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Article ; Online: Structural Insight into the Binding of Cyanovirin-N with the Spike Glycoprotein, M pro and PL pro of SARS-CoV-2

Devashan Naidoo / Pallab Kar / Ayan Roy / Taurai Mutanda / Joseph Bwapwa / Arnab Sen / Akash Anandraj

Molecules, Vol 26, Iss 5114, p

Protein–Protein Interactions, Dynamics Simulations and Free Energy Calculations

2021 Volume 5114

Abstract: The emergence of COVID-19 continues to pose severe threats to global public health. The pandemic has infected over 171 million people and claimed more than 3.5 million lives to date. We investigated the binding potential of antiviral cyanobacterial ... ...

Abstract	The emergence of COVID-19 continues to pose severe threats to global public health. The pandemic has infected over 171 million people and claimed more than 3.5 million lives to date. We investigated the binding potential of antiviral cyanobacterial proteins including cyanovirin-N, scytovirin and phycocyanin with fundamental proteins involved in attachment and replication of SARS-CoV-2. Cyanovirin-N displayed the highest binding energy scores (−16.8 ± 0.02 kcal/mol, −12.3 ± 0.03 kcal/mol and −13.4 ± 0.02 kcal/mol, respectively) with the spike protein, the main protease (M pro ) and the papainlike protease (PL pro ) of SARS-CoV-2. Cyanovirin-N was observed to interact with the crucial residues involved in the attachment of the human ACE2 receptor. Analysis of the binding affinities calculated employing the molecular mechanics-Poisson–Boltzmann surface area (MM-PBSA) approach revealed that all forms of energy, except the polar solvation energy, favourably contributed to the interactions of cyanovirin-N with the viral proteins. With particular emphasis on cyanovirin-N, the current work presents evidence for the potential inhibition of SARS-CoV-2 by cyanobacterial proteins, and offers the opportunity for in vitro and in vivo experiments to deploy the cyanobacterial proteins as valuable therapeutics against COVID-19.
Keywords	SARS-CoV-2 ; spike protein ; M pro ; PL pro ; cyanobacteria ; cyanovirin-N ; Organic chemistry ; QD241-441
Subject code	333
Language	English
Publishing date	2021-08-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Fruit juice of silverberry (Elaeagnus) and bayberry (Myrica) may help in combating against kidney dysfunctions

Pallab Kar / Arnab Kumar Chakraborty / Somit Dutta / Malay Bhattacharya / Tapas Kumar Chaudhuri / Arnab Sen

Clinical Phytoscience, Vol 5, Iss 1, Pp 1-

2019 Volume 9

Abstract: Abstract Background Elaeagnus pyriformis, Myrica nagi and Myrica esculenta are prominent actinorhizal plants of North-East India which produce juicy edible fruits. Native people of this region consume these fruits for nutritional enhancement. Apart from ... ...

Abstract	Abstract Background Elaeagnus pyriformis, Myrica nagi and Myrica esculenta are prominent actinorhizal plants of North-East India which produce juicy edible fruits. Native people of this region consume these fruits for nutritional enhancement. Apart from having immense nutritional value, fruits of these plants have been utilized in traditional medicine for providing protection against various ailments. In our previous study on antioxidant activity and phytochemical fingerprints using GC-MS method; many medicinally potent compounds in fresh fruit juice of the three plants were revealed. We reported the presence of several compounds used to cure renal ailments. In the present study we reported the efficacy of these juices to alleviate nephrotoxicity in rat model. We intend to understand to what extent these fruits could be beneficial. Within the same scope we tried to evaluate whether the bioactive compounds present in the fruits could be responsible for reducing nephrotoxicity by in-silico molecular docking approaches. Methods In this study, three fruit juices namely Elaeagnus pyriformis, Myrica nagi and M. esculenta were evaluated on gentamicin induced nephrotoxicity in rat model. Nephrotoxicity was induced in wistar albino rats by intraperitoneal administration of gentamicin (100 mg/kg/day body weight) for 7 days. The study included a control group which received oral saline only, negative control group received gentamicin, positive control group received gentamicin and cystone, low dose group received gentamicin along with juice (200 mg/kg/day) and high dose group received gentamicin along with juice (400 mg/kg/day). Various enzymatic and biochemical parameters were assessed to study the protective effect of fruit juices in kidney disorders. Results Among the three fruits M. esculenta showed promising result in all in-vivo enzymatic assays (Superoxide dismutase, Glutathione reductase, Lipid peroxidation and catalase). Nevertheless, all the three fruit juice showed high significance value with encouraging range ...
Keywords	Actinorhizal plants ; Gentamicin ; Catalase ; Histology ; Molecular docking ; Medicine ; R ; Homeopathy ; RX1-681
Subject code	630
Language	English
Publishing date	2019-06-01T00:00:00Z
Publisher	SpringerOpen
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Natural compounds from Clerodendrum spp. as possible therapeutic candidates against SARS-CoV-2

Pallab Kar (5154965) / Neeta Raj Sharma (8995220) / Bhupender Singh (1634050) / Arnab Sen (3181959) / Ayan Roy (767372)

An in silico investigation

2020

Abstract: The COVID-19 pandemic caused by the novel coronavirus SARS-CoV-2 has rattled global public health, with researchers struggling to find specific therapeutic solutions. In this context, the present study employed an in silico approach to assess the ... ...

Abstract	The COVID-19 pandemic caused by the novel coronavirus SARS-CoV-2 has rattled global public health, with researchers struggling to find specific therapeutic solutions. In this context, the present study employed an in silico approach to assess the inhibitory potential of the phytochemicals obtained from GC-MS analysis of twelve Clerodendrum species against the imperative spike protein, main protease enzyme M pro and RNA-dependent RNA polymerase (RdRp) of SARS-CoV-2. An extensive molecular docking investigation of the phytocompounds at the active binding pockets of the viral proteins revealed promising inhibitory potential of the phytochemicals taraxerol, friedelin and stigmasterol. Decent physicochemical attributes of the compounds in accordance with Lipinski’s rule of five and Veber’s rule further established them as potential therapeutic candidates against SARS-CoV-2. Molecular mechanics-generalized Born surface area (MM-GBSA) binding free energy estimation revealed that taraxerol was the most promising candidate displaying the highest binding efficacy with all the concerned SARS-CoV-2 proteins included in the present analysis. Our observations were supported by robust molecular dynamics simulations of the complexes of the viral proteins with taraxerol for a timescale of 40 nanoseconds. It was striking to note that taraxerol exhibited better binding energy scores with the concerned viral proteins than the drugs that are specifically targeted against them. The present results promise to provide new avenues to further evaluate the potential of the phytocompound taraxerol in vitro and in vivo towards its successful deployment as a SARS-CoV-2 inhibitor and combat the catastrophic COVID-19. Communicated by Ramaswamy H. Sarma
Keywords	Biophysics ; Biochemistry ; Molecular Biology ; Pharmacology ; Infectious Diseases ; Biological Sciences not elsewhere classified ; Chemical Sciences not elsewhere classified ; Information Systems not elsewhere classified ; SARS-CoV-2 ; Clerodendrum spp ; molecular docking ; drug-likeness ; MM-GBSA ; taraxerol ; molecular dynamics simulations ; covid19
Subject code	540
Publishing date	2020-06-19T09:30:30Z
Publishing country	us
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: β-sitosterol conjugated silver nanoparticle-mediated amelioration of CCl4-induced liver injury in Swiss albino mice

Pallab Kar / Swarnendra Banerjee / Md. Moshfekus Saleh-E-In / Akash Anandraj / Emil Kormuth / Suntheren Pillay / Abdullah Ahmed Al-Ghamdi / Mohammad Ajmal Ali / Joongku Lee / Arnab Sen / Devashan Naidoo / Ayan Roy / Yong Eui Choi

Journal of King Saud University: Science, Vol 34, Iss 5, Pp 102113- (2022)

2022

Abstract: Objective: Drug induced hepatocyte death is a major contributor to acute liver failure. We aimed to determine whether β-sitosterol conjugated silver nanoparticles (BSAgNPs) could ameliorate carbon tetrachloride (CCl4)-induced liver injury in Swiss albino ...

Abstract	Objective: Drug induced hepatocyte death is a major contributor to acute liver failure. We aimed to determine whether β-sitosterol conjugated silver nanoparticles (BSAgNPs) could ameliorate carbon tetrachloride (CCl4)-induced liver injury in Swiss albino mice. Methods: Biogenic silver nanoparticles were synthesized from β-sitosterol to produce β-sitosterol (BS) conjugated silver nanoparticles. Serum liver function assays in mice model with CCl4-induced liver injury revealed that alanine aminotransferase (ALT), aspartate aminotransferase (AST), alkaline phosphatase (ALP), bilirubin and cholesterol levels decreased markedly after treatment with β-sitosterol and BSAgNPs. In vivo liver enzymatic assays, including superoxide dismutase (SOD), catalase and reduced glutathione (GSH) were conducted to assess the antioxidant activity of the treatments. Results: Liver tissue from BSAgNP treated mice displayed significantly elevated SOD activity (73.57 ± 1.48%) when compared to positive control group with silymarin treatment. Catalase activity decreased drastically in CCl4 treated mice (47.14 ± 1.08%), but increased with the administration of BSAgNPs (72.24 ± 2.25%). An increase in transforming growth factor β (TGF-β1) in liver tissue homogenate accompanied a reduction in nuclear factor erythroid-2-related factor 2 (Nrf2) in CCl4 treated mice. β-sitosterol and BSAgNPs mediated the reduction of TGF-β1. In the BSAgNPs treated mice, Nrf2 level was significantly elevated; however, no change was detected following β-sitosterol treatment. Conclusion: Our findings reveal that β-sitosterol conjugated silver nanoparticles (BSAgNPs) may cause activation of the Nrf2 gene, through potential inhibition of TGF β1/Smad signaling. Antifibrotic effect of BSAgNPs may promote the lowering of chronic inflammation, oxidative stress and collagen deposition. Nanoparticle-mediated drug delivery of β-sitosterol may therefore have therapeutic promise against hepatic complications.
Keywords	BSAgNPs ; Hepatotoxicity ; Oxidative stress ; Liver fibrosis ; Nrf2 ; TGF-β ; Science (General) ; Q1-390
Subject code	500
Language	English
Publishing date	2022-07-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: The antioxidant rich active principles of Clerodendrum sp. controls haloalkane xenobiotic induced hepatic damage in murine model

Pallab Kar / Somit Dutta / Arnab Kumar Chakraborty / Ayan Roy / Subhajit Sen / Anoop Kumar / Joongku Lee / Tapas Kumar Chaudhuri / Arnab Sen

Saudi Journal of Biological Sciences, Vol 26, Iss 7, Pp 1539-

2019 Volume 1547

Abstract: Clerodendrum is a plant with potent antioxidant activity and has been frequently employed as a traditional remedy against bronchitis, asthma, liver and stomach disorders. Three species of genus Clerodendrum namely Clerodendrum indicum, C. colebrookianum ... ...

Abstract	Clerodendrum is a plant with potent antioxidant activity and has been frequently employed as a traditional remedy against bronchitis, asthma, liver and stomach disorders. Three species of genus Clerodendrum namely Clerodendrum indicum, C. colebrookianum and C. inerme (Syn. Volkameria inermis) were investigated for their possible activity against oxidative stress induced liver injury. Apart from generation of Reactive Oxygen Species (ROS) in the WRL-68 cell line (human hepatic cell line), in-vitro and in-vivo antioxidant assays were also assessed. Features of immune cell proliferation (MTT) were analyzed thoroughly. Gas Chromatography-Mass Spectrometry (GC–MS) and Fourier Transform Infrared Spectroscopy (FTIR) analyses have been performed to identify the active biological compounds. These active biological compounds were further subjected to molecular docking. The antioxidant activity of three Clerodendrum sp. was significantly high in DPPH, nitric oxide, hydroxyl radical and hydrogen peroxide etc. Biochemical parameters like catalase, superoxide dismutase (SOD) and reduced glutathione (GSH) were generated in excess due to CCl4 administration, which was ameliorated by treating with Clerodendrum extract. The phytochemical 24,25-Dihydroxyvitamin D shows excellent binding affinity in Autodock Vina. The present study provided convincing evidences that C. indicum and C. inerme showed good result but C. colebrookianum performed better by almost all means. Keywords: Clerodendrum, Oxidative stress, ROS, Fibrosis, Silymarin, Molecular docking
Keywords	Biology (General) ; QH301-705.5
Language	English
Publishing date	2019-11-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Antioxidant and pharmaceutical potential of Clerodendrum L.

Pallab Kar / Arvind Kumar Goyal / Abhaya Prasad Das / Arnab Sen

International Journal of Green Pharmacy, Vol 8, Iss 4, Pp 210-

An overview

2014 Volume 216

Abstract: Clerodendrum , with about 580 species, belongs to the family Verbenaceae and is widely distributed in the tropical and warm temperate regions of the world. The leaves of some species of Clerodendrum form an important source of diet in North eastern part ... ...

Abstract	Clerodendrum , with about 580 species, belongs to the family Verbenaceae and is widely distributed in the tropical and warm temperate regions of the world. The leaves of some species of Clerodendrum form an important source of diet in North eastern part of India. Various plant parts such as leaf and root extracts of C. indicum, C. phlomidis, C. serratum, C. trichotomum, C. chinense and C. petasites have been used for the treatment of rheumatism, asthma, inflammatory diseases, coughs, skin diseases, vermifuge, febrifuge, malaria etc. Isolation and identification of different chemical compounds and biological activities of the genus Clerodendrum have been studied by few researchers. The major chemical components reported from the genus are phenolics, steroids, flavonoids, terpenes, volatile oils, etc., This paper presents a comprehensive review on the various aspects of Clerodendrum species with respect to their traditional usage or use as alternative medicine for the treatment of various diseases.
Keywords	Antioxidant ; Clerodendrum ; flavonoids ; pharmaceutical ; phenolics ; steroids ; terpenoids ; Therapeutics. Pharmacology ; RM1-950 ; Medicine ; R
Subject code	590
Language	English
Publishing date	2014-01-01T00:00:00Z
Publisher	Medknow Publications
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Amelioration of CCl4 induced liver injury in swiss albino mice by antioxidant rich leaf extract of Croton bonplandianus Baill.

Somit Dutta / Arnab Kumar Chakraborty / Priyankar Dey / Pallab Kar / Pokhraj Guha / Subhajit Sen / Anoop Kumar / Arnab Sen / Tapas Kumar Chaudhuri

PLoS ONE, Vol 13, Iss 4, p e

2018 Volume 0196411

Abstract: The progress in industrialization has blessed mankind with a technologically superior lifestyle but poor management of industrial waste has in turn poisoned nature. One such chemical is carbon tetra chloride (CCl4), which is a potent environmental toxin ... ...

Abstract	The progress in industrialization has blessed mankind with a technologically superior lifestyle but poor management of industrial waste has in turn poisoned nature. One such chemical is carbon tetra chloride (CCl4), which is a potent environmental toxin emitted from chemical industries and its presence in the atmosphere is increasing at an alarming rate. Presence of CCl4 in human body is reported to cause liver damage through free radical mediated inflammatory processes. Kupffer cells present in the liver are potentially more sensitive to oxidative stress than hepatocytes. Kuffer cells produced tumor necrosis factor-α (TNF-α) in response to reactive oxygen species (ROS), that might further cause inflammation or apoptosis. In this study hepatoprotective capacity of antioxidant rich extract of Croton bonplandianus Baill. (CBL) was evaluated on CCl4 induced acute hepatotoxicity in murine model. Hydro-methanolic extract of C. bonplandianus leaf was used for evaluation of free radical scavenging activity. Liver cells of experimental mice were damaged using CCl4 and subsequently hepatoprotective potential of the plant extract was evaluated using series of in-vivo and in-vitro studies. In the hepatoprotective study, silymarin was used as a positive control. Antioxidant enzymes, pro-inflammatory markers, liver enzymatic and biochemical parameters were studied to evaluate hepatoprotective activity of Croton bonplandianus leaf extract. Free radical scavenging activity of CBL extract was also observed in WRL-68 cell line. The phytochemicals identified by GCMS analysis were scrutinized using in-silico molecular docking procedure. The results showed that CBL extract have potent free radical scavenging capacity. The biochemical parameters were over expressed due to CCl4 administration, which were significantly normalized by CBL extract treatment. This finding was also supported by histopathological evidences showing less hepatocellularnecrosis, inflammation and fibrosis in CBL and silymarin treated group, compared to CCl4 ...
Keywords	Medicine ; R ; Science ; Q
Subject code	500
Language	English
Publishing date	2018-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Ethnobotany, traditional knowledge and socioeconomic importance of native drink among the Oraon tribe of Malda district in India

Manas Ranjan Saha / Ritu Rai / Pallab Kar / Arnab Sen / Dilip De Sarker

Journal of Intercultural Ethnopharmacology, Vol 4, Iss 1, Pp 34-

2015 Volume 39

Abstract: ABSTRACT Aim: Preparation of daily traditional drink by the indigenous tribes is a common phenomenon in India. Oraon tribes in Malda district of West Bengal, India are very much practiced in making of their own native brew, known as chullu. Therefore the ...

Abstract	ABSTRACT Aim: Preparation of daily traditional drink by the indigenous tribes is a common phenomenon in India. Oraon tribes in Malda district of West Bengal, India are very much practiced in making of their own native brew, known as chullu. Therefore the aim of the present study was to explore the whole chullu procedure technology of the region and its socioeconomic effect on Oraon. Ethnomedicinal investigation of local plants involved in chullu preparation was another aspect of this study. Materials and Methods: Present study was conducted from April 2012 to June 2013. Consecutive field surveys were performed to collect information from chullu producers to focus the procedure technology of local brew by means of semi-structured individual interviews, informal interviews and group discussion. A semi-structured questionnaire process was also performed to obtain the information regarding the ethnic use of plant species involved in chullu preparation. Results: Present study revealed that four medicinal plant species along with rice having strong local ethnomedicinal value were used to prepare this indigenous drink. Oraon prepare the brew using their unique home-made distillation process. Commercialization of this local brew represents an alternative income to develop their economic condition, especially for poor households. The Index of Importance Value (IVs) was considered to evaluate the importance, usage, and knowledge of the five studied species. Conclusion: It could be concluded that practices of chullu preparation represent a bonding between ethnic knowledge and Oraon people of the province. Commercialization of chullu may be considered as a source of alternative way of income for poor households in the region. [J Intercult Ethnopharmacol 2015; 4(1.000): 34-39]
Keywords	Chullu ; Alternative income ; Ethnobotany ; Oraon ; Malda district ; Therapeutics. Pharmacology ; RM1-950 ; Medicine ; R
Subject code	390
Language	English
Publishing date	2015-03-01T00:00:00Z
Publisher	SAGEYA Publishing Company
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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