scholarly journals p53 CRISPR Deletion Affects DNA Structure and Nuclear Architecture

2020 ◽  
Vol 9 (2) ◽  
pp. 598 ◽  
Author(s):  
Aline Rangel-Pozzo ◽  
Samuel Booth ◽  
Pak Lok Ivan Yu ◽  
Madhurendra Singh ◽  
Galina Selivanova ◽  
...  
Keyword(s):  
Tumor Suppressor ◽  
Three Dimensional ◽  
Nuclear Architecture ◽  
Super Resolution ◽  
Dna Structure ◽  
Tp53 Gene ◽  
Binding Pocket ◽  
Main Function ◽  
Wild Type ◽  
Independent Manner

The TP53 gene is a key tumor suppressor. Although the tumor suppressor p53 was one of the first to be characterized as a transcription factor, with its main function potentiated by its interaction with DNA, there are still many unresolved questions about its mechanism of action. Here, we demonstrate a novel role for p53 in the maintenance of nuclear architecture of cells. Using three-dimensional (3D) imaging and spectral karyotyping, as well as super resolution microscopy of DNA structure, we observe significant differences in 3D telomere signatures, DNA structure and DNA-poor spaces as well gains or losses of chromosomes, between normal and tumor cells with CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)-deleted or wild-type TP53. Additionally, treatment with Nutlin-3 results in differences in nuclear architecture of telomeres in wild-type but not in p53 knockout MCF-7 (Michigan Cancer Foundation-7) cells. Nutlin-3 binds to the p53-binding pocket of mouse double minute 2 (MDM2) and blocks the p53-MDM2 interaction. Moreover, we demonstrate that another p53 stabilizing small molecule, RITA (reactivation of p53 and induction of tumor cell apoptosis), also induces changes in 3D DNA structure, apparently in a p53 independent manner. These results implicate p53 activity in regulating nuclear organization and, additionally, highlight the divergent effects of the p53 targeting compounds Nutlin-3 and RITA.

scholarly journals Recent Synthetic Approaches towards Small Molecule Reactivators of p53

Biomolecules ◽  
2020 ◽  
Vol 10 (4) ◽  
pp. 635 ◽  
Author(s):  
Jerson L. Silva ◽  
Carolina G. S. Lima ◽  
Luciana P. Rangel ◽  
Giulia D. S. Ferretti ◽  
Fernanda P. Pauli ◽  
...  
Keyword(s):  
Tumor Suppressor ◽  
Small Molecules ◽  
P53 Protein ◽  
Tp53 Gene ◽  
Therapy Resistance ◽  
Main Function ◽  
Tumor Suppressor Function ◽  
Cellular Functions ◽  
Synthetic Approaches ◽  
Integrity Of Dna

The tumor suppressor protein p53 is often called “the genome guardian” and controls the cell cycle and the integrity of DNA, as well as other important cellular functions. Its main function is to trigger the process of apoptosis in tumor cells, and approximately 50% of all cancers are related to the inactivation of the p53 protein through mutations in the TP53 gene. Due to the association of mutant p53 with cancer therapy resistance, different forms of restoration of p53 have been subject of intense research in recent years. In this sense, this review focus on the main currently adopted approaches for activation and reactivation of p53 tumor suppressor function, focusing on the synthetic approaches that are involved in the development and preparation of such small molecules.

scholarly journals In silico investigation of Y220C mutant p53 for lead design

2019 ◽  
Author(s):  
Mayank Roy Chowdhury ◽  
Anamika Tiwari ◽  
G.P. Dubey
Keyword(s):  
Tumor Suppressor ◽  
P53 Protein ◽  
Tp53 Gene ◽  
Docking Studies ◽  
Mutant P53 ◽  
Wild Type ◽  
Dynamic Simulations ◽  
Complex Processes ◽  
Cycle Arrest ◽  
To Come

Abstractp53 protein coded by the Tp53 gene is considered as one of the most intensively researched protein and mainly due to its role as a tumor suppressor, it acts as a tumor suppressor by carrying out two biologically complex processes namely Cell cycle arrest and apoptosis, In the oncogenic Y220C mutant p53, tyrosine is replaced by cysteine at 220th residue of the DNA binding Domain which causes the formation of a surface crevice, this specific mutation is responsible for approx. 100,000 cancer cases per year due to the destabilization and denaturation of the protein, as a result, the protein degrades at room temperature. In this work we carry out intensive Molecular Dynamic Simulations and Molecular Docking Studies to understand the structural dynamics of wild type p53 and changes the occurs in the mutant protein and also try to design lead against the druggable crevice and at the end of our study we used fragment-based optimization to come up with lead molecules which can act as scaffold for further drug development process

scholarly journals Establishment of heterochromatin in domain-size-dependent bursts

2021 ◽  
Vol 118 (15) ◽  
pp. e2022887118
Author(s):  
Jan Fabio Nickels ◽  
Ashleigh Katrine Edwards ◽  
Sebastian Jespersen Charlton ◽  
Amanda Møller Mortensen ◽  
Sif Christine Lykke Hougaard ◽  
...  
Keyword(s):  
Mathematical Modeling ◽  
Dynamic Properties ◽  
Three Dimensional ◽  
Domain Size ◽  
Wild Type ◽  
Independent Manner ◽  
Type Region ◽  
Size Dependent ◽  
Evolutionarily Conserved ◽  
Highly Correlated

Methylation of histone H3K9 is a hallmark of epigenetic silencing in eukaryotes. Nucleosome modifications often rely on positive feedback where enzymes are recruited by modified nucleosomes. A combination of local and global feedbacks has been proposed to account for some dynamic properties of heterochromatin, but the range at which the global feedbacks operate and the exact mode of heterochromatin propagation are not known. We investigated these questions in fission yeast. Guided by mathematical modeling, we incrementally increased the size of the mating-type region and profiled heterochromatin establishment over time. We observed exponential decays in the proportion of cells with active reporters, with rates that decreased with domain size. Establishment periods varied from a few generations in wild type to >200 generations in the longest region examined, and highly correlated silencing of two reporters located outside the nucleation center was observed. On a chromatin level, this indicates that individual regions are silenced in sudden bursts. Mathematical modeling accounts for these bursts if heterochromatic nucleosomes facilitate a deacetylation or methylation reaction at long range, in a distance-independent manner. A likely effector of three-dimensional interactions is the evolutionarily conserved Swi6HP1 H3K9me reader, indicating the bursting behavior might be a general mode of heterochromatin propagation.

Functional plasticity of putative TP53 gain of function mutations in human gastrointestinal tract adenocarcinomas.

2021 ◽  
Vol 39 (15_suppl) ◽  
pp. e15530-e15530
Author(s):  
David R. Braxton ◽  
Joanne Xiu ◽  
Wafik S. El-Deiry ◽  
Sourat Darabi ◽  
Wolfgang Michael Korn ◽  
...  
Keyword(s):  
Tumor Suppressor ◽  
Tp53 Gene ◽  
Immune Checkpoint Blockade ◽  
Missense Mutations ◽  
Cell Cycle Regulators ◽  
Wild Type ◽  
Functional Plasticity ◽  
Gain Of Function ◽  
Multifunctional Protein ◽  
Gi Cancers

e15530 Background: The TP53 gene product is a multifunctional protein and prototypical tumor suppressor. Certain missense mutations occurring in hotspots in the TP53 gene may confer gain of function (GOF) oncogenic properties. A recent mouse model (Kadosh et. al., Nature, 2020) demonstrated that secreted factors in the gut microbiome permit GOF p53 to be oncogenic in lower GI tract cancers (LT). By contrast, the GOF p53 mutants in the upper tract cancers (UT) retained tumor suppressor functions. We aimed to provide evidence of the plasticity of TP53 GOF mutants in human GI cancers. We hypothesized that UT should have a lower rate of TP53 GOF than the LT, and UT cancers with putative GOF TP53 mutations should display a higher degree of co-occurring oncogenic alterations such as dysregulation of CCND1, MYCS, or WNT. We also explored outcome differences for TP53 GOF variants. Methods: Tumors of UT (stomach, esophagus, small intestine) and LT (colorectum, anus) were tested at Caris Life Sciences (Phoenix, AZ) by NGS (NextSeq, 592 or NovoSeq, whole exome). MSI/MMRP status was determined by IHC and NGS. Real-world overall survival (OS) was obtained from payor claims data and Kaplan-Meier estimates were calculated. P values adjusted for multiple correction (q) of < 0.05 was considered significant. Six p53 variants were classified as GOF (p.R175, p.G245, p.R248, p.R249, p.R273, and p.R282). Results: Of the 5311 UT and 14810 LT tumors sequenced, 4799 harbored a TP53 GOF variant. UT had TP53 GOF in 22.9% of cases compared to 27.0% of LT (q < 0.05). 67 genes were enriched for amplification (q < 0.05) in the UT TP53 GOF cancers compared to the LT TP53 GOF, including cell cycle regulators( CCND1, CCNE1, CDK6, CDK12), and oncogenes ( KRAS, ERBB2, EGFR). LT TP53 GOF cancers were enriched for eight gene amplifications, including CDX2, FLT3, and SRC. Differences in SNV/InDel patterns were not remarkable. OS analysis revealed TP53 GOF in UT had shorter OS when compared to TP53 wild-type (WT) (Median OS: 418 vs 515 days; HR: 0.864; 95%CI [0.772-0.966]; p = 0.011), but not when MSI/MMRP status was considered separately. LT TP53 GOF did not show OS difference in aggregate, however, MSI-High TP53 GOF cancers showed a shorter OS (Median OS: 762 vs 1479 days; HR: 1.522; [1.068 - 2.171]; p = 0.019). Sub-analysis of LT MSI-High cancers treated by immune checkpoint blockade showed a non-significant trend toward shorter OS of TP53 GOF versus TP53 wild type cancers (HR: 2.55; [0.90-7.19], p: 0.067), but no such trend was seen in UT (HR: 1.434; [0.304-6.758], p:0.646). Conclusions: Our study is the first to compare putative TP53 GOF variants across UT and LT GI adenocarcinoma. TP53 GOF variants are associated with decreased OS in both UT cancers and MSI-High LT cancers. Our findings support the functional plasticity of TP53 GOF variants in human GI cancers. Therefore, the purported effects of secreted microbiome factors on TP53 GOF variants cannot be ruled out.

Application of Molecular Docking for the Development of Improved HIV-1 Reverse Transcriptase Inhibitors

2020 ◽  
Vol 16 ◽  
Author(s):  
Arash Soltani ◽  
Seyed Isaac Hashemy ◽  
Farnaz Zahedi Avval ◽  
Houshang Rafatpanah ◽  
Seyed Abdolrahim Rezaee ◽  
...  
Keyword(s):  
Reverse Transcriptase ◽  
Binding Capacity ◽  
Binding Pocket ◽  
Ligand Docking ◽  
Binding Modes ◽  
Wild Type ◽  
Parent Molecule ◽  
Discovery Studio ◽  
Approved Drugs ◽  
Hiv 1

Introoduction: Inhibition of the reverse transcriptase (RT) enzyme of human immunodeficiency virus (HIV) by low molecular weight inhibitors is still an active area of research. Here, protein-ligand interactions and possible binding modes of novel compounds with the HIV-1 RT binding pocket (the wild-type as well as Y181C and K103N mutants) were obtained and discussed. Methods: A molecular fragment-based approach using FDA-approved drugs were followed to design novel chemical derivatives using delavirdine, efavirenz, etravirine and rilpivirine as the scaffolds. The drug-likeliness of the derivatives was evaluated using Swiss-ADME. Then the parent molecule and derivatives were docked into the binding pocket of related crystal structures (PDB ID: 4G1Q, 1IKW, 1KLM and 3MEC). Genetic Optimization for Ligand Docking (GOLD) Suite 5.2.2 software was used for docking and the results analyzed in the Discovery Studio Visualizer 4. A derivative was chosen for further analysis, if it passed drug-likeliness and the docked energy was more favorable than that of its parent molecule. Out of the fifty-seven derivatives, forty-eight failed in druglikeness screening by Swiss-ADME or in docking stage. Results: The final results showed that the selected compounds had higher predicted binding affinities than their parent scaffolds in both wild-type and the mutants. Binding energy improvement was higher for the structures designed based on second-generation NNRTIs (etravirine and rilpivirine) than the first-generation NNRTIs (delavirdine and efavirenz). For example, while the docked energy for rilpivirine was -51 KJ/mol, it was improved for its derivatives RPV01 and RPV15 up to -58.3 and -54.5 KJ/mol, respectively. Conclusion: In this study, we have identified and proposed some novel molecules with improved binding capacity for HIV RT using fragment-based approach.

scholarly journals Antitumor Effects of PRIMA-1 and PRIMA-1Met (APR246) in Hematological Malignancies: Still a Mutant P53-Dependent Affair?

Cells ◽  
2021 ◽  
Vol 10 (1) ◽  
pp. 98
Author(s):  
Paola Menichini ◽  
Paola Monti ◽  
Andrea Speciale ◽  
Giovanna Cutrona ◽  
Serena Matis ◽  
...  
Keyword(s):  
Hematological Malignancies ◽  
Cell Metabolism ◽  
Therapy Response ◽  
Tp53 Gene ◽  
Suppressor Gene ◽  
Lower Percentage ◽  
Mutant P53 ◽  
Wild Type ◽  
Antitumor Effects ◽  
Tp53 Tumor Suppressor Gene

Because of its role in the regulation of the cell cycle, DNA damage response, apoptosis, DNA repair, cell migration, autophagy, and cell metabolism, the TP53 tumor suppressor gene is a key player for cellular homeostasis. TP53 gene is mutated in more than 50% of human cancers, although its overall dysfunction may be even more frequent. TP53 mutations are detected in a lower percentage of hematological malignancies compared to solid tumors, but their frequency generally increases with disease progression, generating adverse effects such as resistance to chemotherapy. Due to the crucial role of P53 in therapy response, several molecules have been developed to re-establish the wild-type P53 function to mutant P53. PRIMA-1 and its methylated form PRIMA-1Met (also named APR246) are capable of restoring the wild-type conformation to mutant P53 and inducing apoptosis in cancer cells; however, they also possess mutant P53-independent properties. This review presents the activities of PRIMA-1 and PRIMA-1Met/APR246 and describes their potential use in hematological malignancies.

scholarly journals Deciphering the Role of Residues Involved in Disorder-To-Order Transition Regions in Archaeal tRNA Methyltransferase 5

Genes ◽  
2021 ◽  
Vol 12 (3) ◽  
pp. 399
Author(s):  
Ambuj Srivastava ◽  
Dhanusha Yesudhas ◽  
Shandar Ahmad ◽  
M. Michael Gromiha
Keyword(s):  
Three Dimensional ◽  
Md Simulations ◽  
Order Transition ◽  
Free Form ◽  
Wild Type ◽  
Intrinsically Disordered ◽  
Intrinsically Disordered Regions ◽  
Type Complex ◽  
In The Wild ◽  
Trna Methyltransferase

tRNA methyltransferase 5 (Trm5) enzyme is an S-adenosyl methionine (AdoMet)-dependent methyltransferase which methylates the G37 nucleotide at the N1 atom of the tRNA. The free form of Trm5 enzyme has three intrinsically disordered regions, which are highly flexible and lack stable three-dimensional structures. These regions gain ordered structures upon the complex formation with tRNA, also called disorder-to-order transition (DOT) regions. In this study, we performed molecular dynamics (MD) simulations of archaeal Trm5 in free and complex forms and observed that the DOT residues are highly flexible in free proteins and become stable in complex structures. The energetic contributions show that DOT residues are important for stabilising the complex. The DOT1 and DOT2 are mainly observed to be important for stabilising the complex, while DOT3 is present near the active site to coordinate the interactions between methyl-donating ligands and G37 nucleotides. In addition, mutational studies on the Trm5 complex showed that the wild type is more stable than the G37A tRNA mutant complex. The loss of productive interactions upon G37A mutation drives the AdoMet ligand away from the 37th nucleotide, and Arg145 in DOT3 plays a crucial role in stabilising the ligand, as well as the G37 nucleotide, in the wild-type complex. Further, the overall energetic contribution calculated using MMPBSA corroborates that the wild-type complex has a better affinity between Trm5 and tRNA. Overall, our study reveals that targeting DOT regions for binding could improve the inhibition of Trm5.

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