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Article: Chemical composition, antioxidant and antibacterial activity of

Rahman, Mohammad Mahfuzur / Dipti, Tyeaba Tasnim / Islam, M Nazrul / Abdullah, Abu Tareq Mohammad / Jahan, Sharmin / Alam, Md Morshedul / Karim, M Rezaul

Saudi journal of biological sciences

2023 Volume 30, Issue 6, Page(s) 103663

Abstract: Piper chaba: Practical applications: Natural preservatives are becoming more popular as a result of the different carcinogenic and toxic side effects of conventional preservatives. ...

Abstract	Piper chaba Practical applications: Natural preservatives are becoming more popular as a result of the different carcinogenic and toxic side effects of conventional preservatives.
Language	English
Publishing date	2023-04-29
Publishing country	Saudi Arabia
Document type	Journal Article
ZDB-ID	2515206-3
ISSN	2213-7106 ; 1319-562X
ISSN (online)	2213-7106
ISSN	1319-562X
DOI	10.1016/j.sjbs.2023.103663
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Article ; Online: A structure-based drug design approach for the identification of antiviral compounds targeting the chikungunya virus RdRp protein

Md. Hridoy Ahmed / Gagandeep Singh / Melvin Castrosanto / Alomgir Hossain / Md. Morshedul Islam Rifat / Sadia Hosna Rima / Vandana Gupta / Rajesh K. Kesharwani / Mariusz Jaremko / Abdul-Hamid Emwas / Prawez Alam / Faizul Azam

Chemical Physics Impact, Vol 8, Iss , Pp 100450- (2024)

2024

Abstract: ... We used MD simulations of the three best compounds that bind to the catalytic, palm, and thumb domains ...

Abstract	There are an estimated 3 million Chikungunya virus (CHIKV) infections per year, but no vaccines or specific pharmaceutical treatments are available. RNA-dependent RNA polymerase (RdRp) of CHIKV, encoded by nonstructural protein 4 (nsP4), was targeted to identify potential antiviral compounds in this study. A 3D model of the nsP4 was generated by homology modeling technique and Pockdrug-Server was used to predict ligand binding sites. The pharmacophore hypothesis was developed followed by virtual screening. 300 most potential ligands were selected from a library of 3000 compounds, after filtering for the molecules satisfying Lipinski's Rule of Five. Using molecular docking followed by ADMET analysis, 27 leads were then selected. We used MD simulations of the three best compounds that bind to the catalytic, palm, and thumb domains to find out how the ligand-protein interactions change over time. RMSD, RMSF, radius of gyration, free energy landscapes, and principal component analyses revealed that complexes nsP4-ZINC-12820763 and nsP4-ZINC-33280972 were more stable. Simulated trajectories were further used to compute MMGBSA binding energies of PubChem-135638918 (-22.33 kcal/mol), ZINC-12820763 (-50.19 kcal/mol) and ZINC-33280972 (-32.69 kcal/mol) bound to catalytic, palm and thumb domains, respectively. HOMO and LUMO of potential molecules were also investigated using density functional theory computations. With the support of computational simulations, three compounds were shown to have the potential to inhibit RdRp of CHIKV and need further evaluation using in-vitro and in-vivo analysis.
Keywords	Chikungunya ; Homology modeling ; E-pharmacophore ; Molecular docking ; Molecular dynamics ; Physics ; QC1-999 ; Chemistry ; QD1-999
Subject code	540
Language	English
Publishing date	2024-06-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
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Article ; Online: Contribution of NRF2 to sulfur metabolism and mitochondrial activity

Md Morshedul Alam / Akihiro Kishino / Eunkyu Sung / Hiroki Sekine / Takaaki Abe / Shohei Murakami / Takaaki Akaike / Hozumi Motohashi

Redox Biology, Vol 60, Iss , Pp 102624- (2023)

2023

Abstract: NF-E2-related factor 2 (NRF2) plays a crucial role in the maintenance of cellular homeostasis by regulating various enzymes and proteins that are involved in the redox reactions utilizing sulfur. While substantial impacts of NRF2 on mitochondrial ... ...

Abstract	NF-E2-related factor 2 (NRF2) plays a crucial role in the maintenance of cellular homeostasis by regulating various enzymes and proteins that are involved in the redox reactions utilizing sulfur. While substantial impacts of NRF2 on mitochondrial activity have been described, the precise mechanism by which NRF2 regulates mitochondrial function is still not fully understood. Here, we demonstrated that NRF2 increased intracellular persulfides by upregulating the cystine transporter xCT encoded by Slc7a11, a well-known NRF2 target gene. Persulfides have been shown to play an important role in mitochondrial function. Supplementation with glutathione trisulfide (GSSSG), which is a form of persulfide, elevated the mitochondrial membrane potential (MMP), increased the oxygen consumption rate (OCR) and promoted ATP production. Persulfide-mediated mitochondrial activation was shown to require the mitochondrial sulfur oxidation pathway, especially sulfide quinone oxidoreductase (SQOR). Consistently, NRF2-mediated mitochondrial activation was also dependent on SQOR activity. This study clarified that the facilitation of persulfide production and sulfur metabolism in mitochondria by increasing cysteine availability is one of the mechanisms for NRF2-dependent mitochondrial activation.
Keywords	xCT ; Mitochondria ; Cystine ; Cysteine ; Persulfide ; Mitochondrial membrane potential ; Medicine (General) ; R5-920 ; Biology (General) ; QH301-705.5
Subject code	570
Language	English
Publishing date	2023-04-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
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Article ; Online: Contribution of NRF2 to sulfur metabolism and mitochondrial activity.

Alam, Md Morshedul / Kishino, Akihiro / Sung, Eunkyu / Sekine, Hiroki / Abe, Takaaki / Murakami, Shohei / Akaike, Takaaki / Motohashi, Hozumi

Redox biology

2023 Volume 60, Page(s) 102624

Abstract	NF-E2-related factor 2 (NRF2) plays a crucial role in the maintenance of cellular homeostasis by regulating various enzymes and proteins that are involved in the redox reactions utilizing sulfur. While substantial impacts of NRF2 on mitochondrial activity have been described, the precise mechanism by which NRF2 regulates mitochondrial function is still not fully understood. Here, we demonstrated that NRF2 increased intracellular persulfides by upregulating the cystine transporter xCT encoded by Slc7a11, a well-known NRF2 target gene. Persulfides have been shown to play an important role in mitochondrial function. Supplementation with glutathione trisulfide (GSSSG), which is a form of persulfide, elevated the mitochondrial membrane potential (MMP), increased the oxygen consumption rate (OCR) and promoted ATP production. Persulfide-mediated mitochondrial activation was shown to require the mitochondrial sulfur oxidation pathway, especially sulfide quinone oxidoreductase (SQOR). Consistently, NRF2-mediated mitochondrial activation was also dependent on SQOR activity. This study clarified that the facilitation of persulfide production and sulfur metabolism in mitochondria by increasing cysteine availability is one of the mechanisms for NRF2-dependent mitochondrial activation.
MeSH term(s)	NF-E2-Related Factor 2/genetics ; NF-E2-Related Factor 2/metabolism ; Sulfides/metabolism ; Mitochondria/metabolism ; Cystine
Chemical Substances	persulfides ; NF-E2-Related Factor 2 ; Sulfides ; Cystine (48TCX9A1VT)
Language	English
Publishing date	2023-02-02
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2701011-9
ISSN	2213-2317 ; 2213-2317
ISSN (online)	2213-2317
ISSN	2213-2317
DOI	10.1016/j.redox.2023.102624
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Article ; Online: Supersulfide catalysis for nitric oxide and aldehyde metabolism.

Kasamatsu, Shingo / Nishimura, Akira / Alam, Md Morshedul / Morita, Masanobu / Shimoda, Kakeru / Matsunaga, Tetsuro / Jung, Minkyung / Ogata, Seiryo / Barayeu, Uladzimir / Ida, Tomoaki / Nishida, Motohiro / Nishimura, Akiyuki / Motohashi, Hozumi / Akaike, Takaaki

Science advances

2023 Volume 9, Issue 33, Page(s) eadg8631

Abstract: Abundant formation of endogenous supersulfides, which include reactive persulfide species and sulfur catenated residues in thiols and proteins (supersulfidation), has been observed. We found here that supersulfides ... ...

Abstract	Abundant formation of endogenous supersulfides, which include reactive persulfide species and sulfur catenated residues in thiols and proteins (supersulfidation), has been observed. We found here that supersulfides catalyze
MeSH term(s)	Animals ; Mice ; Nitric Oxide ; Electron Transport ; Aldehydes ; Catalysis ; Glutathione
Chemical Substances	Nitric Oxide (31C4KY9ESH) ; Aldehydes ; Glutathione (GAN16C9B8O)
Language	English
Publishing date	2023-08-18
Publishing country	United States
Document type	Journal Article
ZDB-ID	2810933-8
ISSN	2375-2548 ; 2375-2548
ISSN (online)	2375-2548
ISSN	2375-2548
DOI	10.1126/sciadv.adg8631
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Article: Appraisal of probabilistic human health risks of heavy metals in vegetables from industrial, non-industrial and arsenic contaminated areas of Bangladesh.

Haque, Md Morshedul / Niloy, Nahin Mostofa / Khirul, Md Akhte / Alam, Md Ferdous / Tareq, Shafi M

Heliyon

2021 Volume 7, Issue 2, Page(s) e06309

Abstract: Monitoring of heavy metal content in commonly consumed vegetables is of high priority for food safety, and public health risk assessment. Vegetables were collected from industrial, non-industrial, arsenic contaminated region and one of popular vegetable ... ...

Abstract	Monitoring of heavy metal content in commonly consumed vegetables is of high priority for food safety, and public health risk assessment. Vegetables were collected from industrial, non-industrial, arsenic contaminated region and one of popular vegetable markets of Bangladesh for analyzing heavy metals (As, Cd, Pb, Cu and Zn) using Atomic Absorption Spectroscopy (AAS) with standard digestion procedure. Results showed significant variations of heavy metal content among vegetables and most of cases the metals (except Cu and some of Zn) revealed several times higher concentrations than that of maximum permissible level (MPL) values, which indicated the vegetables were contaminated through either natural or anthropogenic activities. The dietary intake of metals are responsible for association of health risk that evaluated by target hazard quotient (THQ), hazard index (HI), and target carcinogenic risk (TR) calculations. Estimated daily intake (EDI) for all metals were below the maximum tolerable daily intake (MTDI) values of all vegetables. The THQs for single metals were less than 1 (except As and Pb for few vegetables), indicating the inhabitant would not possess health hazard for single metal through vegetables consumption. However, the total target hazard quotient (TTHQ) of all metals were >1 (except Cu and Zn for industrial and non-industrial sites), suggesting potential health risk. HI values were found more than 1 (36.24 for industrial site, 16.74 for non-industrial site, and 15.03 for local market) representing the selected vegetables intake might be affected quality of food safety of densely populated Bangladesh. The probabilistic risk, individual, and total cancer risk (TR) for As and Pb were exceeded the threshold level (10
Language	English
Publishing date	2021-02-24
Publishing country	England
Document type	Journal Article
ZDB-ID	2835763-2
ISSN	2405-8440
ISSN	2405-8440
DOI	10.1016/j.heliyon.2021.e06309
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Article ; Online: Multiomics analysis of altered NRF3 expression reveals poor prognosis in cancer

Md. Morshedul Alam / Kanchan Chakma / Shahriar Mahmud / Mohammad Nazir Hossain / M. Rezaul Karim / Md. Ariful Amin

Informatics in Medicine Unlocked, Vol 29, Iss , Pp 100892- (2022)

2022

Abstract: The alliance of NRF3 expression with human cancer patient survival and the underlying function of this gene in liaison to various cancers progression has not been comprehensively studied. In addition, the molecular mechanism of the NRF3 gene and its ... ...

Abstract	The alliance of NRF3 expression with human cancer patient survival and the underlying function of this gene in liaison to various cancers progression has not been comprehensively studied. In addition, the molecular mechanism of the NRF3 gene and its relationship to cancer patient survival and prognosis are still poorly understood. To elucidate the carcinogenic activity of NRF3, we systematically analyzed the NRF3 expression and its prognostic relevance in diverse cancer patients to decipher the oncogenic function of NRF3. Therefore, we systematically investigated the expression level of NRF3 and its relationship with patient survival as well as the affected pathways in breast, colorectal adenocarcinoma, renal cancer, pancreatic cancer, and thymoma cancer. Relative expression levels of NRF3 were analyzed using the Oncomine, GEPIA2, GENT, UALCAN, cBioPortal, UCSC Xena and The Cancer Genome Atlas (TCGA) databases. Gene copy number of NRF3 was analyzed using cBioPortal, and the subsequent patient prognosis and risk factors were analyzed by obtaining the data from GEPIA2, GENT, and PrognoScan databases. Besides, gene ontology and pathway analysis of co-expressed genes, and transcriptome data analysis were performed using the Enrichr, which revealed NRF3-related pathways in diverse malignancies. Overall, this open database analysis shows a link between NRF3 expression and cancer patient survival and identifies potential NRF3-mediated pathways that could lead to NRF3 being used as a therapeutic target for a variety of human cancers.
Keywords	NRF3 ; Cancer patient ; Poor prognosis ; Patient survival ; Cancer therapeutics ; Computer applications to medicine. Medical informatics ; R858-859.7
Subject code	616
Language	English
Publishing date	2022-01-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Interaction pattern of aldose reductase with β-glucogallin

Md Ashikujjaman Ashik / Tasmia Islam / Michihiko Fujii / Md Morshedul Alam / Mohammad Nazir Hossain, Ph.D.

Informatics in Medicine Unlocked, Vol 30, Iss , Pp 100938- (2022)

Active site exploration and multiple docking analyses

2022

Abstract: The search for an ideal natural drug candidate with minimal side effects has been a never-ending challenge. In diabetes, there are so many potential drug candidates; however, systematic research is necessary to put candidate molecules into effect. β- ... ...

Abstract	The search for an ideal natural drug candidate with minimal side effects has been a never-ending challenge. In diabetes, there are so many potential drug candidates; however, systematic research is necessary to put candidate molecules into effect. β-glucogallin (PubChem CID: 124021) found in Emblica officinalis is explored as a potential candidate molecule to inhibit aldose reductase activity, a key enzyme related to the microvascular complications in diabetic patients. High-resolution crystal structure of human aldose reductase (ALR2) (PDB ID: “1pwm”) from ‘Protein Data Bank’ was retrieved, and active site determination was done using “ CASTp” and blind docking strategies. “Swiss Dock” blind docking revealed a total of 13 active residues, which were found common in the five best binding modes in regard to their free binding energy. The active residues were utilized again to selectively dock β-glucogallin (PubChem CID: 124021) in “Swiss Dock” for which the average free binding energy was −8.07884 kcal/mol calculated from 5 best binding modes. Additionally, a selective docking analysis was performed in ‘Auto Dock 4.2′ using a genetic algorithm where the same binding mode was observed. The lowest binding energy calculated in Auto Dock was −17.37 kcal/mol with an inhibition constant of 186.59 fM, which is substantial to prove the efficacy of this molecule as a potential drug target. In both docking platforms, the interaction pattern stayed in the same orientation. So, this study showed the interactions pattern of β-glucogallin (PubChem CID: 124021) with tentative active sites of aldose reductase (ALR2) (PDB ID: 1pwm) in details which may open up future possibilities for treating patients with diabetic microvascular complications.
Keywords	β-glucogallin ; Aldose reductase ; Docking ; Microvascular complication ; CASTp ; Computer applications to medicine. Medical informatics ; R858-859.7
Subject code	540
Language	English
Publishing date	2022-01-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
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Article ; Online: Chemical composition, antioxidant and antibacterial activity of Piper chaba stem extracts with preservative effects on storage of raw beef patties

Mohammad Mahfuzur Rahman / Tyeaba Tasnim Dipti / M. Nazrul Islam / Abu Tareq Mohammad Abdullah / Sharmin Jahan / Md. Morshedul Alam / M. Rezaul Karim

Saudi Journal of Biological Sciences, Vol 30, Iss 6, Pp 103663- (2023)

2023

Abstract: Piper chaba, a traditional South-east Asian medicinal herb and well-known curry spice, was studied to evaluate its suitability as a source of natural preservatives for beef products. Plant extracts that are high in phenolics and have high antimicrobial ... ...

Abstract	Piper chaba, a traditional South-east Asian medicinal herb and well-known curry spice, was studied to evaluate its suitability as a source of natural preservatives for beef products. Plant extracts that are high in phenolics and have high antimicrobial and antioxidant activities are likely to be useful as a natural preservative. Therefore, the phytochemical composition and the bioactivities of both ethanolic and methanolic extracts of P. chaba stem were examined first. The study revealed a significant antioxidant activities and potential antibacterial activity of P. chaba extracts. Next we investigated the preservation characteristics of P. chaba by using beef patties as a model system. Beef patties were produced and treated with 0.2 % ethanolic extract (mentioned as PEE) of P. chaba and 0.1 % commercial preservative (mentioned as PCP). They were then assessed for various storage quality parameters under refrigerated (4° C ± 1° C) conditions, including free fatty acid, antioxidant contents, and oxidative stability at 0, 6th, 16th, and 33rd days. No significant variations were observed across the products with regard to proximate composition study such as protein, ash and fat contents. In comparison to both PEE and PCP, the control product had higher free fatty acid values throughout the storage period. This indicates that the fat content of the PEE and PCP degraded at a slower rate than the control over the 33-day storage period. Our study also showed that both PCP and PEE had increased antioxidant capacity, implying that lipid oxidation is minimized. In contrast to the control, the oxidative stability of the P. chaba treated products was also higher. Altogether this study revealed that P. chaba could be utilized commercially, particularly in the food industry to preserve muscle foods. Practical Applications: Natural preservatives are becoming more popular as a result of the different carcinogenic and toxic side effects of conventional preservatives. P. chaba, an exquisite culinary herb in Bangladesh, has long ...
Keywords	Piper chaba ; Phytochemicals ; HPLC ; Preservative ; Oxidative stability ; Biology (General) ; QH301-705.5
Subject code	500
Language	English
Publishing date	2023-06-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
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Article ; Online: Appraisal of probabilistic human health risks of heavy metals in vegetables from industrial, non-industrial and arsenic contaminated areas of Bangladesh

Md. Morshedul Haque / Nahin Mostofa Niloy / Md Akhte Khirul / Md. Ferdous Alam / Shafi M. Tareq

Heliyon, Vol 7, Iss 2, Pp e06309- (2021)

2021

Abstract	Monitoring of heavy metal content in commonly consumed vegetables is of high priority for food safety, and public health risk assessment. Vegetables were collected from industrial, non-industrial, arsenic contaminated region and one of popular vegetable markets of Bangladesh for analyzing heavy metals (As, Cd, Pb, Cu and Zn) using Atomic Absorption Spectroscopy (AAS) with standard digestion procedure. Results showed significant variations of heavy metal content among vegetables and most of cases the metals (except Cu and some of Zn) revealed several times higher concentrations than that of maximum permissible level (MPL) values, which indicated the vegetables were contaminated through either natural or anthropogenic activities. The dietary intake of metals are responsible for association of health risk that evaluated by target hazard quotient (THQ), hazard index (HI), and target carcinogenic risk (TR) calculations. Estimated daily intake (EDI) for all metals were below the maximum tolerable daily intake (MTDI) values of all vegetables. The THQs for single metals were less than 1 (except As and Pb for few vegetables), indicating the inhabitant would not possess health hazard for single metal through vegetables consumption. However, the total target hazard quotient (TTHQ) of all metals were >1 (except Cu and Zn for industrial and non-industrial sites), suggesting potential health risk. HI values were found more than 1 (36.24 for industrial site, 16.74 for non-industrial site, and 15.03 for local market) representing the selected vegetables intake might be affected quality of food safety of densely populated Bangladesh. The probabilistic risk, individual, and total cancer risk (TR) for As and Pb were exceeded the threshold level (10−4) and safe limit (10−6), respectively, indicating peoples who have been consuming these vegetables long time, they might be exposed by lifetime cancer risk. Sensitivity analysis revealed that the metal concentration has high influence on carcinogenic risks.
Keywords	Heavy metals ; Common vegetables ; Estimated daily intake (EDI) ; Human health risks ; Probabilistic health risk ; Science (General) ; Q1-390 ; Social sciences (General) ; H1-99
Subject code	500
Language	English
Publishing date	2021-02-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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