenetics; HIV-associated neurodegenerative disorders; Histone deacetylases; Mitochondria; Sirtuins

DOI:  https://doi.org/10.1016/bs.mie.2026.06.023
Methods Enzymol. 2026 ;pii: S0076-6879(26)00230-2. [Epub ahead of print]734 217-234

Evaluation of lysine modified peptides and their cell penetrating peptide conjugates with sirtuin activity inhibition properties and intracellular delivery.

Kamal D Patel, Shalini Aricthota, Gayan Heruka De Zoysa, Vijayalekshmi Sarojini, Devyani Haldar.

  Sirtuins are NAD+ dependent class of histone deacetylase enzymes responsible for post-translational modifications regulating transcription, cell cycle, metabolism, DNA repair and apoptosis. Substrates of sirtuins are histones, α-tubulin, p65, FOXO1 etc. all of which have multiple NƐ-acetyl lysine residues taking part in catalytic reactions of sirtuins with the help of NAD+. In this chapter, we present methods for Solid Phase Peptide Synthesis and solution phase cyclization of a series of substrate-based peptide inhibitors of sirtuins and their cyclic and CPP conjugated derivatives KP 1, Cyc KP 1, Tat KP 1, KP 2, Cyc KP 2, Tat KP 2, KP 3, Cyc KP 3 and Tat KP 3. Further, describe methods that could be used to study sirtuin inhibition activity and cytotoxicity properties of peptides and small molecules. We present data of three peptides from this family Tat KP 1, Tat KP 2 and Tat KP 3 that show promising yeast sirtuin and mammalian SIRT1 inhibition potential (IC50 6-12 µM) comparable to known sirtuin inhibitors suramin and splitomicin and also showed cytotoxicity against HeLa and BE(2)-C cells. Finally, the morphological studies using SEM and TEM showed membrane disruption potential and evidence of apoptosis of Tat conjugated derivatives. This study documents the one of the initial reports of Tat conjugation modification to enhance the sirtuin inhibition potential. Collectively, this chapter provides comprehensive protocols and practical guidance for the characterization and biological evaluation of sirtuin inhibitors which could be used to identify and characterize novel peptides inhibitors of sirtuins with cell penetrating properties.

Keywords:  Apoptosis; BE(2)-C cell lines; HeLa cell lines; Lysine modification; Sirtuin inhibition; Tat peptides

DOI:  https://doi.org/10.1016/bs.mie.2026.06.016
Int J Mol Med. 2026 Nov;pii: 305. [Epub ahead of print]58(5):

Research progress on lysine acetylation (Review).

Minghui Zhang, Yuqi Zhang, Haoxin Yin, Junyuan Yan, Yingling Dong, Xin Zhao, Tianyi Cui, Bin Lv, Xiumei Gao.

  Lysine acetylation is recognized as a critical and reversible post‑translational modification that is essential for numerous cellular functions and biological processes. The dynamic interplay between lysine acetylation and deacetylation to regulates a wide spectrum of processes, including histone modification, gene expression, cell cycle progression, DNA repair and signal transduction. Emerging evidence has demonstrated that the dysregulation of lysine acetylation is strongly associated with multiple diseases, including cancer, cardiovascular diseases, chronic inflammatory diseases and neurological diseases. These alterations can modify gene expression and disrupt cellular homeostasis. The present review aimed to highlight the biological functions of lysine acetyltransferases and lysine deacetylases, their contributions to disease pathogenesis, and the interplay the crosstalk of lysine acetylation with other post‑translational modifications. Drawing on the latest research findings, the therapeutic potential of targeting acetylation pathways is discussed, with the aim of providing new insight into the development of innovative treatment strategies and clinical applications.

Keywords:  acetyltransferases; deacetylases; disease pathogenesis; lysine acetylation; post‑translational modifications

DOI:  https://doi.org/10.3892/ijmm.2026.5976
Front Cell Infect Microbiol. 2026 ;16 1905185

In Silico design and evaluation of a multi-epitope vaccine candidate against Toxoplasma gondii for humans.

Chenchen Yi, Yu Shen, Ye Luo, Qin Wang, Xiaomei Tong.

   Introduction: Toxoplasma gondii is a significant zoonotic pathogen responsible for severe disease in immunocompromised individuals, adverse pregnancy outcomes, and substantial economic losses in the livestock industry. Given the limitations of current therapeutic strategies and vaccines, this study utilized immunoinformatics and reverse vaccinology approaches to design a multi-epitope candidate vaccine.
Methods: A total of 49 T. gondii proteins from the SAG, GRA, MIC, and ROP families were screened. Epitopes were selected based on antigenicity, immunogenicity, cytokine-inducing potential, toxicity, and allergenicity. The selected epitopes were assembled using AAY, GPGPG, and KK linkers, with the 50S ribosomal protein L7/L12 as an adjuvant. Physicochemical properties, molecular docking, molecular dynamics simulations, immune simulations, and codon optimization were subsequently evaluated.
Results: We identified 9 cytotoxic T lymphocyte (CTL), 6 helper T lymphocyte (HTL), and 11 B-cell epitopes. The finalized 556-amino-acid construct (61.13 kDa) demonstrated favorable antigenicity (VaxiJen score: 0.6843), stability (instability index: 39.05), solubility (0.663), and hydrophilicity (GRAVY: -0.502), while maintaining safety profiles. Molecular docking and dynamics simulations confirmed robust and stable binding to TLR2 (-32.8 kcal/mol) and TLR4 (-72.37 kcal/mol). Furthermore, immune simulations predicted a strong, memory-forming humoral and cellular immune response. Codon optimization (CAI: 0.93, GC content: 56.43%) suggested high expression efficiency in Escherichia coli.
Discussion: The rationally designed multi-epitope vaccine demonstrates robust theoretical potential to elicit comprehensive, long-lasting immunity in humans, although its safety and effectiveness require additional experimental validation.

Keywords:  Toxoplasma gondii; immune response; immunoinformatics; multi-epitope vaccine; zoonotic diseases

DOI:  https://doi.org/10.3389/fcimb.2026.1905185
Methods Enzymol. 2026 ;pii: S0076-6879(26)00185-0. [Epub ahead of print]734 327-346

Histone deacetylases: From acetylation homeostasis to oncogenic and neurodegenerative disorders.

Niharika, Samir Kumar Patra.

  Histone deacetylases (HDACs) are central regulators of acetylation homeostasis, governing chromatin architecture, transcriptional dynamics, and diverse cellular processes through reversible lysine deacetylation. Dysregulation of HDAC activity disrupts epigenetic balance and is strongly implicated in oncogenic transformation and the progression of neurodegenerative disorders. This chapter provides a comprehensive overview of HDAC biology with a particular emphasis on experimental and analytical methodologies used to investigate their function. We describe the structural and functional diversity of HDAC classes and their roles in multiprotein complexes that regulate gene expression and cellular signaling. A major focus is placed on screening-compatible and mechanistic assays, including fluorometric, colorimetric, radiometric, fluorescence polarization, TR-FRET, AlphaScreen/AlphaLISA, and differential scanning fluorimetry approaches for quantitative measurement of enzymatic activity and inhibitor profiling. In addition, advanced methodologies such as mass spectrometry-based acetylome analysis, chromatin immunoprecipitation sequencing (ChIP-seq), recombinant enzyme assays, and cell-based reporter systems are discussed in the context of functional genomics and drug discovery. The integration of high-throughput screening, structural biology, and multi-omics strategies is highlighted as essential for dissecting HDAC-mediated regulatory networks. Collectively, this chapter serves as a methodological framework for studying HDAC function and developing targeted epigenetic therapies in cancer and neurodegenerative diseases.

Keywords:  Acetylation; Cancer; Histone deacetylases; Neurodegenerative disorders; Therapy

DOI:  https://doi.org/10.1016/bs.mie.2026.05.057
Front Immunol. 2026 ;17 1883095

SIRT1 deacetylates GAPDH to drive microglial glycolysis and neuroinflammation.

Chou-Yi Hsu, Ibrokhim Sapaev, Ozodbek Nematov, Rustam Turakulov, Sarmad S Abdullah, Zeina T Khaleel, Enas R Alwaily, Majid S Jabir.

   Introduction: Microglial activation drives neuroinflammation through a metabolic switch from oxidative phosphorylation to aerobic glycolysis; however, the molecular mechanisms governing this transition remain poorly defined. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH), sirtuin 1 (SIRT1), lipopolysaccharide (LPS), and interferon-gamma (IFN-γ) are central to this study; GAPDH plays plays a key regulatory role in this switch, and its activity is modulated by reversible acetylation at lysine 254 (K254). It remains unclear whether sirtuin deacetylases regulate this modification in microglia.
Methods: Here, we demonstrate that SIRT1 physically associates with GAPDH in murine microglia and deacetylates K254 under basal conditions. Inflammatory activation using LPS/IFN-γ reduced SIRT1 protein levels and deacetylase activity by approximately 50%, leading to a 2.5-fold increase in K254 acetylation. Pharmacological activation of SIRT1 (SRT1720) reversed this modification and enhanced glycolytic output, mimicking the effects of the deacetylation-mimetic K254R mutant. To isolate the causal role of K254, we replaced endogenous GAPDH with K254R or acetylation-mimetic (K254Q) mutant proteins.
Results: K254R microglia exhibited approximately 35% higher GAPDH enzymatic activity, 40% greater glycolytic flux, and 1.6- to 2.2-fold higher secretion of TNF-α, IL-1β, IL-6, and IL-12p70 than K254Q cells. Glycolytic inhibition with 2-deoxyglucose reduced most of the excess cytokines, confirming enhanced flux as the causal factor in K254-driven inflammatory amplification.
Discussion: Thus, SIRT1-GAPDH signaling represents a post-translational axis linking sirtuin activity directly to glycolytic enzyme function, distinct from SIRT1's traditional transcriptional roles and serving as a viable molecular checkpoint in microglial immunometabolism.

Keywords:  Sirtuin 1; glyceraldehyde-3-phosphate dehydrogenase; glycolysis; lysine acetylation; microglia; neuroinflammation

DOI:  https://doi.org/10.3389/fimmu.2026.1883095
Platelets. 2026 Dec;37(1): 2721783

The mitochondrial deacetylase SIRT3 is nonessential for cyclophilin D-dependent procoagulant platelet formation in mice.

Jens Van Bael, Anne-Sophie Delmote, Inge Pareyn, Laurence Pirotton, Emma de Cartier d'Yves, Sandrine Horman, Yotis A Senis, Johan Auwerx, Simon F De Meyer, Karen Vanhoorelbeke, Claudia Tersteeg.

  Sirtuin 3 (SIRT3) is a nicotinamide adenine dinucleotide (NAD)-dependent mitochondrial deacetylase that regulates protein acetylation and maintains mitochondrial homeostasis in nucleated cells. By deacetylating cyclophilin D (CypD), SIRT3 limits mitochondrial permeability transition pore (mPTP) opening and protects against mitochondrial dysfunction. Although SIRT3 is present in murine and human platelets, its contribution to platelet mitochondrial regulation and procoagulant platelet formation remains unknown. This study investigated whether platelet SIRT3 modulates CypD-dependent procoagulant platelet formation. Platelets obtained from platelet-specific Sirt3 knockout mice (Sirt3plt-/-) and littermate controls (Sirt3plt+/+) were analyzed under resting conditions and after activation with CRP-XL and thrombin. Flow cytometry was used to analyze platelet (activation) markers and procoagulant platelet formation, and mitochondrial respiration was assessed using a Seahorse extracellular flux analyzer. Platelets lacking SIRT3 showed no alterations in basal or agonist-stimulated mitochondrial respiration. Likewise, platelet Sirt3 deletion did not affect the generation of procoagulant platelets in response to strong dual agonist stimulation. These findings indicate that, despite its role in regulating mPTP opening in nucleated cells, platelet SIRT3 is not required for procoagulant platelet formation, suggesting that platelets rely on distinct mechanisms for mPTP regulation.

Keywords:  Mitochondria; SIRT3; platelet; procoagulant

DOI:  https://doi.org/10.1080/09537104.2026.2721783
ACS Chem Biol. 2026 Aug 24.

General Strategy for Controlling Functional Lysine Acetylation via Induced Proximity.

Brianna Hill-Payne, Mohd Younis Bhat, George M Burslem.

Assigning causal function to post-translational modifications (PTMs) remains a central challenge in molecular biology, as most modification events cannot be readily interrogated in their native cellular context. Here, we present a generalizable chemical biology strategy for investigating the functional consequences of lysine acetylation through programmable induced proximity. By combining modular effector recruitment with chemically controlled proximity, this approach enables systematic elucidation of how enzyme identity shapes acetylation outcomes on target proteins in living cells. Across multiple substrates, including histone H3 and p53, we find that distinct acetyltransferases generate reproducible and target-dependent site-selective acetylation patterns, indicating that effector identity encodes predictable features of modification outcomes. These observations establish a framework for linking enzyme recruitment to site-specific PTM deposition and provide a route to identify candidate functional modification events. Rather than providing a single mechanistic insight, this work introduces a broadly applicable strategy for interrogating causal relationships between proximity-driven enzyme recruitment and protein modification, as demonstrated by the impact of p53 acetylation on downstream transcripts. This platform is readily extensible to additional effectors and targets and enables systematic discovery of functional PTMs in cellular systems.

DOI: https://doi.org/10.1021/acschembio.6c00510
Redox Biol. 2026 Aug 22. pii: S2213-2317(26)00356-3. [Epub ahead of print]96 104357

Crosstalk between cysteine and lysine modifications: Integrating redox and metabolic regulation.

Emily C Mitchem, James R Roede, Kristofer S Fritz.

Protein post-translational modifications (PTMs) on amino acid residues enable dynamic cellular responses to changes in metabolic and redox state. Cysteine and lysine are among the most extensively modified amino acid residues, with both undergoing a diversity of acylation and oxidative modifications. Indeed, proximal (<10 Å) cysteine and lysine residues may form integration nodes for crosstalk between metabolism and redox homeostasis pathways. This review highlights the interaction of proximal Cys-Lys residues, including influence on residue pKa by local electrostatics, cysteine-to-lysine transfer of PTM moieties, and covalent crosslinking. We discuss candidate Cys-Lys regulatory pairs in proteins involved in redox regulation, proteostasis, metabolic adaptation and inflammation. We further utilize computational modeling to identify proximity between cysteine and lysine residues in proteins known to be regulated by acylation and oxidative PTMs, and to demonstrate changes in these distances and local electrostatic potential due to lysine acetylation. Finally, we review how mass spectrometry-based proteomics and machine-learning PTM predictive tools can enable the identification, validation, and interpretation of proximal Cys-Lys interactions that regulate cellular responses to oxidative challenge and metabolic flux.

DOI: https://doi.org/10.1016/j.redox.2026.104357
Nat Commun. 2026 Sep 04. pii: 9505. [Epub ahead of print]17(1):

HDAC inhibition via suberoylanilide hydroxamic acid ameliorates doxorubicin-induced cardiotoxicity.

Benay Eksi, Daniel Finke, Synje Michel, Jannek Brauer, Markus B Heckmann, Mohsen Valadan, Leonard M Schanze, Vighnesh Sunder, Kevin Steimel, Jürgen Burhenne, Timon Seeger, Hugo A Katus, Norbert Frey, Johannes Backs, Lorenz H Lehmann.

Anthracycline-induced cardiotoxicity remains a major limitation of cancer therapy, and effective preventive strategies are lacking. Topoisomerase IIb has been implicated as a central driver of this toxicity, suggesting that epigenetic regulators may interfere with the pathological cardiac response. Here, we show that doxorubicin promotes topoisomerase IIb accumulation at cardiomyocyte-specific gene promoters (e.g., Actc1, Myl2, and Myh7) overlapping myocyte enhancer factor 2 binding sites and enhances myocyte enhancer factor 2 -dependent transcription. This response is attenuated by the pan-histone deacetylase inhibitor suberoylanilide hydroxamic acid. Suberoylanilide hydroxamic acid -mediated cardioprotection requires class IIa histone deacetylases, as genetic loss of HDAC4 abolishes its effect. Mechanistically, suberoylanilide hydroxamic acid induces acetylation of the chaperone 14-3-3, disrupting its interaction with HDAC4/5, promoting their nuclear accumulation, and repressing myocyte enhancer factor 2 - driven transcription. In vivo, suberoylanilide hydroxamic acid mitigates doxorubicin-induced cardiotoxicity. These findings identify histone deacetylase inhibition as a cardioprotective repurposing strategy and reveal a mechanistic link between epigenetic regulation and anthracycline-associated cardiotoxicity.

DOI: https://doi.org/10.1038/s41467-026-77428-w
Exp Mol Med. 2026 Sep 02.

Histone deacetylases in cancer metabolic reprogramming.

Yu Hyun Jeon, Hyeyeong Seo, Ji Woo Youn, Jung Yoo, Sang Wu Lee, Soo Yeon Oh, So Hee Kwon.

Cancer cells undergo extensive metabolic reprogramming to sustain rapid proliferation and adapt to heterogeneous tumour microenvironments. These metabolic alterations are tightly linked to epigenetic regulation, which reshapes gene expression and cellular signalling mechanisms. Among epigenetic regulators, histone deacetylases (HDACs) have emerged as key modulators of cancer metabolic reprogramming. Along with their canonical roles in histone deacetylation, HDACs regulate non-histone substrates, including metabolic enzymes and transcription factors, thereby coordinating transcriptional and metabolic programmes. In this review, we summarize current insights into HDAC-mediated regulation of glucose, lipid and amino acid metabolism in cancer and discuss the metabolic mechanisms underlying the anticancer effects of HDAC inhibitors. Collectively, we propose an integrated framework in which HDACs function as central regulators of cancer metabolic reprogramming. We highlight the limitations of HDAC inhibitor studies and discuss the emerging importance of isoform-specific HDAC functions in reprogramming cancer-specific metabolic dependencies and therapeutic strategies.

DOI: https://doi.org/10.1038/s12276-026-01820-1
Methods Enzymol. 2026 ;pii: S0076-6879(26)00188-6. [Epub ahead of print]734 301-326

The extracellular Zinc-finger ubiquitin-binding domain of histone Deacetylase 6 enhances podosome formation in neuronal cells.

Tazeen Qureshi, Abhishek Ankur Balmik, Subashchandrabose Chinnathambi.

  Neurodegenerative disorders are characterized by progressive synaptic failure, neuronal loss, and the accumulation of pathological protein aggregates. A critical but often overlooked driver of this decline is cytoskeletal dysregulation, which compromises essential cellular functions ranging from intracellular transport to morphological stability. Histone Deacetylase 6 (HDAC6) is a central regulator of these dynamics, yet its role in neurodegeneration remains controversial: while its deacetylase activity is often linked to microtubule instability and toxicity, its ubiquitin-binding functions are essential for aggregate clearance. We have previously demonstrated that the ZnF-UBP domain acts as a direct modulator of cytoskeletal architecture, enhancing the formation of actin-rich migratory structures-such as podosomes and lamellipodia-and promoting neuritic outgrowth. It does this by inducing increased localization of actin remodelling proteins to the podosomes, ultimately conferring enhanced migration potential to cells. This chapter highlights the protocols essential for understanding the therapeutic potential of the HDAC6 Zinc Finger Ubiquitin-Binding Protein (ZnF-UBP) domain, in the context of actin remodelling through podosome structures.

Keywords:  Alzheimers disease; Cytoskeleton; Histone deacetylase 6; Podosomes; Tau; Zinc-finger ubiquitin-binding domain (ZnF UBP)

DOI:  https://doi.org/10.1016/bs.mie.2026.05.060
Mol Cell Proteomics. 2026 Sep 01. pii: S1535-9476(26)00147-7. [Epub ahead of print] 101651

Multicomplex Integrative Structural Modeling of a Human Histone Deacetylase Interactome.

Jules Nde, Kartik Majila, Rosalyn C Zimmermann, Cassandra Kempf, Ying Zhang, Joseph Cesare, Janet L Thornton, Jerry L Workman, Laurence Florens, Shruthi Viswanath, Michael P Washburn.

  Histone Deacetylase (HDAC) 1 and 2 are key enzymatic components in multiple large chromatin remodeling complexes including NuRD, SIN3, and CoREST. In addition, both HDAC 1 and 2 contain a large intrinsically disordered region (IDR) within their C-terminal domain (CTD). How HDAC1/2 assemble into these complexes and the structure of the CTD IDR remains poorly understood. Here, we used HDAC1/2 to isolate their protein interaction networks from cells and used crosslinking mass spectrometry (XL-MS) coupled with the Integrative Modeling Platform to build structural models of the NuRD, SIN3A, and CoREST complexes. Next, we implemented an AlphaFold-enabled XL-MS constrained modeling approach to investigate how HDAC1 could assemble into these complexes. We show that the CTD IDR of HDAC1 folds into alpha helices in these complexes. Finally, we built a complete integrative structural model of a NuRD subcomplex including the abundant HDAC1:MBD3:MTA1:GATAD2B:RBBP4 subunits, which included 6 IDRs. The approaches used herein are broadly applicable for the study of protein complexes and protein interaction networks that can provide important insights into IDRs.

Keywords:  CoREST; Crosslinking Mass Spectrometry; Endogenous Complex Structures; HDAC1; HDAC2; Integrative Structural Modeling; Intrinsically Disordered Regions; NuRD; SIN3A

DOI:  https://doi.org/10.1016/j.mcpro.2026.101651
Nat Commun. 2026 Aug 06. pii: 9475. [Epub ahead of print]17(1):

Ribosomal architecture and rRNA modification landscape in the tick-borne parasite Babesia divergens.

Cristina Gutierrez-Vargas, Lee S Izhaki-Tavor, Diana G Calvopina-Chavez, Caroline D Keroack, Pablo Copello, Manoj T Duraisingh, Mélissa Léger-Abraham.

Babesia are tick-borne intracellular apicomplexan parasites that infect a wide range of wild and domestic animals (e.g., cattle), resulting in significant economic losses to the livestock industry. Humans are considered accidental hosts for a few Babesia species. Babesia microti and B. divergens are the most prevalent causes of human babesiosis that are showing a broadening geographic distribution. Due to the complex life cycle of Babesia species, their survival depends on the precise control of gene expression, which is primarily regulated by epigenetic, transcriptional, and post-transcriptional mechanisms. High-resolution structural information on key components of the translation machinery, such as ribosomes, could aid in the development of antiparasitic drugs. Here, we report cryogenic electron microscopy ribosome structures from B. divergens, showing associated tRNAs, an mRNA fragment, and RACK1, a signaling scaffold crucial to translation regulation. Density map analysis displays ribosome regions at high resolution, which, when combined with nanopore sequencing, enabled the comprehensive identification of rRNA modifications. The rRNA modifications localize not only to the reduced B. divergens rRNA expansion segments but also to functionally essential ribosomal sites.

DOI: https://doi.org/10.1038/s41467-026-75282-4
Methods Mol Biol. 2026 ;3022 73-98

Recombinant Production and Characterization of Human Enzymes Responsible for Collagen Lysine Post-translational Modifications.

Daiana Mattoteia, Matteo De Marco, Sristi Raj Rai, Silvia Faravelli, Luigi Scietti, Federico Forneris.

  Biosynthesis of collagen molecules, as well as collagenous segments of non-collagen proteins, requires extensive post-translational modifications (PTMs) that confer specific functional and structural properties to tissues and organs. Within collagen polypeptide sequences, lysine residues are subject to a series of PTMs, resulting in hydroxylation and subsequent O-linked glycosylation of their side chains. These modifications are catalyzed by two distinct metalloenzyme families, named LH/PLOD and GLT25D/COLGALT, which alternatively process modified lysine side chains yielding 5-hydroxylysine (LH/PLOD), β-(1,O)-galactosyl-5-hydroxylysine (GLT25D/COLGALT), and α-(1,2)-glucosyl-β-(1,O)-galactosyl-5-hydroxylysine (LH/PLOD). In this chapter, we illustrate strategies to recombinantly produce human full-length LH3/PLOD3 as well as GLT25D1/COLGALT1, verify the quality of these recombinant preparations, and perform direct and indirect assays to evaluate their enzymatic activities in vitro on synthetic collagen peptides and gelatin.

Keywords:  Enzymatic activity assays; Enzyme; GLT25D/COLGALT; Galactosyltransferase; Glucosyltransferase; LH/PLOD; Lysyl hydroxylase; Post-translational modifications; Protein characterization; Recombinant protein production

DOI:  https://doi.org/10.1007/978-1-0716-5194-0_4
Methods Enzymol. 2026 ;pii: S0076-6879(26)00251-X. [Epub ahead of print]734 79-103

Mechanistic insights on HDAC6 ZnF UBP-Tau interaction through biophysical and computational approaches.

Abhishek Ankur Balmik, Shweta Kishor Sonawane, Nalini Vijay Gorantla, Subashchandrabose Chinnathambi.

  Histone deacetylase 6 is a unique cytoplasmic deacetylase implicated in cellular functions such as microtubule dynamics, protein quality control, ubiquitin-mediated degradation and neurodegenerative disorders. The ZnF UBP (zinc finger ubiquitin binding protein) domain of HDAC6 is known to be directly modulate several cellular processes linked to neurodegeneration such as sequestering polyubiquitinated aggregates and regulating protein aggregate clearance mechanisms in neurons. Microtubule associated protein Tau (MAP Tau) undergoes aggregation in neurodegenerative conditions like Alzheimer's disease (AD) and several other tauopathies. Tau is a natively disordered protein which is functionally regulated by wide array of post-translational modifications (PTMs) as well as by interacting with several proteins. This methodological study aims to understand the molecular interaction between HDAC6 ZnF UBP domain and Tau protein in order to elucidate the role of HDAC6 ZnF UBP domain in Tau aggregation and stability. We employed an integrated biochemical, biophysical and computational workflow to characterize the interaction between HDAC6 ZnF UBP and Tau. NMR spectroscopy, isothermal titration calorimetry and pull-down assay with purified HDAC6 ZnF UBP and Tau proteins demonstrated direct interaction between the two, with interaction associated structural perturbations and favourable binding kinetics as observed in NMR and ITC respectively. Computational analyses further suggest the formation of Tau-HDAC6 ZnF UBP complex and provided underlying molecular interactions involved in the binding of these two proteins. The findings in this study helps to advance the current understanding of regulatory role of HDAC6 specifically in Tau biology and further provides a useful framework for investigating the modulation of aggregation prone proteins via protein-protein interaction in neurodegenerative diseases.

Keywords:  Alzheimer disease; HDAC6; NMR; Protein aggregation; Protein-protein interaction; Tau protein; ZnF UBP

DOI:  https://doi.org/10.1016/bs.mie.2026.07.009
J Phys Chem B. 2026 Sep 03. 130(35): 9007-9020

Machine Learning and Molecular Modeling Reveal HDAC6 as a Key Target of Tanshinone IIA in Multiple Myeloma.

Jian Gao, Jiawen Chu, Pengpeng Li.

Multiple myeloma (MM) is a malignant blood cancer marked by severe bone destruction and immune microenvironment disruption. Yet relapse and drug resistance remain major clinical challenges. Tanshinone IIA (TIIA) exhibits potent antitumor activity, but its molecular targets and mechanisms in MM remain unclear. Here, we systematically elucidate TIIA's pharmacological mechanisms in MM using network pharmacology, transcriptomics, molecular docking, molecular dynamics (MD) simulations, and in vitro cellular experiments. Histone deacetylase 6 (HDAC6) was identified as a key prognostic target in MM via integrative bioinformatics─combining cross-database analysis, machine learning (LASSO, SVM-RFE, random forest), and survival validation in the MMRF-CoMMpass cohort. Molecular docking and MD simulations showed stable binding of TIIA to HDAC6. In vitro, TIIA directly inhibited HDAC6 enzymatic activity and selectively killed U266 and RPMI 8226 myeloma cells in a dose-dependent manner, with minimal toxicity to normal cells. Additionally, gene set enrichment analysis (GSEA) and single-sample GSEA (ssGSEA) immune profiling using the LM22 signature suggested that HDAC6 participates in microenvironmental remodeling by modulating cell adhesion-mediated resistance and orchestrating an immunosuppressive niche characterized by monocyte depletion. This study highlights for the first time the critical role of HDAC6 in TIIA-mediated antimyeloma activity and provides novel mechanistic insights and potential targeted therapeutic strategies for the treatment of MM.

DOI: https://doi.org/10.1021/acs.jpcb.6c03788
Methods Enzymol. 2026 ;pii: S0076-6879(26)00173-4. [Epub ahead of print]734 173-198

Critical structural features of HDAC11 inhibitors.

Indrasis Dasgupta, Srijoni Sinha, Shovanlal Gayen.

  Histone deacetylase 11 (HDAC11), the sole member of the class IV HDACs, has gained significance as a key regulator of a wide range of physiological and pathological processes. The structural characterization of HDAC11 remains challenging due to the absence of an experimentally determined crystal structure. Proper analysis of reported HDAC11 inhibitors can yield valuable insights into the key structural fingerprints essential for inhibition. Using a diverse range of descriptor sets, including various 2D descriptors and fingerprint-based descriptors, it becomes possible to effectively identify critical structural features associated with HDAC11 inhibitory activity. These fingerprints enable the recognition of substructural features that play an important role in binding within the HDAC11 catalytic site and in achieving selective inhibition. In the present chapter, various computational methodologies, including Bayesian classification, Recursive partitioning approaches and machine learning-based classification models, have been discussed in a user-friendly manner to identify the critical structural features required for effective HDAC11 inhibition. The insights derived from these approaches are expected to assist researchers in the rational design of selective HDAC11 inhibitors, which may be further validated through experimental studies.

Keywords:  Bayesian classification; Classification QSAR; Fingerprints; HDAC11; Machine learning; Recursive partitioning

DOI:  https://doi.org/10.1016/bs.mie.2026.05.045
Nat Commun. 2026 07 31. pii: 9323. [Epub ahead of print]17(1):

Molecular mechanism of pore formation by Plasmodium Perforin-like Protein 2.

Yu Zhang, Lijie Zhong, Yun Song, Mingcheng Guo, Keli Ren, Tingting Yang, Yixin Huang, Ilia Sirotkin, Gangshun Yi, Fang Jiao, Peijun Zhang, Robert J C Gilbert, Tao Ni, Xiulian Yu.

Malaria-causing Plasmodium parasites must pass through several host cell types to complete their life cycle. This cell traversal is facilitated by perforin-like proteins (PLPs), among which PLP2 is essential for erythrocyte rupture by gametocytes. However, the mechanism by which PLP2 forms pores is not yet understood. Here, we combine cryo-electron microscopy and tomography to reveal the structural basis of Plasmodium vivax PLP2-mediated membrane attack. PvPLP2 assembles on lipid bilayers into heterogeneous arc- and ring-shaped pores with variable stoichiometries. Among them, we determine the structure of a 17-subunit pore complex in which the pore-forming MACPF domains form the central β-barrel, while the peripheral Apicomplexan PLP C-terminal β-pleated sheet (APCβ) domains anchor the complex to the membrane surface. A disulfide-stabilized mutant captures an intermediate pre-pore complex prior to membrane insertion, delineating the structural transitions that underpin β-barrel deployment. Functionally, PvPLP2 acts preferentially on the inner leaflet of the erythrocyte membrane, a specificity driven by its affinity for negatively charged lipids. Together, these findings establish the pore-formation pathway for a key Plasmodium virulence factor and provide a structural framework for rational design of transmission-blocking agents that prevent gametocyte egress.

DOI: https://doi.org/10.1038/s41467-026-76236-6
J Invertebr Pathol. 2026 Aug 29. pii: S0022-2011(26)00205-3. [Epub ahead of print]220 108729

TCA cycle-related lactate and malate dehydrogenases differentially modulate fungal development, immune evasion and pathogenicity in the entomopathogen Beauveria bassiana.

Hao Zhang, Xin-Yi Wang, Xue-Ting Wang, Ting-Fei Sun, Ben-Jie Gao, Ming-Guang Feng, Sheng-Hua Ying.

  The tricarboxylic acid (TCA) cycle plays a pivotal role in fungal physiological processes. In this study, two TCA-cycle related enzyme were functionally analyzed in a model entomopathogenic fungus Beauveria bassiana, including NAD-dependent lactate dehydrogenase (BbLdh) and malate dehydrogenase (BbMdh1 and 2). Domain annotation indicated all these enzymes contained an Ldh_1 domain. Functional analyses indicated that BbLdh and BbMdh2 had differential contributions to fungal growth, development, stress tolerance, virulence, and mycosis. Notably, BbLdh played a more important role in fungal interaction with the host than BbMdh2, which was attributed to its additional functions in stress tolerance, extracellular acidification, in vivo development, and immune evasion. In contrast, BbMdh2 primarily was involved in cuticle penetration due to its roles in utilization of host nutrients (e.g., lipids and proteins). Comparative transcriptomic analysis revealed that BbLdh mediated numerous metabolic pathways and physiological responses to oxidative stress. Collectively, this study reveals the metabolic mechanisms involved in the B. bassiana adaptation to the host niches, deepening our understanding of metabolic pathways during fungal interaction with the hosts.

Keywords:  Dehydrogenase; Fungal development; Pathogenicity; Stress response; Tricarboxylic acid cycle

DOI:  https://doi.org/10.1016/j.jip.2026.108729
Methods Mol Biol. 2026 ;3070 301-321

Methods to Study CCT Expression and Impact on Cytoskeleton.

Camila Scagnetti, Hugo Yébenes, Silvia Requena, Noa B Martín-Cófreces.

  Chaperones are proteins whose function is to intervene in the correct folding of newly synthesized polypeptides in the ribosome, thus providing their native conformation. CCT belongs to the Hsp60 family of chaperonins and is specifically a Type II subgroup. Here, we describe methods for determining and manipulating the CCT protein and RNA levels, as well as CCT distribution in cells, using complementary biochemical and imaging approaches. Protocols are provided for samples from primary human cells and established cell lines, including electrophoretic separation and immunoblotting. In parallel, procedures for immunofluorescence staining and microscopy are outlined, with emphasis on fixation, permeabilization, and antibody optimization. Critical parameters, appropriate controls, and troubleshooting considerations are discussed to facilitate robust and reproducible detection of CCT across different cellular systems.

Keywords:  CCT; CD4+ T lymphocytes; Chaperonine; Fluorescence microscopy; Immunofluorescence; Jurkat; Western blot; siRNA

DOI:  https://doi.org/10.1007/978-1-0716-5515-3_17
Methods Enzymol. 2026 ;pii: S0076-6879(26)00184-9. [Epub ahead of print]734 347-366

Experimental approaches to study histone deacetylation in Caenorhabditis elegans.

Anam Naseer, Aamir Nazir.

  Histones, being basic in nature, form the core of a nucleosome which governs DNA compaction and regulate the expression of genetic information. These undergo various modifications at their flanking tail region. One such important epigenetic modifications include deacetylation. To study histone deacetylation various experimental models and approaches have been developed till date. However, one of the best in vivo models to study this modification is a soil-dwelling nematode, Caenorhabditis elegans. This tiny, transparent worm shares around 70% genetic homology with humans which becomes a key feature in employing it as a model system. This chapter highlights major experimental approaches for studying histone deacetylation using C. elegans.

Keywords:  Caenorhabditis elegans; Histone deacetylation; Immunofluorescence; RNA interference; Western blotting

DOI:  https://doi.org/10.1016/bs.mie.2026.05.056