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Article ; Online: Effects of theaflavin-gallate

Maiti, Smarajit / Banerjee, Amrita / Kanwar, Mehak

Phytomedicine Plus : International journal of phytotherapy and phytopharmacology

2022 Volume 2, Issue 2, Page(s) 100237

Abstract: ... ...

Abstract	Background
Language	English
Publishing date	2022-02-08
Publishing country	Netherlands
Document type	Journal Article
ISSN	2667-0313
ISSN (online)	2667-0313
DOI	10.1016/j.phyplu.2022.100237
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Article: Molecular dynamic simulation suggests stronger interaction of Omicron-spike with ACE2 than wild but weaker than Delta SARS-CoV-2 can be blocked by engineered S1-RBD fraction.

Santra, Dipannita / Maiti, Smarajit

Structural chemistry

2022 Volume 33, Issue 5, Page(s) 1755–1769

Abstract: The SARS-CoV-2 claimed millions of lives, globally. Occurring from Wuhan (wild type) in December, 2019, it constantly mutated to Omicron (B.1.1.529), the predecessor to Delta. Omicron having ~ 32 spike mutations has variable infectivity-multiplicity- ... ...

Abstract	The SARS-CoV-2 claimed millions of lives, globally. Occurring from Wuhan (wild type) in December, 2019, it constantly mutated to Omicron (B.1.1.529), the predecessor to Delta. Omicron having ~ 32 spike mutations has variable infectivity-multiplicity-immuno-invasive properties. Understanding of its mutational effect on ACE2-binding/disease severity and developing preventive/therapeutic strategies are important. The binding affinities of Wuhan/Delta/Omicron spikes (PDB/GISAID/SWISS-MODEL) were docked (HADDOCK2.4) with ACE2 and compared by competitive-docking (PRODIGY). The protein structural stability was verified by kinetic-data/Ramachandran-plot (Zlab/UMassMedBioinfo). After several trials, a 59 amino acid (453ARG-510VAL) peptide-cut (Expasy-server) of the wild-type spike RBD with some desired mutants (THR500SER/THR500GLY/THR500ALA/THR500CYS) was blindly/competitively docked (PyMOL-V2.2.2) to block the Omicron-ACE2 binding. We examined molecular dynamic simulation (iMOD-server, with 9000 cycles/300 k-heating/1 atm pressure for system equilibration for 50 ns-run) of ACE2 and two CUTs with different SARS-CoV-2 variants. The binding-affinity of Omicron-ACE2 is slightly higher than the rest two in competitive docking setup. During individual (1:1) docking, Omicron showed little higher than wild type but much weaker binding affinity than Delta. Competitive docking suggests ten H-bonding (1.3-2.4 Å) with highly favorable energy values/Van-der-Walls-force/Haddock score for more stable-binding of Omicron-RBD with ACE2. Blind docking of different CUTs (wild/mutants) and Omicron to ACE2 completely rejected the Omicron-RBD from ACE2-target. The best blocking/binding affinity of -16.4 and -13 kcal/mole were observed in the case of THR500SER and THR500GLY, respectively, with multiple H-bonding 1.9-2.2 Å. These are supported by the MD-simulation results. So, the spike binding affinities were Delta > Omicron > wild in 1:1 docking with ACE2. Considering the wild type is non-existing nowadays, Omicron showed less ACE2 binding properties. The 59 cut of spike-RBD and its mutant THR500SER/THR500GLY may be further screened as universal blockers of this virus. Supplementary information: The online version contains supplementary material available at 10.1007/s11224-022-02022-x.
Language	English
Publishing date	2022-08-04
Publishing country	United States
Document type	Journal Article
ZDB-ID	2018832-8
ISSN	1572-9001 ; 1040-0400
ISSN (online)	1572-9001
ISSN	1040-0400
DOI	10.1007/s11224-022-02022-x
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Article ; Online: Significant impact of redox regulation of estrogen-metabolizing proteins on cellular stress responses.

Maiti, Smarajit / Nazmeen, Aarifa / Banerjee, Amrita

Cell biochemistry and function

2023 Volume 41, Issue 4, Page(s) 461–477

Abstract: The ultimate driving force, stress, promotes adaptability/evolution in proliferating organisms, transforming tumorigenic growth. Estradiol (E2) regulates both phenomena. In this study, bioinformatics-tools, site-directed-mutagenesis (human estrogen- ... ...

Abstract	The ultimate driving force, stress, promotes adaptability/evolution in proliferating organisms, transforming tumorigenic growth. Estradiol (E2) regulates both phenomena. In this study, bioinformatics-tools, site-directed-mutagenesis (human estrogen-sulfotransferase/hSULT1E1), HepG2 cells tested with N-acetyl-cysteine (NAC/thiol-inducer) or buthionine-sulfoxamine (BSO/thiol-depletory) were evaluated for hSULT1E1 (estradiol-sulphating/inactivating) functions. Reciprocal redox regulation of steroid sulfatase (STS, E2-desulfating/activating) results in the Cys-formylglycine transition by the formylglycine-forming enzyme (FGE). The enzyme sequences and structures were examined across the phylogeny. Motif/domain and the catalytic conserve sequences and protein-surface-topography (CASTp) were investigated. The E2 binding to SULT1E1 suggests that the conserved-catalytic-domain in this enzyme has critical Cysteine 83 at position. This is strongly supported by site-directed mutagenesis/HepG2-cell research. Molecular-docking and superimposition studies of E2 with the SULT1E1 of representative species and to STS reinforce this hypothesis. SULT1E1-STS are reciprocally activated in response to the cellular-redox-environment by the critical Cys of these two enzymes. The importance of E2 in organism/species proliferation and tissue tumorigenesis is highlighted.
MeSH term(s)	Humans ; Cysteine/metabolism ; Estrogens ; Estradiol ; Oxidation-Reduction ; Mutagenesis, Site-Directed
Chemical Substances	Cysteine (K848JZ4886) ; Estrogens ; Estradiol (4TI98Z838E)
Language	English
Publishing date	2023-05-04
Publishing country	England
Document type	Journal Article
ZDB-ID	283643-9
ISSN	1099-0844 ; 0263-6484
ISSN (online)	1099-0844
ISSN	0263-6484
DOI	10.1002/cbf.3796
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Article ; Online: Evaluation of substrate specificity and catalytic promiscuity of

Paul, Manish / Banerjee, Amrita / Maiti, Smarajit / Mitra, Debanjan / DasMohapatra, Pradeep K / Thatoi, Hrudayanath

Journal of biomolecular structure & dynamics

2023 , Page(s) 1–23

Abstract: Cellulases are enzymes that aid in the hydrolysis of cellulosic fibers and have a wide range of industrial uses. In the ... ...

Abstract	Cellulases are enzymes that aid in the hydrolysis of cellulosic fibers and have a wide range of industrial uses. In the present
Language	English
Publishing date	2023-12-21
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2023.2295971
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Article ; Online: Prediction of Prospective Mutational Landscape of SARS-CoV-2 Spike ssRNA and Evolutionary Basis of Its Host Interaction.

Sarkar, Aniket / Ghosh, Trijit Arka / Bandyopadhyay, Bidyut / Maiti, Smarajit / Panja, Anindya Sundar

Molecular biotechnology

2024

Abstract: Booster doses are crucial against severe COVID-19, as rapid virus mutations and variant emergence prolong the pandemic crisis. The virus's quick evolution, short generation-time, and adaptive changes impact virulence and evolvability, helping predictions ...

Abstract	Booster doses are crucial against severe COVID-19, as rapid virus mutations and variant emergence prolong the pandemic crisis. The virus's quick evolution, short generation-time, and adaptive changes impact virulence and evolvability, helping predictions about variant of concerns' (VOCs') landscapes. Here, in this study, we used a new computational algorithm, to predict the mutational pattern in SARS-CoV-2 ssRNA, proteomics, structural identification, mutation stability, and functional correlation, as well as immune escape mechanisms. Interestingly, the sequence diversity of SARS Coronavirus-2 has demonstrated a predominance of G- > A and C- > U substitutions. The best validation statistics are explored here in seven homologous models of the expected mutant SARS-CoV-2 spike ssRNA and employed for hACE2 and IgG interactions. The interactome profile of SARS-CoV-2 spike with hACE2 and IgG revealed a strong correlation between phylogeny and divergence time. The systematic adaptation of SARS-CoV-2 spike ssRNA influences infectivity and immune escape. Data suggest higher propensity of Adenine rich sequence promotes MHC system avoidance, preferred by A-rich codons. Phylogenetic data revealed the evolution of SARS-CoV-2 lineages' epidemiology. Our findings may unveil processes governing the genesis of immune-resistant variants, prompting a critical reassessment of the coronavirus mutation rate and exploration of hypotheses beyond mechanical aspects.
Language	English
Publishing date	2024-04-15
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	1193057-3
ISSN	1559-0305 ; 1073-6085
ISSN (online)	1559-0305
ISSN	1073-6085
DOI	10.1007/s12033-024-01146-1
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Article ; Online: Synovial macrophages of rheumatoid arthritic mice protectively responded by altered M1/M2 differentiation after antibody blocking of TNFR1 and IL-1R.

Kanwar, Mehak / Dey, Rajen / Maiti, Smarajit / Banerjee, Amrita / Bishayi, Biswadev

International immunopharmacology

2023 Volume 115, Page(s) 109654

Abstract: Rheumatoid arthritis (RA) primarily affecting the synovial tissue, has emerged as a major concern leading to the pressing need to develop effective treatment strategies. In the affected synovial tissue, resident macrophages play a pivotal role in the ... ...

Abstract	Rheumatoid arthritis (RA) primarily affecting the synovial tissue, has emerged as a major concern leading to the pressing need to develop effective treatment strategies. In the affected synovial tissue, resident macrophages play a pivotal role in the pathogenesis of RA. TNF-α and IL-1β released from pro-inflammatory M1 synovial macrophages are the master regulators of chronic joint inflammation. In this study collagen-induced rheumatoid arthritis model was developed in mice and post isolation, macrophages were subjected to administration with neutralizing antibodies IL1R and TNFR1 either alone or in combination. Flow cytometric analysis followed by Western blots, ROS, and IL-1β, TNF-α release assays were performed. Outcomes suggested that post-dual blockade of IL1R and TNFR1 arthritic synovial macrophages showed a shifting of the M1 towards the anti-inflammatory M2 phenotype. Moreover, the switch towards the M2 phenotype might be responsible for decreased levels of IL-1β,TNF-α, and ROS and simultaneous elevation in the activity of antioxidant enzymes like SOD, CAT, and GP
MeSH term(s)	Animals ; Mice ; Antibodies/pharmacology ; Arthritis, Rheumatoid ; Inflammation/metabolism ; Macrophages ; Reactive Oxygen Species/metabolism ; Receptors, Tumor Necrosis Factor, Type I/metabolism ; Tumor Necrosis Factor-alpha/metabolism ; Synovial Membrane/cytology ; Synovial Membrane/metabolism ; Receptors, Interleukin-1/metabolism
Chemical Substances	Antibodies ; Reactive Oxygen Species ; Receptors, Tumor Necrosis Factor, Type I ; Tumor Necrosis Factor-alpha ; Receptors, Interleukin-1
Language	English
Publishing date	2023-01-06
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2043785-7
ISSN	1878-1705 ; 1567-5769
ISSN (online)	1878-1705
ISSN	1567-5769
DOI	10.1016/j.intimp.2022.109654
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Article ; Online: Immunoinformatics and MD-simulation data suggest that Omicron spike epitopes are more interacting to IgG via better MHC recognition than Delta variant.

Sarkar, Aniket / Santra, Dipannita / Sundar Panja, Anindya / Maiti, Smarajit

International immunopharmacology

2023 Volume 123, Page(s) 110636

Abstract: Background: Recently, in Nov 2021, in South Africa, the SARS CoV-2 variant Omicron was found to be highly infectious and transmissible but with the least fatality. It occupies the nasopharynx-oropharynx and easily spreads. The epidemiological data/ ... ...

Abstract	Background: Recently, in Nov 2021, in South Africa, the SARS CoV-2 variant Omicron was found to be highly infectious and transmissible but with the least fatality. It occupies the nasopharynx-oropharynx and easily spreads. The epidemiological data/reports suggest that several vaccines failed to neutralize Omicron. It has a large number of spike mutations and the RNA/protein vaccines were developed from its predecessors that may justify its escape in most neutralization reactions. Its lower immuno-suppression/cytokine-storming/inflammatory-response effects need exploration. Objectives: In the current study, we attempted to delineate the comparative interaction of different variants' spikes with multiple recognition sites on IgG and HLA-typing of MHC class and I and II. Methods: All SARS-CoV-2 spike-proteins/human-IgG/MHC-I & II were obtained from the NCBI/ PDB/GISAID database. Initial 3D-structures of the unavailable proteins were constructed by Homology-Modeling (Swissmodel-Expasy) and optimized (PROCHECK). Molecular-docking of spike-IgG/spike- I & MHC-II was performed (HADDOCK2.4/HawkDock) with active-residue screening (CPORT). Antigenicity of epitopes was determined (Vaxigen v2.0-server) and the epitope-model prepared (PEP-FOLD3-server). The binding-affinity/biological-interfaces/visualize were performed (PRODIGY-PyMOL2). We also examined the genesis of feasible transition pathways of functional docked complexes (iMODs) of MHC with different epitopes and antibodies of IgG with different variants. Further, Molecular-Dynamic-Simulation was performed by GROMACS 2023.1 software package. The MD-simulation was run with 100 ns (300 k-heating/1-atm pressure). Results: Surface-area with interactomes, H-bonding and polar/non-polar bonding were the highest in Omicron spike-IgG interaction. Unlike other variants, both the L and H chains of at least three different recognition sites of IgG interact with the N-terminal and C-terminal RBD of the S1-portion and partially bind to S2. In other cases, binding was observed in either NTD or CTD with a lesser number of bonding-interactomes, especially in Delta spike-Ab interaction. In the case of MHC class-I & II, the highest binding affinity/surface was noticed by Omicron and least by the Delta variant. The MD simulation data of lower RMSD values of the Delta and Omicron variants indicate improved structural stability and less departure from the initial conformation. Better binding to the IgG and MHC molecules explains Omicron's little ability in immune invasion.
MeSH term(s)	Humans ; Epitopes ; COVID-19 ; SARS-CoV-2 ; Molecular Dynamics Simulation
Chemical Substances	Epitopes
Language	English
Publishing date	2023-07-25
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2043785-7
ISSN	1878-1705 ; 1567-5769
ISSN (online)	1878-1705
ISSN	1567-5769
DOI	10.1016/j.intimp.2023.110636
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Article ; Online: Global conserved RBD fraction of SARS-CoV-2 S-protein with T500S mutation in silico significantly blocks ACE2 and rejects viral spike.

Banerjee, Amrita / Kanwar, Mehak / Santra, Dipannita / Maiti, Smarajit

Translational medicine communications

2022 Volume 7, Issue 1, Page(s) 2

Abstract: Background: SARS-CoV-2 developed global-pandemic with millions of infections/deaths. As it is urgently necessary it is assumed that some blockers/inhibitors of ACE2 could be helpful to resist the binding of viral-spike Receptor-Binding-Domain (RBD).: ... ...

Abstract	Background: SARS-CoV-2 developed global-pandemic with millions of infections/deaths. As it is urgently necessary it is assumed that some blockers/inhibitors of ACE2 could be helpful to resist the binding of viral-spike Receptor-Binding-Domain (RBD). Methods: Here, conserved RBD from 186-countries were compared with WUHAN-Hu-1 wild-type (CLUSTAL-X2/Pymol). The RBD of ACE2-bound nCOV2 crystal-structure 6VW1 was analyzed by Haddock-PatchDock. Extensive structural study/trial to introduce point/double/triple mutations in the different locations of CUT4 (most-effective from total 4 proposed fragments; CUTs) were tested with Swiss-Model-Expacy. Results: Blind-docking of mutated-CUTs in ACE2 completely rejected the nCOV2 binding to ACE2. Further, competitive-docking/binding-analyses (by PRODIGY) demonstrated few more bonding (LYS31-PHE490 and GLN42-GLN498) of CUT4 (than wild) and hindered TYR41-THR500 interaction with ACE2. Moreover, mutated-CUT4 even showed higher blocking effect against spike-ACE2 binding. Conclusion: In summary, CUT4-mutant rejects whole glycosylated-nCoV2 in all pre-dock, post-dock and competitive-docking conditions. The present work strategy is relevant because it could be able to block at the first level entry of the virus to the host cells. Supplementary information: The online version contains supplementary material available at 10.1186/s41231-022-00109-5.
Language	English
Publishing date	2022-02-04
Publishing country	England
Document type	Journal Article
ISSN	2396-832X
ISSN (online)	2396-832X
DOI	10.1186/s41231-022-00109-5
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Article ; Online: Global conserved RBD fraction of SARS-CoV-2 S-protein with T500S mutation in silico significantly blocks ACE2 and rejects viral spike

Amrita Banerjee / Mehak Kanwar / Dipannita Santra / Smarajit Maiti

Translational Medicine Communications, Vol 7, Iss 1, Pp 1-

2022 Volume 11

Abstract: Abstract Background SARS-CoV-2 developed global-pandemic with millions of infections/deaths. As it is urgently necessary it is assumed that some blockers/inhibitors of ACE2 could be helpful to resist the binding of viral-spike Receptor-Binding-Domain ( ... ...

Abstract	Abstract Background SARS-CoV-2 developed global-pandemic with millions of infections/deaths. As it is urgently necessary it is assumed that some blockers/inhibitors of ACE2 could be helpful to resist the binding of viral-spike Receptor-Binding-Domain (RBD). Methods Here, conserved RBD from 186-countries were compared with WUHAN-Hu-1 wild-type (CLUSTAL-X2/Pymol). The RBD of ACE2-bound nCOV2 crystal-structure 6VW1 was analyzed by Haddock-PatchDock. Extensive structural study/trial to introduce point/double/triple mutations in the different locations of CUT4 (most-effective from total 4 proposed fragments; CUTs) were tested with Swiss-Model-Expacy. Results Blind-docking of mutated-CUTs in ACE2 completely rejected the nCOV2 binding to ACE2. Further, competitive-docking/binding-analyses (by PRODIGY) demonstrated few more bonding (LYS31-PHE490 and GLN42-GLN498) of CUT4 (than wild) and hindered TYR41-THR500 interaction with ACE2. Moreover, mutated-CUT4 even showed higher blocking effect against spike-ACE2 binding. Conclusion In summary, CUT4-mutant rejects whole glycosylated-nCoV2 in all pre-dock, post-dock and competitive-docking conditions. The present work strategy is relevant because it could be able to block at the first level entry of the virus to the host cells.
Keywords	SARS CoV-2 pandemic ; ACE2 blocking by RBD fragments ; Mutation in RBD ; T500S ; Haddock and Hawkdock ; Medicine ; R
Subject code	540
Language	English
Publishing date	2022-02-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
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Article ; Online: Better binding informatics of delta variants (B.1.617.2) with ACE2 than wild, D614G or N501Y CoV-2 is fully blocked by 84 amino-acid cut of wild spike

Dipannita Santra / Amrita Banerjee / Smarajit Maiti

Informatics in Medicine Unlocked, Vol 29, Iss , Pp 100900- (2022)

2022

Abstract: Background and objective: The B.1.617.2 known as the Delta-variant harbors diverse Spike-mutations with developed transmissibility and immune-evasion more than wild/D614G/N501Y variants. The Delta-variant claimed comparatively a large number of lives ... ...

Abstract	Background and objective: The B.1.617.2 known as the Delta-variant harbors diverse Spike-mutations with developed transmissibility and immune-evasion more than wild/D614G/N501Y variants. The Delta-variant claimed comparatively a large number of lives globally. In the present study, the binding-affinities of these variants’ spikes to the human lung-ACE2 were investigated. Further, a certain portion of the spike-protein with a desired mutation was tested in-silico to block the ACE2. Methods: Structure of spike-variants were retrieved from PDB/GISAID and used for homology-modeling (SWISS-MODEL). A different combination of spike-ACE2 binding 1:1 or competitive blind-docking was performed using the Haddock 2.4 web-server. Eventually, two cut-segments (84 amino-acid of wild-spike, 432–516 Cut1) and its mutant T500S; Cut 2 were screened (Swiss-model Expasy-server) as blocker/inhibitor of all spike-variants (PyMOL-V2.2.2). Results: It is shown that the stability and energy of the Delta binding-affinity to ACE2 is far more than others. The number H-bonding (5), their lengths (1.7 Å-2.8 Å) and energy, Van-der-Walls energy, Haddock-score were highly favorable for more stable-binding of Delta-RBD to ACE2. The Ramachandran-plot (Zlab/UMassMed Bioinfo) data supports this. We observed the best Haddock score as −120.8±2.6 for Delta with Van-der-Walls and electrostatic-energy as −62.9 and −208.7, respectively. The highest binding-affinity (ΔG) was −10.7 kcal/mol. Its THR500 and GLN506 strongly bind with the LYS353 of ACE2. The Cut1 and its mutant T500S completely blocked Delta-spike binding to ACE2 with ΔG -8.4 and −10.6 kcal/mol, respectively. But during the comparison between 2 Cuts, Cut1 showed better results. Conclusions: Fractioned spike-protein from the conserved Receptor-Binding-Domain (RBD) could universally block the virus at entry-level, thus completely protecting any intercellular metabolism. Bioinformatics is an emerging field for screening of some drug/therapeutic targets from numerous options, minimizing time and expenses.
Keywords	SARS CoV-2 ; B.1.617.2- delta-variant ; Higher ACE2 affinity ; Spike-fragment peptide blocker ; Computer applications to medicine. Medical informatics ; R858-859.7
Subject code	572
Language	English
Publishing date	2022-01-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
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