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Article ; Online: In silico

Chaudhary, Meenakshi / Sehgal, Deepak

Journal of biomolecular structure & dynamics

2021 Volume 40, Issue 22, Page(s) 11560–11570

Abstract: Chikungunya Virus (CHIKV) is having a major impact on humans with potentially life-threatening and debilitating arthritis. The lack of a specific antiviral drug against the CHIKV disease has created an alarming situation to identify or develop potent ... ...

Abstract	Chikungunya Virus (CHIKV) is having a major impact on humans with potentially life-threatening and debilitating arthritis. The lack of a specific antiviral drug against the CHIKV disease has created an alarming situation to identify or develop potent chemical molecules for its remedial measures. Antiviral therapies for viral diseases are generally expensive and have adverse side effects. Plant-based antiviral natural compounds are the most suitable and best alternative of current antiviral drugs because of less toxicity. In the present study, non-structural protein 3 macrodomain (nsP3
MeSH term(s)	Humans ; Chikungunya Fever/drug therapy ; Chikungunya virus ; Molecular Docking Simulation ; Antiviral Agents/chemistry ; Virus Replication
Chemical Substances	Antiviral Agents
Language	English
Publishing date	2021-08-06
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2021.1960195
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Article ; Online: In silico identification of chikungunya virus replication inhibitor validated using biochemical and cell-based approaches.

Chaudhary, Meenakshi / Kumar, Akash / Bala Sharma, Kiran / Vrati, Sudhanshu / Sehgal, Deepak

The FEBS journal

2024

Abstract: Discovering an alternative therapy with a long-lasting effect on symptoms caused by chikungunya virus (CHIKV) infection is prompted by the lack of a vaccine and the absence of safe, effective and non-toxic medications. One potential strategy is ... ...

Abstract	Discovering an alternative therapy with a long-lasting effect on symptoms caused by chikungunya virus (CHIKV) infection is prompted by the lack of a vaccine and the absence of safe, effective and non-toxic medications. One potential strategy is synthesizing or identifying small compounds that can specifically target the active site of an essential enzyme and prevent virus replication. Previous site-directed mutagenesis studies have demonstrated the crucial role of the macrodomain, which is a part of non-structural protein 3 (nsP3), in virus replication. Exploiting this fact, the macrodomain can be targeted to discover a natural substance that can inhibit its function and thereby impede virus replication. With this aim, the present study focused on potential CHIKV nsP3 macrodomain (nsP3
Language	English
Publishing date	2024-02-01
Publishing country	England
Document type	Journal Article
ZDB-ID	2173655-8
ISSN	1742-4658 ; 1742-464X
ISSN (online)	1742-4658
ISSN	1742-464X
DOI	10.1111/febs.17066
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Article ; Online: In silico

Suman / Chaudhary, Meenakshi / Nain, Vikrant

Journal of biomolecular structure & dynamics

2020 Volume 39, Issue 3, Page(s) 841–850

Abstract: Cold shock domain (CSD) proteins with nucleic acid binding properties are well conserved from bacteria to higher organisms. In bacteria, the cold shock proteins (CSPs) are single domain RNA chaperones, whereas in animals and plants, CSDs are accompanied ... ...

Abstract	Cold shock domain (CSD) proteins with nucleic acid binding properties are well conserved from bacteria to higher organisms. In bacteria, the cold shock proteins (CSPs) are single domain RNA chaperones, whereas in animals and plants, CSDs are accompanied by additional domains with roles in transcription regulation. Bacterial CSPs (
MeSH term(s)	Bacillus subtilis/genetics ; Bacterial Proteins/genetics ; Base Sequence ; Cold Shock Proteins and Peptides/genetics ; Cold Temperature ; Cold-Shock Response ; Molecular Docking Simulation ; Phylogeny ; RNA, Plant
Chemical Substances	Bacterial Proteins ; Cold Shock Proteins and Peptides ; RNA, Plant
Language	English
Publishing date	2020-02-12
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2020.1719198
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Article ; Online: Molecular docking and dynamic simulation analysis of

Chaudhary, Meenakshi / Nain, Vikrant / Sehgal, Deepak

Journal of biomolecular structure & dynamics

2021 Volume 41, Issue 4, Page(s) 1342–1350

Abstract: The unavailability of a suitable treatment for human Hepatitis E virus (HEV) infection necessitate the development of anti HEV drugs. The HEV papain-like cysteine proteases (HEV PCP) is a crucial target to prevent viral replication and progression. E64 ... ...

Abstract	The unavailability of a suitable treatment for human Hepatitis E virus (HEV) infection necessitate the development of anti HEV drugs. The HEV papain-like cysteine proteases (HEV PCP) is a crucial target to prevent viral replication and progression. E64 is a known HEV PCP inhibitor; however, its molecular mechanism of inhibition is not yet known. Since the crystal structure of HEV PCP is not available, the primary focuses of the present study was to refine the predicted HEV PCP structural model by molecular dynamics (MD) simulation. Further, we performed a 200 ns MD simulation to understand the structural complexity of HEV PCP and the effect of E64 binding with HEV PCP. The E64 binding with active site residues Gln48, Thr51, Gln55, Cys52, Ser81, Gln 98, Cys 132, Arg158, His159, Asn 160 and Ala96 leads to reduced fluctuations in the residue at N-terminal (18-41) that include the CHC motif (26-28). However, most of the other non interacting residues, including the inter-domain linker region (46-87), showed increased fluctuations in the HEV PCP-E64 complex. The residue Asp21 and Ala96 are involved in the formation of interdomain interactions in the HEV PCP apo enzyme. While in the PCP-E64 complex, E64 binds to Ala96 and creates a steric hindrance to prevent interdomain interactions. Thus, the E64 binding reduces interdomain interactions and restrict domain movements in the HEV PCP-E64 complex. This information will be important for the chemically designing more effective derivatives of E64 developing HEV PCP specific inhibitors.Communicated by Ramaswamy H. Sarma.
MeSH term(s)	Humans ; Catalytic Domain ; Endopeptidases ; Hepatitis E virus/enzymology ; Hepatitis E virus/physiology ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Peptide Hydrolases ; Viral Papain-like Proteases/antagonists & inhibitors ; Viral Papain-like Proteases/metabolism
Chemical Substances	Endopeptidases (EC 3.4.-) ; Peptide Hydrolases (EC 3.4.-) ; Viral Papain-like Proteases (EC 3.4.22.-)
Language	English
Publishing date	2021-12-21
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2021.2019124
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Article ; Online: River Ganga pollution: Causes and failed management plans (correspondence on Dwivedi et al. 2018. Ganga water pollution: A potential health threat to inhabitants of Ganga basin. Environment International 117, 327-338).

Chaudhary, Meenakshi / Walker, Tony R

Environment international

2019 Volume 126, Page(s) 202–206

Language	English
Publishing date	2019-02-22
Publishing country	Netherlands
Document type	Letter
ZDB-ID	554791-x
ISSN	1873-6750 ; 0160-4120
ISSN (online)	1873-6750
ISSN	0160-4120
DOI	10.1016/j.envint.2019.02.033
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Article: Inhibition of Hepatitis E Virus Replication by Novel Inhibitor Targeting Methyltransferase

Hooda, Preeti / Chaudhary, Meenakshi / Parvez, Mohammad K. / Sinha, Neha / Sehgal, Deepak

Viruses. 2022 Aug. 15, v. 14, no. 8

2022

Abstract: Hepatitis E Virus (HEV) is a quasi-enveloped virus having a single-stranded, positive-sense RNA genome (~7.2 kb), flanked with a 5′ methylated cap and a 3′ polyadenylated tail. The HEV open reading frame 1 (ORF1) encodes a 186-kDa polyprotein speculated ... ...

Abstract	Hepatitis E Virus (HEV) is a quasi-enveloped virus having a single-stranded, positive-sense RNA genome (~7.2 kb), flanked with a 5′ methylated cap and a 3′ polyadenylated tail. The HEV open reading frame 1 (ORF1) encodes a 186-kDa polyprotein speculated to get processed and produce Methyltransferase (MTase), one of the four essential replication enzymes. In this study, we report the identification of the MTase inhibitor, which may potentially deplete its enzymatic activity, thus causing the cessation of viral replication. Using in silico screening through docking, we identified ten putative compounds, which were tested for their anti-MTase activity. This resulted in the identification of 3-(4-Hydroxyphenyl)propionic acid (HPPA), with an IC₅₀ value of 0.932 ± 0.15 μM, which could be perceived as an effective HEV inhibitor. Furthermore, the compound was tested for inhibition of HEV replication in the HEV culture system. The viral RNA copies were markedly decreased from ~3.2 × 10⁶ in untreated cells to ~4.3 × 10².⁸ copies in 800 μM HPPA treated cells. Therefore, we propose HPPA as a potential drug-like inhibitor against HEV-MTase, which would need further validation through in vivo analysis using animal models and the administration of Pharmacokinetic and Pharmacodynamic (PK/PD) studies.
Keywords	Orthohepevirus A ; animals ; computer simulation ; enzyme activity ; genome ; messenger RNA ; methylation ; methyltransferases ; pharmacodynamics ; pharmacokinetics ; polyproteins ; propionic acid ; virus replication ; viruses
Language	English
Dates of publication	2022-0815
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article
ZDB-ID	2516098-9
ISSN	1999-4915
ISSN	1999-4915
DOI	10.3390/v14081778
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Hepatitis E Virus Cysteine Protease Has Papain Like Properties Validated by

Saraswat, Shweta / Chaudhary, Meenakshi / Sehgal, Deepak

Frontiers in cellular and infection microbiology

2020 Volume 9, Page(s) 478

Abstract: Hepatitis E virus (HEV) has emerged as a global health concern during the last decade. In spite of a high mortality rate in pregnant women with fulminant hepatitis, no antiviral drugs or licensed vaccine is available in India. HEV-protease is a pivotal ... ...

Abstract	Hepatitis E virus (HEV) has emerged as a global health concern during the last decade. In spite of a high mortality rate in pregnant women with fulminant hepatitis, no antiviral drugs or licensed vaccine is available in India. HEV-protease is a pivotal enzyme responsible for ORF1 polyprotein processing leading to cleavage of the non-structural enzymes involved in virus replication. HEV-protease region encoding 432-592 amino acids of Genotype-1 was amplified, expressed in Sf21 cells and purified in its native form. The recombinant enzyme was biochemically characterized using SDS-PAGE, Western blotting and Immunofluorescence. The enzyme activity and the inhibition studies were conducted using Zymography, FTC-casein based protease assay and ORF1 polyprotein digestion. To conduct ORF1 digestion assay, the polyprotein, natural substrate of HEV-protease, was expressed in
MeSH term(s)	Amino Acid Sequence ; Animals ; Baculoviridae ; Catalytic Domain ; Cysteine Proteases/chemistry ; Cysteine Proteases/drug effects ; Cysteine Proteases/genetics ; Cysteine Proteases/metabolism ; DNA Helicases ; Epitopes ; Escherichia coli/genetics ; Hepatitis E virus/enzymology ; Hepatitis E virus/genetics ; Kinetics ; Methyltransferases ; Molecular Docking Simulation ; Open Reading Frames ; Papain/chemistry ; Papain/genetics ; Papain/metabolism ; Peptide Hydrolases ; Protease Inhibitors/pharmacology ; Protein Conformation ; RNA Replicase ; Recombinant Proteins ; Sf9 Cells ; Virus Replication
Chemical Substances	Epitopes ; Protease Inhibitors ; Recombinant Proteins ; Methyltransferases (EC 2.1.1.-) ; RNA Replicase (EC 2.7.7.48) ; Cysteine Proteases (EC 3.4.-) ; Peptide Hydrolases (EC 3.4.-) ; Papain (EC 3.4.22.2) ; DNA Helicases (EC 3.6.4.-)
Keywords	covid19
Language	English
Publishing date	2020-01-23
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2619676-1
ISSN	2235-2988 ; 2235-2988
ISSN (online)	2235-2988
ISSN	2235-2988
DOI	10.3389/fcimb.2019.00478
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Article ; Online: In silico

Chandra, Anshuman / Chaudhary, Meenakshi / Qamar, Imteyaz / Singh, Nagendra / Nain, Vikrant

Journal of biomolecular structure & dynamics

2021 Volume 40, Issue 14, Page(s) 6534–6544

Abstract: The novel Coronavirus disease 2019 (COVID-19) is potentially fatal and caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Due to the unavailability of any proven treatment or vaccination, the outbreak of COVID-19 is wreaking havoc ... ...

Abstract	The novel Coronavirus disease 2019 (COVID-19) is potentially fatal and caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Due to the unavailability of any proven treatment or vaccination, the outbreak of COVID-19 is wreaking havoc worldwide. Hence, there is an urgent need for therapeutics targeting SARS-CoV-2. Since, botanicals are an important resource for several efficacious antiviral agents, natural compounds gaining significant attention for COVID-19 treatment. In the present study, methyltranferase (MTase) of the SARS-CoV-2 is targeted using computational approach. The compounds were identified using molecular docking, virtual screening and molecular dynamics simulation studies. The binding mechanism of each compound was analyzed considering the stability and energetic parameter using
MeSH term(s)	Antiviral Agents/chemistry ; Antiviral Agents/pharmacology ; COVID-19/drug therapy ; Humans ; Methyltransferases ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Protease Inhibitors/chemistry ; SARS-CoV-2
Chemical Substances	Antiviral Agents ; Protease Inhibitors ; Methyltransferases (EC 2.1.1.-)
Language	English
Publishing date	2021-02-15
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2021.1886174
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Article ; Online: Inhibition of Hepatitis E Virus Replication by Novel Inhibitor Targeting Methyltransferase.

Hooda, Preeti / Chaudhary, Meenakshi / Parvez, Mohammad K / Sinha, Neha / Sehgal, Deepak

Viruses

2022 Volume 14, Issue 8

Abstract: Hepatitis E Virus (HEV) is a quasi-enveloped virus having a single-stranded, positive-sense RNA genome (~7.2 kb), flanked with a 5' methylated cap and a 3' polyadenylated tail. The HEV open reading frame 1 (ORF1) encodes a 186-kDa polyprotein speculated ... ...

Abstract	Hepatitis E Virus (HEV) is a quasi-enveloped virus having a single-stranded, positive-sense RNA genome (~7.2 kb), flanked with a 5' methylated cap and a 3' polyadenylated tail. The HEV open reading frame 1 (ORF1) encodes a 186-kDa polyprotein speculated to get processed and produce Methyltransferase (MTase), one of the four essential replication enzymes. In this study, we report the identification of the MTase inhibitor, which may potentially deplete its enzymatic activity, thus causing the cessation of viral replication. Using in silico screening through docking, we identified ten putative compounds, which were tested for their anti-MTase activity. This resulted in the identification of 3-(4-Hydroxyphenyl)propionic acid (HPPA), with an IC
MeSH term(s)	Animals ; Hepatitis E ; Hepatitis E virus/genetics ; Methyltransferases ; Polyproteins ; Virus Replication/physiology
Chemical Substances	Polyproteins ; Methyltransferases (EC 2.1.1.-)
Language	English
Publishing date	2022-08-15
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2516098-9
ISSN	1999-4915 ; 1999-4915
ISSN (online)	1999-4915
ISSN	1999-4915
DOI	10.3390/v14081778
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Article: Baseline assessment of contaminants in marine biota prior to remediation of industrial effluent impacted sediments in a former tidal estuary in Nova Scotia, Canada

Romo, Jessica / Chaudhary, Meenakshi / Walker, Tony R

Marine pollution bulletin. 2019 June 19,

2019

Abstract: Contaminated sediments at a pulp mill and former chor-alkali effluent treatment facility in Nova Scotia, Canada will undergo remediation. However, baseline studies assessing contaminants in marine biota in the marine receiving environment are lacking. ... ...

Abstract	Contaminated sediments at a pulp mill and former chor-alkali effluent treatment facility in Nova Scotia, Canada will undergo remediation. However, baseline studies assessing contaminants in marine biota in the marine receiving environment are lacking. Historical qualitative and quantitative contaminant data in biota from Boat Harbour (a former tidal lagoon which was used to treat industrial effluent since 1967), and surrounding marine environment were reviewed to establish baseline pollution from industrial effluent and contaminated sediments. Elevated metal, dioxins and furan concentrations previously measured in marine biota needs updating to help inform pre-remediation monitoring. Selection of species, contaminants of concern and sampling locations were ad hoc and often inconsistent with environmental effects monitoring requirements under Canadian federal Pulp and Paper Effluent Regulations. These consolidated baseline data are required to determine historical impacts and to assist future monitoring during Boat Harbour sediment remediation to compare against.
Keywords	boats ; dioxins ; environmental impact ; estuaries ; furans ; industrial effluents ; marine environment ; monitoring ; pulp ; remediation ; sediment contamination ; sediments ; water pollution ; Nova Scotia
Language	English
Dates of publication	2019-0619
Publishing place	Elsevier Ltd
Document type	Article
Note	Pre-press version
ZDB-ID	2001296-2
ISSN	1879-3363 ; 0025-326X
ISSN (online)	1879-3363
ISSN	0025-326X
DOI	10.1016/j.marpolbul.2019.06.055
Database	NAL-Catalogue (AGRICOLA)

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