Intercalation process of anticancer copper (II) complexes in DNA

Ternary Copper (II) Complexes (TCC) have shown cytotoxic, genotoxic, and antineoplastic activity in vitro and in vivo. There are evidences that these compounds interact directly with DNA but it is not clear how deep TCC penetrates into the DNA double helix and their specific interactions have not been established. Recently, our group found that the deoxyribose-phosphate group is the specific recognition site of TCC in DNA. Here we report a crystallographic and theoretical study to determine each step of intercalation process of TCC in DNA with the recognition site as starting point. On the basis of crystal structures, Molecular Dynamics, DFT calculations and Electron Density Analysis we found that the family of analyzed TCC prefers the sequence Thymine-Adenine-Thymine to start the insertion. The intercalation process consists of an opening of a base pair as the complex intercalates within a succession of axial ligand exchange. The copper center migrates from phosphate to ribose then to thymine and finally to adenine. It is possible that the biological activity of TCC is related to its capability to evert base pairs and perform the necessary migrations from the recognition site to the complete intercalation

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The deaminase ADAL-pivoted catabolism checkpoint suppresses aberrant DNA N6-methyladenine incorporation

10.21203/rs.3.rs-374831/v1 ◽

2021 ◽

Author(s):

Shaokun Chen ◽

Weiyi Lai ◽

Zhiyi Zhao ◽

Ning Zhang ◽

Yan Liu ◽

...

Keyword(s):

Adenylate Kinase ◽

Patient Survival ◽

Double Helix ◽

Intracellular Degradation ◽

Dna Double Helix ◽

Adenylate Kinase 1 ◽

Phosphorylation Rate

Abstract Abundant RNA N6-methyladenine (m6A) is degraded in RNA decay and potentially induces aberrant DNA N6-methyladenine (6mA) misincorporation. Biophysically, like truly methylated product DNA 6mA, misincorporated 6mA also destabilizes the DNA double helix and thus ditto affects DNA replication and transcription. By heavy stable isotope tracing, we demonstrate that intracellular degradation of RNA m6A cannot induce any misincorporated DNA 6mA, unveiling the existence of a catabolism checkpoint that blocks DNA 6mA misincorporation. We further show that the deaminase ADAL preferentially catabolizes N6-methyl-2’-deoxyadenosine monophosphate (6mdAMP) in vitro and in vivo, and adenylate kinase 1 restricts the phosphorylation rate of 6mdAMP, together contributing to the identified checkpoint. Noteworthy, low ADAL expression reduces dramatically the patient survival in four cancers. Collectively, our data strongly support a pivotal role of ADAL in the suppression of 6mA misincorporation and implicate that both ADAL and misincorporated 6mA may mark cancer abnormalities.

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Activation of p53 Function by Human Transcriptional Coactivator PC4: Role of Protein-Protein Interaction, DNA Bending, and Posttranslational Modifications

Molecular and Cellular Biology ◽

10.1128/mcb.01064-07 ◽

2007 ◽

Vol 27 (21) ◽

pp. 7603-7614 ◽

Cited By ~ 35

Author(s):

Kiran Batta ◽

Tapas K. Kundu

Keyword(s):

Dna Binding ◽

Posttranslational Modifications ◽

Molecular Mechanisms ◽

Double Helix ◽

Dna Bending ◽

Cell Cycle Checkpoints ◽

Transcriptional Coactivator ◽

Dna Double Helix

ABSTRACT Tumor suppressor p53 controls cell cycle checkpoints and apoptosis via the transactivation of several genes that are involved in these processes. The functions of p53 are regulated by a wide variety of proteins, which interact with it either directly or indirectly. The multifunctional human transcriptional coactivator PC4 interacts with p53 in vivo and in vitro and regulates its function. Here we report the molecular mechanisms of the PC4-mediated activation of p53 function. PC4 interacts with the DNA binding and C-terminal domains of p53 through its DNA binding domain, which is essential for the stimulation of p53 DNA binding. Remarkably, ligation-mediated circularization assays reveal that PC4 induces significant bending in the DNA double helix. Deletion mutants defective in DNA bending are found to be impaired in activating p53-mediated DNA binding and apoptosis. Furthermore, acetylation of PC4 enhances, while phosphorylation abolishes, its ability to bend DNA, activate p53 DNA binding, and, thereby, regulate p53 functions. In conclusion, PC4 activates p53 recruitment to p53-responsive promoters (Bax and p21) in vivo through its interaction with p53 and by providing bent substrate for p53 recruitment. These results elucidate the general molecular mechanisms of activation of p53 function, mediated by its coactivators.

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A Paradoxical Mutant GATA Factor

Eukaryotic Cell ◽

10.1128/ec.3.2.393-405.2004 ◽

2004 ◽

Vol 3 (2) ◽

pp. 393-405 ◽

Cited By ~ 29

Author(s):

M. Isabel Muro-Pastor ◽

Joseph Strauss ◽

Ana Ramón ◽

Claudio Scazzocchio

Keyword(s):

Transcription Factor ◽

Dna Binding ◽

Double Helix ◽

Constitutive Expression ◽

Nitrogen Sources ◽

Loss Of Function ◽

Gata Factor ◽

Dna Double Helix

ABSTRACT The niiA (nitrite reductase) and niaD (nitrate reductase) genes of Aspergillus nidulans are subject to both induction by nitrate and repression by ammonium or glutamine. The intergenic region between these genes functions as a bidirectional promoter. In this region, nucleosomes are positioned under nonexpression conditions. On nitrate induction under derepressing conditions, total loss of positioning occurs. This is independent of transcription and of the NirA-specific transcription factor but absolutely dependent on the wide-domain GATA-binding AreA factor. We show here that a 3-amino-acid deletion in the basic carboxy-terminal sequence of the DNA-binding domain results in a protein with paradoxical properties. Its weak DNA binding is consistent with its loss-of-function phenotype on most nitrogen sources. However, it results in constitutive expression and superinducibility of niiA and niaD. Nucleosome loss of positioning is also constitutive. The mutation partially suppresses null mutations in the transcription factor NirA. AreA binds NirA in vitro, and the mutation does not affect this interaction. The in vivo methylation pattern of the promoter is drastically altered, suggesting the recruitment of one or more unknown transcription factors and/or a local distortion on the DNA double helix.

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EJE Prize 2013: Regulation of aldosterone secretion: from physiology to disease

Acta Endocrinologica ◽

10.1530/eje-13-0263 ◽

2013 ◽

Vol 168 (6) ◽

pp. R85-R93 ◽

Cited By ~ 30

Author(s):

Felix Beuschlein

Keyword(s):

High Throughput Sequencing ◽

Secondary Hypertension ◽

Small Sample ◽

Cellular Systems ◽

Common Disease ◽

Aldosterone Secretion ◽

Technical Developments ◽

Starting Point

Arterial hypertension is a major cardiovascular risk factor that affects between 10 and 40% of the population in industrialized countries. Primary aldosteronism (PA) is the most common form of secondary hypertension with an estimated prevalence of around 10% in referral centers and 4% in a primary care setting. Despite its high prevalence until recently, the underlying genetic and molecular basis of this common disease had remained largely obscure. Over the past decade, a number of insights have been achieved that have relied onin vitrocellular systems, wild-type and genetically modifiedin vivomodels, as well as clinical studies in well-characterized patient populations. This progress has been made possible by a number of independent technical developments including that of specific hormone assays that allow measurement in small sample volumes as well as genetic techniques that enable high-throughput sequencing of a large number of samples. Furthermore, animal models have provided important insights into the physiology of aldosterone regulation that have served as a starting point for investigation of mechanisms involved in autonomous aldosterone secretion. Finally, national and international networks that have built up registries and biobanks have been instrumental in fostering translational research endeavors in PA. Therefore, it is to be expected that in the near future, further pathophysiological mechanisms that result in autonomous aldosterone secretion will be unraveled.

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Fiber-Optic Time-Resolved Fluorescence Sensor for in Vitro Serotonin Determination

Applied Spectroscopy ◽

10.1366/0003702934067180 ◽

1993 ◽

Vol 47 (5) ◽

pp. 590-597 ◽

Cited By ~ 8

Author(s):

Stephane Mottin ◽

Canh Tran-Minh ◽

Pierre Laporte ◽

Raymond Cespuglio ◽

Michel Jouvet

Keyword(s):

Chemical Sensor ◽

Fiber Optic ◽

Fiber Optic Sensor ◽

Excitation Wavelength ◽

Nitrogen Laser ◽

Time Resolved ◽

Temporal Effects ◽

Starting Point

At pH 7 and with the excitation at wavelengths above 315 nm, previously unreported fluorescence of 5-HT (5-hydroxytryptamine) is observed. Two fluorescence bands were observed for 5-HT; the first emits at around 390 nm with an associated lifetime near 1 ns, and the other (well known) emits at 340 nm with an associated lifetime of 2.7 ns. With both static and time-resolved fluorescences, the spectral and temporal effects of the excitation wavelength were studied between 285 and 340 nm. With these basic spectroscopic properties as a starting point, a fiber-optic chemical sensor (FOCS) was developed in order to measure 5-HT with a single-fiber configuration, nitrogen laser excitation, and fast digitizing techniques. Temporal effects including fluorescence of the optical fiber were studied and compared with measurements both directly in cuvette and through the fiber-optic sensor. Less than thirty seconds are required for each measurement. A detection limit of 5-HT is reached in the range of 5 μM. Our system, with an improved sensitivity, could therefore be a possible and convenient “tool” for in vivo determination of 5-HT.

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SARS-CoV-2 Spike triggers barrier dysfunction and vascular leak via integrins and TGF-β signaling

10.1101/2021.12.10.472112 ◽

2021 ◽

Author(s):

Scott B Biering ◽

Francielle Tramontini Gomes de Sousa ◽

Laurentia V. Tjang ◽

Felix Pahmeier ◽

Richard Ruan ◽

...

Keyword(s):

Transcriptional Response ◽

Barrier Dysfunction ◽

Vascular Leak ◽

Endothelial Barrier Dysfunction ◽

Mechanistic Insight ◽

Starting Point ◽

Signaling Axis ◽

Insight Into

Severe COVID-19 is associated with epithelial and endothelial barrier dysfunction within the lung as well as in distal organs. While it is appreciated that an exaggerated inflammatory response is associated with barrier dysfunction, the triggers of this pathology are unclear. Here, we report that cell-intrinsic interactions between the Spike (S) glycoprotein of SARS-CoV-2 and epithelial/endothelial cells are sufficient to trigger barrier dysfunction in vitro and vascular leak in vivo, independently of viral replication and the ACE2 receptor. We identify an S-triggered transcriptional response associated with extracellular matrix reorganization and TGF-β signaling. Using genetic knockouts and specific inhibitors, we demonstrate that glycosaminoglycans, integrins, and the TGF-β signaling axis are required for S-mediated barrier dysfunction. Our findings suggest that S interactions with barrier cells are a contributing factor to COVID-19 disease severity and offer mechanistic insight into SARS-CoV-2 triggered vascular leak, providing a starting point for development of therapies targeting COVID-19 pathogenesis.

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(E)-N′-(4-Fluorobenzylidene)-5-methyl-2-(pyridin-3-yl)thiazole-4-carbohydrazide

Molbank ◽

10.3390/m1058 ◽

2019 ◽

Vol 2019 (2) ◽

pp. M1058

Author(s):

Vinuta Kamat ◽

Rangappa Santosh ◽

Suresh Nayak

Keyword(s):

Escherichia Coli ◽

Double Helix ◽

Catalytic Amount ◽

Target Compound ◽

Addition Compound ◽

E Coli ◽

In Vitro Antibacterial Activity ◽

Ft Ir ◽

Dna Double Helix

5-methyl-2-(pyridin-3-yl)-1,3-thiazole-4-carbohydrazide (1) on treatment with 4-fluorobenzaldehyde in presence of catalytic amount of acetic acid, accessed the target compound (2) with the yield of 79%. The target compound was confirmed by 1H-NMR, 13C-NMR, FT-IR and LCMS. In vitro antibacterial activity against Staphylococcus aureus (S. Aureus), Bacillus subtilis (B. subtilis), Escherichia coli (E. coli), and Pseudomonas aeruginosa (P. aeruginosa) were carried out and compound 2 showed promising activity against B. subtilis. In addition, compound 2 was analyzed for DNA binding study. It revealed that compound 2 has a promising affinity towards DNA double helix.

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Based on Principles and Insights of COVID-19 Epidemiology, Genome Sequencing, and Pathogenesis: Retrospective Analysis of Sinigrin and ProlixinRX (Fluphenazine) Provides Off-Label Drug Candidates

SLAS DISCOVERY Advancing Life Sciences ◽

10.1177/2472555220950236 ◽

2020 ◽

Vol 25 (10) ◽

pp. 1123-1140

Author(s):

Jilan Nazeam ◽

Esraa Z. Mohammed ◽

Mariam Raafat ◽

Mariam Houssein ◽

Asmaa Elkafoury ◽

...

Keyword(s):

Natural Products ◽

Evidence Synthesis ◽

Drug Repurposing ◽

New Drugs ◽

Future Research ◽

Nitrogenous Compounds ◽

Future Research Agenda ◽

Starting Point

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative pathogen of pandemic coronavirus disease 2019 (COVID-19). So far, no approved therapy has been developed to halt the spread of the pathogen, and unfortunately, the strategies for developing a new therapy will require a long time and very extensive resources. Therefore, drug repurposing has emerged as an ideal strategy toward a smart, versatile, quick way to confine the lethal disease. In this endeavor, natural products have been an untapped source for new drugs. This review represents the confederated experience of multidisciplinary researchers of 99 articles using several databases: Google Scholar, Science Direct, MEDLINE, Web of Science, Scopus, and PubMed. To establish the hypothesis, a Bayesian perspective of a systematic review was used to outline evidence synthesis. Our docking documentation of 69 compounds and future research agenda assumptions were directed toward finding an effective and economic anti-COVID-19 treatment from natural products. Glucosinolate, flavones, and sulfated nitrogenous compounds demonstrate direct anti-SARS-CoV-2 activity through inhibition protease enzymes and may be considered potential candidates against coronavirus. These findings could be a starting point to initiate an integrative study that may encompass interested scientists and research institutes to test the hypothesis in vitro, in vivo, and in clinics after satisfying all ethical requirements.

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Ratiometric analysis using Raman spectroscopy as a powerful predictor of structural properties of fatty acids

Royal Society Open Science ◽

10.1098/rsos.181483 ◽

2018 ◽

Vol 5 (12) ◽

pp. 181483 ◽

Cited By ~ 9

Author(s):

Lauren E. Jamieson ◽

Angela Li ◽

Karen Faulds ◽

Duncan Graham

Keyword(s):

Fatty Acids ◽

Raman Spectroscopy ◽

Biological Sample ◽

Ex Vivo ◽

Degree Of Saturation ◽

Specific Information ◽

Analytical Technique ◽

Starting Point

Raman spectroscopy has been used extensively for the analysis of biological samples in vitro , ex vivo and in vivo . While important progress has been made towards using this analytical technique in clinical applications, there is a limit to how much chemically specific information can be extracted from a spectrum of a biological sample, which consists of multiple overlapping peaks from a large number of species in any particular sample. In an attempt to elucidate more specific information regarding individual biochemical species, as opposed to very broad assignments by species class, we propose a bottom-up approach beginning with a detailed analysis of pure biochemical components. Here, we demonstrate a simple ratiometric approach applied to fatty acids, a subsection of the lipid class, to allow the key structural features, in particular degree of saturation and chain length, to be predicted. This is proposed as a starting point for allowing more chemically and species-specific information to be elucidated from the highly multiplexed spectrum of multiple overlapping signals found in a real biological sample. The power of simple ratiometric analysis is also demonstrated by comparing the prediction of degree of unsaturation in food oil samples using ratiometric and multivariate analysis techniques which could be used for food oil authentication.

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In Vitro Screening for Drug Repositioning

CrossRef Listing of Deleted DOIs ◽

10.1177/1087057114563024 ◽

2014 ◽

Vol 20 (2) ◽

pp. 167-179 ◽

Cited By ~ 25

Author(s):

Graeme F. Wilkinson ◽

Kevin Pritchard

Keyword(s):

Scientific Literature ◽

Drug Repositioning ◽

Short Review ◽

In Vitro Screening ◽

Compound Libraries ◽

Starting Point ◽

Viable Method ◽

Large Compound

Drug repositioning or repurposing has received much coverage in the scientific literature in recent years and has been responsible for the generation of both new intellectual property and investigational new drug submissions. The literature indicates a significant trend toward the use of computational- or informatics-based methods for generating initial repositioning hypotheses, followed by focused assessment of biological activity in phenotypic assays. Another viable method for drug repositioning is in vitro screening of known drugs or drug-like molecules, initially in disease-relevant phenotypic assays, to identify and validate candidates for repositioning. This approach can use large compound libraries or can focus on subsets of known drugs or drug-like molecules. In this short review, we focus on ways to generate and validate repositioning candidates in disease-related in vitro and phenotypic assays, and we discuss specific examples of this approach as applied to a variety of disease areas. We propose that in vitro screens offer several advantages over biochemical or in vivo methods as a starting point for drug repositioning.

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