bims-toxgon 2025-05-04 papers

bims-toxgon

Biomed News

on Toxoplasma gondii metabolism

Issue of 2025–05–04
27 papers selected by
Lakesh Kumar, BITS Pilani

Toxoplasma gondii RAD51 recombinase is required to overcome DNA replication stress and its inactivation leads to bradyzoite differentiation.
Advancing N,N'-disubstituted diamines in antimalarial drug development: Structure-activity relationships and mechanistic studies.
Dual-mode recognition of tRNAPro isoacceptors by Toxoplasma gondii Prolyl-tRNA synthetase.
Toxoplasma cyst wall CST9 elicits an acute-associated humoral response in humans and mice and protects against chronic infection in immunized mice.
CSP ubiquitylation favours Plasmodium berghei survival during early liver stage infection.
Comparison of a commercial ELISA, an in-house indirect ELISA, and a dot-ELISA developed for the serodetection of Toxoplasma gondii antibodies in farm animals.
SELEX-derived DNA aptamer utilized for sensitive electrochemical biosensing of Toxoplasma gondii surface antigen 1.
Sirtuins in Osteosarcoma: Cracking the Code and Opening Up New Treatment Options.
Drug Discovery for Histone Deacetylase Inhibition: Past, Present and Future of Zinc-Binding Groups.
Toxoplasma gondii chronic infection decreases visceral nociception through peripheral opioid receptor signaling.
Development of a BiAD Sensor for Locus-Specific Detection of Cellular Histone Acetylation Dynamics by Fluorescence Microscopy.
Protein Acetylation as a Novel Post-translational Modification of Plant Peroxisomal Proteins.
Switching off the yeast-to-hyphae transition in Yarrowia lipolytica through histone deacetylase inhibitors.
Acetylation and deacetylation dynamics in stress response to cancer and infections.
SIRT2 inhibition enhances mitochondrial apoptosis in Brucella-infected bovine placental trophoblast cells.
SIRTUINS MODULATORS MITIGATE HYPOXIA-INDUCED CELL DEATH DUE TO CHANGES IN HISTONE 3 ACETYLATION, AND MITOCHONDRIAL FUNCTION, DYNAMICS, AND CONTENT.
Sirtuin 3 Protects Lung Adenocarcinoma from Ferroptosis by Deacetylating and Stabilizing Mitochondrial Glutamate Transporter Solute Carrier Family 25 Member A22.
IDH1 regulates human erythropoiesis by eliciting chromatin state reprogramming.
DNA stimulates the deacetylase SIRT6 to mono-ADP-ribosylate proteins with histidine repeats.
SnRK2s: Kinases or Substrates?
Cytosolic NADK is conditionally essential for folate-dependent nucleotide synthesis.
The protein deacetylase HDAC10 controls DNA replication in malignant lymphoid cells.
Chemically Synthesized Fluorescence based Kinase Sensing Systems for Signaling in Cancer.
Altering metabolism programs cell identity via NAD+-dependent deacetylation.
IPMK depletion influences genome-wide DNA methylation.
Structural basis of multitasking by the apicoplast DNA polymerase from Plasmodium falciparum.
A Computational Approach for Designing a Peptide-Based Acetyl-CoA Synthetase 2 Inhibitor: A New Horizon for Anticancer Development.

bioRxiv. 2025 Apr 08. pii: 2025.04.08.647840. [Epub ahead of print]

Toxoplasma gondii RAD51 recombinase is required to overcome DNA replication stress and its inactivation leads to bradyzoite differentiation.

Ana M Saldarriaga Cartagena, Ayelén Aparicio Arias, Constanza Cristaldi, Agustina Ganuza, M Micaela Gonzalez, María M Corvi, William J Sullivan, Laura Vanagas, Sergio O Angel.

Toxoplasma gondii is an obligate intracellular parasite with a high replication rate that can lead to DNA replicative stress, in turn associated with the generation of DNA double-strand breaks (DSBs). Cells have two main pathways to repair DSBs: non-homologous end joining and homologous recombination repair (NHEJ and HRR respectively). RAD51 is the key recombinase in the HRR pathway. In this work, we achieved endogenous tagging of the RAD51 gene using the Auxin Inducible Degron (AID) system, to generate the clonal line RH RAD51 HA-AID . Here we demonstrate that RAD51 is expressed in replicative tachyzoites and establishes damage foci. Auxin-induced knock-down (KD) affects the correct replication of tachyzoites which show loss of synchronization. The use of the RAD51 inhibitor B02 also affects parasite growth, with an IC 50 of 4.8 µM. B02 produced alterations in tachyzoite replication and arrest in the S phase of the cell cycle. Additionally, B02 induced tachyzoite to bradyzoite differentiation showing small cyst-like structures. In conclusion, the HRR pathway is necessary for maintaining proper tachyzoite replication under normal growth conditions, supporting that replicative stress occurs during the cell cycle. Our findings also suggest that DNA replication stress can induce bradyzoite differentiation.

DOI: https://doi.org/10.1101/2025.04.08.647840
Eur J Med Chem. 2025 Jul 05. pii: S0223-5234(25)00395-2. [Epub ahead of print]291 117630

Advancing N,N'-disubstituted diamines in antimalarial drug development: Structure-activity relationships and mechanistic studies.

Alejandro I Recio-Balsells, Esteban Panozzo-Zénere, Renzo Carlucci, Nirupa Chaurasia, Ashan Manhas, Mercedes Bacelo Fioressi, Georgina N Montagna, Gustavo Arrizabalaga, Shabana I Khan, Babu L Tekwani, Niti Kumar, Guillermo R Labadie.

  Previously we reported the synthesis of thirty N,N'-disubstituted diamines, several of which exhibited potent activity against apicomplexan parasites, including Plasmodium falciparum and Toxoplasma gondii. Building on this, we expanded the series with fifty-four new compounds, which were evaluated against the same parasites. These analogs were synthesized via a one-pot reductive amination of aliphatic diamines with various aromatic aldehydes. The new library showed great potential, with several compounds achieving a pIC50 greater than 6.0 against P. falciparum and with an acceptable selectivity index range (SI ≥ 10). Additionally, some compounds exhibited activity against T. gondii, although no clear correlation in activity was observed between the two apicomplexan parasites which survive in different intracellular niches. A comprehensive structure-activity relationship (SAR) analysis was performed, encompassing both the previously reported collection and the new analogs. Furthermore, selected hits were tested against resistant P. falciparum strains, demonstrating comparable activity to that observed with sensitive strains. To gain insights into the mechanism of action, we examined morphological changes in the parasite for selected hits, observing distinct alterations that suggested diverse mechanisms across the compounds. Finally, we evaluated the invivo activity of three selected hits, though substantial parasite clearance was not observed. This outcome highlights the opportunity to optimize SAR to enhance permeability, solubility, and bioavailability, or it may suggest a parasitostatic rather than parasiticidal mechanism of action. In conclusion, this work highlights the potential of N,N'-disubstituted diamines in antimalarial drug discovery. Future efforts will focus on improving in vivo efficacy and further elucidating the mechanism of action.

Keywords:  Antimalarial activity; Apicomplexa; Polyamines; Resistant Plasmodium falciparum; Structure-activity relationship

DOI:  https://doi.org/10.1016/j.ejmech.2025.117630
EMBO Rep. 2025 Apr 28.

Dual-mode recognition of tRNAPro isoacceptors by Toxoplasma gondii Prolyl-tRNA synthetase.

Indira Rizqita Ivanesthi, Emi Latifah, Shih-Yang Liu, Yi-Kuan Tseng, Hung-Chuan Pan, Chien-Chia Wang.

  Prolyl-tRNA synthetases (ProRSs) exhibit diverse domain architectures and motifs, evolving into prokaryotic (P-type) and eukaryotic/archaeal (E-type) variants. Both types exhibit high specificity for the recognition and aminoacylation of their cognate tRNAs. Interestingly, the parasitic eukaryote Toxoplasma gondii encodes a single E-type ProRS (TgProRS) but utilizes two distinct tRNAPro isoacceptors: a cytosolic E-type (with C72/C73) and an apicoplast P-type (with G72/A73). Our study demonstrates that TgProRS, despite being classified as an E-type enzyme, efficiently charges both tRNAPro isoacceptors and functionally compensates for yeast cytoplasmic and mitochondrial ProRS activities. Notably, while C72/C73 are dispensable for cytosolic tRNAPro charging, G72/A73 are crucial for apicoplast tRNAPro aminoacylation. Furthermore, Mutations in the motif 2 loop selectively affect E- or P-type tRNAPro recognition. While TgProRS exhibits similar susceptibility to azetidine (a proline mimic) when charging both tRNAPro types, cytosolic tRNAPro charging is five times more sensitive to inhibition by halofuginone (a Pro-A76 mimic) compared to apicoplast tRNAPro charging. These findings underscore TgProRS's dual functionality, showcasing its remarkable evolutionary adaptability and providing valuable insights for developing more selective therapeutic agents.

Keywords:  Aminoacyl-tRNA Synthetase; Halofuginone; Parasite; Protein Synthesis; Toxoplasmosis

DOI:  https://doi.org/10.1038/s44319-025-00457-x
Microb Pathog. 2025 Apr 25. pii: S0882-4010(25)00363-8. [Epub ahead of print]205 107638

Toxoplasma cyst wall CST9 elicits an acute-associated humoral response in humans and mice and protects against chronic infection in immunized mice.

Ana M Saldarriaga Cartagena, Elias M Rivera, Edwin F Sánchez-López, Paula M Formigo, Ariel Legarralde, Agustina Ganuza, Andrés M Alonso, Marina Clemente, Sergio O Angel.

   BACKGROUND: Toxoplasma gondii is an obligate intracellular parasite that causes human and animal toxoplasmosis. It is considered an essential zoonotic foodborne infection. Up to now, there is not an adequate determination of acute toxoplasmosis in a single assay or a low-cost, safe vaccine against animal or human toxoplasmosis.
METHODS: We selected three parasite proteins belonging to dense granules and present in the secretome: TGME49_200360 (hypothetical protein), GRA17, and CST9. These recombinant proteins were analyzed using serum from mice experimentally infected with Me49 cysts and using a panel of human sera grouped as acute, chronic, or seronegative by IgG-ELISA. Besides, C57BL mice were immunized with rCST9 combined with alum or PBS + alum and challenged with tachyzoite of RH (100) and Me49 (1000 and 10,000) strains. Survival, serology, and brain cysts were analyzed.
RESULTS: Of the three proteins, only rCST9 showed reactivity with experimentally infected mice, restricted to day 15 post-infection but not on day 21 and beyond. Analysis of human serum samples showed that 36.66 % of acute sera and 4.61 % of chronic sera reacted with rCST9, while the other rAGs showed sensitivities below 5 % in all cases. The immunization of rCST9 combined with alum showed that it could not protect against the virulent strain RH but efficiently control the chronic infection in mice challenged with the avirulent strain Me49.
CONCLUSIONS: These data indicate that rCST9 presents an antigenic exposure restricted to the acute stage and can protect against chronic infection in the mouse model.

Keywords:  Dense granules; Diagnosis; Recombinant antigen; Toxoplasma gondii; Vaccine

DOI:  https://doi.org/10.1016/j.micpath.2025.107638
Sci Rep. 2025 Apr 25. 15(1): 14498

CSP ubiquitylation favours Plasmodium berghei survival during early liver stage infection.

Sara J S Baptista, Aparajita Lahree, Sofia Marques, Inês Bento, João Mello-Vieira, António M Mendes, Vanessa Zuzarte-Luís, Maria M Mota.

The circumsporozoite protein (CSP), an essential protein that covers the surface of the Plasmodium sporozoite, is a key player in multiple stages of the parasite development within the mosquito and during interactions between sporozoites and mammalian hepatocytes. Here, we identify a novel function of Plasmodium berghei CSP: preventing parasite elimination during the early stages of hepatic infection, through its ubiquitylation at two lysine (K) residues, K252 and K258, located in the C-terminal domain. A Plasmodium berghei transgenic line lacking these lysine residues exhibited a significant decrease in hepatic infectivity, with parasites being eliminated 4 h after infection. The reduced infectivity correlated with an increased association of host autophagy markers, LC3 and LAMP1, to the parasitophorous vacuole membrane of the liver stage parasite. Notably, inhibiting the host autophagy pathway fully rescued the mutant parasites from elimination. Collectively, we reveal a strategy employed by Plasmodium to evade early clearance during hepatic infection, which relies on the ubiquitylation of specific CSP lysine residues, that results in reduced parasite elimination via host autophagic and lysosomal activity.

DOI: https://doi.org/10.1038/s41598-025-98294-4
J Vet Diagn Invest. 2025 Apr 27. 10406387251331637

Comparison of a commercial ELISA, an in-house indirect ELISA, and a dot-ELISA developed for the serodetection of Toxoplasma gondii antibodies in farm animals.

Nagwa I Toaleb, Raafat M Shaapan, Dina Aboelsoued.

  Toxoplasma gondii is a widespread intracellular protozoan that can infect humans and animals. We isolated T. gondii strains from sheep, goats, cattle, buffaloes, and camels to develop and evaluate a modified in-house dot-ELISA for the detection of Toxoplasma antibodies in farm animals, and compared the results with a commercial ELISA (IDvet; gold standard). Animal tissue samples (n = 430) were examined microscopically, and infected tissues were bioassayed in mice as a viability test. Egyptian Toxoplasma strains were isolated from sheep, cattle, and camels and identified via PCR using the B1 gene (GenBank OR837022.1, OR837021.1, OR837020.1 from sheep, cattle, and camels, respectively). A T. gondii tachyzoite antigen from a sheep strain had the highest potential for the detection of specific T. gondii antibodies. We characterized this antigen using SDS-PAGE and separated it into 10 polypeptides of 96-12 kDa. Our modified in-house dot-ELISA detected T. gondii seropositivity in 172 of 430 (40%) farm animals with a sensitivity of 96.6% and specificity of 100%. The results of our dot-ELISA were confirmed in comparison with those of our indirect ELISA and the commercial ELISA. In a western blot, a predominant immunogenic reactive antigen band of 65 kDa was detected in T. gondii-positive sera of sheep, cattle, buffaloes, and camels; no cross-reaction occurred with antibodies to other parasitic infections or samples from healthy controls. Our modified in-house dot-ELISA is a rapid and simple test that showed promise for the detection of Toxoplasma antibodies in farm animals.

Keywords:  PCR; Toxoplasma gondii; anti-Toxoplasma IgG; dot-ELISA; indirect ELISA

DOI:  https://doi.org/10.1177/10406387251331637
Int J Biol Macromol. 2025 Apr 25. pii: S0141-8130(25)04082-6. [Epub ahead of print] 143530

SELEX-derived DNA aptamer utilized for sensitive electrochemical biosensing of Toxoplasma gondii surface antigen 1.

Pandiyaraj Kanagavalli, Shahad Alkhaldi, Mohammed Zourob, Shimaa Eissa.

  Toxoplasma gondii (T. gondii) is a global parasitic pathogen with significant health implications. Effective diagnosis is crucial, especially for vulnerable populations like immunocompromised individuals and pregnant women. Here, we developed a novel electrochemical aptasensor for detecting Surface Antigen 1 (SAG1), a key biomarker for acute T. gondii infections. New high-affinity aptamers (SOK3, SOK14, and SOK18) specific to SAG1 were identified using SELEX method. The aptamers were then immobilized onto screen-printed carbon electrodes (SPE) modified with graphene quantum dots (GQDs). Physicochemical characterization confirmed successful aptasensor fabrication. SOK14 was identified as optimal for SAG1 detection due to its lower dissociation constant and distinct current response upon protein binding. Square wave voltammetry (SWV) showed a linear response from 0.01 to 100 nM SAG1 (n = 3), correlating with [Fe(CN)6]3-/4- oxidation peak current changes and achieving a low detection limit of 11.5 pM with relative standard deviations ranging from 3.3 to 4.9 %. Selectivity studies against other nonspecific biomarkers for other pathogens validated the aptasensor's specificity. Application of the aptasensor in spiked serum samples indicated its efficiency in complex biological samples. This platform enables rapid, on-site detection of T. gondii with high sensitivity, selectivity, and reliability in serum samples, supporting early diagnosis and timely treatment to prevent complications.

Keywords:  Electrochemical aptasensor; Graphene quantum dots; SELEX method; Surface antigen 1; Toxoplasma gondii

DOI:  https://doi.org/10.1016/j.ijbiomac.2025.143530
Curr Pharm Biotechnol. 2025 Apr 25.

Sirtuins in Osteosarcoma: Cracking the Code and Opening Up New Treatment Options.

Yushi Zhao, Yong Han, Baichuan Wang, Ting Wang.

  Osteosarcoma (OS) is a frequent primary malignant bone tumor that primarily affects adolescents and the elderly, and it is prone to metastasis and recurrence. The prognostic status of metastatic and recurrent OS has remained stagnant over the past decades despite the availability of an extensive range of chemotherapy drugs in the clinic. To increase the overall survival and quality of life of patients with osteosarcoma, new therapeutic approaches must be developed immediately. In recent years, sirtuins (SIRT1-7) have garnered a lot of attention as researchers investigate the mechanisms underlying OS development and look for efficient treatment approaches. The nicotinamide adenine dinucleotide (NAD+)-dependent histone deacetylases (HDACs) that make up the sirtuin family are engaged in several biologically controlled processes, including proliferation, invasion, metastasis, apoptosis, autophagy, and chemotherapy resistance. Despite their significance in cancer having been avidly studied for decades, their specific functions and mechanisms of action are not yet clear due to limited reports. This review will summarize the current research status and look forward to the directions and prospects of its application in osteosarcoma research, aiming to open up new avenues for the treatment and study of osteosarcoma.

Keywords:  Osteosarcoma; prognosis; sirtuins; therapeutic approaches.; treatment

DOI:  https://doi.org/10.2174/0113892010374421250419163509
Pharmaceuticals (Basel). 2025 Apr 16. pii: 577. [Epub ahead of print]18(4):

Drug Discovery for Histone Deacetylase Inhibition: Past, Present and Future of Zinc-Binding Groups.

Gustavo Salgado Pires, Heber Victor Tolomeu, Daniel Alencar Rodrigues, Lídia Moreira Lima, Carlos Alberto Manssour Fraga, Pedro de Sena Murteira Pinheiro.

  Histone deacetylases (HDACs) are key regulators of gene expression, influencing chromatin remodeling and playing a crucial role in various physiological and pathological processes. Aberrant HDAC activity has been linked to cancer, neurodegenerative disorders, and inflammatory diseases, making these enzymes attractive therapeutic targets. HDAC inhibitors (HDACis) have gained significant attention, particularly those containing zinc-binding groups (ZBGs), which interact directly with the catalytic zinc ion in the enzyme's active site. The structural diversity of ZBGs profoundly impacts the potency, selectivity, and pharmacokinetics of HDACis. While hydroxamic acids remain the most widely used ZBGs, their limitations, such as metabolic instability and off-target effects, have driven the development of alternative scaffolds, including ortho-aminoanilides, mercaptoacetamides, alkylhydrazides, oxadiazoles, and more. This review explores the structural and mechanistic aspects of different ZBGs, their interactions with HDAC isoforms, and their influence on inhibitor selectivity. Advances in structure-based drug design have allowed the fine-tuning of HDACi pharmacophores, leading to more selective and efficacious compounds with improved drug-like properties. Understanding the nuances of ZBG interactions is essential for the rational design of next-generation HDACis, with potential applications in oncology, neuroprotection, and immunotherapy.

Keywords:  HDAC selectivity; drug design; epigenetics; metal chelation; metalloenzyme; structure–activity relationship

DOI:  https://doi.org/10.3390/ph18040577
PLoS Pathog. 2025 Apr 29. 21(4): e1013106

Toxoplasma gondii chronic infection decreases visceral nociception through peripheral opioid receptor signaling.

Alexis Audibert, Xavier Mas-Orea, Léa Rey, Marcy Belloy, Emilie Bassot, Louise Battut, Gilles Marodon, Frederick Masson, Matteo Serino, Nicolas Cenac, Gilles Dietrich, Chrystelle Bonnart, Nicolas Blanchard.

By eliciting immune activation in the digestive tract, intestinal pathogens may perturb gut homeostasis. Some gastrointestinal infections can indeed increase the risk of developing post-infectious irritable bowel syndrome (PI-IBS). Intriguingly, the prevalent foodborne parasite Toxoplasma gondii has not been linked to the development of PI-IBS and the impact of this infection on colon homeostasis remains ill-defined. We show in a mouse model that latent T. gondii decreases visceral nociceptive responses in an opioid signaling-dependent manner. Despite the accumulation of Th1 and cytotoxic T cells in the colon of latently infected mice, the selective invalidation of enkephalin gene in T cells ruled out the involvement of T cell-derived enkephalins in hypoalgesia. These findings provide clues about how this widespread infection durably shapes the gut immune landscape and modifies intestinal physiological parameters. They suggest that in contrast to other gut microbes, T. gondii infection could be negatively associated with abdominal pain.

DOI: https://doi.org/10.1371/journal.ppat.1013106
Genes (Basel). 2025 Apr 10. pii: 444. [Epub ahead of print]16(4):

Development of a BiAD Sensor for Locus-Specific Detection of Cellular Histone Acetylation Dynamics by Fluorescence Microscopy.

Anja R Köhler, Nicole Gutekunst, Annika Harsch, Pavel Bashtrykov, Albert Jeltsch.

   BACKGROUND: Dynamic changes in histone acetylation play crucial roles during cellular differentiation and disease development, but their detection in living cells is still a challenging task.
OBJECTIVES: Here, we developed a Bimolecular Anchor Detector (BiAD) sensor for the detection of locus-specific changes in histone acetylation in living cells by fluorescence microscopy.
METHODS: We used the BRD9 bromodomain cloned as tandem double domain (2xBRD9-BD) as a reader of histone acetylation. It was integrated into a dual-color BiAD chassis that was previously described by us.
RESULTS: We identified the gene body of TTC34 as a potential target for our sensor, because it contains dense histone acetylation and 392 local sequence repeats. Using a binding-deficient mutant of 2xBRD9-BD as a negative control, we established a successful readout of histone acetylation at the TTC34 locus. A single-domain reader did not function, indicating the requirement for the double reader to enhance the affinity and specificity of the chromatin interaction via avidity effects. With this sensor, we could detect dynamic increases in histone acetylation at the TTC34 locus after the treatment of cells with the histone deacetylase inhibitor Trichostatin A for 6 h indicating the applicability of the sensor for single-cell epigenome studies.
CONCLUSIONS: Our data demonstrate that active chromatin modifications can be detected by BiAD sensors using 2xBRD9-BD as a reader. This complements the toolkit of the available BiAD sensors and documents the modularity of BiAD sensors.

Keywords:  bimolecular anchor/detector; bimolecular fluorescence complementation; epigenome modification; fluorescence microscopy; histone acetylation; single-cell analysis; split fluorophore

DOI:  https://doi.org/10.3390/genes16040444
J Exp Bot. 2025 Apr 26. pii: eraf089. [Epub ahead of print]

Protein Acetylation as a Novel Post-translational Modification of Plant Peroxisomal Proteins.

Sigrun Reumann, Athina Parasyri.

  Plant peroxisomes compartmentalize many important metabolic functions, but little is known how these pathways are regulated at the post-translational level. Few plant peroxisomal proteins have been shown to be subjected to reversible phosphorylation or ubiquitination, but other post-translational modifications are hardly known for peroxisomes from animals, fungi, and plants. We here address the question whether plant peroxisomal metabolism might be regulated by protein acetylation. We summarize available knowledge on protein acetylation in plastids and mitochondria, focusing on the catalytic machinery and the regulation of target enzymes. We screened global acetylome studies of Arabidopsis for known proteins of peroxisomes that are N-terminally or Lys acetylated. For selected matrix proteins, we mapped the acetylated Lys sites onto their AlphaFold 3D models to predict their effect on enzyme activity and oligomerization. We also summarize knowledge on two Arabidopsis acetyl transferases that have recently been identified as novel peroxisomal matrix proteins. We deduce their evolution in peroxisomes and partly their functions, as far as they can be predicted from available structural models. This information allows us to identify experimental strategies to define the postulated new regulatory mechanism of protein acetylation for plant peroxisomes in the near future. (193 words, <200).

Keywords:  Acetyl transferases; Arabidopsis; co- and post-translational regulation; peroxisomes; protein acetylation

DOI:  https://doi.org/10.1093/jxb/eraf089
Res Microbiol. 2025 Apr 28. pii: S0923-2508(25)00034-8. [Epub ahead of print] 104299

Switching off the yeast-to-hyphae transition in Yarrowia lipolytica through histone deacetylase inhibitors.

Martha Viviana Roa-Cordero, Christian Alfonso Arenas-Sepúlveda, María Cristina Herrera-Plata, Sandra Milena Leal-Pinto, Nubia Andrea Villota-Salazar, Juan Manuel González-Prieto.

  Fungi can develop a variety of morphotypes to survive, colonize, adapt and prevail under different environmental conditions. In general, two morphological shapes encompass the others: yeast (unicellular) and hyphae (multicellular). Under specific conditions, some fungi can adopt these two cellular morphologies, and for this reason, they are called dimorphic. Histone acetylation and deacetylation are well-known important mechanisms of chromatin remodelling that control cell differentiation processes as dimorphism. The reactions involved are catalysed by histone acetyltransferases (HATs) and histone deacetylases (HDACs), respectively. In the present work, we used Yarrowia lipolytica as a dimorphic fungal model to investigate the effect of HDAC chemical inhibition on the growth and yeast-to-hyphae switch of fungi. For this purpose, we tested the compounds sodium butyrate (SB) and valproic acid (VPA) as epigenetic modulators. Our results indicated that Y. lipolytica tolerates high doses of these inhibitors due to its lipolytic nature. However, once the metabolic capability of the fungus is overcome, SB and VPA strongly suppress hyphal growth, suggesting that histone acetylation plays a pivotal role in the regulation of this process.

Keywords:  Epigenetics; HDAC in fungi; Morphogenesis; chromatin and cell differentiation; dimorphism; sodium butyrate; valproic acid

DOI:  https://doi.org/10.1016/j.resmic.2025.104299
Semin Immunol. 2025 Apr 26. pii: S1044-5323(25)00029-6. [Epub ahead of print]78 101957

Acetylation and deacetylation dynamics in stress response to cancer and infections.

Lili Li, Yanqiong Zeng, Genhong Cheng, Heng Yang.

  In response to stress stimuli, cells have evolved various mechanisms to integrate internal and external signals to achieve dynamic homeostasis. Lysine acetyltransferase (KATs) and deacetyltransferase (KDACs) are the key modulators of epigenetic modifications, enabling cells to modulate cellular responses through the acetylation and deacetylation of both histone and nonhistone proteins. Understanding the signaling pathways involved in cellular stress response, along with the roles of KATs and KDACs may pave the way for the development of novel therapeutic strategies. This review discusses the molecular mechanisms of acetylation and deacetylation in stress responses related to tumorigenesis, viral and bacterial infections. In tumorigenesis section, we focused on the tumor cells' intrinsic and external molecules and signaling pathways regulated by acetylation and deacetylation modification. In viral and bacterial infections, we summarized the update research on acetylation and deacetylation modification in viral and bacterial infections, which systematical introduction on this topic is not too much. Additionally, we provide an overview of current therapeutic interventions and clinical trials involving KAT and KDAC inhibitors in the treatment of cancer, as well as viral and bacterial infection-related diseases.

Keywords:  Acetylation; Bacterial infection; Deacetylation; KATs; KDACs; Stress response; Tumorigenesis; Viral infection

DOI:  https://doi.org/10.1016/j.smim.2025.101957
Vet Res. 2025 May 02. 56(1): 97

SIRT2 inhibition enhances mitochondrial apoptosis in Brucella-infected bovine placental trophoblast cells.

Mengyu Zhang, Lin Qi, Junmei Li, NingQiu Yuan, Yunyi Zhai, Mingyue Hao, Dong Zhou, Wei Liu, Yaping Jin, Aihua Wang.

  Brucella is a successful pathogen that employs a plethora of immune evasion mechanisms. This contributes to pathogenesis and persistence and limits the efficacy of available treatments. An increasing understanding of host‒pathogen interactions suggests that integrating host-directed strategies with existing anti-Brucella treatments could lead to more effective bacterial clearance and a reduction in drug-resistant strains. SIRT2 is a nicotinamide adenine dinucleotide (NAD+)-dependent deacetylase found in mammals. It can deacetylate various transcription factors and regulatory proteins, playing crucial roles in host‒pathogen interactions and pathogen infection-induced apoptosis. In this study, we investigated the role of SIRT2 in Brucella-induced cell apoptosis using bovine placental trophoblast cells. Our results indicate that B. abortus A19 infection upregulates SIRT2 protein expression and significantly induces mitochondrial apoptosis in these cells. Furthermore, inhibition of SIRT2 exacerbates B. abortus A19-induced mitochondrial apoptosis and markedly inhibits intracellular bacterial survival. These results prove the role of SIRT2 in Brucella pathogenesis and the mechanism of action.

Keywords:   Brucella ; SIRT2; bovine placental trophoblast cells; mitochondrial apoptosis

DOI:  https://doi.org/10.1186/s13567-025-01518-8
Neuropharmacology. 2025 Apr 30. pii: S0028-3908(25)00190-X. [Epub ahead of print] 110484

SIRTUINS MODULATORS MITIGATE HYPOXIA-INDUCED CELL DEATH DUE TO CHANGES IN HISTONE 3 ACETYLATION, AND MITOCHONDRIAL FUNCTION, DYNAMICS, AND CONTENT.

Luiz Felipe Souza E Silva, Amanda Siena, Jessica Mayumi Yuzawa, Tatiana Rosado Rosenstock.

  Hypoxia is a key environmental factor linked to neurodevelopmental complications, primarily through its impact on mitochondrial dysfunction. Given that sirtuins regulate mitochondrial and cellular metabolism, we aimed to investigate whether pharmacological modulation of sirtuins could protect neurons from hypoxia-induced mitochondrial dysfunction and cell death. To explore this, primary cortical neurons from male Wistar rats (control) and Spontaneously Hypertensive Rats (a model for neonatal hypoxia and schizophrenia) were exposed to cobalt chloride (CoCl2) to chemically induce hypoxia. Neurons were also treated with Nicotinamide (50 μM), Resveratrol (0.5 μM), and Sirtinol (5 μM) to modulate sirtuin activity. We first assessed histone deacetylation, cell death, mitochondrial calcium retention capacity, mitochondrial membrane potential, and levels of reactive oxygen species (ROS). In addition, we analysed the expression of genes related to mitochondrial metabolism, dynamics, and biogenesis, as well as high-energy compound levels. Our data indicate that both chemical and neonatal hypoxia caused mitochondrial depolarization, reduced calcium retention, increased ROS levels, and elevated Nfe2l2 expression in primary cortical neurons. Hypoxia also led to increased expression of genes associated with mitochondrial biogenesis and fission, as well as reduced ATP levels and elevated pyruvate and lactate levels. Importantly, treatment with sirtuin modulators enhanced neuron viability, likely by further increasing Nfe2l2 expression and reducing ROS production. These modulators also improved metabolic outcomes, including higher ATP levels, and normalized pyruvate and lactate production, as well as mitochondrial fusion gene expression. Collectively, our findings suggest that sirtuin modulators could mitigate hypoxia-induced damage and may represent a potential therapeutic strategy for managing neurodevelopmental disorders.

Keywords:  Hypoxia; Mitochondrial dysfunction; Schizophrenia and Neurons; Sirtuins

DOI:  https://doi.org/10.1016/j.neuropharm.2025.110484
Antioxidants (Basel). 2025 Mar 28. pii: 403. [Epub ahead of print]14(4):

Sirtuin 3 Protects Lung Adenocarcinoma from Ferroptosis by Deacetylating and Stabilizing Mitochondrial Glutamate Transporter Solute Carrier Family 25 Member A22.

Xiangyun Wei, Tiange Wang, Zhengcao Xing, Qinyun Shi, Jianmin Gu, Qiuju Fan, Hao Wang, Bin Chen, Jinke Cheng, Rong Cai.

  Solute carrier family 25 member A22 (SLC25A22) is a glutamate transporter in the inner mitochondrial membrane that is known to suppress ferroptosis in pancreatic ductal adenocarcinoma (PDAC). Sirtuin 3 (SIRT3) is the main mitochondrial deacetylase, and we previously demonstrated that targeting SIRT3 sensitized glioblastoma to ferroptosis by promoting mitophagy and inhibiting SLC7A11. The purpose of this study was to analyze the effect of SIRT3-mediated deacetylation of mitochondrial SLC25A22 on RAS-selective lethal 3 (RSL3)-induced ferroptosis in lung adenocarcinoma (LUAD). We found that the expression of SLC25A22 and SIRT3 had a high positive correlation and that their expression was greater in LUAD tissues than in adjacent tissues. The RSL3-induced ferroptosis of LUAD led to upregulation of SLC25A22 and SIRT3, and SIRT3 protected RSL3-induced LUAD from ferroptosis in vitro and in vivo. At the molecular level, SIRT3 bound with SLC25A22 and deacetylated this protein. Targeting SIRT3 enhanced the acetylation of SLC25A22, decreased its ubiquitination, and promoted 26S proteasome degradation in LUAD cells. Therefore, our results demonstrated that SIRT3 protected LUAD cells from RSL3-induced ferroptosis, and this effect is at least partially due to its deacetylation of SLC25A22, revealing that the SIRT3-SLC25A22 axis has an important role in regulating the ferroptosis of LUAD cells.

Keywords:  Sirtuin 3; ferroptosis; lung adenocarcinoma; solute carrier family 25 member 22

DOI:  https://doi.org/10.3390/antiox14040403
Elife. 2025 Apr 29. pii: RP100406. [Epub ahead of print]13

IDH1 regulates human erythropoiesis by eliciting chromatin state reprogramming.

Mengjia Li, Hengchao Zhang, Xiuyun Wu, Mengqi Yu, Qianqian Yang, Lei Sun, Wei Li, Zhongxing Jiang, Fumin Xue, Ting Wang, Xuili An, Lixiang Chen.

  Isocitrate dehydrogenase 1 (IDH1) is the key enzyme that can modulate cellular metabolism, epigenetic modification, and redox homeostasis. Gain-of-function mutations and decreased expression of IDH1 have been demonstrated to be associated with pathogenesis of various myeloid malignancies characterized by ineffective erythropoiesis, such as acute myeloid leukemia (AML) and myelodysplastic syndrome (MDS). However, the function and mechanism of IDH1 in human erythropoiesis still remains unclear. Here, utilizing the human erythropoiesis system, we present an evidence of IDH1-mediated chromatin state reprogramming besides its well-characterized metabolism effects. We found that knockdown IDH1 induced chromatin reorganization and subsequently led to abnormalities biological events in erythroid precursors, which could not be rescued by addition of reactive oxygen species (ROS) scavengers or supplementation of α-ketoglutarate (α-KG).We further revealed that knockdown IDH1 induces genome-wide changes in distribution and intensity of multiple histone marks, among which H3K79me3 was identified as a critical factor in chromatin state reprogramming. Integrated analysis of ChIP-seq, ATAC-seq, and RNA-seq recognized that SIRT1 was the key gene affected by IDH1 deficiency. Thus, our current work provided novel insights for further clarifying fundamental biological function of IDH1 which has substantial implications for an in-depth understanding of pathogenesis of diseases with IDH1 dysfunction and accordingly development of therapeutic strategies.

Keywords:  H3K79me3; IDH1; SIRT1; chromatin states; genetics; genomics; human erythropoiesis; none

DOI:  https://doi.org/10.7554/eLife.100406
J Biol Chem. 2025 Apr 23. pii: S0021-9258(25)00381-3. [Epub ahead of print] 108532

DNA stimulates the deacetylase SIRT6 to mono-ADP-ribosylate proteins with histidine repeats.

Nicholas J Pederson, Katharine L Diehl.

  Sirtuins are the NAD+-dependent class III lysine deacylases (KDACs). Members of this family have been linked to longevity and a wide array of different diseases, motivating the pursuit of sirtuin modulator compounds. Sirtuin 6 (SIRT6) is a primarily nuclear KDAC that deacetylates histones to facilitate gene repression. In addition to this canonical post-translational modification (PTM) "eraser" function, SIRT6 can use NAD+ instead to "write" mono-ADP-ribosylation (mARylation) on target proteins. This enzymatic function has been primarily associated with SIRT6's role in the DNA damage response. This modification has been challenging to study because it is not clear under what precise cellular contexts it occurs, only a few substrates are known, and potential interference from other ADP-ribosyltransferases in cells, among other reasons. In this work, we used commercially available ADP-ribosylation detection reagents to investigate the mARylation activity of SIRT6 in a reconstituted system. We observed that SIRT6 is activated in its mARylation activity by binding to dsDNA ends. We further identified a surprising target motif within biochemical substrates of SIRT6, polyhistidine (polyHis) repeat tracts, that are present in several previously identified SIRT6 mARylation substrates. This work provides important context for SIRT6 mARylation activity, in contrast to its KDAC activity, and generates a list of new potential SIRT6 mARylation substrates based on the polyHis motif..

Keywords:  ADP-ribosylation; DNA repair; DNA-protein interaction; Post-translational modification (PTM); sirtuins

DOI:  https://doi.org/10.1016/j.jbc.2025.108532
Plants (Basel). 2025 Apr 09. pii: 1171. [Epub ahead of print]14(8):

SnRK2s: Kinases or Substrates?

Yunmin Wei, Linzhu Peng, Xiangui Zhou.

  Throughout their life cycle, plants persistent through environmental adversities that activate sophisticated stress-signaling networks, with protein kinases serving as pivotal regulators of these responses. The sucrose non-fermenting-1-related protein kinase 2 (SnRK2), a plant-specific serine/threonine kinase, orchestrates stress adaptation by phosphorylating downstream targets to modulate gene expression and physiological adjustments. While SnRK2 substrates have been extensively identified, the existing literature lacks a systematic classification of these components and their functional implications. This review synthesizes recent advances in characterizing SnRK2-phosphorylated substrates in Arabidopsis thaliana, providing a mechanistic framework for their roles in stress signaling and developmental regulation. Furthermore, we explore the understudied paradigm of SnRK2 undergoing multilayered post-translational modifications (PTMs), including phosphorylation, ubiquitination, SUMOylation, S-nitrosylation, sulfation (S-sulfination and tyrosine sulfation), and N-glycosylation. These PTMs collectively fine-tune SnRK2 stability, activity, and subcellular dynamics, revealing an intricate feedback system that balances kinase activation and attenuation. By integrating substrate networks with regulatory modifications, this work highlights SnRK2's dual role as both a phosphorylation executor and a PTM-regulated scaffold, offering new perspectives for engineering stress-resilient crops through targeted manipulation of SnRK2 signaling modules.

Keywords:  SnRK2; phosphorylation; post-translational modification; substrates

DOI:  https://doi.org/10.3390/plants14081171
Nat Metab. 2025 May 02.

Cytosolic NADK is conditionally essential for folate-dependent nucleotide synthesis.

Kyle M Flickinger, Carlos A Mellado Fritz, Kimberly S Huggler, Gina M Wade, Gavin R Chang, Kathryn C Fox, Judith A Simcox, Jason R Cantor.

Nicotinamide adenine dinucleotide kinase (NADK) catalyses the phosphorylation of NAD+ to produce NAD phosphate, the oxidized form of NADPH, a cofactor that serves a critical role in driving reductive metabolism. Cancer cells co-express two distinct NAD kinases that differ by localization (NADK, cytosol; NADK2, mitochondria). CRISPR screens performed across hundreds of cancer cell lines indicate that both are dispensable for growth in conventional culture media. By contrast, NADK deletion impaired cell growth in human plasma-like medium. Here we trace this conditional NADK dependence to the availability of folic acid. NADPH is the preferred cofactor of dihydrofolate reductase (DHFR), the enzyme that mediates metabolic activation of folic acid. We find that NADK is required for enabling cytosolic NADPH-driven DHFR activity sufficient to maintain folate-dependent nucleotide synthesis under low folic acid conditions. Our results reveal a basis for conditional NADK essentiality and suggest that folate availability determines whether DHFR activity can be sustained by alternative electron donors such as NADH.

DOI: https://doi.org/10.1038/s42255-025-01272-3
Leukemia. 2025 Apr 29.

The protein deacetylase HDAC10 controls DNA replication in malignant lymphoid cells.

Andreas O Mieland, Giuseppe Petrosino, Mario Dejung, Jia-Xuan Chen, Amitkumar Fulzele, Fereshteh Mahmoudi, Jia-Wey Tu, Al-Hassan M Mustafa, Yanira Zeyn, Christoph Hieber, Matthias Bros, Tina M Schnöder, Florian H Heidel, Sara Najafi, Ina Oehme, Ilse Hofmann, Mike Schutkowski, Sebastian Hilscher, Christian Kosan, Falk Butter, Sanil Bhatia, Wolfgang Sippl, Oliver H Krämer.

Histone deacetylases (HDACs) comprise a family of 18 epigenetic modifiers. The biologically relevant functions of HDAC10 in leukemia cells are enigmatic. We demonstrate that human cultured and primary acute B cell/T cell leukemia and lymphoma cells require the catalytic activity of HDAC10 for their survival. In such cells, HDAC10 controls a MYC-dependent transcriptional induction of the DNA polymerase subunit POLD1. Consequently, pharmacological inhibition of HDAC10 causes DNA breaks and an accumulation of poly-ADP-ribose chains. These processes culminate in caspase-dependent apoptosis. PZ48 does not damage resting and proliferating human normal blood cells. The in vivo activity of PZ48 against ALL cells is verified in a Danio rerio model. These data reveal a nuclear function for HDAC10. HDAC10 controls the MYC-POLD1 axis to maintain the processivity of DNA replication and genome integrity. This mechanistically defined "HDAC10ness" may be exploited as treatment option for lymphoid malignancies.

DOI: https://doi.org/10.1038/s41375-025-02612-8
Chembiochem. 2025 May 02. e202500175

Chemically Synthesized Fluorescence based Kinase Sensing Systems for Signaling in Cancer.

Anindita Roy, Monisha Singha, Subhankar Singha.

  Kinases are an essential class of enzymes that regulate cellular processes through phosphorylation, influencing signal transduction, cell cycle progression, and apoptosis. Dysregulation of kinase activity is a hallmark of cancer, contributing to tumorigenesis, metastasis, and therapeutic resistance. Therefore, precise detection and monitoring of kinase activity are essential for understanding cancer biology and advancing diagnostics and therapeutics. Among various detection methods, fluorescence-based kinase sensing systems have emerged as highly sensitive, real-time tools for investigating kinase function. These systems leverage fluorescent moieties, either genetically encoded or chemically synthesized, to provide spatial and temporal insights into kinase activity in complex biological environments. This review focuses on chemically synthesized fluorescence-based kinase sensing systems, which offer unique advantages, including precise control over concentrations and compatibility with in vitro and in vivo applications. We have classified the chemically synthesized sensing systems into three categories: specific peptide substrate-based, ATP/ADP-recognition-based, and inhibitor-based sensing systems, each tailored to specific kinase activities. Compared to genetically encoded systems, chemically synthesized sensors demonstrate greater versatility and are better suited for quantitative high-throughput applications. This review explores the design, mechanisms, and applications of these systems in cancer biology, highlighting their potential for identifying kinase biomarkers, optimizing targeted therapies, and advancing personalized medicine.

Keywords:  Cancer diagnostics; Fluorescence sensing; Kinase detections; Kinase inhibitors; Kinase substrates

DOI:  https://doi.org/10.1002/cbic.202500175
EMBO J. 2025 Apr 25.

Altering metabolism programs cell identity via NAD+-dependent deacetylation.

Robert A Bone, Molly P Lowndes, Silvia Raineri, Alba R Riveiro, Sarah L Lundregan, Morten Dall, Karolina Sulek, Jose A H Romero, Luna Malzard, Sandra Koigi, Indra J Heckenbach, Victor Solis-Mezarino, Moritz Völker-Albert, Catherine G Vasilopoulou, Florian Meier, Ala Trusina, Matthias Mann, Michael L Nielsen, Jonas T Treebak, Joshua M Brickman.

  Cells change their metabolic profiles in response to underlying gene regulatory networks, but how can alterations in metabolism encode specific transcriptional instructions? Here, we show that forcing a metabolic change in embryonic stem cells (ESCs) promotes a developmental identity that better approximates the inner cell mass (ICM) of the early mammalian blastocyst in cultures. This shift in cellular identity depends on the inhibition of glycolysis and stimulation of oxidative phosphorylation (OXPHOS) triggered by the replacement of D-glucose by D-galactose in ESC media. Enhanced OXPHOS in turn activates NAD + -dependent deacetylases of the Sirtuin family, resulting in the deacetylation of histones and key transcription factors to focus enhancer activity while reducing transcriptional noise, which results in a robustly enhanced ESC phenotype. This exploitation of a NAD + /NADH coenzyme coupled to OXPHOS as a means of programming lineage-specific transcription suggests new paradigms for how cells respond to alterations in their environment, and implies cellular rejuvenation exploits enzymatic activities for simultaneous activation of a discrete enhancer set alongside silencing genome-wide transcriptional noise.

Keywords:  Aging; Enhancers; Metabolism; Pluripotency; Sirtuins

DOI:  https://doi.org/10.1038/s44318-025-00417-0
Biochem Biophys Res Commun. 2025 Apr 22. pii: S0006-291X(25)00588-1. [Epub ahead of print]766 151874

IPMK depletion influences genome-wide DNA methylation.

Zachary Sin, Evan Kinnear, Raj Doshi, Sujan Chatterjee, Houssemeddine Derbel, Prasun Guha, Qian Liu.

Inositol polyphosphate multikinase (IPMK) is emerging as a critical regulator of nuclear functions. While earlier studies in yeast and cell lines linked IPMK to gene expression, recent work reveals its role in modulating histone acetylation through the activation of histone deacetylases 1/3 (HDAC1/3). Interestingly, HDAC1/3 interact with DNA methyltransferase 1 (DNMT1), stabilizing DNMT1 and promoting DNA methylation. As an HDAC1/3 activator, IPMK may thereby influence DNA methylation dynamics. This study investigates how the genetic depletion of IPMK influences DNA methylation, though the role of its kinase activity remains untested. Using long-read Oxford nanopore sequencing, we conducted methylation analysis for >28 millions of CpG sites and discovered that IPMK deletion results in over 22,000 differentially methylated regions (DMRs). Integrating affected genes by DMRs and RNA-seq data, we found that 35 genes show an inverse correlation between methylation in promoter regions and gene expression. Pathway analysis revealed that genes related to tissue remodeling and hematopoiesis are affected. Notably, MMP14 and LIF showed significant methylation changes in promoter regions under IPMK deletion, resulting in decreased mRNA and protein expression. Collectively, this study identifies IPMK as a novel regulator of DNA methylation. While this study did not investigate the role of IPMK's kinase activity in regulating DNA methylation, future studies will determine whether IPMK's effects on DNA methylation are driven by its kinase activity or by kinase-independent mechanisms.

DOI: https://doi.org/10.1016/j.bbrc.2025.151874
bioRxiv. 2025 Apr 09. pii: 2025.04.09.647933. [Epub ahead of print]

Structural basis of multitasking by the apicoplast DNA polymerase from Plasmodium falciparum.

Anamika Kumari, Theodora Enache, Timothy D Craggs, Janice D Pata, Indrajit Lahiri.

Plasmodium falciparum is a unicellular eukaryotic pathogen responsible for the majority of malaria-related fatalities. Plasmodium belongs to the phylum Apicomplexa and like most members of this phylum, contains a non-photosynthetic plastid called the apicoplast. The apicoplast has its own genome, which is replicated by a dedicated apicoplast replisome. Unlike other cellular replisomes, the apicoplast replisome uses a single DNA polymerase (apPol) for copying the apicoplast DNA. Being the only DNA polymerase in the apicoplast, apPol is expected to multitask, catalysing both replicative and lesion bypass synthesis. Replicative synthesis typically relies on a restrictive active site for high accuracy while lesion bypass requires an open active site. This raises the question how does apPol combine the structural features of multiple DNA polymerases in a single protein. Using single particle electron cryomicroscopy (cryoEM), we have solved the structures of apPol bound to its DNA and nucleotide substrates in five pre-chemistry conformational states, allowing us to describe the events leading up to nucleotide incorporation and answer how apPol incorporates features of multiple polymerases. We found that, unlike most replicative polymerases, apPol can accommodate a nascent base pair with the fingers in an open configuration, which might facilitate the lesion bypass activity. In the fingers open state we identified a nascent base pair checkpoint that can preferentially select a Watson-Crick base pair, an essential requirement for replicative synthesis. Taken together these structural features explain how apPol may balance replicative and lesion bypass synthesis.

DOI: https://doi.org/10.1101/2025.04.09.647933
Cell Biochem Biophys. 2025 Apr 27.

A Computational Approach for Designing a Peptide-Based Acetyl-CoA Synthetase 2 Inhibitor: A New Horizon for Anticancer Development.

Musab Ali, Ernest Oduro-Kwateng, Ibrahim Oluwatobi Kehinde, Narasimham L Parinandi, Mahmoud E S Soliman.

  Acetyl-CoA Synthetase 2 (ACSS2) has emerged as a new target for anticancer development owing to its high expression in various tumours and its enhancement of malignancy. Stressing the growing interest in peptide-derived drugs featuring better selectivity and efficacy, a computational protocol was applied to design a peptide inhibitor for ACSS2. Herein, 3600 peptide sequences derived from ACSS2 nucleotide motif were generated by classifying the 20 amino acids into six physiochemical groups. De novo modeling maintained essential binding interactions, and a refined library of 16 peptides was derived using Support Vector Machine filters to ensure proper bioavailability, toxicity, and therapeutic relevance. Structural and folding predictions, along with molecular docking, identified the top candidate, Pep16, which demonstrated significantly higher binding affinity (91.1 ± 1.6 kcal/mol) compared to a known inhibitor (53.7 ± 0.7 kcal/mol). Further molecular dynamics simulations and binding free energy calculations revealed that Pep16 enhances ACSS2 conformational variability, occupies a larger binding interface, and achieved firm binding. MM/GBSA analysis highlighted key electrostatic interactions with specific ACSS2 residues, including ARG 373, ARG 526, ARG 628, ARG 631, and LYS 632. Overall, Pep16 appears to lock the ACSS2 nucleotide pocket into a compact, rigid conformation, potentially blocking ATP binding and catalytic activity, and may serve as a novel specific ACSS2 inhibitor. Though, we urge further research to confirm and compare its therapeutic potential to existing inhibitors. We also believe that this systematic methodology would represent an indispensable tool for prospective peptide-based drug discovery.

Keywords:  ACSS2; Anticancer agents; Molecular docking; Molecular dynamics simulations; Peptide inhibitor

DOI:  https://doi.org/10.1007/s12013-025-01729-y