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Article: Predicted antiviral drugs Darunavir, Amprenavir, Rimantadine and Saquinavir can potentially bind to neutralize SARS-CoV-2 conserved proteins.

Halder, Umesh C

Journal of biological research (Thessalonike, Greece)

2021 Volume 28, Issue 1, Page(s) 18

Abstract: Background: Novel Coronavirus disease 2019 or COVID-19 has become a threat to human society due to fast spreading and increasing mortality. It uses vertebrate hosts and presently deploys humans. Life cycle and pathogenicity of SARS-CoV-2 have already ... ...

Abstract	Background: Novel Coronavirus disease 2019 or COVID-19 has become a threat to human society due to fast spreading and increasing mortality. It uses vertebrate hosts and presently deploys humans. Life cycle and pathogenicity of SARS-CoV-2 have already been deciphered and possible drug target trials are on the way. Results: The present study was aimed to analyze Non-Structural Proteins that include conserved enzymes of SARS-CoV-2 like papain-like protease, main protease, Replicase, RNA-dependent RNA polymerase, methyltransferase, helicase, exoribonuclease and endoribonucleaseas targets to all known drugs. A bioinformatic based web server Drug ReposeER predicted several drug binding motifs in these analyzed proteins. Results revealed that anti-viral drugs Darunavir,Amprenavir, Rimantadine and Saquinavir were the most potent to have 3D-drug binding motifs that were closely associated with the active sites of the SARS-CoV-2 enzymes . Conclusions: Repurposing of the antiviral drugs Darunavir, Amprenavir, Rimantadine and Saquinavir to treat COVID-19 patients could be useful that can potentially prevent human mortality.
Language	English
Publishing date	2021-08-04
Publishing country	Greece
Document type	Journal Article
ZDB-ID	2186880-3
ISSN	2241-5793 ; 1790-045X
ISSN (online)	2241-5793
ISSN	1790-045X
DOI	10.1186/s40709-021-00149-2
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Article: Anti-COVID-19 terpenoid from marine sources: A docking, admet and molecular dynamics study.

Sepay, Nayim / Sekar, Aishwarya / Halder, Umesh C / Alarifi, Abdullah / Afzal, Mohd

Journal of molecular structure

2020 Volume 1228, Page(s) 129433

Abstract: Traditional medicines contain natural products (NPs) as main ingredient which always give new direction and paths to develop new advanced medicines. In the COVID-19 pandemic, NPs can be used or can help to find new compound against it. The SARS ... ...

Abstract	Traditional medicines contain natural products (NPs) as main ingredient which always give new direction and paths to develop new advanced medicines. In the COVID-19 pandemic, NPs can be used or can help to find new compound against it. The SARS coronavirus-2 main protease (SARS CoV-2 M
Keywords	covid19
Language	English
Publishing date	2020-10-10
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	194476-9
ISSN	0022-2860 ; 0377-046X
ISSN	0022-2860 ; 0377-046X
DOI	10.1016/j.molstruc.2020.129433
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Article ; Online: Anti-COVID-19 terpenoid from marine sources

Sepay, Nayim / Sekar, Aishwarya / Halder, Umesh C / Alarifi, Abdullah / Afzal, Mohd

Journal of Molecular Structure

A docking, admet and molecular dynamics study

2020 , Page(s) 129433

Keywords	Inorganic Chemistry ; Organic Chemistry ; Analytical Chemistry ; Spectroscopy ; covid19
Language	English
Publisher	Elsevier BV
Publishing country	us
Document type	Article ; Online
ZDB-ID	194476-9
ISSN	0022-2860 ; 0377-046X
ISSN	0022-2860 ; 0377-046X
DOI	10.1016/j.molstruc.2020.129433
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Anti-COVID-19 terpenoid from marine sources: a docking, ADMET and molecular dynamics study

Sepay, Nayim / Sekar, Aishwarya / Halder, Umesh C / Alarifi, Abdullah / Afzal, Mohd

J Mol Struct

Abstract	Traditional medicines contain natural products (NPs) as main ingredient which always give new direction and paths to develop new advanced medicines. In the COVID-19 pandemic, NPs can be used or can help to find new compound against it. The SARS coronavirus-2 main protease (SARS CoV-2 Mpro) enzyme, arbitrate viral replication and transcription, is target here. The study show that, from the electronic features and binding affinity of all the NPs with the enzyme, the compounds with higher hydrophobicity and lower flexibility can be more favorable inhibitor. More than fifty NPs were screened for the target and one terpenoid (T3) from marine sponge Cacospongia mycofijiensis shows excellent SARS CoV-2 Mpro inhibitory activity in comparison with known peptide based inhibitors. The molecular dynamics simulation studies of the terpenoids with the protein indicates that the complex is stable and hydrogen bonds are involved during the complexation. Considering binding affinity, bioavailability, pharmacokinetics and toxicity of the compounds, it is proposed that the NP T3 can act as a potential drug candidate against COVID-19 virus.
Keywords	covid19
Publisher	WHO
Document type	Article
Note	WHO #Covidence: #846050
Database	COVID19

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Article ; Online: Tryptophan dynamics in the exploration of micro-conformational changes of refolded β-lactoglobulin after thermal exposure: a steady state and time-resolved fluorescence approach.

Halder, Umesh C / Chakraborty, Jishnu / Das, Niloy / Bose, Sayantan

Journal of photochemistry and photobiology. B, Biology

2012 Volume 109, Page(s) 50–57

Abstract: Refolding intermediates of proteins, including molten globules, are likely to undergo dynamic conformational transitions. In this work, thermal unfolding and refolding of bovine β-lactoglobulin (β-lg) have been revisited to encounter such intermediate ... ...

Abstract	Refolding intermediates of proteins, including molten globules, are likely to undergo dynamic conformational transitions. In this work, thermal unfolding and refolding of bovine β-lactoglobulin (β-lg) have been revisited to encounter such intermediate states. Lower thermal range (< 80°C) was selected to avoid irreversible aggregate formation. The gross kinetic refolding as monitored with the fluorophore, Trp19, was likely to be reversible but alteration in time resolved fluorescence parameters ruled out the possibility of micro-structural reversibility for the refolded partner. Time resolved fluorescence showed that the refolded protein still lacks some intact native conformation. Far-UV CD signals lack the signature of any secondary structural distortion in global structural context whereas near-UV CD signals were strongly indicative of perturbation in micro-structure surrounding the aromatic moieties which hardly revives after cooling. Steady state anisotropy results showed successfully the break-down of dimer to monomer form of β-lg within 50°C temperature range and augmentation in anisotropy up on further thermal stress reflected the reorganization of tryptophan residues into more restricted and rigid micro-environment as well as irreversible disulfide-linked dimer formation. Reliability of conformational reversibility in the thermal unfolding-refolding is still enigmatic on micro and global structural perspectives. Intermediate state prior to the completion of refolding of thermally exposed β-lg was identified through fluorescence studies.
MeSH term(s)	Animals ; Cattle ; Fluorescence Polarization ; Hot Temperature ; Lactoglobulins/chemistry ; Models, Molecular ; Protein Conformation ; Protein Refolding ; Protein Unfolding ; Spectrometry, Fluorescence/methods ; Time Factors ; Tryptophan
Chemical Substances	Lactoglobulins ; Tryptophan (8DUH1N11BX)
Language	English
Publishing date	2012-04-02
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	623022-2
ISSN	1873-2682 ; 1011-1344
ISSN (online)	1873-2682
ISSN	1011-1344
DOI	10.1016/j.jphotobiol.2012.01.005
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Article ; Online: A dihydro-pyrido-indole potently inhibits HSV-1 infection by interfering the viral immediate early transcriptional events.

Bag, Paromita / Ojha, Durbadal / Mukherjee, Hemanta / Halder, Umesh C / Mondal, Supriya / Biswas, Aruna / Sharon, Ashoke / Van Kaer, Luc / Chakrabarty, Sekhar / Das, Gobardhan / Mitra, Debashis / Chattopadhyay, Debprasad

Antiviral research

2014 Volume 105, Page(s) 126–134

Abstract: ... in cutaneously infected Balb/C mice. Thus, the interference in the binding of IE complex, a decisive factor ...

Abstract	In our continued quest for identifying novel molecules from ethnomedicinal source we have isolated an alkaloid 7-methoxy-1-methyl-4,9-dihydro-3H-pyrido[3,4-b]indole, also known as Harmaline (HM), from an ethnomedicinal herb Ophiorrhiza nicobarica. The compound exhibited a potent anti-HSV-1 activity against both wild type and clinical isolates of HSV-1. Further we demonstrated that HM did not interfere in viral entry but the recruitment of lysine-specific demethylase-1 (LSD1) and the binding of immediate-early (IE) complex on ICP0 promoter. This leads to the suppression of viral IE gene synthesis and thereby the reduced expression of ICP4 and ICP27. Moreover, HM at its virucidal concentration is nontoxic and reduced virus yields in cutaneously infected Balb/C mice. Thus, the interference in the binding of IE complex, a decisive factor for HSV lytic cycle or latency by HM reveals an interesting target for developing non-nucleotide antiherpetic agent with different mode of action than Acyclovir.
MeSH term(s)	Animals ; Antiviral Agents/isolation & purification ; Antiviral Agents/pharmacology ; Antiviral Agents/therapeutic use ; Disease Models, Animal ; Female ; Harmaline/isolation & purification ; Harmaline/pharmacology ; Harmaline/therapeutic use ; Herpes Simplex/drug therapy ; Herpes Simplex/virology ; Herpesvirus 1, Human/drug effects ; Herpesvirus 1, Human/genetics ; Immediate-Early Proteins/antagonists & inhibitors ; Immediate-Early Proteins/biosynthesis ; Mice, Inbred BALB C ; Rubiaceae/chemistry ; Transcription, Genetic/drug effects
Chemical Substances	Antiviral Agents ; ICP27 protein, human herpesvirus 1 ; Immediate-Early Proteins ; herpes simplex virus, type 1 protein ICP4 ; Harmaline (CN58I4TOET)
Language	English
Publishing date	2014-05
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	306628-9
ISSN	1872-9096 ; 0166-3542
ISSN (online)	1872-9096
ISSN	0166-3542
DOI	10.1016/j.antiviral.2014.02.007
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Article: Loss of structural integrity and hydrophobic ligand binding capacity of acetylated and succinylated bovine β-lactoglobulin

Chakraborty, Jishnu / Das, Niloy / Das, Kali P / Halder, Umesh C

International dairy journal. 2009 Jan., v. 19, no. 1

2009

Abstract: The lysine residues of bovine @b-lactoglobulin (@b-lg) were acetylated and succinylated to investigate the effect of chemical modification on tertiary and secondary structures. Both derivatives showed higher electrophoretic mobility compared with native @ ...

Abstract	The lysine residues of bovine @b-lactoglobulin (@b-lg) were acetylated and succinylated to investigate the effect of chemical modification on tertiary and secondary structures. Both derivatives showed higher electrophoretic mobility compared with native @b-lg. The molar extinction coefficients of modified proteins were lower than native @b-lg. A significant decrease in intrinsic tryptophan fluorescence intensities, and a red shift of emission maxima were observed. The structural stabilities of the derivatives were compared with the native form. Both modified @b-lg structures were less stable against guanidine hydrochloride and urea denaturation. Hydrophobicities decreased, as measured by hydrophobic ligand binding of the modified @b-lg. Circular dichroism spectra of modified forms were different. The beta structural content of modified @b-lactoglobulins decreased substantially with an increase in random coil structure. These modifications changed the tertiary structure, and involved a significant loss of secondary structure of @b-lg.
Keywords	cows ; milk ; lactalbumin ; protein secondary structure ; protein tertiary structure ; lysine ; chemical reactions ; acetylation ; binding capacity ; hydrophobicity ; fluorescence emission spectroscopy ; polyacrylamide gel electrophoresis ; circular dichroism spectroscopy
Language	English
Dates of publication	2009-01
Size	p. 43-49.
Publishing place	[Amsterdam]: Elsevier Science
Document type	Article
ZDB-ID	1076400-8
ISSN	0958-6946
ISSN	0958-6946
DOI	10.1016/j.idairyj.2008.06.011
Database	NAL-Catalogue (AGRICOLA)

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Article: Molecular characterization and localization of Plasmodium falciparum choline kinase.

Choubey, Vinay / Guha, Mithu / Maity, Pallab / Kumar, Sanjay / Raghunandan, Resmi / Maulik, Prakas R / Mitra, Kalyan / Halder, Umesh C / Bandyopadhyay, Uday

Biochimica et biophysica acta

2006 Volume 1760, Issue 7, Page(s) 1027–1038

Abstract: ... confocal microscopy. A model structure of PfCK was constructed based on the crystal structure of choline kinase of C ... of ATP. The K(m) values for choline and ATP are found to be 145+/-20 microM and 2.5+/-0.3 mM ...

Abstract	Generation of phosphocholine by choline kinase is important for phosphatidylcholine biosynthesis via Kennedy pathway and phosphatidylcholine biosynthesis is essential for intraerythrocytic growth of malaria parasite. A putative gene (Gene ID PF14_0020) in chromosome 14, having highest sequence homology with choline kinase, has been identified by BLAST searches from P. falciparum genome sequence database. This gene has been PCR amplified, cloned, over-expressed and characterized. Choline kinase activity of the recombinant protein (PfCK) was validated as it catalyzed the formation of phosphocholine from choline in presence of ATP. The K(m) values for choline and ATP are found to be 145+/-20 microM and 2.5+/-0.3 mM, respectively. PfCK can phosphorylate choline efficiently but not ethanolamine. Southern blotting indicates that PfCK is a single copy gene and it is a cytosolic protein as evidenced by Western immunoblotting and confocal microscopy. A model structure of PfCK was constructed based on the crystal structure of choline kinase of C. elegans to search the structural homology. Consistent with the homology modeling predictions, CD analysis indicates that the alpha and beta content of PfCK are 33% and 14%, respectively. Since choline kinase plays a vital role for growth and multiplication of P. falciparum during intraerythrocytic stages, we can suggest that this well characterized PfCK may be exploited in the screening of new choline kinase inhibitors to evaluate their antimalarial activity.
MeSH term(s)	Adenosine Triphosphate/chemistry ; Amino Acid Sequence ; Animals ; Caenorhabditis elegans ; Choline Kinase/chemistry ; Erythrocytes/metabolism ; Humans ; Kinetics ; Models, Molecular ; Molecular Sequence Data ; Phosphorylcholine/chemistry ; Plasmodium falciparum/enzymology ; Protein Conformation ; Sequence Homology, Amino Acid
Chemical Substances	Phosphorylcholine (107-73-3) ; Adenosine Triphosphate (8L70Q75FXE) ; Choline Kinase (EC 2.7.1.32)
Language	English
Publishing date	2006-07
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	60-7
ISSN	1879-2596 ; 1879-260X ; 1872-8006 ; 1879-2642 ; 1879-2618 ; 1879-2650 ; 0006-3002 ; 0005-2728 ; 0005-2736 ; 0304-4165 ; 0167-4838 ; 1388-1981 ; 0167-4889 ; 0167-4781 ; 0304-419X ; 1570-9639 ; 0925-4439 ; 1874-9399
ISSN (online)	1879-2596 ; 1879-260X ; 1872-8006 ; 1879-2642 ; 1879-2618 ; 1879-2650
ISSN	0006-3002 ; 0005-2728 ; 0005-2736 ; 0304-4165 ; 0167-4838 ; 1388-1981 ; 0167-4889 ; 0167-4781 ; 0304-419X ; 1570-9639 ; 0925-4439 ; 1874-9399
DOI	10.1016/j.bbagen.2006.03.003
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Article ; Online: Silver nanoparticle modulates the aggregation of beta-lactoglobulin and induces to form rod-like aggregates.

Sardar, Subrata / Anas, Md / Maity, Sanhita / Pal, Sampa / Parvej, Hasan / Begum, Shahnaz / Dalui, Ramkrishna / Sepay, Nayim / Halder, Umesh Chandra

International journal of biological macromolecules

2018 Volume 125, Page(s) 596–604

Abstract: ... in 10 mM phosphate buffer at pH 7.5 after thermal exposure at 75 °C. Heat exposed β-lg forms ...

Abstract	Silver nanoparticles (SNPs) have been increasingly used in medicines and biomaterials as a drug carriers and diagnostic or therapeutic material due to their smaller size, large surface area and cell penetration ability. Here we report the preparation of SNPs of diameter 10 ± 3 nm by using silver nitrate and sodium borohydride and the interaction of synthesized SNPs with our model protein β-lactoglobulin (β-lg) in 10 mM phosphate buffer at pH 7.5 after thermal exposure at 75 °C. Heat exposed β-lg forms amyloidal fibrillar aggregates whereas this protein aggregates adopt rod-like shape instead of fibrillar structure in presence of SNP under the same conditions. Size of the synthesized SNPs is confirmed by UV-Visible spectroscopy, SEM and TEM. Interactions and subsequent formation of molecular assembly of heat stressed β-lg with SNP were investigated using Th-T assay and ANS binding assay, DLS, RLS, CD, FT-IR, SEM, TEM. Docking study parallely also support the experimental findings.
MeSH term(s)	Amyloid/metabolism ; Hot Temperature ; Hydrophobic and Hydrophilic Interactions ; Lactoglobulins/metabolism ; Metal Nanoparticles/administration & dosage ; Polymorphism, Single Nucleotide/physiology ; Protein Aggregates/drug effects ; Silver/administration & dosage
Chemical Substances	Amyloid ; Lactoglobulins ; Protein Aggregates ; Silver (3M4G523W1G)
Language	English
Publishing date	2018-12-07
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.2018.12.039
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Article ; Online: Effect of progesterone receptor status on maspin synthesis via nitric oxide production in neutrophils in human breast cancer.

Ganguly Bhattacharjee, Karabi / Bhattacharyya, Mau / Halder, Umesh Chandra / Jana, Pradipta / Sinha, Asru K

Breast cancer (Tokyo, Japan)

2014 Volume 21, Issue 5, Page(s) 605–613

Abstract: ... neutrophils revealed that whereas normal neutrophils had 11.5 × 10(10) PR sites/cell with K d = 47.619 nM, PR+ ... neutrophils had 6.6 × 10(10) PR sites/cell with K d = 47.619 nM. The progesterone negative (PR-) neutrophils ...

Abstract	Background: Although progesterone receptor (PR) status, similarly to estrogen receptor status, is of prognostic importance in breast cancer, the involvement of the PR in breast cancer remains obscure. Studies were conducted to determine the function of the PR in neutrophils in the nitric oxide-induced synthesis of maspin, an anti-breast-cancer protein produced in nonmalignant mammary cells and in neutrophils in the circulation. Methods: PR status was determined by immunohistochemistry. Maspin synthesis was determined by in-vitro translation of messenger RNA and quantified by enzyme-linked immunosorbent assay. Nitric oxide was determined by the methemoglobin method. Results: It was found that PR status in neutrophils was identical with that in malignant breast tissues. A Scatchard plot for progesterone binding to normal and PR-positive (PR+) neutrophils revealed that whereas normal neutrophils had 11.5 × 10(10) PR sites/cell with K d = 47.619 nM, PR+ neutrophils had 6.6 × 10(10) PR sites/cell with K d = 47.619 nM. The progesterone negative (PR-) neutrophils failed to bind to progesterone. Incubation of normal and PR+ neutrophils with 25 nM progesterone produced 1.317 μM NO and 2.329 nM maspin; the PR+ neutrophils produced 0.72 μM NO and 1.138 nM maspin. The PR- neutrophils failed to produce any NO or maspin in the presence of progesterone. Inhibition of progesterone-induced NO synthesis led to complete inhibition of maspin synthesis in all neutrophils. Conclusion: These results suggest that estrogen and progesterone complement each other in NO-induced maspin synthesis, and do not necessarily antagonize in the synthesis of the anti-breast-cancer protein.
MeSH term(s)	Adult ; Aged ; Animals ; Breast Neoplasms/metabolism ; Case-Control Studies ; Dose-Response Relationship, Drug ; Female ; Humans ; Middle Aged ; Neutrophils/drug effects ; Neutrophils/metabolism ; Nitric Oxide/biosynthesis ; Progesterone/metabolism ; Progesterone/pharmacology ; Rabbits ; Receptors, Progesterone/metabolism ; Serpins/genetics ; Serpins/metabolism
Chemical Substances	Receptors, Progesterone ; SERPIN-B5 ; Serpins ; Nitric Oxide (31C4KY9ESH) ; Progesterone (4G7DS2Q64Y)
Language	English
Publishing date	2014-09
Publishing country	Japan
Document type	Journal Article
ZDB-ID	2052429-8
ISSN	1880-4233 ; 1340-6868
ISSN (online)	1880-4233
ISSN	1340-6868
DOI	10.1007/s12282-012-0422-6
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