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Article ; Online: Mitigating climate change and pandemic impacts on global food security: dual sustainable agriculture approach (2S approach).

Sarker, Protup Kumer / Paul, Archi Sundar / Karmoker, Dola

2023 Volume 258, Issue 6, Page(s) 104

Abstract: Main conclusion: Simultaneous application of two sustainability approaches such as the application of biofertilizers to GM plants and microbe bioengineering to enhance physiological response and beneficial interaction with GM plants may have a ... ...

Abstract	Main conclusion: Simultaneous application of two sustainability approaches such as the application of biofertilizers to GM plants and microbe bioengineering to enhance physiological response and beneficial interaction with GM plants may have a significant impact on strengthening global food security amid climate change and the pandemic. The second sustainable development goal (SDG 02, Zero Hunger) aims global agricultural sustainability and food security challenges. The agriculture sector has been an integral part of developing countries for millions of farmers and their families. Their contribution provides stability of raw matter related to food availability. But climate change, higher population growth and worldwide pandemics are the main obstacles to food quality, higher crop productivity and global food security. Scientists are concerned with the manifestation of agriculture sustainability in the modern crop management approach to resolving the issues. It is the only way to higher yield productivity by protecting the environment, conserving natural resources, and slowing climate change. Several strategies can be an option to implement, yet the proposed two sustainability approach or 2S approach will be the significant way toward the goal of zero hunger. The first sustainability approach is an application of genetically modified (S1: GMO) Plants and the other is an application of beneficiary plant growth-promoting microbes (S2: Biofertilizers) to the plants for both higher crops and maintenance of the environment. This study summarizes the essential points of S1 and S2 for the widespread utilization of the 2S approach in agriculture and recommends the potential alternatives to be implemented to produce food for all. Simultaneous application of the 2S approach can defeat all threats to gain sustainability in agriculture.
MeSH term(s)	Humans ; Climate Change ; Pandemics ; Agriculture ; Crop Production ; Crops, Agricultural
Language	English
Publishing date	2023-10-25
Publishing country	Germany
Document type	Journal Article ; Review
ZDB-ID	208909-9
ISSN	1432-2048 ; 0032-0935 ; 1866-2749
ISSN (online)	1432-2048
ISSN	0032-0935 ; 1866-2749
DOI	10.1007/s00425-023-04257-2
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Article ; Online: Antiviral phytochemicals as potent inhibitors against NS3 protease of dengue virus.

Rahman, Md Mahbubur / Biswas, Sourav / Islam, Kazi Jahidul / Paul, Archi Sundar / Mahato, Shiplob Kumar / Ali, Md Ackas / Halim, Mohammad A

Computers in biology and medicine

2021 Volume 134, Page(s) 104492

Abstract: Dengue, a mosquito-borne disease, has appeared as a major infectious disease globally. The virus requires its proteins to replicate and reproduce in the host cell. The NS3 protease converts the polyprotein to functional proteins with the help of the NS2B ...

Abstract	Dengue, a mosquito-borne disease, has appeared as a major infectious disease globally. The virus requires its proteins to replicate and reproduce in the host cell. The NS3 protease converts the polyprotein to functional proteins with the help of the NS2B cofactor. Thus, NS3 protease is a promising target to develop antiviral inhibitors against the dengue virus. A systematic screening including ADMET properties, molecular docking, molecular dynamics (MD) simulation, binding free energy calculation, and QSAR studies is carried out to predict potent inhibitors against the NS3 protease. From the screening of 40 antiviral phytochemicals, ADMET properties analysis was used to screen out ligands that violate ADME rules and have probable toxicity. Cyanidin 3-Glucoside, Dithymoquinone, and Glabridin were predicted to be potent inhibitors against the NS3 protease according to their binding affinity. These ligands showed several noncovalent interactions, including hydrogen bond, hydrophobic interaction, electrostatic interaction, pi-sulfur interactions. The ligand-protein complexes were further scrutinized using 250 ns molecular dynamics simulation. The MM-PBSA binding free energy calculation was conducted to investigate their binding stability in dynamic conditions. The calculated pIC50(mM) value was predicted using the QSAR model with 89.91% goodness of fit. The predicted biologocal activity value for the ligands indicates they might have good potency.
MeSH term(s)	Animals ; Antiviral Agents/pharmacology ; Dengue Virus ; Molecular Docking Simulation ; Peptide Hydrolases ; Phytochemicals/pharmacology ; Protease Inhibitors/pharmacology
Chemical Substances	Antiviral Agents ; Phytochemicals ; Protease Inhibitors ; Peptide Hydrolases (EC 3.4.-)
Language	English
Publishing date	2021-05-14
Publishing country	United States
Document type	Journal Article
ZDB-ID	127557-4
ISSN	1879-0534 ; 0010-4825
ISSN (online)	1879-0534
ISSN	0010-4825
DOI	10.1016/j.compbiomed.2021.104492
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Article ; Online: A molecular modeling approach to identify effective antiviral phytochemicals against the main protease of SARS-CoV-2.

Islam, Rajib / Parves, Md Rimon / Paul, Archi Sundar / Uddin, Nizam / Rahman, Md Sajjadur / Mamun, Abdulla Al / Hossain, Md Nayeem / Ali, Md Ackas / Halim, Mohammad A

Journal of biomolecular structure & dynamics

2020 Volume 39, Issue 9, Page(s) 3213–3224

Abstract: The main protease of SARS-CoV-2 is one of the important targets to design and develop antiviral drugs. In this study, we have selected 40 antiviral phytochemicals to find out the best candidates which can act as potent inhibitors against the main ... ...

Abstract	The main protease of SARS-CoV-2 is one of the important targets to design and develop antiviral drugs. In this study, we have selected 40 antiviral phytochemicals to find out the best candidates which can act as potent inhibitors against the main protease. Molecular docking is performed using AutoDock Vina and GOLD suite to determine the binding affinities and interactions between the phytochemicals and the main protease. The selected candidates strongly interact with the key Cys145 and His41 residues. To validate the docking interactions, 100 ns molecular dynamics (MD) simulations on the five top-ranked inhibitors including hypericin, cyanidin 3-glucoside, baicalin, glabridin, and α-ketoamide-11r are performed. Principal component analysis (PCA) on the MD simulation discloses that baicalin, cyanidin 3-glucoside, and α-ketoamide-11r have structural similarity with the apo-form of the main protease. These findings are also strongly supported by root-mean-square deviation (RMSD), root-mean-square fluctuation (RMSF), radius of gyration (Rg), and solvent accessible surface area (SASA) investigations. PCA is also used to find out the quantitative structure-activity relationship (QSAR) for pattern recognition of the best ligands. Multiple linear regression (MLR) of QSAR reveals the
MeSH term(s)	Antiviral Agents/pharmacology ; COVID-19 ; Humans ; Molecular Docking Simulation ; Peptide Hydrolases ; Phytochemicals/pharmacology ; SARS-CoV-2
Chemical Substances	Antiviral Agents ; Phytochemicals ; Peptide Hydrolases (EC 3.4.-)
Keywords	covid19
Language	English
Publishing date	2020-05-12
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2020.1761883
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Article ; Online: Cysteine focused covalent inhibitors against the main protease of SARS-CoV-2.

Paul, Archi Sundar / Islam, Rajib / Parves, Md Rimon / Mamun, Abdulla Al / Shahriar, Imrul / Hossain, Md Imran / Hossain, Md Nayeem / Ali, Md Ackas / Halim, Mohammad A

Journal of biomolecular structure & dynamics

2020 Volume 40, Issue 4, Page(s) 1639–1658

Abstract: In viral replication and transcription, the main protease (Mpro) of SARS-CoV-2 plays an important role and appears to be a vital target for drug design. In Mpro, there is a Cys-His catalytic dyad, and ligands that interact with the Cys145 assumed to be ... ...

Abstract	In viral replication and transcription, the main protease (Mpro) of SARS-CoV-2 plays an important role and appears to be a vital target for drug design. In Mpro, there is a Cys-His catalytic dyad, and ligands that interact with the Cys145 assumed to be an effective approach to inhibit the Mpro. In this study, approximately 1400 cysteine-focused ligands were screened to identify the best candidates that can act as potent inhibitors against Mpro. Our results show that the selected ligands strongly interact with the key Cys145 and His41 residues. Covalent docking was performed for the selected candidates containing the acrylonitrile group, which can form a covalent bond with Cys145. All atoms molecular dynamics (MD) simulation was performed on the selected four inhibitors including L1, L2, L3 and L4 to validate the docking interactions. Our results were also compared with a control ligand, α-ketoamide (11r). Principal component analysis on structural and energy data obtained from the MD trajectories shows that L1, L3, L4 and α-ketoamide (11r) have structural similarity with the apo-form of the Mpro. Quantitative structure-activity relationship method was employed for pattern recognition of the best ligands, which discloses that ligands containing acrylonitrile and amide warheads can show better performance. ADMET analysis displays that our selected candidates appear to be safer inhibitors. Our combined studies suggest that the best cysteine focused ligands can help to design an effective lead drug for COVID-19 treatment. Communicated by Ramaswamy H. Sarma.
MeSH term(s)	COVID-19 ; Coronavirus 3C Proteases/antagonists & inhibitors ; Cysteine ; Humans ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Protease Inhibitors/pharmacology ; SARS-CoV-2/drug effects ; SARS-CoV-2/enzymology ; Structure-Activity Relationship
Chemical Substances	Protease Inhibitors ; 3C-like proteinase, SARS-CoV-2 (EC 3.4.22.-) ; Coronavirus 3C Proteases (EC 3.4.22.28) ; Cysteine (K848JZ4886)
Keywords	covid19
Language	English
Publishing date	2020-10-13
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2020.1831610
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Article ; Online: A molecular modeling approach to identify effective antiviral phytochemicals against the main protease of SARS-CoV-2

Islam, Rajib / Parves, Md. Rimon / Paul, Archi Sundar / Uddin, Nizam / Rahman, Md. Sajjadur / Mamun, Abdulla Al / Hossain, Md. Nayeem / Ali, Md. Ackas / Halim, Mohammad A.

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	10.1080/07391102.2020.1761883
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Article ; Online: Cysteine focused covalent inhibitors against the main protease of SARS-CoV-2

Paul, Archi Sundar / Islam, Rajib / Parves, Md Rimon / Mamun, Abdulla Al / Shahriar, Imrul / Hossain, Md Imran / Hossain, Md Nayeem / Ali, Md Ackas / Halim, Mohammad A.

Journal of Biomolecular Structure and Dynamics

2020 , Page(s) 1–20

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	10.1080/07391102.2020.1831610
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Cysteine focused covalent inhibitors against the main protease of SARS-CoV-2

Paul, Archi Sundar / Islam, Rajib / Parves, Md Rimon / Mamun, Abdulla Al / Shahriar, Imrul / Hossain, Md Imran / Hossain, Md Nayeem / Ali, Md Ackas / Halim, Mohammad A

J Biomol Struct Dyn

Abstract	In viral replication and transcription, the main protease (Mpro) of SARS-CoV-2 plays an important role and appears to be a vital target for drug design. In Mpro, there is a Cys-His catalytic dyad, and ligands that interact with the Cys145 assumed to be an effective approach to inhibit the Mpro. In this study, approximately 1400 cysteine-focused ligands were screened to identify the best candidates that can act as potent inhibitors against Mpro. Our results show that the selected ligands strongly interact with the key Cys145 and His41 residues. Covalent docking was performed for the selected candidates containing the acrylonitrile group, which can form a covalent bond with Cys145. All atoms molecular dynamics (MD) simulation was performed on the selected four inhibitors including L1, L2, L3 and L4 to validate the docking interactions. Our results were also compared with a control ligand, α-ketoamide (11r). Principal component analysis on structural and energy data obtained from the MD trajectories shows that L1, L3, L4 and α-ketoamide (11r) have structural similarity with the apo-form of the Mpro. Quantitative structure-activity relationship method was employed for pattern recognition of the best ligands, which discloses that ligands containing acrylonitrile and amide warheads can show better performance. ADMET analysis displays that our selected candidates appear to be safer inhibitors. Our combined studies suggest that the best cysteine focused ligands can help to design an effective lead drug for COVID-19 treatment. Communicated by Ramaswamy H. Sarma.
Keywords	covid19
Publisher	WHO
Document type	Article
Note	WHO #Covidence: #851512
Database	COVID19

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Article: A molecular modeling approach to identify effective antiviral phytochemicals against the main protease of SARS-CoV-2

Islam, Rajib / Parves, Md Rimon / Paul, Archi Sundar / Uddin, Nizam / Rahman, Md Sajjadur / Mamun, Abdulla Al / Hossain, Md Nayeem / Ali, Md Ackas / Halim, Mohammad A

J Biomol Struct Dyn

Abstract	The main protease of SARS-CoV-2 is one of the important targets to design and develop antiviral drugs. In this study, we have selected 40 antiviral phytochemicals to find out the best candidates which can act as potent inhibitors against the main protease. Molecular docking is performed using AutoDock Vina and GOLD suite to determine the binding affinities and interactions between the phytochemicals and the main protease. The selected candidates strongly interact with the key Cys145 and His41 residues. To validate the docking interactions, 100 ns molecular dynamics (MD) simulations on the five top-ranked inhibitors including hypericin, cyanidin 3-glucoside, baicalin, glabridin, and α-ketoamide-11r are performed. Principal component analysis (PCA) on the MD simulation discloses that baicalin, cyanidin 3-glucoside, and α-ketoamide-11r have structural similarity with the apo-form of the main protease. These findings are also strongly supported by root-mean-square deviation (RMSD), root-mean-square fluctuation (RMSF), radius of gyration (Rg), and solvent accessible surface area (SASA) investigations. PCA is also used to find out the quantitative structure-activity relationship (QSAR) for pattern recognition of the best ligands. Multiple linear regression (MLR) of QSAR reveals the R2 value of 0.842 for the training set and 0.753 for the test set. Our proposed MLR model can predict the favorable binding energy compared with the binding energy detected from molecular docking. ADMET analysis demonstrates that these candidates appear to be safer inhibitors. Our comprehensive computational and statistical analysis show that these selected phytochemicals can be used as potential inhibitors against the SARS-CoV-2.Communicated by Ramaswamy H. Sarma.
Keywords	covid19
Publisher	WHO
Document type	Article
Note	WHO #Covidence: #143889
Database	COVID19

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Article ; Online: Reducing Ruminal Ammonia Production With Improvement in Feed Utilization Efficiency and Performance of Murrah Buffalo (Bubalus bubalis) Through Dietary Supplementation of Plant-Based Feed Additive Blend

Yendrembam Mery Chanu / Shyam Sundar Paul / Avijit Dey / Satbir Singh Dahiya

Frontiers in Veterinary Science, Vol

2020 Volume 7

Abstract: ... Butyrivibrio fibrisolvens, and Megasphaera elsdenii as well as anaerobic fungi and methanogenic archaea ...

Abstract	The study evaluated the potential of blends of eucalyptus oil and aqueous extract of mulethi (root of Glycyrrhiza glabra) to reduce rate of ruminal ammonia production without affecting feed digestion to improve nitrogen utilization efficiency and performance of Murrah buffalo (Bubalus bubalis). Based on preliminary independent studies with graded doses of eucalyptus oil and mulethi root aqueous extract in modulating in vitro rumen fermentation, four blends of feed additive comprising graded doses (5, 10, 15, and 25 μL) of eucalyptus oil and a fixed quantity (15 μL) of aqueous extract of mulethi roots were prepared and examined for their effects on in vitro rumen fermentation and on methane and gas production in 100-mL calibrated glass syringes by standard IVGP protocol. Rumen liquor was collected from four rumen fistulated Murrah buffaloes fed a total mixed ration. Out of four blends, blend-1 comprising 5 μL of eucalyptus oil and 15 μL of aqueous extract (233.6 g/L DW) of mulethi per 40 mL of in vitro medium was found to reduce ammonia production significantly (p < 0.001) without affecting feed digestibility. An equivalent dose of blend-1 (10.5 mL of eucalyptus oil and 7.35 g of mulethi root powder/h/day) fed to four rumen fistulated buffaloes for 24 days resulted in 50% reduction (p < 0.05) in rumen ammonia level with no inhibition in feed fermentation or short-chain fatty acid production. The total bacterial population including Ruminococcus albus, Fibrobacter succinogenes, Butyrivibrio fibrisolvens, and Megasphaera elsdenii as well as anaerobic fungi and methanogenic archaea remained unaffected (p > 0.05). Twelve buffalo calves (avg. BW 137.5 ± 9.2 kg, 8–12 months old) divided into two groups of six each and fed a total mixed ration (concentrate: roughage; 60:40) with or without supplementation of blend-1 for about 3 months demonstrated 14% increase (p < 0.05) in average daily gain in BW with a trend (p < 0.10) in improvement of feed or protein utilization efficiency (1.4 vs. 1.1 g crude ...
Keywords	eucalyptus oil ; licorice ; nitrogen efficiency ; plant bioactives ; ruminal ammonia production ; Veterinary medicine ; SF600-1100
Subject code	660
Language	English
Publishing date	2020-08-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
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