molecular modeling software package moe  (Chemical Computing Group)

Journal: iScience

Article Title: Antigen-directed single domain antibody-based TNFR1 agonists elicit preferential killing of HER2-overexpressing cancer cells

doi: 10.1016/j.isci.2026.115327

Figure Lengend Snippet: AlphaFold3 models of TNFR1-ICM11 complexes (A) Native TNFR1–TNF reference structure for epitope orientation (adapted from PDB: 1TNR ). The following contact residues defines TNF binding site: Lys18, Ser49, His52, Trp93, Glu95, Arg132, Lys143, Lys144, Glu42, Ser43, His55, Cys56, Cys59, Ser60, Lys61, Arg63, Lys64, Glu65, and Met66. (B–D) AF3 models for 1:1, 2×, and 3× TNFR1-ICM11 assemblies. The AF3 confidences are indicated in the figure: ipTM provides confidence in the interface quality, and pTM summarizes the overall complex topology. The resulting contact residues of the 1:1 complex are: Arg63, Glu65, His91, Tyr92, Trp93, Glu95, Asn96, Gln99, Phe101, Lys118, Arg132, Glu133, Glu135, Glu147, and Lys150. Shared TNFR1 hotspot residues shared by both TNF and ICM11: Arg63, Glu65, Trp93, Glu95, Arg132. Interface/contact residues were computed via Molecular Operating Environment (MOE) software.

Article Snippet: molecular modeling software package MOE (Molecular Operating Environment) , Chemical Computing Group Inc. , RRID: SCR_014882.

Techniques: Binding Assay, Software

Journal: Cancer Immunology Research

Article Title: Systematic Engineering of TROP2-Targeted CAR T-Cell Therapy Overcomes Resistance Pathways in Solid Tumors

doi: 10.1158/2326-6066.CIR-25-0527

Figure Lengend Snippet: VH-only binder discovery, CAR engineering, and screening results in the identification of CARs with high efficacy and capable of binding unique epitopes. A, In vivo activity of selected constructs from (S4) with an orthotopic model of PC9. Mice were injected at day (d) = −14 with PC9 ffLuc + and, after engraftment was confirmed, given irrelevantly targeted control CAR or TROP2 CAR at 0.3E6 CAR + /mouse, as indicated by the arrow. Tumor was measured subsequently by bioluminescence imaging. Data are representative of two different experiments with different donors. B, Survival of mice from ( A ) with statistics shown using log-rank (Mantel–Cox) of hRS7 to VH681. C, In silico protein–protein docking prediction of sacituzumab, modeled from the FASTA primary sequence using antibody homology modeling (MOE), in complex with TROP2. The inset shows putative key residues and their side chains participating in protein–protein contacts, namely van der Waals interactions (pink halos), at the epitope–partatope interface. D, In vitro viability of TROP2 (hRS7-based) CARs against WT, KO, or murine Q237-252 substitution of TROP2. Performed at an E:T ratio of 2:1 and cocultured for 24 hours. Data are representative of two different experiments with different donors, with technical triplicates, with error bars showing SD. E, TROP2 VH binds to distinct epitopes compared with scFv-based CAR constructs. mTROP2 is murine TROP2, whereas mCPD and mCRD are murine CRD and CPD, with the remaining domains derived from the human TROP2 amino acid sequence. Heatmap demonstrates that selected TROP2 VH constructs have activity against a unique domain compared with scFv-based (hRS7 and dato) CAR constructs. Viability is normalized to an irrelevantly targeted control CAR for each construct. Data are representative of two different experiments with different donors. F, In silico protein–protein docking prediction of TROP2 VH375 and VH681, modeled from the FASTA primary sequence using antibody homology modeling (MOE), in complex with TROP2. The inset shows putative key residues and their side chains participating in protein–protein contacts, namely van der Waals interactions (pink halos), at the epitope–partatope interface. P values are reported as follows compared with control: *, P ≤ 0.05; ****, P ≤ 0.0001. TY domain, thyroglobulin type-1 domain.

Article Snippet: Computational studies aimed at modeling the structure and binding interactions of datopotamab and sacituzumab scFvs and three VH binders that demonstrated high cytotoxicity in both PC9 and HCC827GR6 cell lines (VH375, VH377, and VH681) to human TROP2 were performed using the Molecular Operating Environment (MOE) software package (MOE2022.02, Chemical Computing Group).

Techniques: Binding Assay, In Vivo, Activity Assay, Construct, Injection, Control, Imaging, In Silico, Sequencing, In Vitro, Derivative Assay

Journal: Cancer Immunology Research

Article Title: Systematic Engineering of TROP2-Targeted CAR T-Cell Therapy Overcomes Resistance Pathways in Solid Tumors

doi: 10.1158/2326-6066.CIR-25-0527

Figure Lengend Snippet: Rational epitope binding–based design of biparatopic CARs leveraging single-domain VH-only binders overcomes models of resistance to single epitope–targeted approaches. A, Schematic of biparatopic TROP2 VH-based CARs in a second-generation CAR vector with a linker between anti-CRD VH and anti-CPD VH, as well as a hinge/transmembrane domain (H/TM), 4-1BB costimulatory domain, and CD3ζ signaling domain. B, In vitro cytotoxicity of TROP2 scFv, VH, and biparatopic VH CAR against PC9 with various substitutions of TROP2 domains with murine domains as indicated. Performed at a 2:1 E:T ratio and cocultured for 24 hours before viability was assessed via luciferase assay and normalized to an irrelevant BCMA control. Data are representative of two different experiments with different donors. C, In silico protein–protein docking prediction of biparatopic TROP2 VH681_375, modeled from the FASTA primary sequence using antibody homology modeling (MOE), in complex with TROP2. D, In vitro activity in a live-cell imaging assay of TROP2 CARs against PC9. PC9 TROP2 KO was stably transduced with murine CPD and mCherry, and live-cell imaging was performed on Incucyte with counting of red objects. The cytotoxicity index is the red cell object count relative to time (t) = 0 when CARs were applied at an E:T ratio of 0.25:1. Data are representative of two different experiments with different donors, with technical triplicates with error shading showing SEM. E, Similar to ( D ), with PC9 TROP2 murine CRD clone transduced with GFP, with counting of green objects. Data are representative of two different experiments with different donors, with technical triplicates with error shading showing SEM. F, PC9 harboring murine Q237-252 (CPD) or murine CRD tumors were injected subcutaneously into separate flanks of NSG mice, and after tumors reached ∼100 mm 3 , CD19 irrelevant control or TROP2 CARs were administered at a one-time dose of 2.5E6 CAR + cells via the tail vein, as indicated by the arrow. Tumors measured by caliper measurement of the mQ237-252 tumor on the left flank, with individual (dim) and mean (solid) measurements shown for groups. Data are representative of two different experiments with different donors. G, Tumors were measured by caliper measurement of the mCRD tumor on the right flank, with individual (dim) and mean (solid) measurements shown for groups. Data are representative of two different experiments with different donors. H, Survival of mice from F to G with biparatopic TROP2 CAR VH681_375 compared with benchmark hRS7 CAR (60 vs. 36.5 days, P = 0.001). Survival statistics were reported by log-rank (Mantel–Cox) test. P values are reported as follows compared with control: **, P ≤ 0.01; ****, P ≤ 0.0001.

Article Snippet: Computational studies aimed at modeling the structure and binding interactions of datopotamab and sacituzumab scFvs and three VH binders that demonstrated high cytotoxicity in both PC9 and HCC827GR6 cell lines (VH375, VH377, and VH681) to human TROP2 were performed using the Molecular Operating Environment (MOE) software package (MOE2022.02, Chemical Computing Group).

Techniques: Binding Assay, Plasmid Preparation, In Vitro, Luciferase, Control, In Silico, Sequencing, Activity Assay, Live Cell Imaging, Stable Transfection, Transduction, Injection