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Article ; Online: Comparative assessment of RNA-dependent RNA polymerase (RdRp) inhibitors under clinical trials to control SARS-CoV2 using rigorous computational workflow.

Goswami, Dweipayan

RSC advances

2021 Volume 11, Issue 46, Page(s) 29015–29028

Abstract: The devastating effect of SARS-CoV2 continues and the scientific community is pursuing to find the strategy to combat the spread of the virus. The approach is adapted to target this virus with medicine in combination with existing vaccines. For this, the ...

Abstract	The devastating effect of SARS-CoV2 continues and the scientific community is pursuing to find the strategy to combat the spread of the virus. The approach is adapted to target this virus with medicine in combination with existing vaccines. For this, the medications that can specifically inhibit an enzyme essential for viral replication 'RNA-dependant-RNA polymerase (RdRp)' of SARS-CoV2 are being developed. RdRp is the enzyme commonly found in all RNA viruses but is absent in humans. There are in total 60 different RdRp inhibitors already under clinical trials for combating other RNA viruses, which are sought to even work for SARS-CoV2. These inhibitors are classified as nucleoside/nucleotide analogues and nonnucleoside/nonnucleotide analogues. In this study, all the known RdRp inhibitors were computationally targeted in the native form and their active form making the use of molecular docking, MM-GBSA and molecular dynamics (MD) simulations to find the top two of each nucleoside/nucleotide analogues and nonnucleoside/nonnucleotide analogues. The results showed ribavirin 5'-triphosphate and favipiravir ribonucleoside triphosphate (favipiravir-RTP) to be the top two nucleotide analogues while pimodivir and dihydropyrazolopyridinone analogue 8d were the top two nonnucleosides/non-nucleotide analogues.
Language	English
Publishing date	2021-09-02
Publishing country	England
Document type	Journal Article
ISSN	2046-2069
ISSN (online)	2046-2069
DOI	10.1039/d1ra04460e
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Article ; Online: Understanding mastitis: Microbiome, control strategies, and prevalence - A comprehensive review.

Panchal, Janki / Patel, Arun / Patel, Sandip / Goswami, Dweipayan

Microbial pathogenesis

2024 Volume 187, Page(s) 106533

Abstract: Mastitis significantly affects the udder tissue in dairy cattle, leading to inflammation, discomfort, and a decline in both milk yield and quality. The condition can be attributed to an array of microbial agents that access the mammary gland through ... ...

Abstract	Mastitis significantly affects the udder tissue in dairy cattle, leading to inflammation, discomfort, and a decline in both milk yield and quality. The condition can be attributed to an array of microbial agents that access the mammary gland through multiple pathways. The ramifications of this ailment are not merely confined to animal welfare but extend to the financial viability of the livestock industry. This review offers a historical lens on mastitis, tracing its documentation back to 1851, and examines its global distribution with a focus on regional differences in prevalence and antimicrobial resistance (AMR) patterns. Specific microbial genes and communities implicated in both mastitis and AMR are explored, including Staphylococcus aureus, Streptococcus agalactiae,Streptococcus dysagalactiae, Streptococcus uberis Escherichia coli, Klebsiella pneumoniae, Mycoplasma bovis, Corynebacterium bovis, among others. These microorganisms have evolved diverse strategies to elude host immune responses and neutralize commonly administered antibiotics, complicating management efforts. The review aims a comprehensive overview of the current knowledge and research gaps on mastitis and AMR, and to highlight the need for a One Health approach to address this global health issue. Such an approach entails multi-disciplinary cooperation to foster judicious antibiotic use, enhance preventive measures against mastitis, and bolster surveillance and monitoring of AMR in pathogens responsible for mastitis.
MeSH term(s)	Animals ; Female ; Cattle ; Humans ; Prevalence ; Anti-Bacterial Agents/pharmacology ; Anti-Bacterial Agents/therapeutic use ; Anti-Bacterial Agents/metabolism ; Streptococcus agalactiae ; Milk/microbiology ; Escherichia coli ; Microbiota ; Mastitis, Bovine/epidemiology ; Mastitis, Bovine/prevention & control ; Mastitis, Bovine/metabolism
Chemical Substances	Anti-Bacterial Agents
Language	English
Publishing date	2024-01-01
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	632772-2
ISSN	1096-1208 ; 0882-4010
ISSN (online)	1096-1208
ISSN	0882-4010
DOI	10.1016/j.micpath.2023.106533
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Article: Comparative assessment of RNA-dependent RNA polymerase (RdRp) inhibitors under clinical trials to control SARS-CoV2 using rigorous computational workflow

Goswami, Dweipayan

RSC advances. 2021 Sept. 02, v. 11, no. 46

2021

Abstract	The devastating effect of SARS-CoV2 continues and the scientific community is pursuing to find the strategy to combat the spread of the virus. The approach is adapted to target this virus with medicine in combination with existing vaccines. For this, the medications that can specifically inhibit an enzyme essential for viral replication ‘RNA-dependant-RNA polymerase (RdRp)’ of SARS-CoV2 are being developed. RdRp is the enzyme commonly found in all RNA viruses but is absent in humans. There are in total 60 different RdRp inhibitors already under clinical trials for combating other RNA viruses, which are sought to even work for SARS-CoV2. These inhibitors are classified as nucleoside/nucleotide analogues and nonnucleoside/nonnucleotide analogues. In this study, all the known RdRp inhibitors were computationally targeted in the native form and their active form making the use of molecular docking, MM-GBSA and molecular dynamics (MD) simulations to find the top two of each nucleoside/nucleotide analogues and nonnucleoside/nonnucleotide analogues. The results showed ribavirin 5′-triphosphate and favipiravir ribonucleoside triphosphate (favipiravir-RTP) to be the top two nucleotide analogues while pimodivir and dihydropyrazolopyridinone analogue 8d were the top two nonnucleosides/non-nucleotide analogues.
Keywords	RNA ; RNA-directed RNA polymerase ; medicine ; molecular dynamics ; nucleosides ; virus replication ; viruses
Language	English
Dates of publication	2021-0902
Size	p. 29015-29028.
Publishing place	The Royal Society of Chemistry
Document type	Article
ISSN	2046-2069
DOI	10.1039/d1ra04460e
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Article ; Online: Probing the effects of streptomycin on Brassica napus germination and assessing its molecular interactions using extensive molecular dynamics (MD) simulations.

Patel, Rohit / Prajapati, Karan / Goswami, Dweipayan / Saraf, Meenu

Scientific reports

2023 Volume 13, Issue 1, Page(s) 19066

Abstract: Antibiotics are chemical compounds that are used to treat and prevent disease in humans and animals. They have been used in animal feed for over 60 years and are widely used in industrial farming. Antibiotics can have negative environmental impacts, ... ...

Abstract	Antibiotics are chemical compounds that are used to treat and prevent disease in humans and animals. They have been used in animal feed for over 60 years and are widely used in industrial farming. Antibiotics can have negative environmental impacts, including the potential to contribute to the development of antibiotic-resistant organisms. They can enter the environment through various pathways, including the manufacturing process, the direct application of antibiotic-laden manure to fields, and through grazing animals. Antibiotics that are given to animals can be excreted from where they can enter soil and groundwater which enable their entry in plants. Streptomycin is an antibiotic that is used against a range of gram-positive and gram-negative bacteria, but its use has led to the development of antibiotic resistance in some pathogens. It has also been shown to have negative impacts on a range of plant species, including tobacco, tomato, and wheat. Although, the major effect of streptomycin on plant physiology have been studied, the molecular mechanisms at play are barely understood in plant body. In current study, we examined the impact of streptomycin on germination of Brassica napus and then using docking, MM-GBBSA and MD simulations identified key proteins that interact with streptomycin by performing rigorous computational screening of 106 different proteins. Our finding suggest that streptomycin might be interacting with acyl-CoA oxidases, protochlorophyllide reductase B and leucoanthocyanidin dioxygenase based on simulation and docking analysis.
MeSH term(s)	Humans ; Animals ; Streptomycin/pharmacology ; Brassica napus ; Anti-Bacterial Agents/pharmacology ; Molecular Dynamics Simulation ; Gram-Negative Bacteria ; Gram-Positive Bacteria
Chemical Substances	Streptomycin (Y45QSO73OB) ; Anti-Bacterial Agents
Language	English
Publishing date	2023-11-04
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-023-46100-4
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Article ; Online: Pinpointing top inhibitors for GSK3β from pool of indirubin derivatives using rigorous computational workflow and their validation using molecular dynamics (MD) simulations.

Pandya, Vamangi / Rao, Priyashi / Prajapati, Jignesh / Rawal, Rakesh M / Goswami, Dweipayan

Scientific reports

2024 Volume 14, Issue 1, Page(s) 49

Abstract: Glycogen synthase kinase-3β (GSK3β) is a pivotal protein kinase implicated in a spectrum of debilitating diseases, encompassing cancer, diabetes, and neurodegenerative disorders. While the therapeutic potential of GSK3β inhibition is widely recognized, ... ...

Abstract	Glycogen synthase kinase-3β (GSK3β) is a pivotal protein kinase implicated in a spectrum of debilitating diseases, encompassing cancer, diabetes, and neurodegenerative disorders. While the therapeutic potential of GSK3β inhibition is widely recognized, there remains an unmet need for a rigorous, systematic analysis probing the theoretical inhibition dynamics of a comprehensive library of indirubin derivatives against GSK3β using advanced computational methodologies. Addressing this gap, this study embarked on an ambitious endeavor, leveraging indirubin-a renowned scaffold-as a template to curate a vast library of 1000 indirubin derivatives from PubChem. These were enriched with varied substitutions and modifications, identified via a structure similarity search with a Tanimoto similarity threshold of 85%. Harnessing a robust virtual screening workflow, we meticulously identified the top 10 contenders based on XP docking scores. Delving deeper, we gauged the binding free energy differentials (ΔGBind) of these hits, spotlighting the top three compounds that showcased unparalleled binding prowess. A comparative pharmacophore feature mapping with the reference inhibitor OH8, co-crystallized with GSK3β (PDB ID: 6Y9R), was undertaken. The binding dynamics of these elite compounds were further corroborated with 100 ns molecular dynamics simulations, underlining their stable and potent interactions with GSK3β. Remarkably, our findings unveil that these indirubin derivatives not only match but, in certain scenarios, surpass the binding affinity and specificity of OH8. By bridging this research chasm, our study amplifies the therapeutic promise of indirubin derivatives, positioning them as frontrunners in the quest for groundbreaking GSK3β inhibitors, potentially revolutionizing treatments for a myriad of ailments.
MeSH term(s)	Molecular Dynamics Simulation ; Glycogen Synthase Kinase 3 beta ; Workflow ; Indoles/pharmacology ; Molecular Docking Simulation
Chemical Substances	Glycogen Synthase Kinase 3 beta (EC 2.7.11.1) ; indirubin (V86L8P74GI) ; Indoles
Language	English
Publishing date	2024-01-02
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/s41598-023-50992-7
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Article ; Online: Extending the lore of curcumin as dipteran Butyrylcholine esterase (BChE) inhibitor: A holistic molecular interplay assessment.

Rao, Priyashi / Goswami, Dweipayan / Rawal, Rakesh M

PloS one

2022 Volume 17, Issue 5, Page(s) e0269036

Abstract: Since its origin, the emergence of vector-borne infections has taken a toll on incalculable human lives. The use of chemical insecticides is one of the early known methods of vector control and although their use is still a prevalent way to combat insect ...

Abstract	Since its origin, the emergence of vector-borne infections has taken a toll on incalculable human lives. The use of chemical insecticides is one of the early known methods of vector control and although their use is still a prevalent way to combat insect population sadly the perils of insects related transmission still persists. Most commonly, the existing insecticides face the wrath of getting resisted repeatedly, paying way to develop resilient, efficient, and cost-effective natural insecticides. In this study, computational screening was performed using homology modelling, E-pharmacophore feature mapping, molecular docking, Density Function Theory (DFT) assessment, Molecular mechanics generalized Born surface area (MM-GBSA) based binding free energy calculations and Molecular Dynamics (MD) simulation to identify a potential lead phytochemical out of a manually curated library from published literature. The protein target used under this study is insect Butyrylcholine esterase (BChE). Additionally, in vitro insect (Aedes aegypti) BChE inhibition assay was also performed with the top phytochemical identified from in silico assessments. Our research highlights that curcumin leads to inhibition of enzyme BChE of Ae. aegypti. The identified mode of action of curcumin as an insect BChE inhibitor indicates the possibility of its use as an environment friendly and natural futuristic insecticide.
MeSH term(s)	Aedes ; Animals ; Choline/analogs & derivatives ; Cholinesterases/metabolism ; Curcumin/metabolism ; Curcumin/pharmacology ; Enzyme Inhibitors/pharmacology ; Humans ; Insecticide Resistance ; Insecticides/metabolism ; Insecticides/pharmacology ; Molecular Docking Simulation ; Mosquito Vectors/metabolism
Chemical Substances	Enzyme Inhibitors ; Insecticides ; butyrylcholine (3922-86-9) ; Cholinesterases (EC 3.1.1.8) ; Curcumin (IT942ZTH98) ; Choline (N91BDP6H0X)
Language	English
Publishing date	2022-05-26
Publishing country	United States
Document type	Journal Article
ZDB-ID	2267670-3
ISSN	1932-6203 ; 1932-6203
ISSN (online)	1932-6203
ISSN	1932-6203
DOI	10.1371/journal.pone.0269036
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Article ; Online: Molecular insights on ar-turmerone as a structural, functional and pharmacophoric analogue of synthetic mosquito repellent DEET by comprehensive computational assessment.

Rao, Priyashi / Goswami, Dweipayan / Rawal, Rakesh M

Scientific reports

2022 Volume 12, Issue 1, Page(s) 15564

Abstract: Mosquitoes are vectors for a variety of infectious illnesses, and chemical synthetic insecticides have made it possible to control them effectively. Mosquito repellents are a typical means of keeping mosquitos at bay. Because of its main effectiveness of ...

Abstract	Mosquitoes are vectors for a variety of infectious illnesses, and chemical synthetic insecticides have made it possible to control them effectively. Mosquito repellents are a typical means of keeping mosquitos at bay. Because of its main effectiveness of skin permeability, N,N-Diethyl-meta-toluamide (DEET) is one of the most extensively used mosquito repellents but a dangerous synthetic chemical. DEET was identified about a decade ago to inhibit mosquito's Odorant Binding Protein 1 (OBP1), impairing the mosquito's ability to recognise the host body odour. OBP1 has been identified as a possible target for the development of new mosquito repellents since its discovery. Essential oils from different plants, on the other hand, have been used to repel mosquitos since antiquity. One essential oil from the Curcuma longa (Zingiberales: Zingiberaceae) rhizome display mosquito repellent properties, according to the literature. Furthermore, one of the phytochemicals found in abundance in C. longa essential oil, ar-turmerone, exhibits mosquito repellency as comparable to synthetic DEET. Till date studies on in-silico interaction of natural ar-turmerone with OBP1, which we depict in our current work are scarce. Further, there exist no published reports demonstrating the literary evidence on detailed insights of interaction of DEET with OBP1 along with Molecular Dynamics (MD) simulation studies. We further performed detailed molecular investigations using pharmacophore analysis of ar-turmerone and compared it with DEET, where our findings in the current manuscript unveils for the first time that ar-turmerone is a functional, structural and pharmacophoric analogue of DEET.
MeSH term(s)	Animals ; DEET/pharmacology ; Insect Repellents/chemistry ; Insect Repellents/pharmacology ; Insecticides ; Ketones ; Oils, Volatile/chemistry ; Oils, Volatile/pharmacology ; Sesquiterpenes
Chemical Substances	Insect Repellents ; Insecticides ; Ketones ; Oils, Volatile ; Sesquiterpenes ; DEET (134-62-3) ; ar-turmerone (1944T899NO)
Language	English
Publishing date	2022-09-16
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-022-19901-2
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Article: An Anecdote on Prospective Protein Targets for Developing Novel Plant Growth Regulators

Patel, Rohit / Mehta, Krina / Goswami, Dweipayan / Saraf, Meenu

Molecular biotechnology. 2022 Feb., v. 64, no. 2

2022

Abstract: Phytohormones are the main regulatory molecules of core signalling networks associated with plant life cycle regulation. Manipulation of hormone signalling cascade enables the control over physiological traits of plant, which has major applications in ... ...

Abstract	Phytohormones are the main regulatory molecules of core signalling networks associated with plant life cycle regulation. Manipulation of hormone signalling cascade enables the control over physiological traits of plant, which has major applications in field of agriculture and food sustainability. Hence, stable analogues of these hormones are long sought after and many of them are currently known, but the quest for more effective, stable and economically viable analogues is still going on. This search has been further strengthened by the identification of the components of signalling cascade such as receptors, downstream cascade members and transcription factors. Furthermore, many proteins of phytohormone cascades are available in crystallized forms. Such crystallized structures can provide the basis for identification of novel interacting compounds using in silico approach. Plenty of computational tools and bioinformatics software are now available that can aid in this process. Here, the metadata of all the major phytohormone signalling cascades are presented along with discussion on major protein–ligand interactions and protein components that may act as a potential target for manipulation of phytohormone signalling cascade. Furthermore, structural aspects of phytohormones and their known analogues are also discussed that can provide the basis for the synthesis of novel analogues.
Keywords	bioinformatics ; biotechnology ; computer simulation ; computer software ; crystallization ; economic sustainability ; metadata ; plant growth ; plant hormones ; sustainable agriculture
Language	English
Dates of publication	2022-02
Size	p. 109-129.
Publishing place	Springer US
Document type	Article
Note	Review
ZDB-ID	1193057-3
ISSN	1559-0305 ; 1073-6085
ISSN (online)	1559-0305
ISSN	1073-6085
DOI	10.1007/s12033-021-00404-w
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: A clash of quorum sensing vs quorum sensing inhibitors: an overview and risk of resistance

Patel, Rohit / Soni, Mansi / Soyantar, Bilv / Shivangi, Suruchi / Sutariya, Swati / Saraf, Meenu / Goswami, Dweipayan

Arch Microbiol. 2023 Apr., v. 205, no. 4 p.107-107

2023

Abstract: Indiscriminate use of antibiotics to treat microbial pathogens has caused emergence of multiple drug resistant strains. Most infectious diseases are caused by microbes that are capable of intercommunication using signaling molecules, which is known as ... ...

Abstract	Indiscriminate use of antibiotics to treat microbial pathogens has caused emergence of multiple drug resistant strains. Most infectious diseases are caused by microbes that are capable of intercommunication using signaling molecules, which is known as quorum sensing (QS). Such pathogens express their pathogenicity through various QS-regulated virulence factors. Interference of QS could lead to decisive results in controlling such pathogenicity. Hence, QS inhibition has become an attractive new approach for the development of novel drugs. Many quorum sensing inhibitors (QSIs) of diverse origins have been reported. It is imperative that more such anti-QS compounds be found and studied, as they have significant effect on microbial pathogenicity. This review attempts to give a brief account of QS mechanism, its inhibition and describes some compounds with anti-QS potential. Also discussed is the possibility of emergence of quorum sensing resistance.
Keywords	multiple drug resistance ; risk ; virulence
Language	English
Dates of publication	2023-04
Size	p. 107.
Publishing place	Springer Berlin Heidelberg
Document type	Article ; Online
Note	Review
ZDB-ID	124824-8
ISSN	1432-072X ; 0302-8933
ISSN (online)	1432-072X
ISSN	0302-8933
DOI	10.1007/s00203-023-03442-x
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Curcumin interferes with chitin synthesis in Aedes aegypti: a computational and experimental investigation.

Rao, Priyashi / Ninama, Jinal / Dudhat, Mansi / Goswami, Dweipayan / Rawal, Rakesh M

Molecular diversity

2023

Abstract: Throughout history, vector-borne diseases have consistently posed significant challenges to human health. Among the strategies for vector control, chemical insecticides have seen widespread use since their inception. Nevertheless, their effectiveness is ... ...

Abstract	Throughout history, vector-borne diseases have consistently posed significant challenges to human health. Among the strategies for vector control, chemical insecticides have seen widespread use since their inception. Nevertheless, their effectiveness is continually undermined by the steady growth of insecticide resistance within these vector populations. As such, the demand for more robust, efficient, and cost-effective natural insecticides has become increasingly pressing. One promising avenue of research focuses on chitin, a crucial structural component of mosquitoes' exoskeletons and other insects. Chitin not only provides protection and rigidity but also lends flexibility to the insect body. It undergoes substantial transformations during insect molting, a process known as ecdysis. Crucially, the production of chitin is facilitated by an enzyme known as chitin synthase, making it an attractive target for potential novel insecticides. Our recent study delved into the impacts of curcumin, a natural derivative of turmeric, on chitin synthesis and larval development in Aedes aegypti, a mosquito species known to transmit dengue and yellow fever. Our findings demonstrate that even sub-lethal amounts of curcumin can significantly reduce overall chitin content and disrupt the cuticle development in the 4th instar larvae of Aedes aegypti. Further to this, we utilized computational analyses to investigate how curcumin interacts with chitin synthase. Techniques such as molecular docking, pharmacophore feature mapping, and molecular dynamics (MD) simulations helped to illustrate that curcumin binds to the same site as polyoxin D, a recognized inhibitor of chitin synthase. These findings point to curcumin's potential as a natural, bioactive larvicide that targets chitin synthase in mosquitoes and potentially other insects.
Language	English
Publishing date	2023-06-26
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	1376507-3
ISSN	1573-501X ; 1381-1991
ISSN (online)	1573-501X
ISSN	1381-1991
DOI	10.1007/s11030-023-10672-0
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