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Article ; Online: Sepsis among Neonates Admitted to a Neonatal Intensive Care Unit in a Tertiary Care Centre.

Devkota, Kanchan / Kanodia, Piush / Joshi, Bibek

JNMA; journal of the Nepal Medical Association

2024 Volume 62, Issue 270, Page(s) 76–78

Abstract: Introduction: Neonatal sepsis is a condition that carries a high risk for mortality as neonates rapidly transition to extra-uterine life and are subjected to various risk factors. Sepsis prevalence can be reduced by good antenatal care, early detection ... ...

Abstract	Introduction: Neonatal sepsis is a condition that carries a high risk for mortality as neonates rapidly transition to extra-uterine life and are subjected to various risk factors. Sepsis prevalence can be reduced by good antenatal care, early detection and treatment of risk factors. The study aimed to find out the prevalence of sepsis among neonates admitted to a neonatal intensive care unit in a tertiary care centre. Methods: This is a descriptive cross-sectional study conducted among neonates admitted to the neonatal care unit of a tertiary care centre after obtaining ethical approval from the Institutional Review Committee. Data of patients admitted from 12 December 2022 to 30 June 2023 was collected from hospital records. Symptomatic patients admitted to the neonatal intensive care unit were included and those with incomplete data were excluded from the study. A convenience sampling method was used. The point estimate was calculated at a 95% Confidence Interval. Results: Among 379 neonates, the prevalence of sepsis was 138 (36.41%) (28.38-44.44, 95% Confidence Interval). A total of 98 (71.01%) had early-onset neonatal sepsis and 40 (28.99%) had late-onset neonatal sepsis. Conclusions: The prevalence of neonatal sepsis was found to be lower than other studies done in similar settings. Keywords: neonate; neonatal sepsis; prematurity; prevalence.
MeSH term(s)	Pregnancy ; Infant, Newborn ; Humans ; Female ; Neonatal Sepsis/epidemiology ; Neonatal Sepsis/etiology ; Intensive Care Units, Neonatal ; Cross-Sectional Studies ; Tertiary Care Centers ; Sepsis/epidemiology ; Sepsis/complications
Language	English
Publishing date	2024-02-24
Publishing country	Nepal
Document type	Journal Article
ZDB-ID	2209910-4
ISSN	1815-672X ; 0028-2715
ISSN (online)	1815-672X
ISSN	0028-2715
DOI	10.31729/jnma.8431
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: A High-Throughput RNA Displacement Assay for Screening SARS-CoV-2 nsp10-nsp16 Complex toward Developing Therapeutics for COVID-19.

Perveen, Sumera / Khalili Yazdi, Aliakbar / Devkota, Kanchan / Li, Fengling / Ghiabi, Pegah / Hajian, Taraneh / Loppnau, Peter / Bolotokova, Albina / Vedadi, Masoud

SLAS discovery : advancing life sciences R & D

2021 Volume 26, Issue 5, Page(s) 620–627

Abstract: SARS-CoV-2, the coronavirus that causes COVID-19, evades the human immune system by capping its RNA. This process protects the viral RNA and is essential for its replication. Multiple viral proteins are involved in this RNA capping process, including the ...

Abstract	SARS-CoV-2, the coronavirus that causes COVID-19, evades the human immune system by capping its RNA. This process protects the viral RNA and is essential for its replication. Multiple viral proteins are involved in this RNA capping process, including the nonstructural protein 16 (nsp16), which is an
MeSH term(s)	Adenosine/analogs & derivatives ; Adenosine/pharmacology ; Antiviral Agents/pharmacology ; Binding, Competitive ; COVID-19/virology ; Enzyme Inhibitors/pharmacology ; Fluorescence Polarization ; Gene Expression Regulation ; High-Throughput Screening Assays ; Host-Pathogen Interactions/drug effects ; Humans ; Methyltransferases ; Protein Binding ; RNA Caps/antagonists & inhibitors ; RNA Caps/genetics ; RNA Caps/metabolism ; RNA, Viral/antagonists & inhibitors ; RNA, Viral/genetics ; RNA, Viral/metabolism ; SARS-CoV-2/drug effects ; SARS-CoV-2/genetics ; SARS-CoV-2/metabolism ; Signal Transduction ; Small Molecule Libraries/pharmacology ; Viral Nonstructural Proteins/antagonists & inhibitors ; Viral Nonstructural Proteins/genetics ; Viral Nonstructural Proteins/metabolism ; Viral Regulatory and Accessory Proteins/antagonists & inhibitors ; Viral Regulatory and Accessory Proteins/genetics ; Viral Regulatory and Accessory Proteins/metabolism ; Virus Replication ; COVID-19 Drug Treatment
Chemical Substances	Antiviral Agents ; Enzyme Inhibitors ; NSP10 protein, SARS-CoV-2 ; NSP16 protein, SARS-CoV-2 ; RNA Caps ; RNA, Viral ; Small Molecule Libraries ; Viral Nonstructural Proteins ; Viral Regulatory and Accessory Proteins ; Methyltransferases (EC 2.1.1.-) ; Adenosine (K72T3FS567) ; sinefungin (W2U467CIIL)
Language	English
Publishing date	2021-01-10
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2885123-7
ISSN	2472-5560 ; 2472-5552
ISSN (online)	2472-5560
ISSN	2472-5552
DOI	10.1177/2472555220985040
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Article ; Online: A High-Throughput Radioactivity-Based Assay for Screening SARS-CoV-2 nsp10-nsp16 Complex.

Khalili Yazdi, Aliakbar / Li, Fengling / Devkota, Kanchan / Perveen, Sumera / Ghiabi, Pegah / Hajian, Taraneh / Bolotokova, Albina / Vedadi, Masoud

SLAS discovery : advancing life sciences R & D

2021 Volume 26, Issue 6, Page(s) 757–765

Abstract: Frequent outbreaks of novel coronaviruses (CoVs), highlighted by the current severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, necessitate the development of therapeutics that could be easily and effectively administered worldwide. ... ...

Abstract	Frequent outbreaks of novel coronaviruses (CoVs), highlighted by the current severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, necessitate the development of therapeutics that could be easily and effectively administered worldwide. The conserved mRNA-capping process enables CoVs to evade their host immune system and is a target for antiviral development. Nonstructural protein (nsp) 16 in complex with nsp10 catalyzes the final step of coronaviral mRNA capping through its 2'-
MeSH term(s)	Adenosine/analogs & derivatives ; Adenosine/chemistry ; Adenosine/pharmacology ; COVID-19/virology ; Cloning, Molecular ; Enzyme Assays ; Enzyme Inhibitors/chemistry ; Enzyme Inhibitors/pharmacology ; Escherichia coli/genetics ; Escherichia coli/metabolism ; Gene Expression ; Genetic Vectors/chemistry ; Genetic Vectors/metabolism ; High-Throughput Screening Assays ; Humans ; Kinetics ; Methylation ; Methyltransferases ; Models, Molecular ; RNA Caps/antagonists & inhibitors ; RNA Caps/genetics ; RNA Caps/metabolism ; RNA, Viral/antagonists & inhibitors ; RNA, Viral/genetics ; RNA, Viral/metabolism ; Recombinant Proteins/chemistry ; Recombinant Proteins/genetics ; Recombinant Proteins/metabolism ; SARS-CoV-2/drug effects ; SARS-CoV-2/enzymology ; SARS-CoV-2/genetics ; Tritium ; Viral Nonstructural Proteins/antagonists & inhibitors ; Viral Nonstructural Proteins/chemistry ; Viral Nonstructural Proteins/genetics ; Viral Nonstructural Proteins/metabolism ; Viral Regulatory and Accessory Proteins/antagonists & inhibitors ; Viral Regulatory and Accessory Proteins/chemistry ; Viral Regulatory and Accessory Proteins/genetics ; Viral Regulatory and Accessory Proteins/metabolism
Chemical Substances	Enzyme Inhibitors ; NSP10 protein, SARS-CoV-2 ; NSP16 protein, SARS-CoV-2 ; RNA Caps ; RNA, Viral ; Recombinant Proteins ; Viral Nonstructural Proteins ; Viral Regulatory and Accessory Proteins ; Tritium (10028-17-8) ; Methyltransferases (EC 2.1.1.-) ; Adenosine (K72T3FS567) ; sinefungin (W2U467CIIL)
Language	English
Publishing date	2021-04-19
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2885123-7
ISSN	2472-5560 ; 2472-5552
ISSN (online)	2472-5560
ISSN	2472-5552
DOI	10.1177/24725552211008863
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Article ; Online: Structure-Based Discovery of Inhibitors of the SARS-CoV-2 Nsp14 N7-Methyltransferase.

Journal of medicinal chemistry

2023 Volume 66, Issue 12, Page(s) 7785–7803

Abstract: An under-explored target for SARS-CoV-2 is ... ...

Abstract	An under-explored target for SARS-CoV-2 is the
MeSH term(s)	Humans ; Methyltransferases ; SARS-CoV-2/genetics ; Viral Nonstructural Proteins/genetics ; COVID-19 ; RNA, Viral/genetics ; Exoribonucleases
Chemical Substances	Methyltransferases (EC 2.1.1.-) ; Viral Nonstructural Proteins ; RNA, Viral ; Exoribonucleases (EC 3.1.-)
Language	English
Publishing date	2023-06-09
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	218133-2
ISSN	1520-4804 ; 0022-2623
ISSN (online)	1520-4804
ISSN	0022-2623
DOI	10.1021/acs.jmedchem.2c02120
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Article ; Online: The Structure-Based Design of SARS-CoV-2 nsp14 Methyltransferase Ligands Yields Nanomolar Inhibitors.

Otava, Tomáš / Šála, Michal / Li, Fengling / Fanfrlík, Jindřich / Devkota, Kanchan / Perveen, Sumera / Chau, Irene / Pakarian, Paknoosh / Hobza, Pavel / Vedadi, Masoud / Boura, Evzen / Nencka, Radim

ACS infectious diseases

2021 Volume 7, Issue 8, Page(s) 2214–2220

Abstract: In this study, we have focused on the structure-based design of the inhibitors of one of the two SARS-CoV-2 methyltransferases (MTases), nsp14. This MTase catalyzes the transfer of the methyl group ... ...

Abstract	In this study, we have focused on the structure-based design of the inhibitors of one of the two SARS-CoV-2 methyltransferases (MTases), nsp14. This MTase catalyzes the transfer of the methyl group from
MeSH term(s)	COVID-19 ; Exoribonucleases ; Humans ; Ligands ; Methyltransferases/genetics ; SARS-CoV-2 ; Viral Nonstructural Proteins
Chemical Substances	Ligands ; Viral Nonstructural Proteins ; Methyltransferases (EC 2.1.1.-) ; Exoribonucleases (EC 3.1.-)
Language	English
Publishing date	2021-06-21
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2373-8227
ISSN (online)	2373-8227
DOI	10.1021/acsinfecdis.1c00131
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Article ; Online: A high-throughput radioactivity-based assay for screening SARS-CoV-2 nsp10-nsp16 complex

Khalili Yazdi, Aliakbar / Li, Fengling / Devkota, Kanchan / Perveen, Sumera / Ghiabi, Pegah / Hajian, Taraneh / Bolotokova, Albina / Vedadi, Masoud

bioRxiv

Abstract: Frequent outbreaks of novel coronaviruses (CoVs), highlighted by the current SARS-CoV-2 pandemic, necessitate the development of therapeutics that could be easily and effectively administered world-wide. The conserved mRNA-capping process enables CoVs to ...

Abstract	Frequent outbreaks of novel coronaviruses (CoVs), highlighted by the current SARS-CoV-2 pandemic, necessitate the development of therapeutics that could be easily and effectively administered world-wide. The conserved mRNA-capping process enables CoVs to evade their host immune system and is a target for antiviral development. Nonstructural protein (nsp) 16 in complex with nsp10 catalyzes the final step of coronaviral mRNA-capping through its 2′-O-methylation activity. Like other methyltransferases, SARS-CoV-2 nsp10-nsp16 complex is druggable. However, the availability of an optimized assay for high-throughput screening (HTS) is an unmet need. Here, we report the development of a radioactivity-based assay for methyltransferase activity of nsp10-nsp16 complex in a 384-well format, and kinetic characterization, and optimization of the assay for HTS (Z′-factor: 0.83). Considering the high conservation of nsp16 across known CoV species, the potential inhibitors targeting SARS-CoV-2 nsp10-nsp16 complex may also be effective against other emerging pathogenic CoVs.
Keywords	covid19
Language	English
Publishing date	2021-02-03
Publisher	Cold Spring Harbor Laboratory
Document type	Article ; Online
DOI	10.1101/2021.02.03.429625
Database	COVID19

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Article ; Online: Peptide Inhibitors of the α-Cobratoxin-Nicotinic Acetylcholine Receptor Interaction.

Lynagh, Timothy / Kiontke, Stephan / Meyhoff-Madsen, Maria / Gless, Bengt H / Johannesen, Jónas / Kattelmann, Sabrina / Christiansen, Anders / Dufva, Martin / Laustsen, Andreas H / Devkota, Kanchan / Olsen, Christian A / Kümmel, Daniel / Pless, Stephan Alexander / Lohse, Brian

Journal of medicinal chemistry

2020 Volume 63, Issue 22, Page(s) 13709–13718

Abstract: Venomous snakebites cause >100 000 deaths every year, in many cases via potent depression of human neuromuscular signaling by snake α-neurotoxins. Emergency therapy still relies on antibody-based antivenom, hampered by poor access, frequent adverse ... ...

Abstract	Venomous snakebites cause >100 000 deaths every year, in many cases via potent depression of human neuromuscular signaling by snake α-neurotoxins. Emergency therapy still relies on antibody-based antivenom, hampered by poor access, frequent adverse reactions, and cumbersome production/purification. Combining high-throughput discovery and subsequent structure-function characterization, we present simple peptides that bind α-cobratoxin (α-Cbtx) and prevent its inhibition of nicotinic acetylcholine receptors (nAChRs) as a lead for the development of alternative antivenoms. Candidate peptides were identified by phage display and deep sequencing, and hits were characterized by electrophysiological recordings, leading to an 8-mer peptide that prevented α-Cbtx inhibition of nAChRs. We also solved the peptide:α-Cbtx cocrystal structure, revealing that the peptide, although of unique primary sequence, binds to α-Cbtx by mimicking structural features of the nAChR binding pocket. This demonstrates the potential of small peptides to neutralize lethal snake toxins in vitro, establishing a potential route to simple, synthetic, low-cost antivenoms.
MeSH term(s)	Animals ; Binding Sites/drug effects ; Binding Sites/physiology ; Cobra Neurotoxin Proteins/antagonists & inhibitors ; Cobra Neurotoxin Proteins/chemistry ; Cobra Neurotoxin Proteins/metabolism ; Crystallography, X-Ray ; Dose-Response Relationship, Drug ; Female ; Peptide Fragments/chemistry ; Peptide Fragments/metabolism ; Peptide Fragments/pharmacology ; Protein Structure, Secondary ; Receptors, Nicotinic/chemistry ; Receptors, Nicotinic/metabolism ; Xenopus laevis
Chemical Substances	Cobra Neurotoxin Proteins ; Peptide Fragments ; Receptors, Nicotinic ; alpha-cobratoxin (69344-74-7)
Language	English
Publishing date	2020-11-03
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	218133-2
ISSN	1520-4804 ; 0022-2623
ISSN (online)	1520-4804
ISSN	0022-2623
DOI	10.1021/acs.jmedchem.0c01202
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Article: A fluorescence resonance energy transfer-based method for histone methyltransferases

Devkota, Kanchan / Brian Lohse / Camilla Nyby Jakobsen / Jens Berthelsen / Rasmus Prætorius Clausen

Analytical biochemistry. 2015 May 01, v. 476

2015

Abstract: A simple dye–quencher fluorescence resonance energy transfer (FRET)-based assay for methyltransferases was developed and used to determine kinetic parameters and inhibitory activity at EHMT1 and EHMT2. Peptides mimicking the truncated histone H3 tail ... ...

Abstract	A simple dye–quencher fluorescence resonance energy transfer (FRET)-based assay for methyltransferases was developed and used to determine kinetic parameters and inhibitory activity at EHMT1 and EHMT2. Peptides mimicking the truncated histone H3 tail were functionalized in each end with a dye and a quencher, respectively. When lysine-9 residues in the peptides were methylated, they were protected from cleavage by endoproteinase–EndoLysC, whereas unmethylated peptides were cleaved, resulting in an increase in fluorescent intensity.
Keywords	energy transfer ; fluorescence ; histones ; methyltransferases ; peptides
Language	English
Dates of publication	2015-0501
Size	p. 78-80.
Publishing place	Elsevier Inc.
Document type	Article
ZDB-ID	1110-1
ISSN	1096-0309 ; 0003-2697
ISSN (online)	1096-0309
ISSN	0003-2697
DOI	10.1016/j.ab.2015.02.012
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: A fluorescence resonance energy transfer-based method for histone methyltransferases.

Devkota, Kanchan / Lohse, Brian / Jakobsen, Camilla Nyby / Berthelsen, Jens / Clausen, Rasmus Prætorius

Analytical biochemistry

2015 Volume 476, Page(s) 78–80

Abstract: A simple dye-quencher fluorescence resonance energy transfer (FRET)-based assay for methyltransferases was developed and used to determine kinetic parameters and inhibitory activity at EHMT1 and EHMT2. Peptides mimicking the truncated histone H3 tail ... ...

Abstract	A simple dye-quencher fluorescence resonance energy transfer (FRET)-based assay for methyltransferases was developed and used to determine kinetic parameters and inhibitory activity at EHMT1 and EHMT2. Peptides mimicking the truncated histone H3 tail were functionalized in each end with a dye and a quencher, respectively. When lysine-9 residues in the peptides were methylated, they were protected from cleavage by endoproteinase-EndoLysC, whereas unmethylated peptides were cleaved, resulting in an increase in fluorescent intensity.
MeSH term(s)	Biological Assay/methods ; Fluorescence Resonance Energy Transfer/methods ; Histone-Lysine N-Methyltransferase/chemistry ; Histone-Lysine N-Methyltransferase/metabolism
Chemical Substances	histone methyltransferase (EC 2.1.1.-) ; Histone-Lysine N-Methyltransferase (EC 2.1.1.43)
Language	English
Publishing date	2015-05-01
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1110-1
ISSN	1096-0309 ; 0003-2697
ISSN (online)	1096-0309
ISSN	0003-2697
DOI	10.1016/j.ab.2015.02.012
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Article ; Online: A high throughput RNA displacement assay for screening SARS-CoV-2 nsp10-nsp16 complex towards developing therapeutics for COVID-19

Perveen, Sumera / Khalili Yazdi, Aliakbar / Devkota, Kanchan / Li, Fengling / Ghiabi, Pegah / Hajian, Taraneh / Loppnau, Peter / Bolotokova, Albina / Vedadi, Masoud

bioRxiv

Abstract	SARS-CoV-2, the coronavirus that causes COVID-19, evades the human immune system by capping its RNA. This process protects the viral RNA and is essential for its replication. Multiple viral proteins are involved in this RNA capping process including the nonstructural protein 16 (nsp16) which is an S-adenosyl-L-methionine (SAM)-dependent 29-O-methyltransferase. Nsp16 is significantly active when in complex with another nonstructural protein, nsp10, which plays a key role in its stability and activity. Here we report the development of a fluorescence polarization (FP)-based RNA displacement assay for nsp10-nsp16 complex in 384-well format with a Z′-Factor of 0.6, suitable for high throughput screening. In this process, we purified the nsp10-nsp16 complex to higher than 95% purity and confirmed its binding to the methyl donor SAM, product of the reaction, SAH, and a common methyltransferase inhibitor, sinefungin using Isothermal Titration Calorimetry (ITC). The assay was further validated by screening a library of 1124 drug-like compounds. This assay provides a cost-effective high throughput method for screening nsp10-nsp16 complex for RNA-competitive inhibitors towards developing COVID-19 therapeutics.
Keywords	covid19
Language	English
Publishing date	2020-10-15
Publisher	Cold Spring Harbor Laboratory
Document type	Article ; Online
DOI	10.1101/2020.10.14.340034
Database	COVID19

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