Journal: bioRxiv

Article Title: PRMT5 as an Epigenetic Target for Group 3 (MYC-driven) Medulloblastoma

doi: 10.64898/2026.04.09.717536

Figure Lengend Snippet: (A) qPCR analysis for the expression of PRMT5/MYC mRNA in two MYC-amplified cell lines with transiently knocked-down of PRMT5 (using siRNAs) at 72 h. ****, p<0.0001 (student t test, SCR vs siPRMT5). (B) Effect of PRMT5 knockdown (siRNAs) on MYC-luciferase reporter gene (MYC-Luc) activity in HD-MB03 cells. *, p<0.05 (student t test) (C) ChIP analyses for the enrichment of PRMT5 and H4R3me2s on the proximal promoter region of the MYC gene in HD-MB03 cells. ****, p<0.0001 (student t test). ChIP analyses for the enrichment/binding of PRMT5 (D) and H4R3me2s (E) to the proximal promoter region of MYC gene, in PRMT5 knockdown (siRNAs) HD-MB03 cells. ( F ) Co-immunoprecipitation of BRD4 with PRMT5. ( G ) ChIP analyses for the enrichment/binding of PRMT5 and BRD4 to the proximal promoter region of MYC gene, in BRD4 knockdown (siRNAs) HD-MB03 cells. *, p<0.05; **, p<0.05 (student t test).

Article Snippet: Four PRMT5 inhibitors (EPZ015666, GSK332595, LLY-283, JNJ64619178) were purchased from MedChemExpress LLC or Selleckchem Company.

Techniques: Expressing, Amplification, Knockdown, Luciferase, Activity Assay, Binding Assay, Immunoprecipitation

Journal: bioRxiv

Article Title: PRMT5 as an Epigenetic Target for Group 3 (MYC-driven) Medulloblastoma

doi: 10.64898/2026.04.09.717536

Figure Lengend Snippet: RNA-sequencing was used to assess global gene expression changes in HD-MB03 cells 24 h after treatment with DMSO (vehicle) or JNJ64619178 (1 µM). (A) Volcano plot displaying genes significantly upregulated or downregulated in response to PRMT5 inhibition. (B) Gene Ontology Biological Process (GO-BP) functional analysis for top 10 pathways altered by JNJ. (C) Gene sets enrichment analysis (GSEA) (with p<0.01 and FDR<0.2) for top 10 pathways/gene sets (including MYC-associated target gene sets, RNA splicing, metabolism) altered by PRMT5 inhibition. (D) Number of the aberrant splicing events in protein coding genes disrupted by PRMT5 inhibition. (E) GO-BP functional analysis for the aberrant splicing events altered by PRMT5 inhibition. (F) Volcano plot represents all the significant (p<0.05) splicing events. Selected genes from the indicated GO-BP functional classification are highlighted. Metabolism associated genes GGT6, GPT2 and C1QBP1 are identified.

Article Snippet: Four PRMT5 inhibitors (EPZ015666, GSK332595, LLY-283, JNJ64619178) were purchased from MedChemExpress LLC or Selleckchem Company.

Techniques: RNA Sequencing, Gene Expression, Inhibition, Functional Assay

Journal: bioRxiv

Article Title: PRMT5 as an Epigenetic Target for Group 3 (MYC-driven) Medulloblastoma

doi: 10.64898/2026.04.09.717536

Figure Lengend Snippet: (A) MTT assay showing the effects of PRMT5 inhibitors (1-50 µM) on cell growth of MYC-amplified MB (HD-MB03, D341), non-MYC MB (ONS-76) and normal human astrocyte (NHA) cell lines. (B) IC 50 values of PRMT5 inhibitors in the indicated cell lines. (C) Annexin-V assay showing effects of PRMT5 inhibitors (JNJ, EPZ) on apoptosis in HD-MB03 cells. **, p<0.01, ***, p<0.001 (relative to ‘0’ (vehicle control)). (D) Cell cycle profile in HD-MB03 cells treated with PRMT5 inhibitors (EPZ, JNJ). (E) Western blot analysis for the expression of the indicated key proteins in JNJ-treated HD-MB03 cells. ( F) Quantification of spheres following treatment of JNJ and EPZ in two PDX-derived MB cell lines (MED-411FH, MED-114FH) at 72 h. Values, mean ± SEM. * p < 0.05; ** p < 0.01; *** p < 0.005; *** p < 0.001 (Student- t -test). (G) Representative sphere (MED-411FH) images showing disruption of spheres in each treatment. (H) Western blot results showing the expression of indicated proteins in MED-411 spheres treated with JNJ and EPZ.

Article Snippet: Four PRMT5 inhibitors (EPZ015666, GSK332595, LLY-283, JNJ64619178) were purchased from MedChemExpress LLC or Selleckchem Company.

Techniques: MTT Assay, Amplification, Annexin V Assay, Control, Western Blot, Expressing, Derivative Assay, Disruption

Journal: bioRxiv

Article Title: PRMT5 as an Epigenetic Target for Group 3 (MYC-driven) Medulloblastoma

doi: 10.64898/2026.04.09.717536

Figure Lengend Snippet: (A ) JNJ brain concentration in BALB/c mice (N=3) following oral administration of 10 mg/kg JNJ at different timepoints. **p<0.01 (Student’s t-test). (B) NSG mice (N=5) with subcutaneously xenografted HD-MB03 cells were treated orally with vehicle or JNJ (10 mg/kg) five times a week for three weeks. Tumor volume measurement of xenografted mice following treatments. The differences noted between treatment groups show comparison by Student ‘s t-test of the tumor volumes on 21 days post treatment (p<0.005). (C) Representative IHC images (40 × magnification with 60 µm scale bar) of PRMT5, MYC, Ki-67, and CC3 expression in xenografts 21 days post-treatment, as indicated. Bar graphs below show the percentages of PRMT5, MYC, Ki-67 and CC3 positive cells derived from immunohistology scores, which were semi-quantitated in the tumors of three xenografted mice. **p<0.01; ***p<0.005 (Student’s t-test). (D) NSG mice (N=6) with orthotopically xenografted HD-MB03 cells were treated daily with vehicle or JNJ (10 mg/kg) or JNJ (F) (10 mg/kg) for two weeks. Survival analysis of xenografted mice using Kaplan-Meier (long-rank test). *p<0.05, **p<0.01, ***p<0.001. (E) Representative IHC images (4x magnification with 600 µm scale bar) and respective quantification showing MYC-positive tumors in the mouse cerebellum. The percentage of MYC, derived from immunohistology scores, was semi-quantitated in the tumors of three xenografted mice 21 days post-treatment. *p< **p<0.01 (Student’s t-test).

Article Snippet: Four PRMT5 inhibitors (EPZ015666, GSK332595, LLY-283, JNJ64619178) were purchased from MedChemExpress LLC or Selleckchem Company.

Techniques: Concentration Assay, Comparison, Expressing, Derivative Assay

Journal: Journal of Chemical Theory and Computation

Article Title: Exploring the Structural Basis of Cryptic Pocket Formation Driven by Extensive Protein Conformational Changes in Drug Targets

doi: 10.1021/acs.jctc.5c02016

Figure Lengend Snippet: Cryptic pockets and the case of protein arginine methyltransferase 5. (A) Illustrates how early experimentally resolved structures of unliganded drug targets lacked satisfactory pockets for drug discovery but dynamic structural changes revealed cryptic pockets enabling ligand binding. (B) Shows PRMT5′s functional “double E” loop (red), cofactor SAM (magenta) and an example substrate arginine (cyan). An overlay of experimentally resolved structures with the EE loop in its default position is also shown, along with an experimentally resolved state (PDB ID 6UXY ) with the exposed cryptic pocket (circled in red). (C) Shows a structure and sequence alignment (EE loop boxed in black, Clustal2 coloring) of PRMT5 with the other PRMT family members, highlighting EE loop conservation.

Article Snippet: To limit bias arising from different research groups and crystallization conditions, the highest resolution PRMT5 structure resolved by Merck & Co., who solved the allosteric states, showing the EE loop in its default conformation was selected as starting structure: PDB ID 7KIC .

Techniques: Drug discovery, Ligand Binding Assay, Functional Assay, Sequencing

Journal: Journal of Chemical Theory and Computation

Article Title: Exploring the Structural Basis of Cryptic Pocket Formation Driven by Extensive Protein Conformational Changes in Drug Targets

doi: 10.1021/acs.jctc.5c02016

Figure Lengend Snippet: SLICE sampling method based on close contact CVs and OPES Explore biases. Here, the key steps involved in the developed sampling method SLICE are depicted. Knowledge of the target biology is used first to manually set the start and end sequence position to define a region of interest, upon which close contacts are automatically defined and disrupted through OPES Explore biases in a molecular dynamics simulation. PRMT5 is shown as an example here, with panel 4 illustrating various sampled conformations of the EE loop and its close contacts.

Article Snippet: To limit bias arising from different research groups and crystallization conditions, the highest resolution PRMT5 structure resolved by Merck & Co., who solved the allosteric states, showing the EE loop in its default conformation was selected as starting structure: PDB ID 7KIC .

Techniques: Sampling, Sequencing

Journal: Journal of Chemical Theory and Computation

Article Title: Exploring the Structural Basis of Cryptic Pocket Formation Driven by Extensive Protein Conformational Changes in Drug Targets

doi: 10.1021/acs.jctc.5c02016

Figure Lengend Snippet: Pocket analysis and results for PRMT5. (A) Depicts our approach to define ligandable cryptic pockets, where binding regions identified by SiteMap (cyan spheres, SiteScore > 1.0, DScore > 1.0) in the SLICE simulations are only retained if there is no significant (>20%) overlap with binding regions identified by SiteMap in the standard MD simulations. (B) Shows the resulting identified ligandable cryptic pocket for PRMT5 (cyan spheres), along with the crystallized (red, PDB ID 7KIC , 6UXY, and 6UXX) and example simulated (black) EE loop conformations. For reference, the cocrystallized allosteric ligands (black sticks) are also shown but they were not part of the simulations or pocket definitions.

Article Snippet: To limit bias arising from different research groups and crystallization conditions, the highest resolution PRMT5 structure resolved by Merck & Co., who solved the allosteric states, showing the EE loop in its default conformation was selected as starting structure: PDB ID 7KIC .

Techniques: Binding Assay

Journal: Journal of Chemical Theory and Computation

Article Title: Exploring the Structural Basis of Cryptic Pocket Formation Driven by Extensive Protein Conformational Changes in Drug Targets

doi: 10.1021/acs.jctc.5c02016

Figure Lengend Snippet: Mechanistic insights into cryptic pocket formation in the targets studied, showing illustrative snapshots from SLICE simulations in which cryptic pockets formed, highlighting the bias region (red), cryptic ligand (transparent red) and key residues (boxed). (A) PRMT5: D442-R604 dissociate first to facilitate F440 movement. (B) PRMT6: M373-H163 disperse followed by L161 displacement. (C) Abl1: rearrangements between M388-I360 and W405-A365 enable R386 to approach E286, facilitated by A380 and V299 displacement, causing R386 to disrupt E286- K271. (D) SMARCA2: E890-K857 disperse and M856 readjusts. (E) PI3Kα: H940 dissociates from E1012 and Q809, enabling the loop/helix segment to vacate the cryptic pocket area.

Article Snippet: To limit bias arising from different research groups and crystallization conditions, the highest resolution PRMT5 structure resolved by Merck & Co., who solved the allosteric states, showing the EE loop in its default conformation was selected as starting structure: PDB ID 7KIC .

Techniques: