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Article ; Online: Trypsin is inhibited by phytocompounds liquiritin and terpinen-4-ol from the herb

Abhithaj, J / Sharanya, C S / Arun, K G / Jayadevi Variyar, E / Sadasivan, C

Journal of biomolecular structure & dynamics

2023 Volume 42, Issue 6, Page(s) 2957–2964

Abstract: Serine proteases are a class of hydrolytic enzymes involved in various physiological functions like digestion, coagulation, fibrinolysis and immunity. The present study evaluates the serine protease inhibitory potential of phytochemicals liquiritin and ... ...

Abstract	Serine proteases are a class of hydrolytic enzymes involved in various physiological functions like digestion, coagulation, fibrinolysis and immunity. The present study evaluates the serine protease inhibitory potential of phytochemicals liquiritin and terpinen-4-ol present in the herb
MeSH term(s)	Trypsin ; Serine Proteases ; Serine Endopeptidases ; Glycyrrhiza ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Glucosides ; Terpenes ; Flavanones
Chemical Substances	Trypsin (EC 3.4.21.4) ; liquiritin (T0O79T74CD) ; terpinenol-4 (562-74-3) ; Serine Proteases (EC 3.4.-) ; Serine Endopeptidases (EC 3.4.21.-) ; Glucosides ; Terpenes ; Flavanones
Language	English
Publishing date	2023-05-15
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2023.2212784
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Article ; Online: Lipoxygenase inhibitory synthetic derivatives of methyl gallate regulate gene expressions of COX-2 and cytokines to reduce animal model arthritis.

Sharanya, C S / Abhithaj, J / Arun, K G / Eeda, Koti Reddy / Bhat, Vignesh / Variyar, E J / Sabu, A / Haridas, M

Scientific reports

2023 Volume 13, Issue 1, Page(s) 10644

Abstract: Mammalian lipoxygenases (LOXs) are involved in the biosynthesis of mediators of anaphylactic reactions and have been implicated in cell maturation, the pathogenesis of bronchial asthma, atherosclerosis, rheumatoid arthritis, cardiovascular diseases, ... ...

Abstract	Mammalian lipoxygenases (LOXs) are involved in the biosynthesis of mediators of anaphylactic reactions and have been implicated in cell maturation, the pathogenesis of bronchial asthma, atherosclerosis, rheumatoid arthritis, cardiovascular diseases, Alzheimer's disease and osteoporosis. Hence LOX inhibition in chronic conditions can lead to reducing the disease progression, which can be a good target for treating these diseases. The present study deals with designing methyl gallate derivatives and their anti-inflammatory effect by in silico, in vitro and in vivo methods. Designed derivatives were docked against LOX enzyme, and molecular dynamic simulations were carried out. Following the synthesis of derivatives, in vitro LOX inhibition assay, enzyme kinetics and fluorescence quenching studies were performed. One of the derivatives of methyl gallate (MGSD 1) was demonstrated as an anti-inflammatory agent for the treatment of rheumatoid arthritis in the animal model. Amelioration of Freund's complete adjuvant (FCA)-induced arthritis by methyl gallate and its derivative with a concentration of 10-40 mg.kg
MeSH term(s)	Animals ; Cytokines ; Lipoxygenase ; Cyclooxygenase 2/genetics ; Tumor Necrosis Factor-alpha ; Diclofenac ; Arthritis, Rheumatoid ; Lipoxygenases ; Gene Expression ; Mammals
Chemical Substances	Cytokines ; Lipoxygenase (EC 1.13.11.12) ; Cyclooxygenase 2 (EC 1.14.99.1) ; Tumor Necrosis Factor-alpha ; methyl gallate (623D3XG80C) ; Diclofenac (144O8QL0L1) ; Lipoxygenases (EC 1.13.11.-)
Language	English
Publishing date	2023-06-30
Publishing country	England
Document type	Journal Article
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-023-37613-z
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Article ; Online: Compounds of

Haridas, M / Sasidhar, Vijith / Nath, Prajeesh / Abhithaj, J / Sabu, A / Rammanohar, P

Future journal of pharmaceutical sciences

2021 Volume 7, Issue 1, Page(s) 13

Abstract: Background: The nasal carriage of SARS-CoV-2 has been reported as the key factor transmitting COVID-19. Interventions that can reduce viral shedding from the nasopharynx could potentially mitigate the severity of the disease and its contagiousness. ... ...

Abstract	Background: The nasal carriage of SARS-CoV-2 has been reported as the key factor transmitting COVID-19. Interventions that can reduce viral shedding from the nasopharynx could potentially mitigate the severity of the disease and its contagiousness. Herbal formulation of Results: The proteins of SARS-CoV-2, essential for its entry into human cells and highly expressed in the goblet and ciliated cells of nasal epithelium, play a significant role in contagiousness of the virus. Docking studies indicated that the specific compounds present in Conclusion: In silico studies suggest that the phytochemical compounds in
Language	English
Publishing date	2021-01-09
Publishing country	Egypt
Document type	Journal Article
ZDB-ID	2834845-X
ISSN	2314-7253 ; 2314-7253
ISSN (online)	2314-7253
ISSN	2314-7253
DOI	10.1186/s43094-020-00171-6
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Article ; Online: Repurposing of Streptomyces antibiotics as adenosine deaminase inhibitors by pharmacophore modeling, docking, molecular dynamics, and

Arun, K G / Sharanya, C S / Abhithaj, J / Sadasivan, C

Journal of receptor and signal transduction research

2020 Volume 40, Issue 1, Page(s) 77–88

Abstract: Adenosine deaminase (ADA) is an enzyme present in purine metabolic pathway. Its inhibitors are considered to be potent drug lead compounds against inflammatory and malignant diseases. This study aimed to test ADA inhibitory activity of some Streptomyces ... ...

Abstract	Adenosine deaminase (ADA) is an enzyme present in purine metabolic pathway. Its inhibitors are considered to be potent drug lead compounds against inflammatory and malignant diseases. This study aimed to test ADA inhibitory activity of some Streptomyces secondary metabolites by using computational and
MeSH term(s)	Adenosine Deaminase/metabolism ; Adenosine Deaminase Inhibitors/chemistry ; Adenosine Deaminase Inhibitors/pharmacology ; Aminoglycosides/chemistry ; Aminoglycosides/pharmacology ; Anti-Bacterial Agents/pharmacology ; Catalytic Domain ; Drug Evaluation, Preclinical ; Drug Repositioning ; Enzyme Assays ; Humans ; Least-Squares Analysis ; Ligands ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Novobiocin/chemistry ; Novobiocin/pharmacology ; Quantitative Structure-Activity Relationship ; Spectrometry, Fluorescence ; Streptomyces/chemistry
Chemical Substances	Adenosine Deaminase Inhibitors ; Aminoglycosides ; Anti-Bacterial Agents ; Ligands ; Novobiocin (17EC19951N) ; nikkomycin (9Z22C3QQCJ) ; Adenosine Deaminase (EC 3.5.4.4)
Language	English
Publishing date	2020-01-23
Publishing country	England
Document type	Journal Article
ZDB-ID	1230969-2
ISSN	1532-4281 ; 1079-9893
ISSN (online)	1532-4281
ISSN	1079-9893
DOI	10.1080/10799893.2020.1715432
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Article ; Online: Drug repurposing against SARS-CoV-2 using E-pharmacophore based virtual screening, molecular docking and molecular dynamics with main protease as the target.

Arun, K G / Sharanya, C S / Abhithaj, J / Francis, Dileep / Sadasivan, C

Journal of biomolecular structure & dynamics

2020 Volume 39, Issue 13, Page(s) 4647–4658

Abstract: Since its first report in December 2019 from China, the COVID-19 pandemic caused by the beta-coronavirus SARS-CoV-2 has spread at an alarming pace infecting about 5.59 million, and claiming the lives of more than 0.35 million individuals across the globe. ...

Abstract	Since its first report in December 2019 from China, the COVID-19 pandemic caused by the beta-coronavirus SARS-CoV-2 has spread at an alarming pace infecting about 5.59 million, and claiming the lives of more than 0.35 million individuals across the globe. The lack of a clinically approved vaccine or drug remains the biggest bottleneck in combating the pandemic. Drug repurposing can expedite the process of drug development by identifying known drugs which are effective against SARS-CoV-2. The SARS-CoV-2 main protease is a promising drug target due to its indispensable role in viral multiplication inside the host. In the present study an E-pharmacophore hypothesis was generated using a crystal structure of the viral protease in complex with an imidazole carbaximide inhibitor. Drugs available in the superDRUG2 database were used to identify candidate drugs for repurposing. The hits obtained from the pharmacophore based screening were further screened using a structure based approach involving molecular docking at different precisions. The binding energies of the most promising compounds were estimated using MM-GBSA. The stability of the interactions between the selected drugs and the target were further explored using molecular dynamics simulation at 100 ns. The results showed that the drugs Binifibrate and Bamifylline bind strongly to the enzyme active site and hence they can be repurposed against SARS-CoV-2. However, U.S Food and Drug Administration have withdrawn Binifibrate from the market as it was having some adverse health effects on patients.Communicated by Ramaswamy H. Sarma.
MeSH term(s)	COVID-19 ; Drug Repositioning ; Humans ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Pandemics ; Peptide Hydrolases ; Protease Inhibitors ; SARS-CoV-2
Chemical Substances	Protease Inhibitors ; Peptide Hydrolases (EC 3.4.-)
Keywords	covid19
Language	English
Publishing date	2020-06-22
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	10.1080/07391102.2020.1779819
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Article ; Online: Lipoxygenase inhibitory synthetic derivatives of methyl gallate regulate gene expressions of COX-2 and cytokines to reduce animal model arthritis

C.S. Sharanya / J. Abhithaj / K.G. Arun / Koti Reddy Eeda / Vignesh Bhat / E.J. Variyar / A. Sabu / M. Haridas

Scientific Reports, Vol 13, Iss 1, Pp 1-

2023 Volume 19

Abstract: Abstract Mammalian lipoxygenases (LOXs) are involved in the biosynthesis of mediators of anaphylactic reactions and have been implicated in cell maturation, the pathogenesis of bronchial asthma, atherosclerosis, rheumatoid arthritis, cardiovascular ... ...

Abstract	Abstract Mammalian lipoxygenases (LOXs) are involved in the biosynthesis of mediators of anaphylactic reactions and have been implicated in cell maturation, the pathogenesis of bronchial asthma, atherosclerosis, rheumatoid arthritis, cardiovascular diseases, Alzheimer’s disease and osteoporosis. Hence LOX inhibition in chronic conditions can lead to reducing the disease progression, which can be a good target for treating these diseases. The present study deals with designing methyl gallate derivatives and their anti-inflammatory effect by in silico, in vitro and in vivo methods. Designed derivatives were docked against LOX enzyme, and molecular dynamic simulations were carried out. Following the synthesis of derivatives, in vitro LOX inhibition assay, enzyme kinetics and fluorescence quenching studies were performed. One of the derivatives of methyl gallate (MGSD 1) was demonstrated as an anti-inflammatory agent for the treatment of rheumatoid arthritis in the animal model. Amelioration of Freund’s complete adjuvant (FCA)-induced arthritis by methyl gallate and its derivative with a concentration of 10–40 mg.kg−1 has been assessed in vivo in a 28-day-long study. TNF-α and COX-2 gene expression were also studied. Methyl gallate synthetic derivatives (MGSDs) inhibited LOX with an IC50 of 100 nM, 304 nM, and 226 nM for MGSD 1, MGSD 2, and MGSD 3, respectively. Fluorescence quenching methods also prove their binding characteristics, and 200 ns simulations studies showed that the RMSDs for the entire complex were less than 2.8 Å. The in vivo results showed that methyl gallate was required approximately five times diclofenac for the same level of effect, and the synthesised (MGSD 1) compound required only approximately 1/12 of diclofenac for the same level of effect in in-vivo studies. The preeminent expression of COX-2 and TNF-α genes was significantly decreased after the treatment of the methyl gallate derivative. Hence, the in vivo results showed that the referenced synthetic derivative might have more ...
Keywords	Medicine ; R ; Science ; Q
Subject code	610
Language	English
Publishing date	2023-06-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Isozymes inhibited by active site blocking: versatility of calcium indifferent hesperidin binding to phospholipase A

Abhithaj, J / Arun, K G / Sharanya, C S / Haridas, M / Jayadevi Variyar, E

Journal of receptor and signal transduction research

2019 Volume 39, Issue 1, Page(s) 60–66

Abstract: ... ...

Abstract	sPLA
MeSH term(s)	Amino Acid Sequence ; Calcium ; Catalytic Domain ; Computer Simulation ; Group II Phospholipases A2/antagonists & inhibitors ; Group II Phospholipases A2/metabolism ; Group V Phospholipases A2/antagonists & inhibitors ; Group V Phospholipases A2/metabolism ; Group X Phospholipases A2/antagonists & inhibitors ; Group X Phospholipases A2/metabolism ; Hesperidin/pharmacology ; Humans ; Isoenzymes ; Ligands ; Molecular Docking Simulation ; Protein Conformation ; Sequence Homology
Chemical Substances	Isoenzymes ; Ligands ; Hesperidin (E750O06Y6O) ; Group II Phospholipases A2 (EC 3.1.1.4) ; Group V Phospholipases A2 (EC 3.1.1.4) ; Group X Phospholipases A2 (EC 3.1.1.4) ; Calcium (SY7Q814VUP)
Language	English
Publishing date	2019-05-14
Publishing country	England
Document type	Journal Article
ZDB-ID	1230969-2
ISSN	1532-4281 ; 1079-9893
ISSN (online)	1532-4281
ISSN	1079-9893
DOI	10.1080/10799893.2019.1606239
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Book ; Online: Drug Repurposing to Identify Therapeutics Against COVID 19 with SARS-Cov-2 Spike Glycoprotein and Main Protease as Targets

arun kumar / Sharanya C.S / Abhithaj J / Sadasivan C

An in Silico Study

2020

Abstract: The total cases of novel corona virus (SARS-CoV-2) infections is more than one million and total deaths recorded is more than fifty thousand. The research for developing vaccines and drugs against SARS-CoV-2 is going on in different parts of the world. ... ...

Abstract	The total cases of novel corona virus (SARS-CoV-2) infections is more than one million and total deaths recorded is more than fifty thousand. The research for developing vaccines and drugs against SARS-CoV-2 is going on in different parts of the world. Aim of the present study was to identify potential drug candidates against SARS-CoV-2 from existing drugs using in silico molecular modeling and docking. The targets for the present study was the spike protein and the main protease of SARS-CoV-2. The study was able to identify some drugs that can either bind to the spike protein receptor binding domain or the main protease of SARS-CoV-2. These include some of the antiviral drugs. These drugs might have the potential to inhibit the infection and viral replication.
Keywords	Drug Discovery and Drug Delivery Systems ; COVID 19 ; spike glycoprotein ; main protease ; covid19
Subject code	572
Publishing date	2020-04-10T07:34:28Z
Document type	Book ; Online
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Book ; Online: Drug Repurposing for COVID-19 from FDA Approved and Experiment Stage Drugs by in Silico Methods with SARS CoV-2 Spike Protein

Sharanya CS / arun kumar / Abhithaj J / Sabu A / Haridas Madathilkovilakathu

2020

Abstract: E-pharmacophore based virtual screening of DrugBank database is carried out to identify candidate drugs for repurposing. The dug molecules were screened based on the pharmacophore generated and filtered through the 6000 drug molecule to obtain better ... ...

Abstract	E-pharmacophore based virtual screening of DrugBank database is carried out to identify candidate drugs for repurposing. The dug molecules were screened based on the pharmacophore generated and filtered through the 6000 drug molecule to obtain better 2000 of them. This filtered drug molecules further screened via structure based approach, involving molecular docking at different precisions. From the large database seven drug lead molecules were selected as hits and their binding energy with the spike protein were calculated. Cladribine, Clofarabine, Fludarabine from approved category and 7-methyl-guanosine-5'-triphosphate-5'-guanosine, Adenosine-2'-5'-Diphosphate, 8-Bromo-Adenosine-5'-Monophosphate, Alpha-Methylene Adenosine Monophosphate in the experimental category were found to be potent inhibitors of SARS CoV-2 spike protein to repurpose as drugs for COVID-19.
Keywords	Bioinformatics and Computational Biology ; Chemical Biology ; Drug Discovery and Drug Delivery Systems ; SARS CoV-2 ; spike protein ; DrugBank molecules ; e-Pharmacophore model ; Virtual Screening Workflows ; Molecular Docking Approaches ; covid19
Publishing date	2020-05-20T06:45:20Z
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Drug repurposing against SARS-CoV-2 using E-pharmacophore based virtual screening, molecular docking and molecular dynamics with main protease as the target

Arun, K. G. / Sharanya, C. S / Abhithaj, J. / Francis, Dileep / Sadasivan, C.

Journal of Biomolecular Structure and Dynamics

2020 , Page(s) 1–12

Keywords	Molecular Biology ; Structural Biology ; General Medicine ; covid19
Language	English
Publisher	Informa UK Limited
Publishing country	uk
Document type	Article ; Online
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2020.1779819
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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