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Article ; Online: In silico molecular docking analysis for repurposing therapeutics against multiple proteins from SARS-CoV-2.

Deshpande, Rujuta R / Tiwari, Arpita Pandey / Nyayanit, Narendra / Modak, Manisha

2020 Volume 886, Page(s) 173430

Abstract: SARS-CoV-2 has devastated the world with its rapid spread and fatality. The researchers across the globe are struggling hard to search a drug to treat this infection. Understanding the time constraint, the best approach is to study clinically approved ... ...

Abstract	SARS-CoV-2 has devastated the world with its rapid spread and fatality. The researchers across the globe are struggling hard to search a drug to treat this infection. Understanding the time constraint, the best approach is to study clinically approved drugs for control of this deadly pandemic of COVID 19. The repurposing of such drugs can be supported with the study of molecular interactions to enhance the possibility of application. The present work is a molecular docking study of proteins responsible for viral propagation namely 3Clpro, Nsp10/16, Spike protein, SARS protein receptor binding domain, Nsp 9 viral single strand binding protein and viral helicase. The protein through virus enters the host cell-human angiotensin-converting enzyme 2 (ACE2) receptor, is also used as a target for molecular docking. The docking was done with most discussed drugs for SARS-CoV-2 like Ritonavir, Lopinavir, Remdesivir, Chloroquine, Hydroxychloroquine (HCQ), routine antiviral drugs like Oseltamivir and Ribavirin. In addition, small molecules with anti-inflammatory actions like Mycophenolic acid (MPA), Pemirolast, Isoniazid and Eriodictyol were also tested. The generated data confirms the potential of Ritonavir, Lopinavir and Remdesivir as a therapeutic candidate against SARS-CoV-2. It is observed that Eriodictyol binds to almost all selected target proteins with good binding energy, suggesting its importance in treatment of COVID 19. Molecular interactions of Ritonavir, Lopinavir and Remdesivir against SARS-CoV-2 proteins enhanced their potential as a candidate drug for treatment of COVID-19. Eriodictyol had emerged as a new repurposing drug that can be used in COVID-19.
MeSH term(s)	Antiviral Agents/metabolism ; Antiviral Agents/pharmacology ; Betacoronavirus/drug effects ; Betacoronavirus/metabolism ; Computer Simulation ; Drug Repositioning ; Molecular Docking Simulation ; Protein Conformation ; SARS-CoV-2 ; Viral Proteins/chemistry ; Viral Proteins/metabolism
Chemical Substances	Antiviral Agents ; Viral Proteins
Keywords	covid19
Language	English
Publishing date	2020-08-03
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	80121-5
ISSN	1879-0712 ; 0014-2999
ISSN (online)	1879-0712
ISSN	0014-2999
DOI	10.1016/j.ejphar.2020.173430
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: In silico molecular docking analysis for repurposing therapeutics against multiple proteins from SARS-CoV-2

Deshpande, Rujuta R. / Tiwari, Arpita Pandey / Nyayanit, Narendra / Modak, Manisha

European Journal of Pharmacology

2020 Volume 886, Page(s) 173430

Keywords	Pharmacology ; covid19
Language	English
Publisher	Elsevier BV
Publishing country	us
Document type	Article ; Online
ZDB-ID	80121-5
ISSN	1879-0712 ; 0014-2999
ISSN (online)	1879-0712
ISSN	0014-2999
DOI	10.1016/j.ejphar.2020.173430
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Enteric bacterial infection in Drosophila induces whole-body alterations in metabolic gene expression independently of the immune deficiency signaling pathway.

Deshpande, Rujuta / Lee, Byoungchun / Grewal, Savraj S

G3 (Bethesda, Md.)

2022 Volume 12, Issue 11

Abstract: When infected by intestinal pathogenic bacteria, animals initiate both local and systemic defence responses. These responses are required to reduce pathogen burden and also to alter host physiology and behavior to promote infection tolerance, and they ... ...

Abstract	When infected by intestinal pathogenic bacteria, animals initiate both local and systemic defence responses. These responses are required to reduce pathogen burden and also to alter host physiology and behavior to promote infection tolerance, and they are often mediated through alterations in host gene expression. Here, we have used transcriptome profiling to examine gene expression changes induced by enteric infection with the Gram-negative bacteria Pseudomonas entomophila in adult female Drosophila. We find that infection induces a strong upregulation of metabolic gene expression, including gut and fat body-enriched genes involved in lipid transport, lipolysis, and beta-oxidation, as well as glucose and amino acid metabolism genes. Furthermore, we find that the classic innate immune deficiency (Imd)/Relish/NF-KappaB pathway is not required for, and in some cases limits, these infection-mediated increases in metabolic gene expression. We also see that enteric infection with Pseudomonas entomophila downregulates the expression of many transcription factors and cell-cell signaling molecules, particularly those previously shown to be involved in gut-to-brain and neuronal signaling. Moreover, as with the metabolic genes, these changes occurred largely independent of the Imd pathway. Together, our study identifies many metabolic, signaling, and transcription factor gene expression changes that may contribute to organismal physiological and behavioral responses to enteric pathogen infection.
MeSH term(s)	Animals ; Female ; Drosophila/genetics ; Drosophila/metabolism ; Drosophila Proteins/metabolism ; Signal Transduction ; Bacterial Infections ; Gene Expression ; Drosophila melanogaster/metabolism ; Immunity, Innate/genetics
Chemical Substances	Drosophila Proteins
Language	English
Publishing date	2022-06-30
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2629978-1
ISSN	2160-1836 ; 2160-1836
ISSN (online)	2160-1836
ISSN	2160-1836
DOI	10.1093/g3journal/jkac163
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: In silico molecular docking analysis for repurposing therapeutics against multiple proteins from SARS-CoV-2

Deshpande, Rujuta R / Tiwari, Arpita Pandey / Nyayanit, Narendra / Modak, Manisha

Eur J Pharmacol

Abstract	SARS-CoV-2 has devastated the world with its rapid spread and fatality. The researchers across the globe are struggling hard to search a drug to treat this infection. Understanding the time constraint, the best approach is to study clinically approved drugs for control of this deadly pandemic of COVID 19. The repurposing of such drugs can be supported with the study of molecular interactions to enhance the possibility of application. The present work is a molecular docking study of proteins responsible for viral propagation namely 3Clpro, Nsp10/16, Spike protein, SARS protein receptor binding domain, Nsp 9 viral single strand binding protein and viral helicase. The protein through virus enters the host cell-human angiotensin-converting enzyme 2 (ACE2) receptor, is also used as a target for molecular docking. The docking was done with most discussed drugs for SARS-CoV-2 like Ritonavir, Lopinavir, Remdesivir, Chloroquine, Hydroxychloroquine (HCQ), routine antiviral drugs like Oseltamivir and Ribavirin. In addition, small molecules with anti-inflammatory actions like Mycophenolic acid (MPA), Pemirolast, Isoniazid and Eriodictyol were also tested. The generated data confirms the potential of Ritonavir, Lopinavir and Remdesivir as a therapeutic candidate against SARS-CoV-2. It is observed that Eriodictyol binds to almost all selected target proteins with good binding energy, suggesting its importance in treatment of COVID 19. Molecular interactions of Ritonavir, Lopinavir and Remdesivir against SARS-CoV-2 proteins enhanced their potential as a candidate drug for treatment of COVID-19. Eriodictyol had emerged as a new repurposing drug that can be used in COVID-19.
Keywords	covid19
Publisher	WHO
Document type	Article
Note	WHO #Covidence: #691915
Database	COVID19

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Article ; Online: TOR signalling is required for host lipid metabolic remodelling and survival following enteric infection in Drosophila.

Deshpande, Rujuta / Lee, Byoungchun / Qiao, Yuemeng / Grewal, Savraj S

Disease models & mechanisms

2022 Volume 15, Issue 5

Abstract: When infected by enteric pathogenic bacteria, animals need to initiate local and whole-body defence strategies. Although most attention has focused on the role of innate immune anti-bacterial responses, less is known about how changes in host metabolism ... ...

Abstract	When infected by enteric pathogenic bacteria, animals need to initiate local and whole-body defence strategies. Although most attention has focused on the role of innate immune anti-bacterial responses, less is known about how changes in host metabolism contribute to host defence. Using Drosophila as a model system, we identify induction of intestinal target-of-rapamycin (TOR) kinase signalling as a key adaptive metabolic response to enteric infection. We find that enteric infection induces both local and systemic induction of TOR independently of the Immune deficiency (IMD) innate immune pathway, and we see that TOR functions together with IMD signalling to promote infection survival. These protective effects of TOR signalling are associated with remodelling of host lipid metabolism. Thus, we see that TOR is required to limit excessive infection-mediated wasting of host lipid stores by promoting an increase in the levels of gut- and fat body-expressed lipid synthesis genes. Our data support a model in which induction of TOR represents a host tolerance response to counteract infection-mediated lipid wasting in order to promote survival. This article has an associated First Person interview with the first author of the paper.
MeSH term(s)	Animals ; Drosophila ; Drosophila Proteins/metabolism ; Humans ; Immunity, Innate ; Lipids ; Sirolimus
Chemical Substances	Drosophila Proteins ; Lipids ; Sirolimus (W36ZG6FT64)
Language	English
Publishing date	2022-05-09
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2451104-3
ISSN	1754-8411 ; 1754-8403
ISSN (online)	1754-8411
ISSN	1754-8403
DOI	10.1242/dmm.049551
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Ras/ERK-signalling promotes tRNA synthesis and growth via the RNA polymerase III repressor Maf1 in Drosophila.

Sriskanthadevan-Pirahas, Shrivani / Deshpande, Rujuta / Lee, Byoungchun / Grewal, Savraj S

PLoS genetics

2018 Volume 14, Issue 2, Page(s) e1007202

Abstract: The small G-protein Ras is a conserved regulator of cell and tissue growth. These effects of Ras are mediated largely through activation of a canonical RAF-MEK-ERK kinase cascade. An important challenge is to identify how this Ras/ERK pathway alters ... ...

Abstract	The small G-protein Ras is a conserved regulator of cell and tissue growth. These effects of Ras are mediated largely through activation of a canonical RAF-MEK-ERK kinase cascade. An important challenge is to identify how this Ras/ERK pathway alters cellular metabolism to drive growth. Here we report on stimulation of RNA polymerase III (Pol III)-mediated tRNA synthesis as a growth effector of Ras/ERK signalling in Drosophila. We find that activation of Ras/ERK signalling promotes tRNA synthesis both in vivo and in cultured Drosophila S2 cells. We also show that Pol III function is required for Ras/ERK signalling to drive proliferation in both epithelial and stem cells in Drosophila tissues. We find that the transcription factor Myc is required but not sufficient for Ras-mediated stimulation of tRNA synthesis. Instead we show that Ras signalling promotes Pol III function and tRNA synthesis by phosphorylating, and inhibiting the nuclear localization and function of the Pol III repressor Maf1. We propose that inhibition of Maf1 and stimulation of tRNA synthesis is one way by which Ras signalling enhances protein synthesis to promote cell and tissue growth.
MeSH term(s)	Animals ; Animals, Genetically Modified ; Cell Proliferation/genetics ; Cells, Cultured ; Drosophila Proteins/genetics ; Drosophila Proteins/physiology ; Drosophila melanogaster/embryology ; Drosophila melanogaster/genetics ; Embryo, Nonmammalian ; MAP Kinase Signaling System/physiology ; Protein Biosynthesis/genetics ; RNA Polymerase III/antagonists & inhibitors ; RNA, Transfer/biosynthesis ; RNA, Transfer/genetics ; Repressor Proteins/genetics ; Repressor Proteins/physiology ; Signal Transduction/physiology ; Transcription Elongation, Genetic ; Transcription Factor TFIIIB/genetics ; Transcription Factor TFIIIB/physiology ; Wings, Animal/embryology ; Wings, Animal/metabolism ; ras Proteins/physiology
Chemical Substances	Brf protein, Drosophila ; Drosophila Proteins ; Maf1 protein, Drosophila ; Repressor Proteins ; Transcription Factor TFIIIB ; RNA, Transfer (9014-25-9) ; RNA Polymerase III (EC 2.7.7.6) ; ras Proteins (EC 3.6.5.2)
Language	English
Publishing date	2018-02-05
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2186725-2
ISSN	1553-7404 ; 1553-7390
ISSN (online)	1553-7404
ISSN	1553-7390
DOI	10.1371/journal.pgen.1007202
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: The Immune Deficiency Pathway Regulates Metabolic Homeostasis in

Davoodi, Saeideh / Galenza, Anthony / Panteluk, Andrew / Deshpande, Rujuta / Ferguson, Meghan / Grewal, Savraj / Foley, Edan

Journal of immunology (Baltimore, Md. : 1950)

2019 Volume 202, Issue 9, Page(s) 2747–2759

Abstract: Immune and metabolic pathways collectively influence host responses to microbial invaders, and mutations in one pathway frequently disrupt activity in another. We used ... ...

Abstract	Immune and metabolic pathways collectively influence host responses to microbial invaders, and mutations in one pathway frequently disrupt activity in another. We used the
MeSH term(s)	Animals ; Drosophila melanogaster ; Homeostasis/genetics ; Homeostasis/immunology ; Immunity, Innate ; Mutation ; Signal Transduction/genetics ; Signal Transduction/immunology
Language	English
Publishing date	2019-03-22
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	3056-9
ISSN	1550-6606 ; 0022-1767 ; 1048-3233 ; 1047-7381
ISSN (online)	1550-6606
ISSN	0022-1767 ; 1048-3233 ; 1047-7381
DOI	10.4049/jimmunol.1801632
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Zs.MG 28: Show issues

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Article: Efficiency of Biosynthesized Silver and Zinc Nanoparticles Against Multi-Drug Resistant Pathogens.

Punjabi, Kapil / Mehta, Sourabh / Chavan, Rujuta / Chitalia, Vidushi / Deogharkar, Dhanashree / Deshpande, Sunita

Frontiers in microbiology

2018 Volume 9, Page(s) 2207

Abstract: Biosynthesis of metallic nanoparticles has acquired particular attention due to its economic feasibility, low toxicity, and simplicity of the process. In this study, extracellular synthesis of silver and zinc nanoparticle was carried out ... ...

Abstract	Biosynthesis of metallic nanoparticles has acquired particular attention due to its economic feasibility, low toxicity, and simplicity of the process. In this study, extracellular synthesis of silver and zinc nanoparticle was carried out by
Language	English
Publishing date	2018-09-20
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2587354-4
ISSN	1664-302X
ISSN	1664-302X
DOI	10.3389/fmicb.2018.02207
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Article ; Online: Short term analysis of healed post-tubercular kyphosis in younger children based on principles of congenital kyphosis.

Deshpande, Shantanu S / Mehta, Rujuta / Yagnik, Mg

Indian journal of orthopaedics

2012 Volume 46, Issue 2, Page(s) 179–185

Abstract: Background: The patients with healed severe progressive tubercular kyphosis may develop late-onset paraplegia. A particular subgroup of these children (Type IB progression) may benefit from the management principles of congenital kyphosis. Self- ... ...

Abstract	Background: The patients with healed severe progressive tubercular kyphosis may develop late-onset paraplegia. A particular subgroup of these children (Type IB progression) may benefit from the management principles of congenital kyphosis. Self-correction may be observed by selective continued growth of anterior vertebral epiphyseal end-plates over the posterior fused mass. We report a series of cases with posterior fusion of progressive post-tubercular kyphosis with an aim to prevent further progression of kyphosis and to assess if any gradual self correction is seen in followup. Materials and methods: Twelve children fulfilling inclusion criteria of clinicoradiological, hematological diagnosis of healed spine TB having no or <2 spine at risk signs having documented progression of kyphosis and neural deficit underwent posterior fusion in situ without instrumentation, using autogenous iliac crest grafts as well as allograft donor bone graft. They were followed up to maximum of 5 years. Results: All 12 children had a progressive increase in angle preoperatively. Mean followup was 3.6 years. Post surgery, 66% showed a clinical improvement and correction, 25% had static angle, and worsening in one patient. Thus, overall 91% have a favorable result. Conclusion: The mechanism of correction of deformity in presence of posterior fusion is continued growth of the anterior epiphyseal end plates and hence this leads to selective differential anterior column growth giving gradual correction of kyphosis. This avoids anterior, technically demanding and complex, internal gibbus surgeries. This procedure is simple, safe, and less morbid with good results, avoiding long term disability to the patients in selected group of patients.
Language	English
Publishing date	2012-03-22
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	603194-8
ISSN	1998-3727 ; 0019-5413
ISSN (online)	1998-3727
ISSN	0019-5413
DOI	10.4103/0019-5413.93687
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Article ; Online: TOR signalling is required for host lipid metabolic remodelling and survival following enteric infection in Drosophila

Rujuta Deshpande / Byoungchun Lee / Yuemeng Qiao / Savraj S. Grewal

Disease Models & Mechanisms, Vol 15, Iss

2022 Volume 5

Abstract	When infected by enteric pathogenic bacteria, animals need to initiate local and whole-body defence strategies. Although most attention has focused on the role of innate immune anti-bacterial responses, less is known about how changes in host metabolism contribute to host defence. Using Drosophila as a model system, we identify induction of intestinal target-of-rapamycin (TOR) kinase signalling as a key adaptive metabolic response to enteric infection. We find that enteric infection induces both local and systemic induction of TOR independently of the Immune deficiency (IMD) innate immune pathway, and we see that TOR functions together with IMD signalling to promote infection survival. These protective effects of TOR signalling are associated with remodelling of host lipid metabolism. Thus, we see that TOR is required to limit excessive infection-mediated wasting of host lipid stores by promoting an increase in the levels of gut- and fat body-expressed lipid synthesis genes. Our data support a model in which induction of TOR represents a host tolerance response to counteract infection-mediated lipid wasting in order to promote survival. This article has an associated First Person interview with the first author of the paper.
Keywords	drosophila ; tor ; infection ; lipid metabolism ; physiology ; Medicine ; R ; Pathology ; RB1-214
Subject code	570
Language	English
Publishing date	2022-05-01T00:00:00Z
Publisher	The Company of Biologists
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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