A goldilocks computational protocol for inhibitor discovery targeting DNA damage responses including replication-repair functions DOI Creative Commons
Davide Moiani, John A. Tainer

Frontiers in Molecular Biosciences, Journal Year: 2024, Volume and Issue: 11

Published: Nov. 28, 2024

While many researchers can design knockdown and knockout methodologies to remove a gene product, this is mainly untrue for new chemical inhibitor designs that empower multifunctional DNA Damage Response (DDR) networks. Here, we present robust Goldilocks (GL) computational discovery protocol efficiently innovate tools preclinical drug candidates cellular structural biologists without requiring extensive virtual screen (VS) synthesis expertise. By computationally targeting DDR replication repair proteins, exemplify the identification of target sites compounds probe cancer biology. Our GL pipeline integrates experimental predicted structures discover leads, allowing early-structure early-testing (ESET) experiments by laboratories. employing an efficient VS examine protein-protein interfaces (PPIs) allosteric interactions, identify ligand binding beyond active sites, leveraging

Language: Английский

Quantitative, titratable and high-throughput reporter assays to measure DNA double strand break repair activity in cells DOI Creative Commons
Eeson Rajendra, Diego Grande, Bethany Mason

et al.

Nucleic Acids Research, Journal Year: 2023, Volume and Issue: 52(4), P. 1736 - 1752

Published: Dec. 18, 2023

Abstract Repair of DNA damage is essential for the maintenance genome stability and cell viability. double strand breaks (DSBs) constitute a toxic class lesion multiple cellular pathways exist to mediate their repair. Robust titratable assays DSB repair (DSBR) are important functionally interrogate integrity efficiency these mechanisms in disease models as well response genetic or pharmacological perturbations. Several variants DSBR reporters available, however often limited by throughput restricted specific models. Here, we describe generation validation suite extrachromosomal reporter that can efficiently measure major homologous recombination (HR), classical nonhomologous end joining (cNHEJ), microhomology-mediated (MMEJ) single annealing (SSA). We demonstrate be adapted high-throughput screening format they sensitive modulation, thus providing mechanistic quantitative insights into compound potency, selectivity, on-target specificity. propose serve tools dissect interplay pathway networks cells will have broad implications studies basic research drug discovery.

Language: Английский

Citations

4
POLQ mediates replication-stress induced structural variant formation throughout common fragile sites during mitosis DOI Creative Commons
Thomas E. Wilson, Samreen Ahmed, Amanda Winningham

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: May 29, 2024

Abstract Genomic structural variants (SVs) greatly impact human health and disease, but much is unknown about their generative mechanisms, especially for the large class of nonrecurrent alterations. Common fragile sites (CFSs) are unstable loci that provide a model SV formation, deletions, under replication stress. We studied junction formation as it occurred in cells by applying error-minimized capture sequencing to CFS DNA harvested during junctions formed throughout genes at 5-fold higher rate after passed from G2 into M-phase. Neither nor expression depended on mitotic synthesis (MiDAS), an error-prone form conservative active CFSs. Instead, analysis tens thousands de novo combined with repair pathway inhibition revealed primary role polymerase theta (POLQ)-mediated end-joining (TMEJ) M-phase formation. propose important TMEJ genome wide.

Language: Английский

Citations

1
Where Do We Stand in Targeted Therapy Against BRCA1/2 Deficient Cancers? DOI Creative Commons

Zoe Manuel-Epstein

Undergraduate Research in Natural and Clinical Science and Technology (URNCST) Journal, Journal Year: 2024, Volume and Issue: 8(8), P. 1 - 11

Published: Aug. 20, 2024

Introduction: BRCA1 and BRCA2 are tumour suppressor genes that, when mutated, majorly increase the risk of cancer, particularly breast ovarian cancers. Cancer patients with BRCA mutations more likely to have aggressive forms cancer. Targeted therapy is a key component treatment for BRCA-deficient An important focus targeted synthetic lethality. Synthetic lethality loss viability from disruption two genes, but not either gene alone. The most established cancers poly (ADP-ribose) polymerase inhibitors (PARPi). This paper aims summarize advancements in against provide future directions. Methods: Relevant articles were found using search engines PubMed Google Scholar. Search terms relevant included "BRCA1", "BRCA2", "targeted therapies", "BRCA-deficient cancer", "synthetic lethality". Results: PARPi widely used clinical settings only approved by FDA use. exploits HR pathway cells trapping PARP at sites DNA damage, obstructing replication machinery, generating an accumulation DSBs, leading cell death. In addition PARPi, there has been further research into use other lethal interactors approaches target cancers, such as RAD52 inhibitors, FANCD2 immunotherapy, FEN1 APE2 PLK1 Damage Response Kinase RNF168 inhibitors. Discussion Conclusion: One major limitation rapid development resistance. Future steps must be taken overcome resistance improve sensitivity finding therapies alone create synergistic therapy. sum, ongoing BRCA-targeted occurring, efficacy will patient outcomes quality life.

Language: Английский

Citations

1
PARG inhibitor sensitivity correlates with accumulation of single-stranded DNA gaps in preclinical models of ovarian cancer DOI Creative Commons
Ramya Ravindranathan, Ozge Somuncu, Alexandre André Balieiro Anastácio da Costa

et al.

Proceedings of the National Academy of Sciences, Journal Year: 2024, Volume and Issue: 121(47)

Published: Nov. 15, 2024

Poly (ADP-ribose) glycohydrolase (PARG) is a dePARylating enzyme which promotes DNA repair by removal of poly (PAR) from PARylated proteins. Loss or inhibition PARG results in replication stress and sensitizes cancer cells to DNA-damaging agents. inhibitors are now undergoing clinical development for patients having tumors with homologous recombination deficiency (HRD), such as germline somatic

Language: Английский

Citations

1
Polθ Inhibitor (ART558) Demonstrates a Synthetic Lethal Effect with PARP and RAD52 Inhibitors in Glioblastoma Cells DOI Open Access
Gabriela Barszczewska-Pietraszek, Piotr Czarny, Małgorzata Drzewiecka

et al.

International Journal of Molecular Sciences, Journal Year: 2024, Volume and Issue: 25(17), P. 9134 - 9134

Published: Aug. 23, 2024

DNA repair proteins became the popular targets in research on cancer treatment. In our studies we hypothesized that inhibition of polymerase theta (Polθ) and its combination with Poly (ADP-ribose) 1 (PARP1) or RAD52 alkylating drug temozolomide (TMZ) has an anticancer effect glioblastoma cells (GBM21), whereas it a low impact normal human astrocytes (NHA). The compounds was assessed by analysis cell viability, apoptosis, proliferation, damage cycle distribution, as well gene expression. main results show Polθ causes significant decrease viability. It induces which is accompanied reduction proliferation damage. Moreover, stronger when dual PARP1 applied, further enhanced addition TMZ. much lower, especially considering viability conclusion, would like to highlight used great potential kill cells, shows synthetic lethal effect, while sparing astrocytes.

Language: Английский

Citations

0
Cryo-EM structures of the Plasmodium falciparum apicoplast DNA polymerase DOI
Chen‐Yu Lo,

Adron Robert Ung,

Tirthankar Koley

et al.

Journal of Molecular Biology, Journal Year: 2024, Volume and Issue: unknown, P. 168842 - 168842

Published: Oct. 1, 2024

Language: Английский

Citations

0
Replication stress induces POLQ-mediated structural variant formation throughout common fragile sites after entry into mitosis DOI Creative Commons
Thomas E. Wilson, Samreen Ahmed, Amanda Winningham

et al.

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: Nov. 6, 2024

Abstract Genomic structural variants (SVs) greatly impact human health, but much is unknown about the mechanisms that generate largest class of nonrecurrent alterations. Common fragile sites (CFSs) are unstable loci provide a model for SV formation, especially large deletions, under replication stress. We study junction formation as it occurs in cell lines by applying error-minimized capture sequencing to CFS DNA harvested after low-dose aphidicolin treatment. junctions form throughout genes at 5-fold higher rate cells pass from G2 into M-phase. Neither nor expression depend on mitotic synthesis (MiDAS), an error-prone active CFSs. Instead, analysis tens thousands de novo combined with repair pathway inhibition reveal primary role polymerase theta (POLQ)-mediated end-joining (TMEJ). propose important TMEJ genome wide.

Language: Английский

Citations

0
A goldilocks computational protocol for inhibitor discovery targeting DNA damage responses including replication-repair functions DOI Creative Commons
Davide Moiani, John A. Tainer

Frontiers in Molecular Biosciences, Journal Year: 2024, Volume and Issue: 11

Published: Nov. 28, 2024

While many researchers can design knockdown and knockout methodologies to remove a gene product, this is mainly untrue for new chemical inhibitor designs that empower multifunctional DNA Damage Response (DDR) networks. Here, we present robust Goldilocks (GL) computational discovery protocol efficiently innovate tools preclinical drug candidates cellular structural biologists without requiring extensive virtual screen (VS) synthesis expertise. By computationally targeting DDR replication repair proteins, exemplify the identification of target sites compounds probe cancer biology. Our GL pipeline integrates experimental predicted structures discover leads, allowing early-structure early-testing (ESET) experiments by laboratories. employing an efficient VS examine protein-protein interfaces (PPIs) allosteric interactions, identify ligand binding beyond active sites, leveraging

Language: Английский

Citations

0