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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: 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
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: In Silico Approaches in Predictive Genetic Toxicology.

Sinha, Meetali / Dhawan, Alok / Parthasarathi, Ramakrishnan

Methods in molecular biology (Clifton, N.J.)

2019 Volume 2031, Page(s) 351–373

Abstract: Genetic toxicology testing is a weight-of-evidence approach to identify and characterize chemical substances that can cause genetic modifications in somatic and/or germ cells. Prediction of genetic toxicology using computational tools is gaining more ... ...

Abstract	Genetic toxicology testing is a weight-of-evidence approach to identify and characterize chemical substances that can cause genetic modifications in somatic and/or germ cells. Prediction of genetic toxicology using computational tools is gaining more attention and preferred by regulatory authorities as an alternate safety assessment for in vivo or in vitro approaches. Due to the cost and time associated with experimental genetic toxicity tests, it is essential to develop more robust in silico methods to predict chemical genetic toxicity. A number of in silico genotoxicity predictive tools/models are developed based on the experimental data gathered over the years. These in silico tools are divided into statistical quantitative structure-activity relationships (QSAR)-based approaches and expert-based systems. This chapter covers the state of the art in silico toxicology approaches and standardized protocols, essential for conducting genetic toxicity predictions of chemicals. This chapter also highlights various parameters for the validation of the prediction results obtained from QSAR models.
MeSH term(s)	Animals ; Computer Simulation ; Humans ; Models, Biological ; Mutagenicity Tests/methods ; Mutagens/chemistry ; Mutagens/toxicity ; Quantitative Structure-Activity Relationship ; Software
Chemical Substances	Mutagens
Language	English
Publishing date	2019-08-31
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-4939-9646-9_20
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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: Differential interactions of α-synuclein conformers affect refolding and activity of proteins.

Bagree, Gayatri / Srivastava, Tulika / Mahasivam, Sanje / Sinha, Meetali / Bansal, Vipul / Ramanathan, Rajesh / Priya, Smriti / Sharma, Sandeep K

Journal of biochemistry

2022 Volume 173, Issue 2, Page(s) 107–114

Abstract: The accumulation of protein aggregates as intracellular inclusions interferes with cellular protein homeostasis leading to protein aggregation diseases. Protein aggregation results in the formation of several protein conformers including oligomers and ... ...

Abstract	The accumulation of protein aggregates as intracellular inclusions interferes with cellular protein homeostasis leading to protein aggregation diseases. Protein aggregation results in the formation of several protein conformers including oligomers and fibrils, where each conformer has its own structural characteristic and proteotoxic potential. The present study explores the effect of alpha-synuclein (α-syn) conformers on the activity and spontaneous refolding of firefly luciferase. Of the different conformers, α-syn monomers delayed the inactivation of luciferase under thermal stress conditions and enhanced the spontaneous refolding of luciferase. In contrast, the α-syn oligomers and fibrils adversely affected luciferase activity and refolding, where the oligomers inhibited spontaneous refolding, whereas a pronounced effect on the inactivation of native luciferase was observed in the case of fibrils. These results indicate that the oligomers and fibrils of α-syn interfere with the refolding of luciferase and promote its misfolding and aggregation. The study reveals the differential propensities of various conformers of a pathologically relevant protein in causing inactivation, structural modifications and misfolding of other proteins, consequently resulting in altered protein homeostasis.
MeSH term(s)	Humans ; alpha-Synuclein/chemistry ; alpha-Synuclein/metabolism ; Parkinson Disease/metabolism ; Protein Aggregates ; Protein Folding ; Fireflies ; Luciferases/chemistry ; Luciferases/metabolism
Chemical Substances	alpha-Synuclein ; Protein Aggregates ; SNCA protein, human ; Luciferases (EC 1.13.12.-)
Language	English
Publishing date	2022-11-11
Publishing country	England
Document type	Journal Article
ZDB-ID	218073-x
ISSN	1756-2651 ; 0021-924X
ISSN (online)	1756-2651
ISSN	0021-924X
DOI	10.1093/jb/mvac095
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Article ; Online: A natural small molecule-mediated inhibition of alpha-synuclein aggregation leads to neuroprotection in Caenorhabditis elegans.

Srivastava, Tulika / Tyagi, Divya / Fatima, Siraj / Sathyan, Malur Thirumalesh Vishnu / Raj, Ritu / Sharma, Aniket / Chaturvedi, Minal / Sinha, Meetali / Shishodia, Sonia Kumari / Kumar, Dinesh / Sharma, Sandeep K / Shankar, Jata / Satish, Aruna / Priya, Smriti

Journal of neurochemistry

2023

Abstract: Small molecules are being explored intensively for their applications as therapeutic molecules in the management of metabolic and neurological disorders. The natural small molecules can inhibit protein aggregation and underlying cellular pathogenesis of ... ...

Abstract	Small molecules are being explored intensively for their applications as therapeutic molecules in the management of metabolic and neurological disorders. The natural small molecules can inhibit protein aggregation and underlying cellular pathogenesis of neurodegenerative diseases involving multi-factorial mechanisms of action. Certain natural small molecular inhibitors of pathogenic protein aggregation are highly efficient and have shown promising therapeutic potential. In the present study, Shikonin (SHK), a natural plant-based naphthoquinone has been investigated for its aggregation inhibition activity against α-synuclein (α-syn) and the neuroprotective potential in Caenorhabditis elegans (C. elegans). SHK significantly inhibited aggregation of α-syn at sub-stochiometric concentrations, delayed the linear lag phase and growth kinetics of seeded and unseeded α-syn aggregation. The binding of SHK to the C-terminus of α-syn maintained α-helical and disordered secondary structures with reduced beta-sheet content and complexity of aggregates. Further, in C. elegans transgenic PD models, SHK significantly reduced α-syn aggregation, improved locomotor activity and prevented dopaminergic (DA) neuronal degeneration, indicating the neuroprotective role of SHK. The present study highlights the potential of natural small molecules in the prevention of protein aggregation that may further be explored for their therapeutic efficacy in the management of protein aggregation and neurodegenerative diseases.
Language	English
Publishing date	2023-07-10
Publishing country	England
Document type	Journal Article
ZDB-ID	80158-6
ISSN	1471-4159 ; 0022-3042 ; 1474-1644
ISSN (online)	1471-4159
ISSN	0022-3042 ; 1474-1644
DOI	10.1111/jnc.15907
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Article ; Online: Study of Caspase 8 Inhibition for the Management of Alzheimer’s Disease

Syed Sayeed Ahmad / Meetali Sinha / Khurshid Ahmad / Mohammad Khalid / Inho Choi

Molecules, Vol 25, Iss 2071, p

A Molecular Docking and Dynamics Simulation

2020 Volume 2071

Abstract: Alzheimer's disease (AD) is the most common type of dementia and usually manifests as diminished episodic memory and cognitive functions. Caspases are crucial mediators of neuronal death in a number of neurodegenerative diseases, and caspase 8 is ... ...

Abstract	Alzheimer's disease (AD) is the most common type of dementia and usually manifests as diminished episodic memory and cognitive functions. Caspases are crucial mediators of neuronal death in a number of neurodegenerative diseases, and caspase 8 is considered a major therapeutic target in the context of AD. In the present study, we performed a virtual screening of 200 natural compounds by molecular docking with respect to their abilities to bind with caspase 8. Among them, rutaecarpine was found to have the highest (negative) binding energy (−6.5 kcal/mol) and was further subjected to molecular dynamics (MD) simulation analysis. Caspase 8 was determined to interact with rutaecarpine through five amino acid residues, specifically Thr337, Lys353, Val354, Phe355, and Phe356, and two hydrogen bonds (ligand: H35-A: LYS353:O and A:PHE355: N-ligand: N5). Furthermore, a 50 ns MD simulation was conducted to optimize the interaction, to predict complex flexibility, and to investigate the stability of the caspase 8–rutaecarpine complex, which appeared to be quite stable. The obtained results propose that rutaecarpine could be a lead compound that bears remarkable anti-Alzheimer's potential against caspase 8.
Keywords	Alzheimer’s disease ; caspase 8 ; molecular dynamics ; RMSD ; RMSF ; Organic chemistry ; QD241-441
Subject code	540
Language	English
Publishing date	2020-04-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Study of Caspase 8 Inhibition for the Management of Alzheimer's Disease: A Molecular Docking and Dynamics Simulation.

Ahmad, Syed Sayeed / Sinha, Meetali / Ahmad, Khurshid / Khalid, Mohammad / Choi, Inho

Molecules (Basel, Switzerland)

2020 Volume 25, Issue 9

Abstract	Alzheimer's disease (AD) is the most common type of dementia and usually manifests as diminished episodic memory and cognitive functions. Caspases are crucial mediators of neuronal death in a number of neurodegenerative diseases, and caspase 8 is considered a major therapeutic target in the context of AD. In the present study, we performed a virtual screening of 200 natural compounds by molecular docking with respect to their abilities to bind with caspase 8. Among them, rutaecarpine was found to have the highest (negative) binding energy (-6.5 kcal/mol) and was further subjected to molecular dynamics (MD) simulation analysis. Caspase 8 was determined to interact with rutaecarpine through five amino acid residues, specifically Thr337, Lys353, Val354, Phe355, and Phe356, and two hydrogen bonds (ligand: H35-A: LYS353:O and A:PHE355: N-ligand: N5). Furthermore, a 50 ns MD simulation was conducted to optimize the interaction, to predict complex flexibility, and to investigate the stability of the caspase 8-rutaecarpine complex, which appeared to be quite stable. The obtained results propose that rutaecarpine could be a lead compound that bears remarkable anti-Alzheimer's potential against caspase 8.
MeSH term(s)	Alzheimer Disease/drug therapy ; Alzheimer Disease/etiology ; Alzheimer Disease/metabolism ; Binding Sites ; Caspase 8/chemistry ; Caspase Inhibitors/chemistry ; Caspase Inhibitors/pharmacology ; Chemical Phenomena ; Humans ; Hydrogen Bonding ; Ligands ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Protein Binding ; Quantitative Structure-Activity Relationship
Chemical Substances	Caspase Inhibitors ; Ligands ; Caspase 8 (EC 3.4.22.-)
Language	English
Publishing date	2020-04-29
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	1413402-0
ISSN	1420-3049 ; 1431-5165 ; 1420-3049
ISSN (online)	1420-3049
ISSN	1431-5165 ; 1420-3049
DOI	10.3390/molecules25092071
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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
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