bims-toxgon 2025-12-28 papers

bims-toxgon

Biomed News

on Toxoplasma gondii metabolism

Issue of 2025–12–28
nineteen papers selected by
Lakesh Kumar, BITS Pilani

DNA damage-regulated autophagy modulator 1 (DRAM1)-induced lipophagy facilitates Toxoplasma gondii nutrient acquisition and infection.
Cysteine-S-nitrosylation inhibits Rop5-mediated immune evasion in Toxoplasma gondii.
Protective Efficacy of Two Novel DNA Vaccine Candidates Encoding TgGRA28 and TgGRA83 with an IL-28B Molecular Adjuvant Against Acute and Chronic Toxoplasmosis in Mice.
Toxoplasma gondii infection inhibits invasion and migration of human extravillous trophoblasts through dysregulation of FOXO1- and FOXO3a-dependent and -independent mechanisms.
PI3K/Akt/mTOR signaling pathway mediates energy metabolic reprogramming and regulates mitochondrial homeostasis in host cells exposed to Toxoplasma gondii.
The early human interferon gamma response to Toxoplasma gondii is driven by Vγ9Vδ2 T-cell sensing of host phosphoantigens and subsequent NK-cell activation.
Next-Generation HDAC Inhibitors: Advancing Zinc-Binding Group Design for Enhanced Cancer Therapy.
Quinazolinone and Phthalazinone Inhibitors of the HDAC6/Ubiquitin Protein-Protein Interaction.
Publisher Correction: Toxoplasma gondii VIP1 mediates parasitophorous vacuole-host endoplasmic reticulum interactions to facilitate parasite development.
Modular Design of Mitochondrion-Targeted Iron Chelators Allows Highly Selective Antiparasitic Activity against Trypanosomes and Apicomplexan Parasites.
Drug Development.
Metabolites beyond metabolism: Exploring their atypical roles in protein modification and signaling transduction.
The role of the flexible loop region in the substrate binding and catalytic activity of malate dehydrogenases.
An integrated bioinformatics and multi-omics investigation of the sirtuin family to identify their prognostic importance in human cancers.
The biological functions of protein lactylation.
HDAC5 deacetylates cytosolic ACTN4 during skin reepithelialization and represents a therapeutic target for chronic wound healing.
Mitochondrial membrane junction-mediated ATP channeling drives activity-dependent glucose metabolism.
MoSAIC: An Integrated and Modular Workflow for Confident Analysis of Protein Post-Translational Modification Landscapes.
HDAC6-mediated PFKL deacetylation enhances aerobic glycolysis and promotes VSMC proliferation.

Microbiol Res. 2025 Oct 30. pii: S0944-5013(25)00342-8. [Epub ahead of print]305 128383

DNA damage-regulated autophagy modulator 1 (DRAM1)-induced lipophagy facilitates Toxoplasma gondii nutrient acquisition and infection.

Yongheng Hou, Shiguang Huang, Xin-Zhuan Su, Fangli Lu.

  Autophagy is a catabolic process that responds to various environmental stresses, such as nutrient deficiency and intracellular pathogen infection. Toxoplasma gondii is an intracellular parasite that acquires nutrients from the host cells for its proliferation; however, the molecular mechanisms of T. gondii parasites' nutritional acquisition and metabolism are not fully understood. Here, we found that T. gondii type I RH strain induced host cell autophagy for nutrient acquisition and growth. T. gondii RH strain infection induced DNA damage-regulated autophagy modulator 1 (DRAM1) expression in host cells, and mechanistic analyses suggest an involvement of the IL-33-MyD88-p38/NF-κB signaling pathway in this process. DRAM1 knockdown decreased T. gondii parasite growth, while DRAM1 overexpression increased T. gondii parasite growth by hyperactivating autophagy, especially lipophagy, to provide fatty acids for T. gondii proliferation, which led to increased tissue pathology. This study identified DRAM1 as a critical molecule in regulating type I T. gondii-induced lipophagy, parasite proliferation, and liver pathology in mice. The results provide crucial insights into how T. gondii leverages host autophagy for its gain and identify a target for potential disease management, which may offer new avenues for developing novel drugs against this parasite.

Keywords:  DRAM1; Lipophagy; Nutrient acquisition; Proliferation; Toxoplasma gondii

DOI:  https://doi.org/10.1016/j.micres.2025.128383
bioRxiv. 2025 Dec 08. pii: 2025.12.08.693015. [Epub ahead of print]

Cysteine-S-nitrosylation inhibits Rop5-mediated immune evasion in Toxoplasma gondii.

S L Lempke, P C DiMare, B Nichols, A M Chaudry, L F Fitzsimmons, M L Reese, S E Ewald.

Reactive nitrogen species (RNS) are a mechanism to control microbial infections conserved across the host species of the obligate intracellular parasite Toxoplasma gondii. Cysteine S-nitrosylation (SNO) is a reversible post-translational modification that controls complex cell behaviors by regulating protein interactions and signal transduction events. Here we identified a cluster of T. gondii secreted effector proteins that are SNO-modified in a host inducible nitric oxide synthetase (iNOS)-dependent manner. Among these were the rhoptry protein 5 (ROP5) paralogs, which are the major virulence determinants in T. gondii and an immunodominant antigen in B6 mice. ROP5 was necessary for Type I and Type II parasites to evade IFN-γ-mediated immune clearance in iNOS-deficient macrophages. RNS led to the loss of ROP5 association with the parasitophorous vacuole membrane, which is necessary for the known functions of ROP5. Infection with ROP5 knockout parasites rescued the susceptibility of iNOS-deficient mice to infection with Type II T. gondii. Together, these data indicate that RNS can promote cell-autonomous parasite clearance by inhibiting the function of ROP5 paralogs at the parasitophorous vacuole membrane.
Importance: RNS are necessary for cell-autonomous immunity to T. gondii infection; however, the molecular mechanisms by which RNS regulate parasite control remain poorly understood. Our findings support a model where post-translational modification of ROP5 by RNS is a conserved mechanism of inhibiting the functions of divergent ROP5 paralogs. These data provide a specific example of how host RNS are used to counter T. gondii immune evasion effectors that can be applied to understand how nitrosylation regulates the function of other parasite effectors and the role of RNS in the control of other intracellular pathogens.

DOI: https://doi.org/10.64898/2025.12.08.693015
Vaccines (Basel). 2025 Nov 21. pii: 1180. [Epub ahead of print]13(12):

Protective Efficacy of Two Novel DNA Vaccine Candidates Encoding TgGRA28 and TgGRA83 with an IL-28B Molecular Adjuvant Against Acute and Chronic Toxoplasmosis in Mice.

Jun Fang, Jingqi Mu, Rui Li, Jia Chen.

   BACKGROUND: Toxoplasma gondii is a globally distributed apicomplexan parasite capable of causing congenital infections and spontaneous abortions in humans. While the parasite-secreted effector proteins TgGRA28 and TgGRA83 are known to mediate virulence or immune modulation, their potential as vaccine targets remains unexplored. Despite its immunomodulatory properties, the role of IL-28B (a type III interferon) in enhancing DNA vaccine efficacy against T. gondii infection remains unclear.
METHODS: In this study, we constructed eukaryotic expression plasmids pVAX-GRA28, pVAX- GRA83 and pVAX-IL-28B. After transfection into -293-T cell, protein expression encoding TgGRA28 and TgGRA83 was confirmed via indirect immunofluorescence assay (IFA), while IL-28B expression was analyzed by ELISA. Subsequently, C57BL/6J or IFNαR1 knockout mice were immunized with single or dual-antigen DNA vaccines, with or without the molecular adjuvant pVAX-IL-28B. Immune responses were assessed through Toxoplasma-specific antibody levels, cytotoxic T lymphocyte (CTL) activity, cytokine profiling (IFN-γ, IL-2, IL-12p40, IL-12p70), and flow cytometric analysis of lymphocyte subsets and dendritic cells (DCs). Protective efficacy was determined by survival rates and brain cyst burden following challenge with 100 or 10 ME49 T. gondii cysts, respectively.
RESULTS: Vaccination with pVAX-GRA28 and pVAX-GRA83 elicited robust humoral immune responses with increased T. gondii-specific IgG levels and also Th1-polarized immunity, characterized by elevated IgG2a/IgG1 ratio, IFN-γ-dominant cytokine responses, and enhanced DCs, CD4+ and CD8+ T-cell activation. The cocktail vaccine conferred superior protection compared to single-antigen formulations, significantly improving survival and reducing cyst formation. Co-administration of pVAX-IL-28B further augmented vaccine-induced immunity, enhancing both cellular and humoral responses. Moreover, these DNA immunization with pVAX-GRA28 and pVAX-GRA83 plus pVAX-IL-28B induced robust protective immunity that was largely independent of type I IFN signaling, consistent with type III IFN biology.
CONCLUSIONS: Our findings demonstrate that TgGRA28 and TgGRA83 are promising vaccine candidates against toxoplasmosis, capable of inducing protective immunity against acute and chronic infection. Moreover, IL-28B serves as a potent genetic adjuvant, warranting further investigation for its broader application in vaccines targeting apicomplexan parasites.

Keywords:  DNA vaccine; IL-28B; TgGRA28; TgGRA83; Toxoplasma gondii; protective immunity

DOI:  https://doi.org/10.3390/vaccines13121180
Front Cell Infect Microbiol. 2025 ;15 1651142

Toxoplasma gondii infection inhibits invasion and migration of human extravillous trophoblasts through dysregulation of FOXO1- and FOXO3a-dependent and -independent mechanisms.

Aurore Lebourg, Louis-Philippe Leroux, Visnu Chaparro, Sophie Chagneau, Cathy Vaillancourt, Maritza Jaramillo.

  The protozoan parasite Toxoplasma gondii causes severe pathologies in the infected fetus following vertical transmission during pregnancy. Primary T. gondii infection increases the risk of miscarriage during the first trimester of gestation; however, the cellular and molecular mechanisms are not fully understood. Extravillous trophoblasts (EVTs) are fetal cells that migrate and invade the maternal decidua to allow placenta formation and embryo implantation. The transcription factors Forkhead box O3a (FOXO3a) and FOXO1 play a central role in the regulation of EVT migration and invasion. Hence, impairment of EVT functions is associated with FOXO3a/FOXO1 dysregulation and poor pregnancy outcomes. Interestingly, T. gondii-driven inactivation of FOXO3a and FOXO1 was reported in fibroblasts and macrophages. Using a combination of cell imaging, reverse genetics and biochemical approaches in the human trophoblast cell line HTR-8/SVneo, herein we provide evidence that infection with type I RH T. gondii strain inhibits invasiveness and migratory activities in EVTs by repressing FOXO3a-and FOXO1-dependent and independent gene expression. Indeed, either T. gondii infection or single knockdown of FOXO3a and FOXO1 reduced invasion and migration properties in EVTs. Selective chemical blockade of parasite motility and host cell entry indicates that active infection is indispensable for reduced EVT migration but is only partially required for T. gondii-driven repression of EVT invasiveness. Mechanistically, T. gondii infection led to AKT-sensitive phosphorylation and nuclear exclusion of FOXO3a and FOXO1 in EVTs. An RT-qPCR-based screening identified a subset of invasion-and migration-associated genes downregulated in T. gondii-infected EVTs (MMP2, MMP3, MMP14, TIMP2, MUC1, and ITGB3). Transcription of genes encoding MMP3 and integrin β3 decreased in FOXO3a KD and FOXO1 KD EVT cell lines, respectively. These data along with pharmacological inhibition of AKT in infected cells provide evidence that T. gondii downregulates MMP3 and ITGB3 gene expression in EVTs in an AKT-FOXO3a/FOXO1-dependent fashion. In all, we have uncovered a novel regulatory mechanism involved in the repression of EVT migration and invasion properties during T. gondii infection. Further investigation using in vivo and ex vivo models of placental infection is required to determine whether T. gondii-driven dysregulation of EVT functions contributes to pregnancy complications associated with congenital toxoplasmosis.

Keywords:  AKT; FOXO1; FOXO3a; Toxoplasma gondii; extravillous trophoblasts; invasion; migration

DOI:  https://doi.org/10.3389/fcimb.2025.1651142
Microbiol Spectr. 2025 Dec 22. e0138525

PI3K/Akt/mTOR signaling pathway mediates energy metabolic reprogramming and regulates mitochondrial homeostasis in host cells exposed to Toxoplasma gondii.

Kangzhi Xu, Shifan Zhu, Jing Ma, Mingyue Zu, Jin Yang, Fan Xu, Linwei Dai, Dandan Liu, Yanhong Wang, Xinjun Zhang, Siyang Huang, Jinjun Xu, Zhiming Pan, Jianping Tao, Zhaofeng Hou.

  Toxoplasma gondii (T. gondii) relies on host cells for energy and nutrition. Our previous studies showed that T. gondii regulates host cell apoptosis via the mitochondrial pathway, highlighting the essential role of mitochondria in its parasitism. In this study, T. gondii infection was found to significantly affect mitochondrial morphology and dynamic homeostasis in porcine kidney-15 (PK-15) cells, characterized by aggregated, swollen, fragmented, and oval-shaped mitochondria with disappearing cristae, accompanied by increased fusion and decreased fission. Additionally, the energy metabolic reprogramming of PK-15 cells exposed to T. gondii was affirmed from the perspectives of glucose consumption; changes in NAD+/NADH, lactate, pyruvate, and ATP production; and expressions of proteins related to glycolysis and oxidative phosphorylation (OXPHOS). T. gondii-induced mitochondrial damage impaired the OXPHOS process; however, the glycolysis level was significantly increased. Mechanistically, we demonstrated that activation of phosphatidylinositol 3-kinase (PI3K)/protein kinase B (Akt)/mammalian target of rapamycin (mTOR) signaling pathway played a critical role in energy metabolic reprogramming and mitochondrial damage induced by T. gondii, and this effect could be attenuated by LY294002 (a PI3K inhibitor), which significantly reduced intracellular proliferation of T. gondii through inhibiting PI3K/Akt/mTOR signaling pathway. These findings highlight the PI3K/Akt/mTOR pathway as a key mediator of T. gondii-induced cellular metabolic reprogramming and mitochondrial dysfunction; however, its potential as a therapeutic target remains to be validated in vivo.IMPORTANCEToxoplasma gondii, a globally distributed obligate intracellular protozoan parasite, poses severe health risks to immunocompromised individuals and pregnant women, causing miscarriage and fetal abnormalities. Current therapies suffer from high toxicity and limited targets, with unclear mechanisms underlying host-parasite interactions. This study reveals a novel parasitic strategy: T. gondii hijacks host mitochondrial dynamics and energy metabolism. Infection disrupts mitochondrial morphology and suppresses oxidative phosphorylation while activating the PI3K/Akt/mammalian target of rapamycin (mTOR) pathway to drive metabolic reprogramming, enhancing glycolysis to meet energy demands. Critically, inhibiting PI3K/Akt/mTOR with LY294002 reduces intracellular parasite proliferation, validating this pathway as a therapeutic target. Conventional antiparasitic drugs targeting the parasite directly face resistance challenges. By focusing on host metabolic regulation via PI3K/Akt/mTOR, this work advances understanding of parasitism and proposes host-directed therapies to disrupt parasite proliferation by modulating the metabolic microenvironment, highlighting its therapeutic potential against toxoplasmosis.

Keywords:  LY294002; PI3K/Akt/mTOR; Toxoplasma gondii; energy metabolic reprogramming; mitochondrial dynamics

DOI:  https://doi.org/10.1128/spectrum.01385-25
PLoS Pathog. 2025 Dec 26. 21(12): e1013829

The early human interferon gamma response to Toxoplasma gondii is driven by Vγ9Vδ2 T-cell sensing of host phosphoantigens and subsequent NK-cell activation.

Felipe Rodriguez, Jeroen P J Saeij.

Toxoplasma gondii is a globally prevalent intracellular parasite that infects ~40 million Americans. The murine immune response to Toxoplasma relies on both toll-like receptor (TLR) 11/12 and immunity related GTPase-mediated (IRGs) responses, which humans lack, making it unclear how the human immune response detects and responds to the parasite. We investigated whether human Vγ9Vδ2 T cells, which detect phosphoantigens through the BTN3A1 receptor, shape the early immune response to the parasite. Using primary human peripheral blood mononuclear cells (PBMCs), we show that Vγ9Vδ2 T cells are activated by Toxoplasma-infected cells in a BTN3A1-dependent manner leading to secretion of interferon gamma (IFNγ) and tumor necrosis factor-alpha (TNFα). Additionally, these T cells potentiate IFNγ production by natural killer (NK) cells, via TNFα and interleukin (IL)-12 produced during infection. Active parasite invasion is required to stimulate the IFNγ response, and inhibition of the host mevalonate pathway, which limits the synthesis of the phosphoantigen isopentenyl pyrophosphate (IPP), attenuates the cytokine response, indicating Toxoplasma infection increases host phosphoantigens leading to Vγ9Vδ2 T cell activation. Our findings identify Vγ9Vδ2 T cells as key effectors that potentiate NK cells in the early human immune response to Toxoplasma, bridging innate and adaptive immunity in the absence of TLR11/12 signaling.

DOI: https://doi.org/10.1371/journal.ppat.1013829
Cells. 2025 Dec 15. pii: 1997. [Epub ahead of print]14(24):

Next-Generation HDAC Inhibitors: Advancing Zinc-Binding Group Design for Enhanced Cancer Therapy.

Mohammed Hawash.

  Histone deacetylases (HDACs) are pivotal epigenetic regulators that control gene expression, cell proliferation, and differentiation, and their dysregulation is closely associated with the onset and progression of multiple cancers. The therapeutic importance of these enzymes is reflected by FDA approval of HDAC inhibitors for oncology indications. Despite this clinical success, most FDA-approved agents employ conventional zinc-binding groups (ZBGs) such as hydroxamic acid and 2-aminoanilide, which are frequently linked to metabolic instability, genotoxicity, and poor pharmacokinetic behavior. These limitations have spurred the development of structurally diverse and safer HDAC inhibitors incorporating alternative ZBGs. This review provides a comprehensive analysis of recently developed HDAC inhibitors reported in the last few years, emphasizing their structure-activity relationships (SARs), chemical scaffolds, and binding features-including cap, linker, and ZBG motifs. Both hydroxamate-based and non-hydroxamate inhibitors, such as benzamides, hydrazides, and thiol-containing analogs, are critically evaluated. Moreover, the potency and selectivity profiles of these inhibitors are summarized across different cancer and normal cell lines, as well as specific HDAC isoforms, providing a clearer understanding of their therapeutic potential. Emerging dual-target HDAC inhibitors, such as HDAC-tubulin, HDAC-PI3K and HDAC-CDK hybrids, are also discussed for their synergistic anticancer effects.

Keywords:  SAR; anticancer; cells; histone deacetylases; hydroxamate; non-hydroxamate inhibitors; zinc-binding groups

DOI:  https://doi.org/10.3390/cells14241997
bioRxiv. 2025 Dec 20. pii: 2025.12.18.695271. [Epub ahead of print]

Quinazolinone and Phthalazinone Inhibitors of the HDAC6/Ubiquitin Protein-Protein Interaction.

Sydney Gordon, Jordi C J Hintzen, Sebastian Dilones, Callie E W Crawford, George M Burslem.

Histone deacetylase 6 (HDAC6) is a class IIb histone deacetylase that regulates diverse cytosolic acetylation through its two catalytic deacetylase domains and a C-terminal zinc finger ubiquitin-binding domain (ZnF-UBD) which mediates key protein-protein interactions (PPIs) that couple deacetylation and ubiquitin-dependent degradation. While most HDAC6 inhibitors target the catalytic domains, the ZnF-UBD represents an underexplored target. Here, we report the development of small-molecule inhibitors of the HDAC6 ZnF-UBD/ubiquitin interaction based on quinazolinone and phthalazinone scaffolds. Starting from known quinazolinone inhibitors, a modeling-guided scaffold hop revealed a novel phthalazinone series and late-stage diversification yield compounds with improved predicted physicochemical properties. Furthermore, machine-learning-based co-folding affinity predictions reproduced experimental IC□□ rank order, highlighting their utility in PPI inhibitor design. These studies expand the chemical space of HDAC6 ZnF-UBD inhibitors and provide a foundation for future therapeutic and mechanistic exploration of HDAC6-ubiquitin signaling.

DOI: https://doi.org/10.64898/2025.12.18.695271
Nat Microbiol. 2025 Dec 22.

Publisher Correction: Toxoplasma gondii VIP1 mediates parasitophorous vacuole-host endoplasmic reticulum interactions to facilitate parasite development.

Julia D Romano, Ruth Buh, Tanner Grudda, Julia R Box, John Beltran, Shahbaz M Khan, Isabelle Coppens.

DOI: https://doi.org/10.1038/s41564-025-02255-6
ACS Infect Dis. 2025 Dec 22.

Modular Design of Mitochondrion-Targeted Iron Chelators Allows Highly Selective Antiparasitic Activity against Trypanosomes and Apicomplexan Parasites.

Ronald Malych, Yann Bordat, Kristýna Klanicová, Dominik Arbon, Farnaz Zahedifard, Anna Šipková, Eliška Drncová, Viktoriya Levytska, Jan Mach, Laura Plutowski-Wrobel, Marta Machado, Jan Štursa, Jaroslav Truksa, Markus Ganter, Daniel Sojka, Martin Zoltner, Sébastien Besteiro, Lukáš Werner, Robert Sutak.

  Parasitic protozoa exhibit a high demand for iron, with mitochondrial iron metabolism representing a vulnerable target for chemotherapeutic intervention. We recently demonstrated that mitochondrial targeting of the iron chelator deferoxamine (DFO) via triphenylphosphonium (TPP) conjugation enhances its antiparasitic efficacy. To expand upon this strategy, mitochondrially targeted derivatives of DFO and deferasirox (DFX) were synthesized and evaluated for their activity against important human parasites. The DFX derivative mitoDFX was effective against Trypanosoma spp. and Toxoplasma gondii with remarkable selectivity. The fact that mitoDFX is a promising anticancer agent, which is likely safe to use in the context of human health, highlights the potential for drug repurposing in parasitology. Structure-activity relationship (SAR) studies and iron distribution analyses in trypanosomes revealed that mitochondrial targeting of the compounds, rather than iron chelation per se, is the main driver of the antiparasitic effects, underscoring the critical role of phosphonium salts in bioactivity.

Keywords:  Toxoplasma; Trypanosoma; antiparasitic agents; drug repurposing; iron chelators; mitochondrion

DOI:  https://doi.org/10.1021/acsinfecdis.5c00548
Alzheimers Dement. 2025 Dec;21 Suppl 5 e104774

Drug Development.

Thabo Brighton Makgoba, Jacques Joubert, Erika Kapp.

BACKGROUND: Histone deacetylases (HDACs) are epigenetic enzymes linked to several biological functions and diseases. Among HDACs, the class I enzymes show high similarity in protein sequence and active site. Non-selective inhibition of HDACs has side effects. However, HDAC3-selective inhibitors in preclinical studies showed promise in non-communicable diseases with fewer complications. Most HDAC3-selective inhibitors contain a benzamide zinc-binding group (ZBG). Hydroxamates are highly potent HDAC inhibitors, but they exhibit toxicity, poor pharmacokinetic and selectivity profiles. Benzamide-based inhibitors offer improved selectivity but lack potency and often optimisation compromises potency. There is a need for HDAC3 inhibitors with novel ZBGs, balanced potency and selectivity, while maintaining good safety and pharmacokinetic profiles. This study aims to identify HDAC3-selective inhibitors with novel ZBGs using in silico techniques.
METHOD: The in silico tools PROCHECK, VERIFY3D, Molecular Operating Environment, and ProteinsPlus, were utilised to validate HDAC3 protein structure, active site prediction and consensus confirmation, and predict zinc ion coordination geometry. Schrodinger Maestro was used for protein and ligand preparation, and molecular docking. Benchmarking was performed through re-docking and docking of actives and decoys to evaluate and validate the docking program, docking parameters and algorithm. Structure-based virtual screening with predefined criteria identified 22 structurally diverse compounds from focused libraries for purchase and subsequent in vitro evaluation.
RESULT: Out of the 22 compounds tested against HDAC3, 11 compounds showed inhibitory activity. Compound a showed the highest inhibitory activity (89.93%), compound k showed the lowest inhibitory activity (0.61%) at a 20 µM screening concentration. Compound a showed IC50 of 0.99 µM against HDAC3 but it showed poor selectivity against HDAC1 and HDAC2. Compound b showed an IC50 of 15.5 µM and it showed 7.4- and 5.7-fold selectivity against HDAC1 and 2 respectively. Neither compound inhibited HDAC8, and they were predicted to be blood brain barrier (BBB) impermeant. Toxicity predictions showed that compound a may cause neurotoxicity and respiratory toxicity and compound b may cause neurotoxicity and hepatotoxicity.
CONCLUSION: The study identified novel compounds with HDAC3 inhibition. However, it also highlighted the need for further structural optimisation to improve inhibitory activity, maintain selectivity, ensure BBB permeability and reduce toxicity.

DOI: https://doi.org/10.1002/alz70859_104774
Chin Med J (Engl). 2025 Dec 24.

Metabolites beyond metabolism: Exploring their atypical roles in protein modification and signaling transduction.

Wenjuan Yang, Jingxia Wu, Guoliang Cui.

   ABSTRACT: This comprehensive review explores the atypical metabolic roles of metabolites, extending beyond their conventional functions in energy production and biosynthesis. It systematically discusses how metabolites serve as substrates for post-translational protein modifications (PTMs), including lactylation, acetylation, and palmitoylation, detailing their metabolic origins, enzymatic regulation, and impacts on development, homeostasis, and diseases. Additionally, the review highlights how metabolites and metabolic enzymes act as signaling molecules to modulate intracellular and intercellular signal transduction, influencing processes like cell differentiation, survival, and proliferation. Unlike previous reviews, this work integrates PTM mechanisms with metabolic signaling networks, aiming to inspire research on metabolic regulation in health and disease, and to identify novel therapeutic targets.

Keywords:  Acetylation; Glycosylation; Lactylation; Lipidation modification; Metabolism; Metabolite; Palmitoylation; Post-ranslational protein modification; Signal transduction

DOI:  https://doi.org/10.1097/CM9.0000000000003939
Protein Sci. 2026 Jan;35(1): e70418

The role of the flexible loop region in the substrate binding and catalytic activity of malate dehydrogenases.

Varuni K Jamburuthugoda, Christopher E Berndsen, Jing Zhang, Jessica K Bell, Wai Cheung-Tung, Daniel Maskovsky, Kayla Kester, Tina Abelson, Ethan Huynh, John Ellis Bell.

  Malate dehydrogenase (MDH) is a ubiquitous enzyme found across all organisms, playing a central role in cellular metabolism. It catalyzes the interconversion between malate and oxaloacetate (OAA), utilizing NAD(H) or NADP(H) as a cofactor. In this study, we investigated the roles of several amino acid residues within the conserved "flexible loop" region of glyoxysomal MDH from Citrullus lanatus (wgMDH). Specifically, we examined how mutations in this region affect structure, substrate binding, catalysis, and substrate inhibition by OAA. We used kinetic experiments and molecular dynamics simulations to explore these effects. Our results demonstrated the importance of the flexible loop region in positioning the substrate for optimal catalysis, specifically for OAA binding. Several mutants exhibited a significant reduction in affinity for OAA binding while showing minimal effects on NADH binding and little or no decrease in overall catalytic activity. Further, two of the mutations showed decreased Ki for OAA, supporting the impact on OAA binding. Modeling of the effects of the loop on the structure and dynamics of MDH revealed that mutations changed the position of the loop relative to the catalytic histidine, leading to defects in binding and catalysis. These findings suggest that alterations in the dynamics of the flexible loop region influence substrate binding over catalysis.

Keywords:  active site mobile loop; enzyme kinetics; malate dehydrogenase; molecular dynamics; substrate inhibition

DOI:  https://doi.org/10.1002/pro.70418
Tumour Biol. 2025 Jan-Dec;47:47 14230380251410470

An integrated bioinformatics and multi-omics investigation of the sirtuin family to identify their prognostic importance in human cancers.

Md Shahedur Rahman, Rizone Al Hasib, Md Rezanur Rahman, Polash Kumar Biswas, Abu Reza, Munzura Khatun, Mohammad Abu Hena Mostofa Jamal.

  BackgroundIn recent years, the significance of sirtuins in cancer biology has become increasingly evident, but their molecular mechanisms and prognostic impacts remain elusive.ObjectiveThe present study aimed to investigate the differential expression of the sirtuin gene family across cancers and to evaluate their prognostic value.MethodsWe used various bioinformatics databases and methodologies, including Oncomine, GEPIA, OncoDB, cBioPortal, R2 Kaplan-Meier Scanner, STRING, etc., to determine the expression pattern of the sirtuin family genes, along with their mutations and prognostic values in human cancers.ResultsIn the current study, SIRT1, SIRT2, SIRT4, and SIRT5 were downregulated in lymphoma, whereas SIRT6 and SIRT7 were overexpressed. In breast cancer, SIRT3, SIRT5, and SIRT7 were overexpressed, and in terms of kidney cancer, higher expression of SIRT2, SIRT3, and SIRT5 was observed. In contrast, for leukemia, bladder, and brain cancers, most sirtuin family members showed reduced expression. We found that most mutations occurred in uterine cancer, chRCC (chromophobe renal cell carcinoma), DLBCL (diffuse large B-cell lymphoma), melanoma, pRCC (papillary renal cell carcinoma), and esophageal cancer. Moreover, we identified the relevant functional proteins through protein-protein interaction analysis to evaluate copy number alterations (CNAs) in sirtuins. The most frequent alterations were amplifications and deep deletions. Survival analysis demonstrated that SIRT1 and SIRT2 overexpression correlated with improved overall survival in low-grade glioma but predicted poorer outcomes in ovarian cancer. Downregulation of SIRT1, SIRT3, and SIRT5 was associated with better prognosis in DLBCL, while SIRT3 and SIRT4 upregulation predicted favorable survival in testicular germ cell tumors. SIRT6 overexpression was linked to favorable prognosis in esophageal carcinoma and sarcoma, while unfavorable outcomes were observed in hepatocellular carcinoma and cholangiocarcinoma. SIRT7 upregulation was significantly associated with reduced survival in esophageal, liver, and uterine cancers, but surprisingly correlated with improved outcomes in urothelial carcinoma and cervical squamous cell carcinoma.ConclusionsTogether, this multi-omics analysis reveals the correlation and prognostic values of sirtuins across multiple types of human cancers and suggests that sirtuins may serve as promising biomarkers for different cancers.

Keywords:  biomarkers; cancers; copy number alterations; sirtuins; survival analysis

DOI:  https://doi.org/10.1177/14230380251410470
Sheng Li Xue Bao. 2025 Dec 25. 77(6): 1035-1046

The biological functions of protein lactylation.

Jia-Qi Chen, Yue-Jing He, Hui-Ling Zheng, Yuan Yuan, Zhi-Wen Jiang, Jia-Jin Chen, Xin-Yi Zheng, Xin-Guang Liu, Xue-Rong Sun.

Lactylation is one of the post-translational modifications of proteins, a process in which lactyl residues bind to the lysine residues of proteins. This modification can alter the structure, stability, and function of proteins, which in turn regulates cellular metabolism, aging, and the onset of disease. This review classifies proteins with lactylation effects into histones and non-histone proteins and analyzes their functional roles when lactylation occurs. The in-depth exploration of lactylation is still in its infancy, and many aspects of its regulation, functional significance and therapeutic potential need to be further explored.

DOI: https://doi.org/10.13294/j.aps.2025.0094
Sci Transl Med. 2025 Dec 24. 17(830): eads0594

HDAC5 deacetylates cytosolic ACTN4 during skin reepithelialization and represents a therapeutic target for chronic wound healing.

Yifan Zhang, Dongsheng Wen, Chiakang Ho, Yangdan Liu, Xin Wang, Zhiyuan Zhou, Ya Gao, Qingfeng Li.

Skin repair after injury is a complex multistage process. Reepithelialization is a vital component of skin wound healing and involves intricate molecular regulations that are still not fully understood. Here, using a combination of human tissue and animal models, we identified histone deacetylase 5 (HDAC5) as a key mediator of reepithelialization through a mechanism involving nucleocytoplasmic shuttling to regulate deacetylation of a nonhistone protein. We conducted functional validation through a conditional gene knockout mouse model. In addition, parallel studies using ex vivo human skin confirmed that HDAC5 cytoplasmic localization is necessary for efficient wound closure. Liquid chromatography-mass spectrometry of mouse wounds revealed that cytoplasmic HDAC5 interacts with alpha-actinin-4 (ACTN4). Site-directed mutagenesis, immunofluorescence, and luciferase assays demonstrated that HDAC5 deacetylates ACTN4 at the K417 site, allowing nuclear translocation of ACTN4 and subsequent modulation of transcriptional activity of Y-box-binding protein 1 (YBX1). Single-cell transcriptome analysis of mouse wounds revealed cystatin A as a key factor downstream of the HDAC5/ACTN4/YBX1 axis that enhanced reepithelialization and wound healing. We further identified an HDAC5-selective activator, G194-0712, and showed that it improved wound healing in three mouse models of chronic wounds: diabetic wounds, ischemic wounds, and radiation injury. Together, these results highlight a previously unappreciated mechanism involved in skin repair and suggest that HDAC5 activation may hold promise for the treatment of nonhealing skin wounds.

DOI: https://doi.org/10.1126/scitranslmed.ads0594
bioRxiv. 2025 Dec 19. pii: 2025.12.18.695286. [Epub ahead of print]

Mitochondrial membrane junction-mediated ATP channeling drives activity-dependent glucose metabolism.

Dengbao Yang, Gemma Molinaro, Nadine Nijem, Chuanhai Zhang, Dylen Penny, Meijuan Bai, Mei-Jung Lin, Xiaodong Wen, Salvador Pena, Janaka Wansapura, Maria Gaitanou, Rebecca Matsas, Boyuan Wang, Hamid Baniasadi, Yan Han, Jay Gibson, Kimberly Huber, Xing Zeng.

Neurons and brown adipocytes rely on rapid ATP production from accelerated glucose metabolism to sustain bursts of activity upon stimulation, a process known as activity-dependent glucose metabolism. The first committed step in this pathway, the hexokinase I (HK1)-catalyzed phosphorylation of glucose, consumes ATP, raising the question of how this reaction can be accelerated when cytosolic ATP becomes limiting during stimulation. We identify Cell Cycle Exit and Neuronal Differentiation protein 1 (CEND1), expressed in both cell types, as a critical regulator of this process. Loss of CEND1 impairs activity-dependent glucose utilization, ATP generation, and stimulation-evoked activity both in vitro and in vivo . Mechanistically, CEND1 assembles a complex with HK1, voltage-dependent anion channel 1 (VDAC1), and adenine nucleotide translocase 1 (ANT1) at hemifusion-like membrane junction between the outer/inner mitochondrial membrane, channeling mitochondrially derived ATP directly to HK1. These findings uncover a previously unrecognized mechanism that sustains activity-dependent glucose metabolism, with broad implications for energy homeostasis in specialized cell types.

DOI: https://doi.org/10.64898/2025.12.18.695286
Mol Cell Proteomics. 2025 Dec 24. pii: S1535-9476(25)00601-2. [Epub ahead of print] 101502

MoSAIC: An Integrated and Modular Workflow for Confident Analysis of Protein Post-Translational Modification Landscapes.

Yuanwei Xu, Lijun Chen, T Mamie Lih, Yingwei Hu, Hui Zhang.

  Investigating multiple protein post-translational modifications (PTMs) is critical for unraveling the complexities of protein regulation and the dynamic interplay among PTMs, a growing focus in proteomics. However, simultaneous analysis of diverse PTMs remains a significant technical challenge, as existing workflows struggle to balance throughput, sensitivity, and reproducibility, particularly when sample amounts are limited. To address these limitations, we present MoSAIC, a multi-PTM workflow integrating co-enrichment strategies, multiplexing, fractionation, hybrid data acquisition, and unified data analysis, optimized for clinically relevant biological samples. This approach targets phosphorylation, glycosylation, acetylation, and ubiquitination, enabling comprehensive interrogation of these modifications simultaneously. Compared to the traditional CPTAC workflow, MoSAIC doubles PTM coverage (4 vs. 2 PTMs) while maintaining the same instrument time (24 MS runs), achieving increased identifications of PTM-modified peptides. By leveraging fractionation and tandem mass tag (TMT) labeling, we achieved concurrent identification and quantification of PTM-specific peptides from the same sample, enhancing throughput and data consistency. This robust workflow addresses key limitations in multi-PTM proteomics, providing a cost-effective and efficient platform to advance biological and clinical research.

Keywords:  Acetylation; Data-dependent acquisition (DDA); Data-independent acquisition (DIA); Glycosylation; Mass spectrometry (MS); PTM crosstalk; Phosphorylation; Post-translational modifications (PTMs); Proteomics workflow; Tandem mass tag (TMT); Ubiquitination

DOI:  https://doi.org/10.1016/j.mcpro.2025.101502
J Biol Chem. 2025 Dec 18. pii: S0021-9258(25)02927-8. [Epub ahead of print] 111075

HDAC6-mediated PFKL deacetylation enhances aerobic glycolysis and promotes VSMC proliferation.

Zhao-Kun Hu, Zhi-Yan Ren, Jie-Xin Pang, Hui Li, Meng-Nan Yang, Li-Hua Dong.

  Post-translational modifications (PTMs) of the glycolytic enzyme phosphofructokinase, liver type (PFKL) play a vital role in regulating its activity and function. Recently, we observed a reduction of PFKL acetylation in platelet-derived growth factor (PDGF)-BB-induced synthetic vascular smooth muscle cells (VSMCs). However, the function of acetylated PFKL has not be defined. This study aims to elucidate the effects and mechanisms of PFKL acetylation on development and progression of vascular diseases. We found that the expression of PFKL is up-regulated and its acetylation level is decreased in PDGF-BB-induced proliferative VSMCs. HDAC6, acts as the deacetylase of PFKL, could interact with PFKL to enhance enzymatic activity of PFKL by accelerating PFKL tetrameric formation and aerobic glycolysis process, thereby promoting VSMC proliferation, which can be hindered through the application of HDAC inhibitor Trichostatin A (TSA) or siHDAC6. Site prediction and experimental validation revealed that K563 was the main PFKL acetylation site. The recombinant adenoviral vector carrying PFKL K563R mutant aggravated, while the K563Q mutant attenuated PDGF-BB-induced VSMC proliferation and ligation-induced neointimal formation. Thus, PFKL may be a potential target for vascular reconstruction diseases treatment.

Keywords:  PFKL; VSMC proliferation; acetylation; aerobic glycolysis

DOI:  https://doi.org/10.1016/j.jbc.2025.111075