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1.
J Biol Chem ; 299(12): 105451, 2023 Dec.
Article in English | MEDLINE | ID: mdl-37951306

ABSTRACT

Cryptochromes (CRYs) are essential components of the circadian clock, playing a pivotal role as transcriptional repressors. Despite their significance, the precise mechanisms underlying CRYs' involvement in the circadian clock remain incompletely understood. In this study, we identified a rare CRY2 variant, p.Ser420Phe, from the 1000 Genomes Project and Ensembl database that is located in the functionally important coiled-coil-like helix (CC-helix) region. Functional characterization of this variant at the cellular level revealed that p.Ser420Phe CRY2 had reduced repression activity on CLOCK:BMAL1-driven transcription due to its reduced affinity to the core clock protein PER2 and defective translocation into the nucleus. Intriguingly, the CRY2 variant exhibited an unexpected resistance to degradation via the canonical proteasomal pathway, primarily due to the loss of interactions with E3 ligases (FBXL3 and FBXL21), which suggests Ser-420 of CRY2 is required for the interaction with E3 ligases. Further studies revealed that wild-type and CRY2 variants are degraded by the lysosomal-mediated degradation pathway, a mechanism not previously associated with CRY2. Surprisingly, our complementation study with Cry1-/-Cry2-/- double knockout mouse embryonic fibroblast cells indicated that the CRY2 variant caused a 7 h shorter circadian period length in contrast to the observed prolonged period length in CRY2-/- cell lines. In summary, this study reveals a hitherto unknown degradation pathway for CRY2, shedding new light on the regulation of circadian rhythm period length.


Subject(s)
Amino Acid Substitution , Circadian Clocks , Cryptochromes , Animals , Humans , Mice , Circadian Clocks/physiology , Circadian Rhythm/physiology , CLOCK Proteins/metabolism , Cryptochromes/genetics , Cryptochromes/metabolism , Fibroblasts/metabolism , Lysosomes/metabolism , Ubiquitin-Protein Ligases/metabolism , Cell Line
2.
Biochem Pharmacol ; 218: 115896, 2023 12.
Article in English | MEDLINE | ID: mdl-37898388

ABSTRACT

Cryptochromes (CRYs), transcriptional repressors of the circadian clock in mammals, inhibit cAMP production when glucagon activates G-protein coupled receptors. Therefore, molecules that modulate CRYs have the potential to regulate gluconeogenesis. In this study, we discovered a new molecule called TW68 that interacts with the primary pockets of mammalian CRY1/2, leading to reduced ubiquitination levels and increased stability. In cell-based circadian rhythm assays using U2OS Bmal1-dLuc cells, TW68 extended the period length of the circadian rhythm. Additionally, TW68 decreased the transcriptional levels of two genes, Phosphoenolpyruvate carboxykinase 1 (PCK1) and Glucose-6-phosphatase (G6PC), which play crucial roles in glucose biosynthesis during glucagon-induced gluconeogenesis in HepG2 cells. Oral administration of TW68 in mice showed good tolerance, a good pharmacokinetic profile, and remarkable bioavailability. Finally, when administered to fasting diabetic animals from ob/ob and HFD-fed obese mice, TW68 reduced blood glucose levels by enhancing CRY stabilization and subsequently decreasing the transcriptional levels of Pck1 and G6pc. These findings collectively demonstrate the antidiabetic efficacy of TW68 in vivo, suggesting its therapeutic potential for controlling fasting glucose levels in the treatment of type 2 diabetes mellitus.


Subject(s)
Circadian Clocks , Diabetes Mellitus, Type 2 , Animals , Mice , Cryptochromes/genetics , Blood Glucose , Mice, Obese , Glucagon , Diabetes Mellitus, Type 2/drug therapy , Circadian Rhythm/physiology , Mammals , Fasting
3.
J Biomol Struct Dyn ; : 1-12, 2023 Sep 13.
Article in English | MEDLINE | ID: mdl-37705288

ABSTRACT

Cryptochromes (CRYs) are essential components of the molecular clock that generates circadian rhythm. They inhibit BMAL1/CLOCK-driven transcription at the molecular level. There are two CRYs that have differential functions in the circadian clock in mammals. It is not precisely known how they achieve such differential functions. In this study, we performed molecular dynamic simulations on eight CRY mutants that have been experimentally shown to exhibit reduced repressor activities. Our results revealed that mutations in CRY1 affect the dynamic behavior of the serine loop and the availability of the secondary pocket, but not in CRY2. Further analysis of these CRY1 mutants indicated that the differential flexibility of the serine loop leads to changes in the volume of the secondary pocket. We also investigated the weak interactions between the amino acids in the serine loop and those in close proximity. Our findings highlighted the crucial roles of S44 and S45 in the dynamic behavior of the serine loop, specifically through their interactions with E382 in CRY1. Considering the clinical implications of altered CRY1 function, our study opens up new possibilities for the development of drugs that target the allosteric regulation of CRY1.Communicated by Ramaswamy H. Sarma.

4.
Adv Protein Chem Struct Biol ; 137: 17-37, 2023.
Article in English | MEDLINE | ID: mdl-37709375

ABSTRACT

Circadian rhythm is an endogenous timing system that allows an organism to anticipate and adapt to daily changes and regulate various physiological variables such as the sleep-wake cycle. This rhythm is governed by a molecular circadian clock mechanism, generated by a transcriptional and translational feedback loop (TTFL) mechanism. In mammals, TTFL is determined by the interaction of four main clock proteins: BMAL1, CLOCK, Cryptochromes (CRY), and Periods (PER). BMAL1 and CLOCK form dimers and initiate the transcription of clock-controlled genes (CCG) by binding an E-box element with the promotor genes. Among CCGs, PERs and CRYs accumulate in the cytosol and translocate into the nucleus, where they interact with the BMAL1/CLOCK dimer and inhibit its activity. Several epidemiological and genetic studies have revealed that circadian rhythm disruption causes various types of disease. In this chapter, we summarize the effect of core clock gene SNPs on circadian rhythm and diseases in humans.


Subject(s)
ARNTL Transcription Factors , Polymorphism, Single Nucleotide , Humans , Animals , ARNTL Transcription Factors/genetics , Phenotype , Cryptochromes/genetics , Cytosol , Polymers , Mammals
5.
J Biol Rhythms ; 38(2): 171-184, 2023 04.
Article in English | MEDLINE | ID: mdl-36762608

ABSTRACT

The circadian timing system controls absorption, distribution, metabolism, and elimination processes of drug pharmacokinetics over a 24-h period. Exposure of target tissues to the active form of the drug and cytotoxicity display variations depending on the chronopharmacokinetics. For anticancer drugs with narrow therapeutic ranges and dose-limiting side effects, it is particularly important to know the temporal changes in pharmacokinetics. A previous study indicated that pharmacokinetic profile of capecitabine was different depending on dosing time in rat. However, it is not known how such difference is attributed with respect to diurnal rhythm. Therefore, in this study, we evaluated capecitabine-metabolizing enzymes in a diurnal rhythm-dependent manner. To this end, C57BL/6J male mice were orally treated with 500 mg/kg capecitabine at ZT1, ZT7, ZT13, or ZT19. We then determined pharmacokinetics of capecitabine and its metabolites, 5'-deoxy-5-fluorocytidine (5'DFCR), 5'-deoxy-5-fluorouridine (5'DFUR), 5-fluorouracil (5-FU), in plasma and liver. Results revealed that plasma Cmax and AUC0-6h (area under the plasma concentration-time curve from 0 to 6 h) values of capecitabine, 5'DFUR, and 5-FU were higher during the rest phase (ZT1 and ZT7) than the activity phase (ZT13 and ZT19) (p < 0.05). Similarly, Cmax and AUC0-6h values of 5'DFUR and 5-FU in liver were higher during the rest phase than activity phase (p < 0.05), while there was no significant difference in liver concentrations of capecitabine and 5'DFCR. We determined the level of the enzymes responsible for the conversion of capecitabine and its metabolites at each ZT. Results indicated the levels of carboxylesterase 1 and 2, cytidine deaminase, uridine phosphorylase 2, and dihydropyrimidine dehydrogenase (p < 0.05) are being rhythmically regulated and, in turn, attributed different pharmacokinetics profiles of capecitabine and its metabolism. This study highlights the importance of capecitabine administration time to increase the efficacy with minimum adverse effects.


Subject(s)
Antimetabolites, Antineoplastic , Circadian Rhythm , Male , Mice , Rats , Animals , Capecitabine/pharmacokinetics , Antimetabolites, Antineoplastic/pharmacokinetics , Antimetabolites, Antineoplastic/therapeutic use , Mice, Inbred C57BL , Fluorouracil/metabolism , Fluorouracil/therapeutic use
6.
J Biol Chem ; 299(1): 102794, 2023 01.
Article in English | MEDLINE | ID: mdl-36528063

ABSTRACT

Photolyases (PLs) reverse UV-induced DNA damage using blue light as an energy source. Of these PLs, (6-4) PLs repair (6-4)-lesioned photoproducts. We recently identified a gene from Vibrio cholerae (Vc) encoding a (6-4) PL, but structural characterization is needed to elucidate specific interactions with the chromophore cofactors. Here, we determined the crystal structure of Vc (6-4) PL at 2.5 Å resolution. Our high-resolution structure revealed that the two well-known cofactors, flavin adenine dinucleotide and the photoantenna 6,7-dimethyl 8-ribityl-lumazin (DMRL), stably interact with an α-helical and an α/ß domain, respectively. Additionally, the structure has a third cofactor with distinct electron clouds corresponding to a [4Fe-4S] cluster. Moreover, we identified that Asp106 makes a hydrogen bond with water and DMRL, which indicates further stabilization of the photoantenna DMRL within Vc (6-4) PL. Further analysis of the Vc (6-4) PL structure revealed a possible region responsible for DNA binding. The region located between residues 478 to 484 may bind the lesioned DNA, with Arg483 potentially forming a salt bridge with DNA to stabilize further the interaction of Vc (6-4) PL with its substrate. Our comparative analysis revealed that the DNA lesion could not bind to the Vc (6-4) PL in a similar fashion to the Drosophila melanogaster (Dm, (6-4)) PL without a significant conformational change of the protein. The 23rd helix of the bacterial (6-4) PLs seems to have remarkable plasticity, and conformational changes facilitate DNA binding. In conclusion, our structure provides further insight into DNA repair by a (6-4) PL containing three cofactors.


Subject(s)
Deoxyribodipyrimidine Photo-Lyase , Vibrio cholerae , Animals , Deoxyribodipyrimidine Photo-Lyase/genetics , Deoxyribodipyrimidine Photo-Lyase/chemistry , Deoxyribodipyrimidine Photo-Lyase/metabolism , Vibrio cholerae/genetics , Vibrio cholerae/metabolism , Drosophila melanogaster/metabolism , DNA Repair , DNA/chemistry , Flavin-Adenine Dinucleotide/metabolism
7.
Nat Commun ; 13(1): 6742, 2022 11 08.
Article in English | MEDLINE | ID: mdl-36347873

ABSTRACT

Cryptochromes are negative transcriptional regulators of the circadian clock in mammals. It is not clear how reducing the level of endogenous CRY1 in mammals will affect circadian rhythm and the relation of such a decrease with apoptosis. Here, we discovered a molecule (M47) that destabilizes Cryptochrome 1 (CRY1) both in vitro and in vivo. The M47 selectively enhanced the degradation rate of CRY1 by increasing its ubiquitination and resulted in increasing the circadian period length of U2OS Bmal1-dLuc cells. In addition, subcellular fractionation studies from mice liver indicated that M47 increased degradation of the CRY1 in the nucleus. Furthermore, M47-mediated CRY1 reduction enhanced oxaliplatin-induced apoptosis in Ras-transformed p53 null fibroblast cells. Systemic repetitive administration of M47 increased the median lifespan of p53-/- mice by ~25%. Collectively our data suggest that M47 is a promising molecule to treat forms of cancer depending on the p53 mutation.


Subject(s)
Circadian Clocks , Cryptochromes , Animals , Mice , Circadian Clocks/genetics , Circadian Rhythm/genetics , Cryptochromes/genetics , Cryptochromes/metabolism , Longevity , Mammals/metabolism , Mice, Knockout , Transcription Factors/metabolism , Tumor Suppressor Protein p53/genetics
8.
J Biol Chem ; 298(9): 102334, 2022 09.
Article in English | MEDLINE | ID: mdl-35933018

ABSTRACT

Human clock-gene variations contribute to the phenotypic differences observed in various behavioral and physiological processes, such as diurnal preference, sleep, metabolism, mood regulation, addiction, and fertility. However, little is known about the possible effects of identified variations at the molecular level. In this study, we performed a functional characterization at the cellular level of rare cryptochrome 2 (CRY2) missense variations that were identified from the Ensembl database. Our structural studies revealed that three variations (p.Pro123Leu, p.Asp406His, and p.Ser410Ile) are located at the rim of the secondary pocket of CRY2. We show that these variants were unable to repress CLOCK (circadian locomotor output cycles kaput)/BMAL1 (brain and muscle ARNT-like-1)-driven transcription in a cell-based reporter assay and had reduced affinity to CLOCK-BMAL1. Furthermore, our biochemical studies indicated that the variants were less stable than the WT CRY2, which could be rescued in the presence of period 2 (PER2), another core clock protein. Finally, we found that these variants were unable to properly localize to the nucleus and thereby were unable to rescue the circadian rhythm in a Cry1-/-Cry2-/- double KO mouse embryonic fibroblast cell line. Collectively, our data suggest that the rim of the secondary pocket of CRY2 plays a significant role in its nuclear localization independently of PER2 and in the intact circadian rhythm at the cellular level.


Subject(s)
ARNTL Transcription Factors , CLOCK Proteins , Circadian Rhythm , Cryptochromes , ARNTL Transcription Factors/metabolism , Animals , CLOCK Proteins/metabolism , Circadian Rhythm/physiology , Cryptochromes/chemistry , Cryptochromes/genetics , Cryptochromes/metabolism , Fibroblasts , Humans , Mice , Protein Domains , Protein Stability
9.
Adv Protein Chem Struct Biol ; 131: 207-233, 2022.
Article in English | MEDLINE | ID: mdl-35871891

ABSTRACT

Circadian rhythm is a 24-h cycle that regulates the biochemical and behavioral changes of organisms. It controls a wide range of functions, from gene expression to behavior, allowing organisms to anticipate daily changes in their environment. In mammals, circadian rhythm is generated by a complex transcriptional and translational feedback loop mechanism. The binding of CLOCK/BMAL1 heterodimer to the E-box of DNA located within the promoter region initiates transcription of clock control genes including the transcription of the other two core clock genes of Periods (Pers) and Cryptochromes (Crys). Then PERs and CRYs along with casein kinase 1ɛ/Δ translocate into the nucleus where they suppress CLOCK/BMAL1 transactivation and, in turn, clock-regulated gene expression. Various clock components must be operational to aid in their stabilization and period extension in circadian rhythm. In this review, we have highlighted the recent progress for the core clock interacting proteins to maintain and to stabilize circadian rhythm in mammals.


Subject(s)
ARNTL Transcription Factors , CLOCK Proteins , ARNTL Transcription Factors/metabolism , Animals , CLOCK Proteins/genetics , CLOCK Proteins/metabolism , Circadian Rhythm/genetics , Cryptochromes/metabolism , Mammals/metabolism , Protein Interaction Maps
10.
Methods Mol Biol ; 2482: 15-34, 2022.
Article in English | MEDLINE | ID: mdl-35610417

ABSTRACT

Circadian rhythms are part of the body's clock, which regulates several physiological and biochemical variables according to the 24-h cycle. Ample evidence indicated disturbance of the circadian clock leads to an increased susceptibility to several diseases. Therefore, a great effort has been made to find small molecules that regulate circadian rhythm by high-throughput methods. Having crystal structures of core clock proteins, makes them amenable to structure-based drug design studies. Here, we describe virtual screening methods that can be utilized for the identification of small molecules regulating the activity of core clock protein Cryptochrome 1.


Subject(s)
CLOCK Proteins , Circadian Clocks , CLOCK Proteins/metabolism , Circadian Rhythm/physiology , Molecular Docking Simulation
11.
Funct Integr Genomics ; 22(3): 407-421, 2022 Jun.
Article in English | MEDLINE | ID: mdl-35286570

ABSTRACT

In this study, we characterized the fatty acid production in Neochloris aquatica at transcriptomics and biochemical levels under limiting, normal, and excess nitrate concentrations in different growth phases. At the stationary phase, N. aquatica mainly produced saturated fatty acids such as stearic acid under the limiting nitrate concentration, which is suitable for biodiesel production. However, it produced polyunsaturated fatty acids such as α-linolenic acid under the excess nitrate concentration, which has nutritional values as food supplements. In addition, RNA-seq was employed to identify genes and pathways that were being affected in N. aquatica for three growth phases in the presence of the different nitrate amounts. Genes that are responsible for the production of saturated fatty acids were upregulated in the cells grown under a limiting nitrogen amount while genes that are responsible for the production of polyunsaturated fatty acid were upregulated in the cells grown under excess nitrogen amount. Further analysis showed more genes differentially expressed (DEGs) at the logarithmic phase in all conditions while a relatively steady trend was observed during the transition from the logarithmic phase to the stationary phase under limiting and excess nitrogen. Our results provide a foundation for identifying developmentally important genes and understanding the biological processes in the different growth phases of the N. aquatica in terms of biomass and lipid production.


Subject(s)
Fatty Acids , Transcriptome , Biomass , Fatty Acids/metabolism , Nitrates , Nitrogen/metabolism
12.
Proteins ; 90(6): 1315-1330, 2022 06.
Article in English | MEDLINE | ID: mdl-35122331

ABSTRACT

Circadian rhythms are a series of endogenous autonomous 24-h oscillations generated by the circadian clock. At the molecular level, the circadian clock is based on a transcription-translation feedback loop, in which BMAL1 and CLOCK transcription factors of the positive arm activate the expression of CRYPTOCHROME (CRY) and PERIOD (PER) genes of the negative arm as well as the circadian clock-regulated genes. There are three PER proteins, of which PER2 shows the strongest oscillation at both stability and cellular localization level. Protein-protein interactions (PPIs) or interactome of the circadian clock proteins have been investigated using classical methods such as two-dimensional gel electrophoresis, immunoprecipitation-coupled mass spectrometry, and yeast-two hybrid assay where the dynamic and weak interactions are difficult to catch. To identify the interactome of PER2 we have adopted proximity-dependent labeling with biotin and mass spectrometry-based identification of labeled proteins (BioID). In addition to known interactions with such as CRY1 and CRY2, we have identified several new PPIs for PER2 and confirmed some of them using co-immunoprecipitation technique. This study characterizes the PER2 protein interactions in depth, and it also implies that using a fast BioID method with miniTurbo or TurboID coupled to other major circadian clock proteins might uncover other interactors in the clock that have yet to be discovered.


Subject(s)
Circadian Clocks , Period Circadian Proteins , ARNTL Transcription Factors/genetics , ARNTL Transcription Factors/metabolism , CLOCK Proteins/genetics , CLOCK Proteins/metabolism , Circadian Clocks/genetics , Period Circadian Proteins/genetics , Period Circadian Proteins/metabolism , Proteome/metabolism
13.
Sci Rep ; 11(1): 18510, 2021 09 16.
Article in English | MEDLINE | ID: mdl-34531414

ABSTRACT

Circadian rhythm is an important mechanism that controls behavior and biochemical events based on 24 h rhythmicity. Ample evidence indicates disturbance of this mechanism is associated with different diseases such as cancer, mood disorders, and familial delayed phase sleep disorder. Therefore, drug discovery studies have been initiated using high throughput screening. Recently the crystal structures of core clock proteins (CLOCK/BMAL1, Cryptochromes (CRY), Periods), responsible for generating circadian rhythm, have been solved. Availability of structures makes amenable core clock proteins to design molecules regulating their activity by using in silico approaches. In addition to that, the implementation of classification features of molecules based on their toxicity and activity will improve the accuracy of the drug discovery process. Here, we identified 171 molecules that target functional domains of a core clock protein, CRY1, using structure-based drug design methods. We experimentally determined that 115 molecules were nontoxic, and 21 molecules significantly lengthened the period of circadian rhythm in U2OS cells. We then performed a machine learning study to classify these molecules for identifying features that make them toxic and lengthen the circadian period. Decision tree classifiers (DTC) identified 13 molecular descriptors, which predict the toxicity of molecules with a mean accuracy of 79.53% using tenfold cross-validation. Gradient boosting classifiers (XGBC) identified 10 molecular descriptors that predict and increase in the circadian period length with a mean accuracy of 86.56% with tenfold cross-validation. Our results suggested that these features can be used in QSAR studies to design novel nontoxic molecules that exhibit period lengthening activity.


Subject(s)
CLOCK Proteins/metabolism , Circadian Rhythm/physiology , Cryptochromes/metabolism , Animals , Databases, Protein , Mice , Molecular Docking Simulation , Molecular Dynamics Simulation , Protein Conformation
14.
Front Neurosci ; 15: 652608, 2021.
Article in English | MEDLINE | ID: mdl-34248476

ABSTRACT

Light-activated biointerfaces provide a non-genetic route for effective control of neural activity. InP quantum dots (QDs) have a high potential for such biomedical applications due to their uniquely tunable electronic properties, photostability, toxic-heavy-metal-free content, heterostructuring, and solution-processing ability. However, the effect of QD nanostructure and biointerface architecture on the photoelectrical cellular interfacing remained unexplored. Here, we unravel the control of the photoelectrical response of InP QD-based biointerfaces via nanoengineering from QD to device-level. At QD level, thin ZnS shell growth (∼0.65 nm) enhances the current level of biointerfaces over an order of magnitude with respect to only InP core QDs. At device-level, band alignment engineering allows for the bidirectional photoelectrochemical current generation, which enables light-induced temporally precise and rapidly reversible action potential generation and hyperpolarization on primary hippocampal neurons. Our findings show that nanoengineering QD-based biointerfaces hold great promise for next-generation neurostimulation devices.

15.
FEBS J ; 288(2): 614-639, 2021 01.
Article in English | MEDLINE | ID: mdl-32383312

ABSTRACT

Circadian disruption influences metabolic health. Metabolism modulates circadian function. However, the mechanisms coupling circadian rhythms and metabolism remain poorly understood. Here, we report that cystathionine ß-synthase (CBS), a central enzyme in one-carbon metabolism, functionally interacts with the core circadian protein cryptochrome 1 (CRY1). In cells, CBS augments CRY1-mediated repression of the CLOCK/BMAL1 complex and shortens circadian period. Notably, we find that mutant CBS-I278T protein, the most common cause of homocystinuria, does not bind CRY1 or regulate its repressor activity. Transgenic CbsZn/Zn  mice, while maintaining circadian locomotor activity period, exhibit reduced circadian power and increased expression of E-BOX outputs. CBS function is reciprocally influenced by CRY1 binding. CRY1 modulates enzymatic activity of the CBS. Liver extracts from Cry1-/- mice show reduced CBS activity that normalizes after the addition of exogenous wild-type (WT) CRY1. Metabolomic analysis of WT, CbsZn/Zn , Cry1-/- , and Cry2-/- samples highlights the metabolic importance of endogenous CRY1. We observed temporal variation in one-carbon and transsulfuration pathways attributable to CRY1-induced CBS activation. CBS-CRY1 binding provides a post-translational switch to modulate cellular circadian physiology and metabolic control.


Subject(s)
Circadian Clocks/genetics , Circadian Rhythm/genetics , Cryptochromes/genetics , Cystathionine beta-Synthase/genetics , Metabolome/genetics , Protein Processing, Post-Translational , ARNTL Transcription Factors/genetics , ARNTL Transcription Factors/metabolism , Amino Acid Sequence , Animals , CLOCK Proteins/genetics , CLOCK Proteins/metabolism , Cryptochromes/deficiency , Cystathionine beta-Synthase/metabolism , E-Box Elements , Female , HEK293 Cells , Humans , Male , Metabolic Networks and Pathways/genetics , Mice , Mice, Knockout , Mutation , Period Circadian Proteins/genetics , Period Circadian Proteins/metabolism , Protein Binding , Sequence Alignment , Sequence Homology, Amino Acid , Signal Transduction
16.
Funct Integr Genomics ; 21(1): 1-16, 2021 Jan.
Article in English | MEDLINE | ID: mdl-33111200

ABSTRACT

We have previously reported that the deletion of BMAL1 gene has opposite effects in respect to its contribution to the pathways that are effective in the multistage carcinogenesis process. BMAL1 deletion sensitized nearly normal breast epithelial (MCF10A) and invasive breast cancer cells (MDA-MB-231) to cisplatin- and doxorubicin-induced apoptosis, while this deletion also aggravated the invasive potential of MDA-MB-231 cells. However, the mechanistic relationship of the seemingly opposite contribution of BMAL1 deletion to carcinogenesis process is not known at genome-wide level. In this study, an RNA-seq approach was taken to uncover the differentially expressed genes (DEGs) and pathways after treating BMAL1 knockout (KO) or wild-type (WT) MDA-MB-231 cells with cisplatin and doxorubicin to initiate apoptosis. Gene set enrichment analysis with the DEGs demonstrated that enrichment in multiple genes/pathways contributes to sensitization to cisplatin- or doxorubicin-induced apoptosis in BMAL1-dependent manner. Additionally, our DEG analysis suggested that non-coding transcript RNA (such as lncRNA and processed pseudogenes) may have role in cisplatin- or doxorubicin-induced apoptosis. Protein-protein interaction network obtained from common DEGs in cisplatin and doxorubicin treatments revealed that GSK3ß, NACC1, and EGFR are the principal genes regulating the response of the KO cells. Moreover, the analysis of DEGs among untreated BMAL1 KO and WT cells revealed that epithelial-mesenchymal transition genes are up-regulated in KO cells. As a negative control, we have also analyzed the DEGs following treatment with an endoplasmic reticulum (ER) stress-inducing agent, tunicamycin, which was affected by BMAL1 deletion minimally. Collectively, the present study suggests that BMAL1 regulates many genes/pathways of which the alteration in BMAL1 KO cells may shed light on pleotropic phenotype observed.


Subject(s)
ARNTL Transcription Factors/genetics , Carcinogenesis/genetics , Transcriptome , ARNTL Transcription Factors/metabolism , Apoptosis , Carcinogenesis/metabolism , Cell Line, Tumor , Gene Deletion , Gene Expression Regulation, Neoplastic , Gene Regulatory Networks , Humans
17.
J Biomol Struct Dyn ; 39(17): 6772-6791, 2021 Oct.
Article in English | MEDLINE | ID: mdl-32752938

ABSTRACT

Despite strict measures taken by many countries, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to be an issue of global concern. Currently, there are no clinically proven pharmacotherapies for coronavirus disease 2019, despite promising initial results obtained from drugs such as azithromycin and hydroxychloroquine. Therefore, the repurposing of clinically approved drugs for use against SARS-CoV-2 has become a viable strategy. Here, we searched for drugs that target SARS-CoV-2 3C-like protease (3CLpro) and viral RNA-dependent RNA polymerase (RdRp) by in silico screening of the U.S. Food and Drug Administration approved drug library. Well-tolerated and widely used drugs were selected for molecular dynamics (MD) simulations to evaluate drug-protein interactions and their persistence under physiological conditions. Tetracycline, dihydroergotamine, ergotamine, dutasteride, nelfinavir, and paliperidone formed stable interactions with 3CLpro based on MD simulation results. Similar analysis with RdRp showed that eltrombopag, tipranavir, ergotamine, and conivaptan bound to the enzyme with high binding free energies. Docking results suggest that ergotamine, dihydroergotamine, bromocriptine, dutasteride, conivaptan, paliperidone, and tipranavir can bind to both enzymes with high affinity. As these drugs are well tolerated, cost-effective, and widely used, our study suggests that they could potentially to be used in clinical trials for the treatment of SARS-CoV-2-infected patients.Communicated by Ramaswamy H. Sarma.


Subject(s)
COVID-19 , Pharmaceutical Preparations , Antiviral Agents , Humans , Molecular Docking Simulation , Molecular Dynamics Simulation , Peptide Hydrolases , Protease Inhibitors , RNA-Dependent RNA Polymerase , SARS-CoV-2
18.
Biomed Opt Express ; 11(11): 6068-6077, 2020 Nov 01.
Article in English | MEDLINE | ID: mdl-33282475

ABSTRACT

Artificial control of neural activity allows for understanding complex neural networks and improving therapy of neurological disorders. Here, we demonstrate that utilization of photovoltaic biointerfaces combined with light waveform shaping can generate safe capacitive currents for bidirectional modulation of neurons. The differential photoresponse of the biointerface due to double layer capacitance facilitates the direction control of capacitive currents depending on the slope of light intensity. Moreover, the strength of capacitive currents is controlled by changing the rise and fall time slope of light intensity. This approach allows for high-level control of the hyperpolarization and depolarization of membrane potential at single-cell level. Our results pave the way toward advanced bioelectronic functionalities for wireless and safe control of neural activity.

19.
J Biol Chem ; 295(50): 17187-17199, 2020 12 11.
Article in English | MEDLINE | ID: mdl-33028638

ABSTRACT

Mammalian circadian clocks are driven by transcription/translation feedback loops composed of positive transcriptional activators (BMAL1 and CLOCK) and negative repressors (CRYPTOCHROMEs (CRYs) and PERIODs (PERs)). CRYs, in complex with PERs, bind to the BMAL1/CLOCK complex and repress E-box-driven transcription of clock-associated genes. There are two individual CRYs, with CRY1 exhibiting higher affinity to the BMAL1/CLOCK complex than CRY2. It is known that this differential binding is regulated by a dynamic serine-rich loop adjacent to the secondary pocket of both CRYs, but the underlying features controlling loop dynamics are not known. Here we report that allosteric regulation of the serine-rich loop is mediated by Arg-293 of CRY1, identified as a rare CRY1 SNP in the Ensembl and 1000 Genomes databases. The p.Arg293His CRY1 variant caused a shortened circadian period in a Cry1-/-Cry2-/- double knockout mouse embryonic fibroblast cell line. Moreover, the variant displayed reduced repressor activity on BMAL1/CLOCK driven transcription, which is explained by reduced affinity to BMAL1/CLOCK in the absence of PER2 compared with CRY1. Molecular dynamics simulations revealed that the p.Arg293His CRY1 variant altered a communication pathway between Arg-293 and the serine loop by reducing its dynamicity. Collectively, this study provides direct evidence that allosterism in CRY1 is critical for the regulation of circadian rhythm.


Subject(s)
CLOCK Proteins , Circadian Rhythm , Cryptochromes , Molecular Dynamics Simulation , ARNTL Transcription Factors/chemistry , ARNTL Transcription Factors/genetics , ARNTL Transcription Factors/metabolism , Allosteric Regulation , Amino Acid Substitution , Animals , Arginine/chemistry , Arginine/genetics , Arginine/metabolism , CLOCK Proteins/chemistry , CLOCK Proteins/genetics , CLOCK Proteins/metabolism , Cryptochromes/chemistry , Cryptochromes/genetics , Cryptochromes/metabolism , HEK293 Cells , Humans , Mice , Mice, Knockout , Mutation, Missense , Period Circadian Proteins/chemistry , Period Circadian Proteins/genetics , Period Circadian Proteins/metabolism , Polymorphism, Single Nucleotide , Protein Binding , Protein Structure, Secondary , Transcription, Genetic
20.
ACS Appl Mater Interfaces ; 12(38): 42997-43008, 2020 Sep 23.
Article in English | MEDLINE | ID: mdl-32852189

ABSTRACT

Neural interfaces are the fundamental tools to understand the brain and cure many nervous-system diseases. For proper interfacing, seamless integration, efficient and safe digital-to-biological signal transduction, and long operational lifetime are required. Here, we devised a wireless optoelectronic pseudocapacitor converting the optical energy to safe capacitive currents by dissociating the photogenerated excitons in the photovoltaic unit and effectively routing the holes to the supercapacitor electrode and the pseudocapacitive electrode-electrolyte interfacial layer of PEDOT:PSS for reversible faradic reactions. The biointerface showed high peak capacitive currents of ∼3 mA·cm-2 with total charge injection of ∼1 µC·cm-2 at responsivity of 30 mA·W-1, generating high photovoltages over 400 mV for the main eye photoreception colors of blue, green, and red. Moreover, modification of PEDOT:PSS controls the charging/discharging phases leading to rapid capacitive photoresponse of 50 µs and effective membrane depolarization at the single-cell level. The neural interface has a device lifetime of over 1.5 years in the aqueous environment and showed stability without significant performance decrease after sterilization steps. Our results demonstrate that adopting the pseudocapacitance phenomenon on organic photovoltaics paves an ultraefficient, safe, and robust way toward communicating with biological systems.


Subject(s)
Biocompatible Materials/chemistry , Bridged Bicyclo Compounds, Heterocyclic/chemistry , Neurons/physiology , Photic Stimulation , Polymers/chemistry , Polystyrenes/chemistry , Animals , Electrodes , Electrolytes , Gold/chemistry , Humans , Particle Size , Rats , Surface Properties , Tumor Cells, Cultured
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