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Article ; Online: Computational Risk Assessment of Persistence, Bioaccumulation, and Toxicity of Novel Flame-Retardant Chemicals.

Singh, Prakrity / Pandit, Shraddha / Sinha, Meetali / Yadav, Dhvani / Parthasarathi, Ramakrishnan

The journal of physical chemistry. A

2023 Volume 127, Issue 51, Page(s) 10747–10757

Abstract: Novel brominated flame retardants (NBFRs) have emerged as chemicals of environmental concern, as they have been widely used as an alternative to polybrominated diphenyl ethers (PBDEs). Considering the similar structural features of NBFRs and PBDEs ... ...

Abstract	Novel brominated flame retardants (NBFRs) have emerged as chemicals of environmental concern, as they have been widely used as an alternative to polybrominated diphenyl ethers (PBDEs). Considering the similar structural features of NBFRs and PBDEs necessitates a comprehensive investigation to understand the physicochemical relationships of these compounds and their ability to alter biological functions. In this study, we investigated the persistent nature of NBFRs in terms of thyroid-disrupting potential by understanding the structure-stability aspects using density functional theory (DFT)-based reactivity parameters and interactions via molecular docking and molecular dynamics (MD) simulations. The results indicate that the DFT-based stability descriptor (chemical hardness) is associated with the persistent nature of NBFRs. The computed molecular interaction profile revealed prominent interactions between thyroid receptor-β (TR-β) and NBFRs. Stable trajectory and interactions with TR-β were obtained with ATE,
MeSH term(s)	Environmental Monitoring/methods ; Flame Retardants/analysis ; Halogenated Diphenyl Ethers/analysis ; Halogenated Diphenyl Ethers/chemistry ; Bioaccumulation ; Molecular Docking Simulation
Chemical Substances	Flame Retardants ; Halogenated Diphenyl Ethers
Language	English
Publishing date	2023-12-18
Publishing country	United States
Document type	Journal Article
ISSN	1520-5215
ISSN (online)	1520-5215
DOI	10.1021/acs.jpca.3c04160
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Inheritance and maintenance of small RNA-mediated epigenetic effects.

Quarato, Piergiuseppe / Singh, Meetali / Bourdon, Loan / Cecere, Germano

BioEssays : news and reviews in molecular, cellular and developmental biology

2022 Volume 44, Issue 6, Page(s) e2100284

Abstract: Heritable traits are predominantly encoded within genomic DNA, but it is now appreciated that epigenetic information is also inherited through DNA methylation, histone modifications, and small RNAs. Several examples of transgenerational epigenetic ... ...

Abstract	Heritable traits are predominantly encoded within genomic DNA, but it is now appreciated that epigenetic information is also inherited through DNA methylation, histone modifications, and small RNAs. Several examples of transgenerational epigenetic inheritance of traits have been documented in plants and animals. These include even the inheritance of traits acquired through the soma during the life of an organism, implicating the transfer of epigenetic information via the germline to the next generation. Small RNAs appear to play a significant role in carrying epigenetic information across generations. This review focuses on how epigenetic information in the form of small RNAs is transmitted from the germline to the embryos through the gametes. We also consider how inherited epigenetic information is maintained across generations in a small RNA-dependent and independent manner. Finally, we discuss how epigenetic traits acquired from the soma can be inherited through small RNAs.
MeSH term(s)	Animals ; DNA Methylation/genetics ; Epigenesis, Genetic ; Germ Cells ; Heredity ; Inheritance Patterns/genetics ; RNA/genetics ; RNA/metabolism
Chemical Substances	RNA (63231-63-0)
Language	English
Publishing date	2022-03-25
Publishing country	United States
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ZDB-ID	50140-2
ISSN	1521-1878 ; 0265-9247
ISSN (online)	1521-1878
ISSN	0265-9247
DOI	10.1002/bies.202100284
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Article: Inheritance and maintenance of small RNA‐mediated epigenetic effects

Quarato, Piergiuseppe / Singh, Meetali / Bourdon, Loan / Cecere, Germano

BioEssays. 2022 June, v. 44, no. 6

2022

Abstract	Heritable traits are predominantly encoded within genomic DNA, but it is now appreciated that epigenetic information is also inherited through DNA methylation, histone modifications, and small RNAs. Several examples of transgenerational epigenetic inheritance of traits have been documented in plants and animals. These include even the inheritance of traits acquired through the soma during the life of an organism, implicating the transfer of epigenetic information via the germline to the next generation. Small RNAs appear to play a significant role in carrying epigenetic information across generations. This review focuses on how epigenetic information in the form of small RNAs is transmitted from the germline to the embryos through the gametes. We also consider how inherited epigenetic information is maintained across generations in a small RNA‐dependent and independent manner. Finally, we discuss how epigenetic traits acquired from the soma can be inherited through small RNAs.
Keywords	DNA ; DNA methylation ; epigenetics ; germ cells ; histones
Language	English
Dates of publication	2022-06
Publishing place	John Wiley & Sons, Ltd
Document type	Article
Note	JOURNAL ARTICLE
ZDB-ID	50140-2
ISSN	1521-1878 ; 0265-9247
ISSN (online)	1521-1878
ISSN	0265-9247
DOI	10.1002/bies.202100284
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Article ; Online: Integrated QSAR and Adverse Outcome Pathway Analysis of Chemicals Released on 3D Printing Using Acrylonitrile Butadiene Styrene.

Pandit, Shraddha / Singh, Prakrity / Sinha, Meetali / Parthasarathi, Ramakrishnan

Chemical research in toxicology

2021 Volume 34, Issue 2, Page(s) 355–364

Abstract: Additive manufacturing commonly known as 3D printing has numerous applications in several domains including material and biomedical technologies and has emerged as a tool of capabilities by providing fast, highly customized, and cost-effective solutions. ...

Abstract	Additive manufacturing commonly known as 3D printing has numerous applications in several domains including material and biomedical technologies and has emerged as a tool of capabilities by providing fast, highly customized, and cost-effective solutions. However, the impact of the printing materials and chemicals present in the printing fumes has raised concerns about their adverse potential affecting humans and the environment. Thus, it is necessary to understand the properties of the chemicals emitted during additive manufacturing for developing safe and biocompatible fibers having controlled emission of fumes including its sustainable usage. Therefore, in this study, we have developed a computational predictive risk-assessment framework on the comprehensive list of chemicals released during 3D printing using the acrylonitrile butadiene styrene (ABS) filament. Our results showed that the chemicals present in the fumes of the ABS-based fiber used in additive manufacturing have the potential to lead to various toxicity end points such as inhalation toxicity, oral toxicity, carcinogenicity, hepatotoxicity, and teratogenicity. Moreover, because of their absorption, distribution in the body, metabolism, and excretion properties, most of the chemicals exhibited a high absorption level in the intestine and the potential to cross the blood-brain barrier. Furthermore, pathway analysis revealed that signaling like alpha-adrenergic receptor signaling, heterotrimeric G-protein signaling, and Alzheimer's disease-amyloid secretase pathway are significantly overrepresented given the identified target proteins of these chemicals. These findings signify the adversities associated with 3D printing fumes and the necessity for the development of biodegradable and considerably safer fibers for 3D printing technology.
MeSH term(s)	Acrylonitrile/adverse effects ; Butadienes/adverse effects ; Humans ; Inhalation Exposure/adverse effects ; Molecular Structure ; Printing, Three-Dimensional ; Quantitative Structure-Activity Relationship ; Styrene/adverse effects
Chemical Substances	Butadienes ; Styrene (44LJ2U959V) ; Acrylonitrile (MP1U0D42PE)
Language	English
Publishing date	2021-01-08
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	639353-6
ISSN	1520-5010 ; 0893-228X
ISSN (online)	1520-5010
ISSN	0893-228X
DOI	10.1021/acs.chemrestox.0c00274
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Article: ToxDP2 Database: Toxicity prediction of dietary polyphenols

Sinha, Meetali / Sachan, Deepak Kumar / Bhattacharya, Roshni / Singh, Prakrity / Parthasarathi, Ramakrishnan

Food chemistry. 2022 Feb. 15, v. 370

2022

Abstract: Polyphenols are bioactive substances that minimize the risk of a variety of chronic diseases. Exposure to polyphenol bioactive compounds in our diet has increased across the globe, with amplified expectations from consumers, industry, and regulators ... ...

Abstract	Polyphenols are bioactive substances that minimize the risk of a variety of chronic diseases. Exposure to polyphenol bioactive compounds in our diet has increased across the globe, with amplified expectations from consumers, industry, and regulators centered on the potential benefits and essential safety of these compounds. Several data resources for beneficial properties of dietary polyphenols are present; however, toxicological information remains partial. We present a dynamic web-based database to assess dietary polyphenols' safety and fulfill the toxicity data gaps in the domain of food safety. The database (ToxDP2) comprises 415 dietary polyphenolic compounds, distributed into 15 subclasses with 25,792 collected and predicted data points. This web server facilitates the exploration of polyphenols for divergent applications. The data-driven approach on the ToxDP2 provides researchers with an understanding of polyphenols structure–function-toxicity relationships beneficial for developing nutraceuticals, pharmaceuticals, herbal supplements, and formulations.
Keywords	Internet ; databases ; dietary supplements ; food chemistry ; food safety ; industry ; polyphenols ; prediction ; risk ; toxicity ; toxicology
Language	English
Dates of publication	2022-0215
Publishing place	Elsevier Ltd
Document type	Article
ZDB-ID	243123-3
ISSN	1873-7072 ; 0308-8146
ISSN (online)	1873-7072
ISSN	0308-8146
DOI	10.1016/j.foodchem.2021.131350
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Article ; Online: ToxDP2 Database: Toxicity prediction of dietary polyphenols.

Sinha, Meetali / Sachan, Deepak Kumar / Bhattacharya, Roshni / Singh, Prakrity / Parthasarathi, Ramakrishnan

Food chemistry

2021 Volume 370, Page(s) 131350

Abstract	Polyphenols are bioactive substances that minimize the risk of a variety of chronic diseases. Exposure to polyphenol bioactive compounds in our diet has increased across the globe, with amplified expectations from consumers, industry, and regulators centered on the potential benefits and essential safety of these compounds. Several data resources for beneficial properties of dietary polyphenols are present; however, toxicological information remains partial. We present a dynamic web-based database to assess dietary polyphenols' safety and fulfill the toxicity data gaps in the domain of food safety. The database (ToxDP2) comprises 415 dietary polyphenolic compounds, distributed into 15 subclasses with 25,792 collected and predicted data points. This web server facilitates the exploration of polyphenols for divergent applications. The data-driven approach on the ToxDP2 provides researchers with an understanding of polyphenols structure-function-toxicity relationships beneficial for developing nutraceuticals, pharmaceuticals, herbal supplements, and formulations.
MeSH term(s)	Diet ; Dietary Supplements ; Polyphenols/analysis
Chemical Substances	Polyphenols
Language	English
Publishing date	2021-10-07
Publishing country	England
Document type	Journal Article
ZDB-ID	243123-3
ISSN	1873-7072 ; 0308-8146
ISSN (online)	1873-7072
ISSN	0308-8146
DOI	10.1016/j.foodchem.2021.131350
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Article ; Online: Germline inherited small RNAs facilitate the clearance of untranslated maternal mRNAs in C. elegans embryos

Piergiuseppe Quarato / Meetali Singh / Eric Cornes / Blaise Li / Loan Bourdon / Florian Mueller / Celine Didier / Germano Cecere

Nature Communications, Vol 12, Iss 1, Pp 1-

2021 Volume 14

Abstract: In animal embryos, maternally deposited mRNAs are degraded by several different mechanisms. Here the authors show that C. elegans embryos inherit antisense pool of small RNAs which are loaded into CSR-1 and cleave complementary maternal mRNAs. ...

Abstract	In animal embryos, maternally deposited mRNAs are degraded by several different mechanisms. Here the authors show that C. elegans embryos inherit antisense pool of small RNAs which are loaded into CSR-1 and cleave complementary maternal mRNAs.
Keywords	Science ; Q
Language	English
Publishing date	2021-03-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Translation and codon usage regulate Argonaute slicer activity to trigger small RNA biogenesis

Meetali Singh / Eric Cornes / Blaise Li / Piergiuseppe Quarato / Loan Bourdon / Florent Dingli / Damarys Loew / Simone Proccacia / Germano Cecere

Nature Communications, Vol 12, Iss 1, Pp 1-

2021 Volume 18

Abstract: 22G-RNAs are single-stranded antisense small RNAs that are expressed in C. elegans germline. Here the authors show that CSR-1 dependent 22G-RNAs are produced in the cytosol on mRNAs actively engaged in translation and that codon usage of an mRNA ... ...

Abstract	22G-RNAs are single-stranded antisense small RNAs that are expressed in C. elegans germline. Here the authors show that CSR-1 dependent 22G-RNAs are produced in the cytosol on mRNAs actively engaged in translation and that codon usage of an mRNA regulates the biogenesis of CSR-1 dependent 22G-RNAs.
Keywords	Science ; Q
Language	English
Publishing date	2021-06-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: The dual role of phytochemicals on SARS-CoV-2 inhibition by targeting host and viral proteins.

Singh, Prakrity / Chauhan, Shweta Singh / Pandit, Shraddha / Sinha, Meetali / Gupta, Shristee / Gupta, Anshika / Parthasarathi, Ramakrishnan

Journal of traditional and complementary medicine

2021 Volume 12, Issue 1, Page(s) 90–99

Abstract: Background: The severe acute respiratory syndrome-2019 has affected more than 190 million people around the world and caused severe crises throughout the globe. Due to rapid mutation in the viral genome, its became important to simultaneously improvise ... ...

Abstract	Background: The severe acute respiratory syndrome-2019 has affected more than 190 million people around the world and caused severe crises throughout the globe. Due to rapid mutation in the viral genome, its became important to simultaneously improvise the host immunity while targeting viral proteins to reduce the severity of infection. Aim: The current computational work focuses on multi-level rigorous screening of 47 medicinal plant-based phytochemicals for discovering effective phytochemical inhibitors against the host and viral targets. Experimental procedure: A total of 586 phytochemicals were analyzed in detail based on their drug-likeness, pharmacological properties, and structure-based activity against the viral proteins (Spike glycoprotein, Papain-like protease, and Main protease) and host proteins (ACE2, Importin-subunit α-5, and β-1). Phytochemicals showing higher binding affinity with the dual capacity to target both the categories of proteins were further analyzed by profiling of their chemical reactivity using Density-Functional Theory (DFT) based quantum chemical methods. Finally, detailed molecular dynamics simulations were performed to analyze the interactions of the complexes. Results and conclusion: The results revealed that the selected phytochemicals from
Language	English
Publishing date	2021-09-08
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2709698-1
ISSN	2225-4110
ISSN	2225-4110
DOI	10.1016/j.jtcme.2021.09.001
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Analogue discovery of safer alternatives to HCQ and CQ drugs for SAR-CoV-2 by computational design.

Sinha, Meetali / Gupta, Anshika / Gupta, Shristee / Singh, Prakrity / Pandit, Shraddha / Chauhan, Shweta Singh / Parthasarathi, Ramakrishnan

Computers in biology and medicine

2021 Volume 130, Page(s) 104222

Abstract: COVID-19 outbreak poses a severe health emergency to the global community. Due to availability of limited data, the selection of an effective treatment is a challenge. Hydroxychloroquine (HCQ), a chloroquine (CQ) derivative administered for malaria and ... ...

Abstract	COVID-19 outbreak poses a severe health emergency to the global community. Due to availability of limited data, the selection of an effective treatment is a challenge. Hydroxychloroquine (HCQ), a chloroquine (CQ) derivative administered for malaria and autoimmune diseases, has been shown to be effective against both Severe Acute Respiratory Syndrome (SARS-CoV-1) and SARS-CoV-2. Apart from the known adverse effects of these drugs, recently the use of CQ and HCQ as a potential treatment for COVID-19 is under flux globally. In this study, we focused on identifying a more potent analogue of HCQ and CQ against the spike protein of SAR-CoV-2 that can act as an effective antiviral agent for COVID-19 treatment. Systematic pharmacokinetics, drug-likeness, basicity predictions, virtual screening and molecular dynamics analysis (200 ns) were carried out to predict the inhibition potential of the analogous compounds on the spike protein. This work identifies the six potential analogues, out of which two compounds, namely 1-[1-(6-Chloroquinolin-4-yl) piperidin-4-yl]piperidin-3-ol and (1R,2R)-2-N-(7-Chloroquinolin-4-yl)cyclohexane-1,2-diamine interact with the active site of the spike protein similar to HCQ and CQ respectively with augmented safety profile.
MeSH term(s)	Drug Discovery ; Humans ; Hydroxychloroquine/analogs & derivatives ; Hydroxychloroquine/chemistry ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; SARS-CoV-2/chemistry ; Spike Glycoprotein, Coronavirus/antagonists & inhibitors ; Spike Glycoprotein, Coronavirus/chemistry ; COVID-19 Drug Treatment
Chemical Substances	Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2 ; Hydroxychloroquine (4QWG6N8QKH)
Language	English
Publishing date	2021-01-20
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	127557-4
ISSN	1879-0534 ; 0010-4825
ISSN (online)	1879-0534
ISSN	0010-4825
DOI	10.1016/j.compbiomed.2021.104222
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