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Article ; Online: An in silico investigation on the interactions of curcumin and epigallocatechin-3-gallate with NLRP3 Inflammasome complex.

Jena, Atala B / Dash, Umesh C / Duttaroy, Asim K

Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie

2022 Volume 156, Page(s) 113890

Abstract: Interleukin-1β (IL-1β) and IL-18 are the underlying factors of the inflammatory response and are necessary for the host's reaction and pathogen resistance. The NLRP3 inflammasome involves in the secretion of pro-inflammatory cytokines IL-1β/IL-18 in ... ...

Abstract	Interleukin-1β (IL-1β) and IL-18 are the underlying factors of the inflammatory response and are necessary for the host's reaction and pathogen resistance. The NLRP3 inflammasome involves in the secretion of pro-inflammatory cytokines IL-1β/IL-18 in response to microbial infection and cellular damage. Curcumin and epigallocatechin-3-gallate (EGCG) suppress the activation of the NLRP3 inflammasome; however, the exact mechanisms are not yet well known. In the current study, we investigated the interaction of curcumin and EGCG, the plant-derived compounds, with NLRP3 complex using in silico approach. The molecular docking and protein-protein interaction were used to investigate the apparent binding processes and affinities between components of the NLRP3 complex with curcumin and EGCG. Our data showed that NLRP3 had a higher binding affinity for curcumin and EGCG than other complex proteins, with - 8.2 Kcal/mol and - 9.6 Kcal/mol, respectively. Similarly, ASC had a lower binding affinity for curcumin and EGCG, with - 5.0 Kcal/mol and - 7.4 Kcal/mol, respectively. The higher binding affinity of both compounds for the key NLRP3 protein in their complexes as compared to that of MCC950 (a selective inhibitor of NLRP3 complex) suggests that curcumin and EGCG may impact the complex's function. Protein-protein interaction studies also corroborated the efficacy of these two polyphenols in hindering the formation of NLRP3 complex. The therapeutic effect of curcumin and EGCG may be due to the inhibition of inflammasome activation. The molecular and protein-protein interaction data indicated that the therapeutic effects of these two polyphenols are mediated by preventing the development of the NLRP3 complex. Proposed mechanisms to prevent the development of the NLRP3 complex by antioxidant curcumin and catechin.
MeSH term(s)	NLR Family, Pyrin Domain-Containing 3 Protein/metabolism ; Inflammasomes/metabolism ; Curcumin/pharmacology ; Catechin/pharmacology ; Interleukin-18 ; Molecular Docking Simulation ; Interleukin-1beta/metabolism ; Polyphenols
Chemical Substances	NLR Family, Pyrin Domain-Containing 3 Protein ; Inflammasomes ; Curcumin (IT942ZTH98) ; epigallocatechin gallate (BQM438CTEL) ; Catechin (8R1V1STN48) ; Interleukin-18 ; Interleukin-1beta ; Polyphenols
Language	English
Publishing date	2022-10-19
Publishing country	France
Document type	Journal Article
ZDB-ID	392415-4
ISSN	1950-6007 ; 0753-3322 ; 0300-0893
ISSN (online)	1950-6007
ISSN	0753-3322 ; 0300-0893
DOI	10.1016/j.biopha.2022.113890
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Article ; Online: Thermodynamics of benzoquinone-induced conformational changes in nucleic acids and human serum albumin.

Jena, Atala B / Samal, Rashmi R / Dandapat, Jagneshwar / Subudhi, Umakanta

Chemico-biological interactions

2022 Volume 369, Page(s) 110281

Abstract: ... describes the chemico-biological interaction between benzene metabolite para-benzoquinone (BQ) with B-form ... of nucleic acids (B-DNA) and human serum albumin (HSA). The binding ability of HSA towards bromocresol green (BCG ... of numerous endogenous and exogenous molecules. Similarly, BQ interacts directly to the GC region of B ...

Abstract	Biological macromolecules such as proteins, nucleic acids, carbohydrates and lipids, play a crucial role in biochemical and molecular processes. Thus, the study of the structure-function relationship of biomolecules in presence of ligands is an important aspect of structural biology. The current communication describes the chemico-biological interaction between benzene metabolite para-benzoquinone (BQ) with B-form of nucleic acids (B-DNA) and human serum albumin (HSA). The binding ability of HSA towards bromocresol green (BCG) was significantly suppressed when exposed to increasing concentrations of BQ in the presence of various physiological buffers. Further, the native fluorescence of HSA was drastically reduced and the secondary structures of HSA were significantly compromised with increasing concentrations of BQ. In vitro and in silico studies also revealed that BQ binds to domains I and II of HSA and thus altering the conformation of HSA which may potentially affect plasma osmotic pressure, as well as the binding and transport of numerous endogenous and exogenous molecules. Similarly, BQ interacts directly to the GC region of B-DNA particularly in the minor groove which was also assessed by computational docking studies. Isothermal titration calorimetry data suggest higher binding affinity of BQ towards DNA than HSA. Various spectroscopic observations also suggest that BQ binds to DNA preferably in the minor grooves. Thus, the results revealed that BQ may play a key role in inducing mutagenicity, either by formation of adducts on GC regions or by accelerating oxidative damage to biomacromolecules through chemico-biological interactions.
Language	English
Publishing date	2022-11-25
Publishing country	Ireland
Document type	Journal Article
ZDB-ID	218799-1
ISSN	1872-7786 ; 0009-2797
ISSN (online)	1872-7786
ISSN	0009-2797
DOI	10.1016/j.cbi.2022.110281
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Article ; Online: Author Correction: Catechin and curcumin interact with S protein of SARS-CoV2 and ACE2 of human cell membrane: insights from computational studies.

Jena, Atala B / Kanungo, Namrata / Nayak, Vinayak / Chainy, G B N / Dandapat, Jagneshwar

Scientific reports

2021 Volume 11, Issue 1, Page(s) 8482

Language	English
Publishing date	2021-04-13
Publishing country	England
Document type	Published Erratum
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-021-88218-3
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Article ; Online: Therapeutic Potential and Ethnopharmacology of Dominant Mangroves of Bhitarkanika National Park, Odisha, India.

Das, Sudipta K / Das, Bikash / Jena, Atala B / Pradhan, Chinmay / Sahoo, Gunanidhi / Dandapat, Jagneshwar

Chemistry & biodiversity

2022 Volume 19, Issue 3, Page(s) e202100857

Abstract: Bhitarkanika National Park is the second largest contiguous mangrove forest of India. Approximately 0.15 million mangrove depending population are found residing in and around 307 villages within the National Park. Despite being one of the most diverse ... ...

Abstract	Bhitarkanika National Park is the second largest contiguous mangrove forest of India. Approximately 0.15 million mangrove depending population are found residing in and around 307 villages within the National Park. Despite being one of the most diverse mangrove habitations of India, the ethnopharmacological practices are meager in comparison to the other mangrove regions of India and Southeast Asia. The present review is aimed to congregate information on the therapeutic potential and ethnopharmacology of nine dominant mangrove species of the National Park, such as Aegiceras corniculatum, Avicenia marina, Avicenia officinalis, Ceriops decandra, Excoecaria agallocha, Heritiera fomes, Lumnitzera racemosa, Rhizophora mucronata, and Sonneratia apetala. Our aim is to generate social awareness among the mangrove dwellers to promote uses of folklore medicine using these tremendously potential mangrove plants, as a complementary step to strengthen community health. Further, we also want to grab the attention of researchers working in related disciplines, for their holistic and extensive studies towards bio-prospectation of the dominant mangrove plants of Bhitarkanika National Park.
MeSH term(s)	Ethnopharmacology ; Euphorbiaceae ; India ; Parks, Recreational ; Phytotherapy ; Rhizophoraceae ; Wetlands
Language	English
Publishing date	2022-02-23
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2139001-0
ISSN	1612-1880 ; 1612-1872
ISSN (online)	1612-1880
ISSN	1612-1872
DOI	10.1002/cbdv.202100857
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Article ; Online: Author Correction

Atala B. Jena / Namrata Kanungo / Vinayak Nayak / G. B. N. Chainy / Jagneshwar Dandapat

Scientific Reports, Vol 11, Iss 1, Pp 1-

Catechin and curcumin interact with S protein of SARS-CoV2 and ACE2 of human cell membrane: insights from computational studies

2021 Volume 1

Abstract: An amendment to this paper has been published and can be accessed via a link at the top of the paper. ...

Abstract	An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Keywords	Medicine ; R ; Science ; Q
Language	English
Publishing date	2021-04-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Catechin and curcumin interact with S protein of SARS-CoV2 and ACE2 of human cell membrane

Atala B. Jena / Namrata Kanungo / Vinayak Nayak / G. B. N. Chainy / Jagneshwar Dandapat

Scientific Reports, Vol 11, Iss 1, Pp 1-

insights from computational studies

2021 Volume 14

Abstract: Abstract The recent outbreak of the coronavirus (SARS-CoV2) is an unprecedented threat to human health and society across the globe. In this context, development of suitable interventions is the need of the hour. The viral spike protein (S Protein) and ... ...

Abstract	Abstract The recent outbreak of the coronavirus (SARS-CoV2) is an unprecedented threat to human health and society across the globe. In this context, development of suitable interventions is the need of the hour. The viral spike protein (S Protein) and the cognate host cell receptor ACE2 can be considered as effective and appropriate targets for interventions. It is evident from the present computational study, that catechin and curcumin, not only exhibit strong binding affinity to viral S Protein and host receptor ACE2 but also to their complex (receptor-binding domain (RBD) of the spike protein of SARS-CoV2 and ACE2; RBD/ACE2-complex). The binding affinity values of catechin and curcumin for the S protein, ACE2 and RBD/ACE2-complex are − 10.5 and − 7.9 kcal/mol; − 8.9 and − 7.8 kcal/mol; and − 9.1 and − 7.6 kcal/mol, respectively. Curcumin directly binds to the receptor binding domain (RBD) of viral S Protein. Molecular simulation study over a period of 100 ns further substantiates that such interaction within RBD site of S Protein occurs during 40–100 ns out of 100 ns simulation trajectory. Contrary to this, catechin binds with amino acid residues present near the RBD site of S Protein and causes fluctuation in the amino acid residues of the RBD and its near proximity. Both catechin and curcumin bind the interface of ‘RBD/ACE2-complex’ and intervene in causing fluctuation of the alpha helices and beta-strands of the protein complex. Protein–protein interaction studies in presence of curcumin or catechin also corroborate the above findings suggesting the efficacy of these two polyphenols in hindering the formation of S Protein-ACE2 complex. In conclusion, this computational study for the first time predicts the possibility of above two polyphenols for therapeutic strategy against SARS-CoV2.
Keywords	Medicine ; R ; Science ; Q
Subject code	612
Language	English
Publishing date	2021-01-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Catechin and curcumin interact with S protein of SARS-CoV2 and ACE2 of human cell membrane: insights from computational studies.

Jena, Atala B / Kanungo, Namrata / Nayak, Vinayak / Chainy, G B N / Dandapat, Jagneshwar

Scientific reports

2021 Volume 11, Issue 1, Page(s) 2043

Abstract: The recent outbreak of the coronavirus (SARS-CoV2) is an unprecedented threat to human health and society across the globe. In this context, development of suitable interventions is the need of the hour. The viral spike protein (S Protein) and the ... ...

Abstract	The recent outbreak of the coronavirus (SARS-CoV2) is an unprecedented threat to human health and society across the globe. In this context, development of suitable interventions is the need of the hour. The viral spike protein (S Protein) and the cognate host cell receptor ACE2 can be considered as effective and appropriate targets for interventions. It is evident from the present computational study, that catechin and curcumin, not only exhibit strong binding affinity to viral S Protein and host receptor ACE2 but also to their complex (receptor-binding domain (RBD) of the spike protein of SARS-CoV2 and ACE2; RBD/ACE2-complex). The binding affinity values of catechin and curcumin for the S protein, ACE2 and RBD/ACE2-complex are - 10.5 and - 7.9 kcal/mol; - 8.9 and - 7.8 kcal/mol; and - 9.1 and - 7.6 kcal/mol, respectively. Curcumin directly binds to the receptor binding domain (RBD) of viral S Protein. Molecular simulation study over a period of 100 ns further substantiates that such interaction within RBD site of S Protein occurs during 40-100 ns out of 100 ns simulation trajectory. Contrary to this, catechin binds with amino acid residues present near the RBD site of S Protein and causes fluctuation in the amino acid residues of the RBD and its near proximity. Both catechin and curcumin bind the interface of 'RBD/ACE2-complex' and intervene in causing fluctuation of the alpha helices and beta-strands of the protein complex. Protein-protein interaction studies in presence of curcumin or catechin also corroborate the above findings suggesting the efficacy of these two polyphenols in hindering the formation of S Protein-ACE2 complex. In conclusion, this computational study for the first time predicts the possibility of above two polyphenols for therapeutic strategy against SARS-CoV2.
MeSH term(s)	Amino Acid Sequence ; Angiotensin-Converting Enzyme 2/chemistry ; Angiotensin-Converting Enzyme 2/metabolism ; Binding Sites ; COVID-19/drug therapy ; COVID-19/metabolism ; COVID-19/virology ; Catechin/chemistry ; Catechin/metabolism ; Catechin/pharmacology ; Cell Membrane/metabolism ; Computational Biology/methods ; Curcumin/chemistry ; Curcumin/metabolism ; Curcumin/pharmacology ; Humans ; Molecular Docking Simulation ; Protein Binding ; Protein Domains ; SARS-CoV-2/drug effects ; SARS-CoV-2/metabolism ; Spike Glycoprotein, Coronavirus/chemistry ; Spike Glycoprotein, Coronavirus/metabolism
Chemical Substances	Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2 ; Catechin (8R1V1STN48) ; ACE2 protein, human (EC 3.4.17.23) ; Angiotensin-Converting Enzyme 2 (EC 3.4.17.23) ; Curcumin (IT942ZTH98)
Language	English
Publishing date	2021-01-21
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-021-81462-7
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Article ; Online: Cyclic peptides nanospheres: A '2-in-1' self-assembled delivery system for targeting nucleus and cytoplasm.

Panigrahi, Bijayananda / Singh, Rohit Kumar / Suryakant, Uday / Mishra, Sourav / Potnis, Akhilesh A / Jena, Atala B / Kerry, Rout George / Rajaram, Hema / Ghosh, Sunil K / Mandal, Dindyal

European journal of pharmaceutical sciences : official journal of the European Federation for Pharmaceutical Sciences

2022 Volume 171, Page(s) 106125

Abstract: Vascular endothelial growth factor (VEGF) is considered as one of the vital growth factors for angiogenesis, which is primarily responsible for the progress and maintenance of new vascular network in tumor. Numerous studies report that inhibition of VEGF- ...

Abstract	Vascular endothelial growth factor (VEGF) is considered as one of the vital growth factors for angiogenesis, which is primarily responsible for the progress and maintenance of new vascular network in tumor. Numerous studies report that inhibition of VEGF-induced angiogenesis is a potent technique for cancer suppression. Recently, RNA interference, especially small interfering RNA (siRNA) signified a promising approach to suppress the gene expression. However, the clinical implementation of biological macromolecules such as siRNA is significantly limited because of stability and bioavailability issues. Herein, self-assembled peptide nanospheres have been generated from L,L-cyclic peptides using hydrophobic (Trp), positively charged (Arg) and cysteine (Cys) amino acid residues and demonstrated as vehicles for intracellular delivery of VEGF siRNA and VEGF antisense oligonucleotide. Formation of peptide nanostructures is confirmed by HR-TEM, AFM, SEM and DLS analysis. Possible mechanism of self-assembly of the cyclic peptides and their binding with macromolecules are demonstrated by in-silico analysis. Gel electrophoresis reveals that the newly generated peptide based organic materials exhibit strong binding affinity toward siRNAs / antisense oligonucleotides (ASOs) at optimum concentration. Flow cytometry and confocal microscopy results confirm the efficiency of the new biomaterials toward the intracellular delivery of fluorescent labeled siRNA / ASOs. Furthermore, VEGF expression evaluated by western blot and RT-PCR upon the delivery of functional VEGF siRNA/ASOs suggests that very low concentrations of VEGF siRNA/ASOs cause significant gene knockdown at protein and mRNA levels, respectively.
MeSH term(s)	Cell Line, Tumor ; Cytoplasm/metabolism ; Nanospheres ; Peptides, Cyclic ; RNA, Small Interfering/genetics ; Vascular Endothelial Growth Factor A/metabolism
Chemical Substances	Peptides, Cyclic ; RNA, Small Interfering ; Vascular Endothelial Growth Factor A
Language	English
Publishing date	2022-01-14
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	1154366-8
ISSN	1879-0720 ; 0928-0987
ISSN (online)	1879-0720
ISSN	0928-0987
DOI	10.1016/j.ejps.2022.106125
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Article ; Online: The benzene metabolite p-benzoquinone inhibits the catalytic activity of bovine liver catalase: A biophysical study.

Jena, Atala B / Samal, Rashmi R / Kumari, Kanchan / Pradhan, Jyotsnarani / Chainy, Gagan B N / Subudhi, Umakanta / Pal, Satyanarayan / Dandapat, Jagnehswar

International journal of biological macromolecules

2020 Volume 167, Page(s) 871–880

Abstract: The current communication reports the inhibitory effect of para-benzoquinone (p-BQ) on the structure and function of bovine liver catalase (BLC), a vital antioxidant enzyme. Both BLC and p-BQ were dissolved in respective buffers and the biophysical ... ...

Abstract	The current communication reports the inhibitory effect of para-benzoquinone (p-BQ) on the structure and function of bovine liver catalase (BLC), a vital antioxidant enzyme. Both BLC and p-BQ were dissolved in respective buffers and the biophysical interaction was studied at physiological concentrations. For the first time our data reveals an enthalpy-driven interaction between BLC and p-BQ which is due to hydrogen bonding and van der Waals interactions. The binding affinity of p-BQ with BLC is nearly 2.5 folds stronger in MOPS buffer than Phosphate buffer. Importantly, the binding affinity between BLC and p-BQ was weak in HEPES buffer as compared to other buffers being the strongest in Tris buffer. Molecular docking studies reveal that binding affinity of p-BQ with BLC differ depending upon the nature of buffers rather than on the participating amino acid residues of BLC. This is further supported by the differential changes in secondary structures of BLC. The p-BQ-induced conformational change in BLC was evident from the reduced BLC activity in presence of different buffers in the following order, Phosphate>MOPS>Tris>HEPES. The absorbance peak of BLC was gradually increased and fluorescence spectra of BLC were drastically decreased when BLC to p-BQ molar ratio was incrementally enhanced from 0 to 10,000 times in presence of all buffers. Nevertheless, the declined activity of BLC was positively correlated with the reduced fluorescence and negatively correlated with the enhanced absorbance. Electrochemical study with cyclic voltammeter also suggests a direct binding of p-BQ with BLC in presence of different buffers. Thus, p-BQ-mediated altered secondary structure in BLC results into compromised activity of BLC.
MeSH term(s)	Animals ; Benzene Derivatives/chemistry ; Benzene Derivatives/pharmacology ; Benzoquinones/chemistry ; Benzoquinones/pharmacology ; Catalase/chemistry ; Catalase/metabolism ; Catalysis/drug effects ; Cattle ; Chemical Phenomena ; Enzyme Activation ; Kinetics ; Liver/enzymology ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Molecular Structure ; Protein Binding ; Spectrum Analysis ; Structure-Activity Relationship ; Thermodynamics
Chemical Substances	Benzene Derivatives ; Benzoquinones ; Catalase (EC 1.11.1.6)
Language	English
Publishing date	2020-11-10
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	282732-3
ISSN	1879-0003 ; 0141-8130
ISSN (online)	1879-0003
ISSN	0141-8130
DOI	10.1016/j.ijbiomac.2020.11.044
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Article ; Online: Near infrared-responsive quinacrine-gold hybrid nanoparticles deregulate HSP-70/P300-mediated H3K14 acetylation in ER/PR+ breast cancer stem cells.

Dash, Somya Ranjan / Das, Chinmay / Das, Biswajit / Jena, Atala Bihari / Paul, Subarno / Sinha, Saptarshi / Tripathy, Jasaswini / Kundu, Chanakya Nath

Nanomedicine (London, England)

2024 Volume 19, Issue 7, Page(s) 581–596

Abstract: Aim: ...

Abstract	Aim:
MeSH term(s)	Animals ; Mice ; Acetylation ; Gold ; Histone Acetyltransferases ; Nanoparticles ; Neoplasms ; Neoplastic Stem Cells ; Quinacrine/pharmacology ; Transforming Growth Factor beta ; Humans ; Female
Chemical Substances	Gold (7440-57-5) ; Histone Acetyltransferases (EC 2.3.1.48) ; Quinacrine (H0C805XYDE) ; Transforming Growth Factor beta
Language	English
Publishing date	2024-01-31
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2277839-1
ISSN	1748-6963 ; 1743-5889
ISSN (online)	1748-6963
ISSN	1743-5889
DOI	10.2217/nnm-2023-0269
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