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1.
iScience ; 26(11): 108151, 2023 Nov 17.
Artículo en Inglés | MEDLINE | ID: mdl-37915607

RESUMEN

DIRAS3 is an imprinted tumor suppressor gene encoding a GTPase that has a distinctive N-terminal extension (NTE) not found in other RAS proteins. This NTE and the prenylated C-terminus are required for DIRAS3-mediated inhibition of RAS/MAP signaling and PI3K activity at the plasma membrane. In this study, we applied biochemical, biophysical, and computational methods to characterize the structure and function of the NTE. The NTE peptide recognizes phosphoinositides PI(3,4,5)P3 and PI(4,5)P2 with rapid kinetics and strong affinity. Lipid binding induces NTE structural change from disorder to amphipathic helix. Mass spectrometry identified N-myristoylation of DIRAS3. All-atom molecular dynamic simulations predict DIRAS3 could adhere to the membrane through both termini, suggesting the NTE is involved in targeting and stabilizing DIRAS3 on the membrane by double anchoring. Overall, our results are consistent with DIRAS3's function as a tumor suppressor, whereby the membrane-bound DIRAS3 can effectively target PI3K and KRAS at the membrane.

2.
Front Artif Intell ; 6: 1069353, 2023.
Artículo en Inglés | MEDLINE | ID: mdl-37035534

RESUMEN

Accurate prediction of drug response is a crucial step in personalized medicine. Recently, deep learning techniques have been witnessed with significant breakthroughs in a variety of areas including biomedical research and chemogenomic applications. This motivated us to develop a novel deep learning platform to accurately and reliably predict the response of cancer cells to different drug treatments. In the present work, we describe a Java-based implementation of deep neural network method, termed JavaDL, to predict cancer responses to drugs solely based on their chemical features. To this end, we devised a novel cost function and added a regularization term which suppresses overfitting. We also adopted an early stopping strategy to further reduce overfit and improve the accuracy and robustness of our models. To evaluate our method, we compared with several popular machine learning and deep neural network programs and observed that JavaDL either outperformed those methods in model building or obtained comparable predictions. Finally, JavaDL was employed to predict drug responses of several aggressive breast cancer cell lines, and the results showed robust and accurate predictions with r 2 as high as 0.81.

3.
Clin Cancer Res ; 29(2): 446-457, 2023 01 17.
Artículo en Inglés | MEDLINE | ID: mdl-36346691

RESUMEN

PURPOSE: Several MCL-1 inhibitors (MCL-1i), including AMG-176 and AZD5991, have shown promise in preclinical studies and are being tested for the treatment of hematologic malignancies. A unique feature of these agents is induction and stability of Mcl-1 protein; however, the precise mechanism is unknown. We aim to study the mechanism of MCL-1i-induced Mcl-1 protein stability. EXPERIMENTAL DESIGN: Using several B-cell leukemia and lymphoma cell lines and primary chronic lymphocytic leukemia (CLL) lymphocytes, we evaluated molecular events associated with Mcl-1 protein stability including protein half-life, reverse-phase protein array, protein-protein interaction, phosphorylation, ubiquitination, and de-ubiquitination, followed by molecular simulation and modeling. RESULTS: Using both in vivo and in vitro analysis, we demonstrate that MCL-1i-induced Mcl-1 protein stability is predominantly associated with defective Mcl-1 ubiquitination and concurrent apoptosis induction in both cell lines and primary CLL subjects. These MCL1i also induced ERK-mediated Mcl-1Thr163 phosphorylation, which partially contributed to Mcl-1 stability. Disruption of Mcl-1:Noxa interaction followed by Noxa degradation, enhanced Mcl-1 de-ubiquitination by USP9x, and Mule destabilization are the major effects of these inhibitors. However, unlike other BH3 proteins, Mule:Mcl-1 interaction was unaffected by MCL-1i. WP1130, a global deubiquitinase (DUB) inhibitor, abrogated Mcl-1 induction reaffirming a critical role of DUBs in the observed Mcl-1 protein stability. Further, in vitro ubiquitination studies of Mcl-1 showed distinct difference among these inhibitors. CONCLUSIONS: We conclude that MCL-1i blocked Mcl-1 ubiquitination via enhanced de-ubiquitination and dissociation of Mcl-1 from Noxa, Bak and Bax, and Mule de-stabilization. These are critical events associated with increased Mcl-1 protein stability with AMG-176 and AZD5991.


Asunto(s)
Antineoplásicos , Leucemia Linfocítica Crónica de Células B , Humanos , Antineoplásicos/uso terapéutico , Apoptosis , Proteínas Reguladoras de la Apoptosis , Línea Celular Tumoral , Leucemia Linfocítica Crónica de Células B/tratamiento farmacológico , Leucemia Linfocítica Crónica de Células B/genética , Proteína 1 de la Secuencia de Leucemia de Células Mieloides/genética , Proteína 1 de la Secuencia de Leucemia de Células Mieloides/metabolismo , Estabilidad Proteica , Proteínas Proto-Oncogénicas c-bcl-2/genética , Proteínas Proto-Oncogénicas c-bcl-2/metabolismo , Ubiquitina Tiolesterasa/metabolismo
4.
Nat Commun ; 13(1): 2543, 2022 05 10.
Artículo en Inglés | MEDLINE | ID: mdl-35538070

RESUMEN

Bone metastases occur in 50-70% of patients with late-stage breast cancers and effective therapies are needed. The expression of enhancer of zeste homolog 2 (EZH2) is correlated with breast cancer metastasis, but its function in bone metastasis hasn't been well-explored. Here we report that EZH2 promotes osteolytic metastasis of breast cancer through regulating transforming growth factor beta (TGFß) signaling. EZH2 induces cancer cell proliferation and osteoclast maturation, whereas EZH2 knockdown decreases bone metastasis incidence and outgrowth in vivo. Mechanistically, EZH2 transcriptionally increases ITGB1, which encodes for integrin ß1. Integrin ß1 activates focal adhesion kinase (FAK), which phosphorylates TGFß receptor type I (TGFßRI) at tyrosine 182 to enhance its binding to TGFß receptor type II (TGFßRII), thereby activating TGFß signaling. Clinically applicable FAK inhibitors but not EZH2 methyltransferase inhibitors effectively inhibit breast cancer bone metastasis in vivo. Overall, we find that the EZH2-integrin ß1-FAK axis cooperates with the TGFß signaling pathway to promote bone metastasis of breast cancer.


Asunto(s)
Neoplasias Óseas , Neoplasias de la Mama , Proteína Potenciadora del Homólogo Zeste 2 , Quinasa 1 de Adhesión Focal , Proteína-Tirosina Quinasas de Adhesión Focal , Integrina beta1 , Factor de Crecimiento Transformador beta , Neoplasias Óseas/genética , Neoplasias Óseas/metabolismo , Neoplasias Óseas/secundario , Neoplasias de la Mama/genética , Neoplasias de la Mama/metabolismo , Neoplasias de la Mama/patología , Línea Celular Tumoral , Movimiento Celular , Proteína Potenciadora del Homólogo Zeste 2/genética , Proteína Potenciadora del Homólogo Zeste 2/metabolismo , Femenino , Quinasa 1 de Adhesión Focal/metabolismo , Proteína-Tirosina Quinasas de Adhesión Focal/metabolismo , Humanos , Integrina beta1/genética , Integrina beta1/metabolismo , Transducción de Señal , Factor de Crecimiento Transformador beta/genética , Factor de Crecimiento Transformador beta/metabolismo
5.
Mol Genet Metab ; 135(3): 171-178, 2022 03.
Artículo en Inglés | MEDLINE | ID: mdl-35101330

RESUMEN

More than 1280 variants in the phenylalanine hydroxylase (PAH) gene are responsible for a broad spectrum of phenylketonuria (PKU) phenotypes. While the genotype-phenotype correlation is reaching 88%, for some inconsistent phenotypes with the same genotype additional factors like tetrahydrobiopterin (BH4), the PAH co-chaperone DNAJC12, phosphorylation of the PAH residues or epigenetic factors may play an important role. Very recently an additional player, the long non-coding RNA (lncRNA) transcript HULC, was described to regulate PAH activity and enhance residual enzyme activity of some PAH variants (e.g., the most common p.R408W) by using HULC mimics. In this review we present an overview of the lncRNA function and in particular the interplay of the HUCL transcript with the PAH and discuss potential applications for the future treatment of some PKU patients.


Asunto(s)
Fenilalanina Hidroxilasa , Fenilcetonurias , ARN Largo no Codificante , Humanos , Mutación , Fenotipo , Fenilalanina Hidroxilasa/química , Fenilalanina Hidroxilasa/genética , Fenilcetonurias/genética , Fenilcetonurias/terapia , ARN Largo no Codificante/genética
6.
Sci Rep ; 12(1): 2478, 2022 02 15.
Artículo en Inglés | MEDLINE | ID: mdl-35169199

RESUMEN

The ubiquitination of SKP2, an oncoprotein, is controlled by its E3 ligases, including APC/CFZR1 and deubiquitinases such as USP10. We identified a two-gene signature for the ubiquitination of SKP2, consisting of the copy number of FZR1 compared to the copy number of USP10. The signature reflects the level of SKP2 activity, stratifying BC patients into two groups with significantly different protein levels of SKP2 ubiquitination substrate p27 (t-test p < 0.01) and recapitulating the expression patterns of SKP2 between tumor and normal tissue (Spearman's ρ = 0.39.) The signature is also highly associated with clinical outcome in luminal BC but not other subtypes, characterizing patients into two groups with significantly different overall survival times (log-rank p = 0.006). In addition, it is dramatically associated with tumor grade (Chi-squared p = 6.7 × 10-3), stage (Chi-squared p = 1.6 × 10-11), and the number of positive lymph nodes (negative binomial regression coefficient p = 2.0 × 10-3). Our study provides a rationale for targeting the SKP2 ubiquitination pathway in luminal BC and for further investigation of the use of ubiquitinase/deubiquitinase genes as prognosis and treatment biomarkers.


Asunto(s)
Neoplasias de la Mama/genética , Proteínas Quinasas Asociadas a Fase-S/genética , Neoplasias de la Mama/metabolismo , Neoplasias de la Mama/mortalidad , Neoplasias de la Mama/patología , Enzimas Desubicuitinizantes/metabolismo , Femenino , Humanos , Metástasis Linfática , Pronóstico , Proteínas Quinasas Asociadas a Fase-S/metabolismo , Tasa de Supervivencia , Ubiquitina Tiolesterasa/metabolismo , Ubiquitina-Proteína Ligasas/metabolismo , Ubiquitinación
7.
Entropy (Basel) ; 24(10)2022 Oct 09.
Artículo en Inglés | MEDLINE | ID: mdl-37420459

RESUMEN

Dimethyl carbonate is an important green chemical that has been widely used in the chemical industry. In the production of dimethyl carbonate, methanol oxidative carbonylation has been studied, but the conversion ratio of dimethyl carbonate using this method is too low, and the subsequent separation requires a large amount of energy due to methanol and dimethyl carbonate being azeotrope. In this paper, the strategy of "reaction instead of separation" is proposed. Based on this strategy, a novel process is developed to combine the production of DMC with that of dimethoxymethane (DMM) and dimethyl ether (DME). The co-production process was simulated using Aspen Plus software, and the product purity was up to 99.9%. The exergy analysis of the co-production process and the existing process was carried out. The exergy destruction and exergy efficiency were compared with those of the existing production processes. The results show that the exergy destruction of the co-production process is about 276% less than that of the single-production processes, and the exergy efficiencies in the developed co-production process are significantly improved. The utility loads of the co-production process are significantly lower than that of the single-production process. The developed co-production process increases the methanol conversion ratio to 95%, with a reduced energy requirement. It is proved that the developed co-production process can provide an advantageous option over the existing processes with improved energy efficiency and material savings. The strategy of "reaction instead of separation" is feasible. A new strategy is proposed for azeotrope separation.

8.
Mol Biol Rep ; 49(1): 313-320, 2022 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-34741708

RESUMEN

BACKGROUND: Common vetch (Vicia sativa L.) is an annual legume with excellent suitability in cold and dry regions. Despite its great applied potential, the genomic information regarding common vetch currently remains unavailable. METHODS AND RESULTS: In the present study, the whole genome survey of common vetch was performed using the next-generation sequencing (NGS). A total of 79.84 Gbp high quality sequence data were obtained and assembled into 3,754,145 scaffolds with an N50 length of 3556 bp. According to the K-mer analyses, the genome size, heterozygosity rate and GC content of common vetch genome were estimated to be 1568 Mbp, 0.4345 and 35%, respectively. In addition, a total of 76,810 putative simple sequence repeats (SSRs) were identified. Among them, dinucleotide was the most abundant SSR type (44.94%), followed by Tri- (35.82%), Tetra- (13.22%), Penta- (4.47%) and Hexanucleotide (1.54%). Furthermore, a total of 58,175 SSR primer pairs were designed and ten of them were validated in Chinese common vetch. Further analysis showed that Chinese common vetch harbored high genetic diversity and could be clustered into two main subgroups. CONCLUSION: This is the first report about the genome features of common vetch, and the information will help to design whole genome sequencing strategies. The newly identified SSRs in this study provide basic molecular markers for germplasm characterization, genetic diversity and QTL mapping studies for common vetch.


Asunto(s)
Repeticiones de Microsatélite , Vicia sativa/genética , Secuenciación Completa del Genoma/métodos , Composición de Base , China , Mapeo Cromosómico , Tamaño del Genoma , Genoma de Planta , Secuenciación de Nucleótidos de Alto Rendimiento , Filogenia
9.
Exp Cell Res ; 409(2): 112930, 2021 12 15.
Artículo en Inglés | MEDLINE | ID: mdl-34800542

RESUMEN

Plekha7 (Pleckstrin homology [PH] domain containing, family A member 7) regulates the assembly of proteins of the cytoplasmic apical zonula adherens junction (AJ), thus ensuring cell-cell adhesion and tight-junction barrier integrity. Little is known of Plekha7 function in cancer. In colorectal cancer (CRC) Plekha7 expression is elevated compared to adjacent normal tissue levels, increasing with clinical stage. Plekha7 was present at plasma membrane AJ with wild-type KRas (wt-KRas) but was dispersed in cells expressing mutant KRas (mut-KRas). Fluorescence lifetime imaging microscopy (FLIM) indicated a direct Plekha7 interaction with wt-KRas but scantily with mut-KRas. Inhibiting Plekha7 specifically decreased mut-KRas cell signaling, proliferation, attachment, migration, and retarded mut-KRAS CRC tumor growth. Binding of diC8-phosphoinositides (PI) to the PH domain of Plekha7 was relatively low affinity. This may be because a D175 amino acid residue plays a "sentry" role preventing PI(3,4)P2 and PI(3,4,5)P3 binding. Molecular or pharmacological inhibition of the Plekha7 PH domain prevented the growth of mut-KRas but not wt-KRas cells. Taken together the studies suggest that Plekha7, in addition to maintaining AJ structure plays a role in mut-KRas signaling and phenotype through interaction of its PH domain with membrane mut-KRas, but not wt-KRas, to increase the efficiency of mut-KRas downstream signaling.


Asunto(s)
Biomarcadores de Tumor/metabolismo , Proteínas Portadoras/metabolismo , Neoplasias Colorrectales/patología , Regulación Neoplásica de la Expresión Génica , Mutación , Proteínas Proto-Oncogénicas p21(ras)/genética , Apoptosis , Biomarcadores de Tumor/genética , Proteínas Portadoras/genética , Adhesión Celular , Proliferación Celular , Neoplasias Colorrectales/genética , Neoplasias Colorrectales/metabolismo , Humanos , Uniones Intercelulares , Transducción de Señal , Uniones Estrechas , Células Tumorales Cultivadas
10.
Science ; 373(6555): 662-673, 2021 08 06.
Artículo en Inglés | MEDLINE | ID: mdl-34353949

RESUMEN

The functional role of long noncoding RNAs (lncRNAs) in inherited metabolic disorders, including phenylketonuria (PKU), is unknown. Here, we demonstrate that the mouse lncRNA Pair and human HULC associate with phenylalanine hydroxylase (PAH). Pair-knockout mice exhibited excessive blood phenylalanine (Phe), musty odor, hypopigmentation, growth retardation, and progressive neurological symptoms including seizures, which faithfully models human PKU. HULC depletion led to reduced PAH enzymatic activities in human induced pluripotent stem cell-differentiated hepatocytes. Mechanistically, HULC modulated the enzymatic activities of PAH by facilitating PAH-substrate and PAH-cofactor interactions. To develop a therapeutic strategy for restoring liver lncRNAs, we designed GalNAc-tagged lncRNA mimics that exhibit liver enrichment. Treatment with GalNAc-HULC mimics reduced excessive Phe in Pair -/- and Pah R408W/R408W mice and improved the Phe tolerance of these mice.


Asunto(s)
Fenilalanina Hidroxilasa/metabolismo , Fenilalanina/metabolismo , Fenilcetonurias/genética , ARN Largo no Codificante/genética , Acetilgalactosamina , Animales , Biopterinas/análogos & derivados , Biopterinas/metabolismo , Biopterinas/uso terapéutico , Dieta , Modelos Animales de Enfermedad , Femenino , Hepatocitos/metabolismo , Humanos , Hígado/embriología , Hígado/metabolismo , Masculino , Ratones , Ratones Noqueados , Conformación de Ácido Nucleico , Fenilalanina/administración & dosificación , Fenilalanina Hidroxilasa/deficiencia , Fenilalanina Hidroxilasa/genética , Fenilcetonurias/tratamiento farmacológico , Fenilcetonurias/metabolismo , Unión Proteica , ARN Largo no Codificante/química , ARN Largo no Codificante/metabolismo , ARN Largo no Codificante/uso terapéutico
11.
Chem Sci ; 12(10): 3526-3543, 2021 Jan 13.
Artículo en Inglés | MEDLINE | ID: mdl-34163626

RESUMEN

In recent decades it has become increasingly clear that induction of autophagy plays an important role in the development of treatment resistance and dormancy in many cancer types. Unfortunately, chloroquine (CQ) and hydroxychloroquine (HCQ), two autophagy inhibitors in clinical trials, suffer from poor pharmacokinetics and high toxicity at therapeutic dosages. This has prompted intense interest in the development of targeted autophagy inhibitors to re-sensitize disease to treatment with minimal impact on normal tissue. We utilized Scanning Unnatural Protease Resistant (SUPR) mRNA display to develop macrocyclic peptides targeting the autophagy protein LC3. The resulting peptides bound LC3A and LC3B-two essential components of the autophagosome maturation machinery-with mid-nanomolar affinities and disrupted protein-protein interactions (PPIs) between LC3 and its binding partners in vitro. The most promising LC3-binding SUPR peptide accessed the cytosol at low micromolar concentrations as measured by chloroalkane penetration assay (CAPA) and inhibited starvation-mediated GFP-LC3 puncta formation in a concentration-dependent manner. LC3-binding SUPR peptides re-sensitized platinum-resistant ovarian cancer cells to cisplatin treatment and triggered accumulation of the adapter protein p62 suggesting decreased autophagic flux through successful disruption of LC3 PPIs in cell culture. In mouse models of metastatic ovarian cancer, treatment with LC3-binding SUPR peptides and carboplatin resulted in almost complete inhibition of tumor growth after four weeks of treatment. These results indicate that SUPR peptide mRNA display can be used to develop cell-penetrating macrocyclic peptides that target and disrupt the autophagic machinery in vitro and in vivo.

12.
J Am Chem Soc ; 143(20): 7655-7670, 2021 05 26.
Artículo en Inglés | MEDLINE | ID: mdl-33988982

RESUMEN

Aptamers, synthetic single-strand oligonucleotides that are similar in function to antibodies, are promising as therapeutics because of their minimal side effects. However, the stability and bioavailability of the aptamers pose a challenge. We developed aptamers converted from RNA aptamer to modified DNA aptamers that target phospho-AXL with improved stability and bioavailability. On the basis of the comparative analysis of a library of 17 converted modified DNA aptamers, we selected aptamer candidates, GLB-G25 and GLB-A04, that exhibited the highest bioavailability, stability, and robust antitumor effect in in vitro experiments. Backbone modifications such as thiophosphate or dithiophosphate and a covalent modification of the 5'-end of the aptamer with polyethylene glycol optimized the pharmacokinetic properties, improved the stability of the aptamers in vivo by reducing nuclease hydrolysis and renal clearance, and achieved high and sustained inhibition of AXL at a very low dose. Treatment with these modified aptamers in ovarian cancer orthotopic mouse models significantly reduced tumor growth and the number of metastases. This effective silencing of the phospho-AXL target thus demonstrated that aptamer specificity and bioavailability can be improved by the chemical modification of existing aptamers for phospho-AXL. These results lay the foundation for the translation of these aptamer candidates and companion biomarkers to the clinic.


Asunto(s)
Anticuerpos/inmunología , Aptámeros de Nucleótidos/inmunología , Neoplasias/inmunología , Anticuerpos/química , Aptámeros de Nucleótidos/química , Humanos , Neoplasias/terapia
13.
Blood ; 138(9): 758-772, 2021 09 02.
Artículo en Inglés | MEDLINE | ID: mdl-33786575

RESUMEN

Recirculation of chronic lymphocytic leukemia (CLL) cells between the peripheral blood and lymphoid niches plays a critical role in disease pathophysiology, and inhibiting this process is one of the major mechanisms of action for B-cell receptor (BCR) inhibitors such as ibrutinib and idelalisib. Migration is a complex process guided by chemokine receptors and integrins. However, it remains largely unknown how CLL cells integrate multiple migratory signals while balancing survival in the peripheral blood and the decision to return to immune niches. Our study provided evidence that CXCR4/CD5 intraclonal subpopulations can be used to study the regulation of migration of CLL cells. We performed RNA profiling of CXCR4dimCD5bright vs CXCR4brightCD5dim CLL cells and identified differential expression of dozens of molecules with a putative function in cell migration. GRB2-associated binding protein 1 (GAB1) positively regulated CLL cell homing capacity of CXCR4brightCD5dim cells. Gradual GAB1 accumulation in CLL cells outside immune niches was mediated by FoxO1-induced transcriptional GAB1 activation. Upregulation of GAB1 also played an important role in maintaining basal phosphatidylinositol 3-kinase (PI3K) activity and the "tonic" AKT phosphorylation required to sustain the survival of resting CLL B cells. This finding is important during ibrutinib therapy, because CLL cells induce the FoxO1-GAB1-pAKT axis, which represents an adaptation mechanism to the inability to home to immune niches. We have demonstrated that GAB1 can be targeted therapeutically by novel GAB1 inhibitors, alone or in combination with BTK inhibition. GAB1 inhibitors induce CLL cell apoptosis, impair cell migration, inhibit tonic or BCR-induced AKT phosphorylation, and block compensatory AKT activity during ibrutinib therapy.


Asunto(s)
Proteínas Adaptadoras Transductoras de Señales/biosíntesis , Movimiento Celular , Proteína Forkhead Box O1/metabolismo , Regulación Leucémica de la Expresión Génica , Leucemia Linfocítica Crónica de Células B/metabolismo , Proteínas Proto-Oncogénicas c-akt/metabolismo , Transducción de Señal , Regulación hacia Arriba , Adenina/análogos & derivados , Adenina/farmacología , Línea Celular Tumoral , Humanos , Leucemia Linfocítica Crónica de Células B/tratamiento farmacológico , Leucemia Linfocítica Crónica de Células B/patología , Piperidinas/farmacología
14.
Biochemistry ; 59(35): 3225-3234, 2020 09 08.
Artículo en Inglés | MEDLINE | ID: mdl-32786414

RESUMEN

RNA helices are often punctuated with non-Watson-Crick features that may be targeted by chemical compounds, but progress toward identifying such compounds has been slow. We embedded a tandem UU:GA mismatch motif (5'-UG-3':5'-AU-3') within an RNA hairpin stem to identify compounds that bind the motif specifically. The three-dimensional structure of the RNA hairpin and its interaction with a small molecule identified through virtual screening are presented. The G-A mismatch forms a sheared pair upon which the U-U base pair stacks. The hydrogen bond configuration of the U-U pair involves O2 of the U adjacent to the G and O4 of the U adjacent to the A. The G-A and U-U pairs are flanked by A-U and G-C base pairs, respectively, and the stability of the mismatch is greater than when the motif is within the context of other flanking base pairs or when the 5'-3' orientation of the G-A and U-U pairs is swapped. Residual dipolar coupling constants were used to generate an ensemble of structures against which a virtual screen of 64480 small molecules was performed. The tandem mismatch was found to be specific for one compound, 2-amino-1,3-benzothiazole-6-carboxamide, which binds with moderate affinity but extends the motif to include the flanking A-U and G-C base pairs. The finding that the affinity for the UU:GA mismatch is dependent on flanking sequence emphasizes the importance of the motif context and potentially increases the number of small noncanonical features within RNA that can be specifically targeted by small molecules.


Asunto(s)
Disparidad de Par Base , Benzotiazoles/farmacocinética , ARN/química , ARN/metabolismo , Amidas/farmacocinética , Disparidad de Par Base/efectos de los fármacos , Emparejamiento Base/efectos de los fármacos , Secuencia de Bases/fisiología , Fenómenos Biofísicos , Enlace de Hidrógeno , Espectroscopía de Resonancia Magnética , Modelos Moleculares , Conformación de Ácido Nucleico , ARN/efectos de los fármacos , ARN no Traducido/química , ARN no Traducido/efectos de los fármacos , ARN no Traducido/metabolismo , Especificidad por Sustrato , Termodinámica
15.
Cancer Res ; 80(20): 4500-4513, 2020 10 15.
Artículo en Inglés | MEDLINE | ID: mdl-32699135

RESUMEN

Pancreatic cancer is a lethal disease owing to its intrinsic and acquired resistance to therapeutic modalities. The altered balance between pro- and antiapoptosis signals within cancer cells is critical to therapeutic resistance. However, the molecular mechanisms underlying increased antiapoptosis signals remain poorly understood. In this study, we report that PRMT1 expression is increased in pancreatic cancer tissues and is associated with higher tumor grade, increased aggressiveness, and worse prognosis. PRMT1 overexpression increased arginine methylation of HSPs of 70 kDa (HSP70); this methylation enhanced HSP70 binding and stabilization of BCL2 mRNA through AU-rich elements in 3'-untranslated region and consequentially increased BCL2 protein expression and protected cancer cells from apoptosis induced by cellular stresses and therapeutics. RNA binding and regulation function of HSP70 was involved in pancreatic cancer drug resistance and was dependent on protein arginine methylation. These findings not only reveal a novel PRMT1-HSP70-BCL2 signaling axis that is crucial to pancreatic cancer cell survival and therapeutic resistance, but they also provide a proof of concept that targeted inhibition of this axis may represent a new therapeutic strategy. SIGNIFICANCE: This study demonstrates that a PRMT1-mediated stabilization of BCL2 mRNA contributes to therapeutic resistance in pancreatic cancer and that targeting this pathway could overcome said resistance.


Asunto(s)
Carcinoma Ductal Pancreático/tratamiento farmacológico , Resistencia a Antineoplásicos/fisiología , Proteínas HSP70 de Choque Térmico/metabolismo , Neoplasias Pancreáticas/tratamiento farmacológico , Proteínas Proto-Oncogénicas c-bcl-2/genética , Anciano , Animales , Arginina/metabolismo , Carcinoma Ductal Pancreático/mortalidad , Carcinoma Ductal Pancreático/patología , Resistencia a Antineoplásicos/efectos de los fármacos , Femenino , Proteínas HSP70 de Choque Térmico/genética , Humanos , Masculino , Metilación , Ratones Endogámicos C57BL , Persona de Mediana Edad , Neoplasias Pancreáticas/mortalidad , Neoplasias Pancreáticas/patología , Unión Proteica , Proteína-Arginina N-Metiltransferasas/genética , Proteína-Arginina N-Metiltransferasas/metabolismo , Proteínas Proto-Oncogénicas c-bcl-2/metabolismo , Estabilidad del ARN , ARN Mensajero/genética , ARN Mensajero/metabolismo , Proteínas Represoras/genética , Proteínas Represoras/metabolismo , Ensayos Antitumor por Modelo de Xenoinjerto
16.
Expert Opin Drug Discov ; 15(9): 1025-1044, 2020 09.
Artículo en Inglés | MEDLINE | ID: mdl-32452701

RESUMEN

INTRODUCTION: In recent years, computational polypharmacology has gained significant attention to study the promiscuous nature of drugs. Despite tremendous challenges, community-wide efforts have led to a variety of novel approaches for predicting drug polypharmacology. In particular, some rapid advances using machine learning and artificial intelligence have been reported with great success. AREAS COVERED: In this article, the authors provide a comprehensive update on the current state-of-the-art polypharmacology approaches and their applications, focusing on those reports published after our 2017 review article. The authors particularly discuss some novel, groundbreaking concepts, and methods that have been developed recently and applied to drug polypharmacology studies. EXPERT OPINION: Polypharmacology is evolving and novel concepts are being introduced to counter the current challenges in the field. However, major hurdles remain including incompleteness of high-quality experimental data, lack of in vitro and in vivo assays to characterize multi-targeting agents, shortage of robust computational methods, and challenges to identify the best target combinations and design effective multi-targeting agents. Fortunately, numerous national/international efforts including multi-omics and artificial intelligence initiatives as well as most recent collaborations on addressing the COVID-19 pandemic have shown significant promise to propel the field of polypharmacology forward.


Asunto(s)
Descubrimiento de Drogas , Polifarmacología , Biología Computacional , Química Computacional , Desarrollo de Medicamentos , Humanos , Terapia Molecular Dirigida
17.
Sci Rep ; 10(1): 520, 2020 01 16.
Artículo en Inglés | MEDLINE | ID: mdl-31949258

RESUMEN

The tyrosine kinase receptor EphB4 is frequently overexpressed in ovarian and other solid tumors and is involved in interactions between tumor cells and the tumor microenvironment, contributing to metastasis. Trans-interaction between EphB4 and its membrane-bound ligand ephrin B2 (EFNB2) mediates bi-directional signaling: forward EFNB2-to-EphB4 signaling suppresses tumor cell proliferation, while reverse EphB4-to-EFNB2 signaling stimulates the invasive and angiogenic properties of endothelial cells. Currently, no small molecule-based, dual-function, EphB4-binding peptides are available. Here, we report our discovery of a bi-directional ephrin agonist peptide, BIDEN-AP which, when selectively internalized via receptor-mediated endocytosis, suppressed invasion and epithelial-mesenchymal transition of ovarian cancer cells. BIDEN-AP also inhibited endothelial migration and tube formation. In vivo, BIDEN-AP and its nanoconjugate CCPM-BIDEN-AP significantly reduced growth of orthotopic ovarian tumors, with CCPM-BIDEN-AP displaying greater antitumor potency than BIDEN-AP. Both BIDEN-AP and CCPM-BIDEN-AP compromised angiogenesis by downregulating epithelial-mesenchymal transition and angiogenic pathways. Thus, we report a novel EphB4-based therapeutic approach against ovarian cancer.


Asunto(s)
Efrina-B2/metabolismo , Efrinas/agonistas , Neoplasias Ováricas/tratamiento farmacológico , Péptidos/administración & dosificación , Péptidos/farmacología , Receptor EphB4/metabolismo , Animales , Línea Celular Tumoral , Proliferación Celular/efectos de los fármacos , Supervivencia Celular/efectos de los fármacos , Transición Epitelial-Mesenquimal/efectos de los fármacos , Femenino , Humanos , Ratones , Micelas , Neoplasias Ováricas/metabolismo , Péptidos/genética , Fosforilación , Unión Proteica/efectos de los fármacos , Transducción de Señal/efectos de los fármacos , Microambiente Tumoral/efectos de los fármacos , Ensayos Antitumor por Modelo de Xenoinjerto
18.
AAPS J ; 22(1): 14, 2019 12 18.
Artículo en Inglés | MEDLINE | ID: mdl-31853739

RESUMEN

Aurora kinase B (AKB), a Ser/Thr kinase that plays a crucial role in mitosis, is overexpressed in several cancers. Clinical inhibitors targeting AKB bind to the active DFG "in" conformation of the kinase. It would be beneficial, however, to understand if AKB is susceptible to type II kinase inhibitors that bind to the inactive, DFG "out" conformation, since type II inhibitors achieve higher kinome selectivity and higher potency in vivo. The DFG "out" conformation of AKB is not yet experimentally determined which makes the design of type II inhibitors exceedingly difficult. An alternate approach is to simulate the DFG "out" conformation from the experimentally determined DFG "in" conformation using atomistic molecular dynamics (MD) simulation. In this work, we employed metadynamics (MTD) approach to simulate the DFG "out" conformation of AKB by choosing the appropriate collective variables. We examined structural changes during the DFG-flip and determined the interactions crucial to stabilize the kinase in active and inactive states. Interestingly, the MTD approach also identified a unique transition state (DFG "up"), which can be targeted by small molecule inhibitors. Structural insights about these conformations is essential for structure-guided design of next-generation AKB inhibitors. This work also emphasizes the usefulness of MTD simulations in predicting macromolecular conformational changes at reduced computational costs.


Asunto(s)
Aurora Quinasa B/química , Simulación del Acoplamiento Molecular/métodos , Simulación de Dinámica Molecular , Oligopéptidos/química , Animales , Aurora Quinasa B/metabolismo , Humanos , Oligopéptidos/metabolismo , Estructura Secundaria de Proteína , Xenopus laevis
20.
Nat Commun ; 10(1): 4363, 2019 09 25.
Artículo en Inglés | MEDLINE | ID: mdl-31554794

RESUMEN

The LKB1/AMPK pathway plays a major role in cellular homeostasis and tumor suppression. Down-regulation of LKB1/AMPK occurs in several human cancers and has been implicated in metabolic diseases. However, the precise upstream regulation of LKB1-AMPK pathway is largely unknown. Here, we report that AMPK activation by LKB1 is regulated by tankyrases. Tankyrases interact with and ribosylate LKB1, promoting its K63-linked ubiquitination by an E3 ligase RNF146, which blocks LKB1/STRAD/MO25 complex formation and LKB1 activation. LKB1 activation by tankyrase inhibitors induces AMPK activation and suppresses tumorigenesis. Similarly, the tankyrase inhibitor G007-LK effectively regulates liver metabolism and glycemic control in diabetic mice in a LKB1-dependent manner. In patients with lung cancer, tankyrase levels negatively correlate with p-AMPK levels and poor survival. Taken together, these findings suggest that tankyrase and RNF146 are major up-stream regulators of LKB1-AMPK pathway and provide another focus for cancer and metabolic disease therapies.


Asunto(s)
Proteínas Quinasas Activadas por AMP/antagonistas & inhibidores , Metabolismo Energético/efectos de los fármacos , Inhibidores Enzimáticos/farmacología , Neoplasias/tratamiento farmacológico , Proteínas Serina-Treonina Quinasas/antagonistas & inhibidores , Tanquirasas/antagonistas & inhibidores , Quinasas de la Proteína-Quinasa Activada por el AMP , Proteínas Quinasas Activadas por AMP/metabolismo , Animales , Carcinogénesis/efectos de los fármacos , Carcinogénesis/genética , Línea Celular Tumoral , Células HeLa , Homeostasis/efectos de los fármacos , Humanos , Células MCF-7 , Ratones Endogámicos BALB C , Ratones Endogámicos C57BL , Ratones Desnudos , Neoplasias/genética , Neoplasias/metabolismo , Proteínas Serina-Treonina Quinasas/metabolismo , Transducción de Señal/efectos de los fármacos , Transducción de Señal/genética , Sulfonas/farmacología , Tanquirasas/metabolismo , Triazoles/farmacología , Ensayos Antitumor por Modelo de Xenoinjerto/métodos , para-Aminobenzoatos/farmacología
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