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Zhang Y, Sheikh AM, Tabassum S, Iwasa K, Shibly AZ, Zhou X, Wang R, Bhuiya J, Abdullah FB, Yano S, Aoki Y, Nagai A. Effect of high-fat diet on cerebral pathological changes of cerebral small vessel disease in SHR/SP rats. GeroScience 2024:10.1007/s11357-024-01074-7. [PMID: 38319539 DOI: 10.1007/s11357-024-01074-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 01/10/2024] [Indexed: 02/07/2024] Open
Abstract
Cerebral small vessel diseases (CSVD) are neurological disorders associated with microvessels, manifested pathologically as white matter (WM) changes and cortical microbleeds, with hypertension as a risk factor. Additionally, a high-fat diet (HFD) can affect peripheral vessel health. Our study explored how HFD affects cerebral small vessels in normotensive WKY, hypertensive SHR, and SHR/SP rats. The MRI results revealed that HFD specifically increased WM hyperintensity in SHR/SP rats. Pathologically, it increased WM pallor and vacuolation in SHR and SHR/SP rats. Levels of blood-brain barrier (BBB) protein claudin 5 were decreased in SHR and SHR/SP compared to WKY, with HFD having minimal impact on these levels. Conversely, collagen IV levels remained consistent among the rat strains, which were increased by HFD. Consequently, HFD caused vessel leakage in all rat strains, particularly within the corpus callosum of SHR/SP rats. To understand the underlying mechanisms, we assessed the levels of hypoxia-inducible factor-1α (HIF-1α), Gp91-phox, and neuroinflammatory markers astrocytes, and microglia were increased in SHR and SHR/SP compared to WKY and were further elevated by HFD in all rat strains. Gp91-phox was also increased in SHR and SHR/SP compared to WKY, with HFD causing an increase in WKY but little effect in SHR and SHR/SP. In conclusion, our study demonstrates that HFD, in combined with hypertension, intensifies cerebral pathological alterations in CSVD rats. This exacerbation involves increased oxidative stress and HIF-1α in cerebral vessels, triggering neuroinflammation, vascular basement membrane remodeling, IgG leakage, and ultimately WM damage.
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Affiliation(s)
- Yuchi Zhang
- Department of Neurology, Faculty of Medicine, Shimane University, 89-1 Enya-Cho, Izumo, 693-8501, Japan
- Department of Pharmacology, School of Basic Medical Sciences, Heilongjiang University of Chinese Medicine, Harbin, 150040, China
| | - Abdullah Md Sheikh
- Department of Laboratory Medicine, Faculty of Medicine, Shimane University, Izumo, 693-8501, Japan
| | - Shatera Tabassum
- Department of Laboratory Medicine, Faculty of Medicine, Shimane University, Izumo, 693-8501, Japan
| | - Kenichi Iwasa
- Department of Neurology, Faculty of Medicine, Shimane University, 89-1 Enya-Cho, Izumo, 693-8501, Japan
| | - Abu Zaffar Shibly
- Department of Neurology, Faculty of Medicine, Shimane University, 89-1 Enya-Cho, Izumo, 693-8501, Japan
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Santosh, Tangail, 1902, Bangladesh
| | - Xiaojing Zhou
- Department of Neurology, Faculty of Medicine, Shimane University, 89-1 Enya-Cho, Izumo, 693-8501, Japan
- Department of Neurology, Zhoushan Hospital, Zhoushan, 316004, China
| | - Ruochen Wang
- Department of Neurology, Faculty of Medicine, Shimane University, 89-1 Enya-Cho, Izumo, 693-8501, Japan
| | - Jubo Bhuiya
- Department of Neurology, Faculty of Medicine, Shimane University, 89-1 Enya-Cho, Izumo, 693-8501, Japan
| | - Fatema Binte Abdullah
- Department of Neurology, Faculty of Medicine, Shimane University, 89-1 Enya-Cho, Izumo, 693-8501, Japan
| | - Shozo Yano
- Department of Laboratory Medicine, Faculty of Medicine, Shimane University, Izumo, 693-8501, Japan
| | - Yoshihito Aoki
- Department of Neurology, Faculty of Medicine, Shimane University, 89-1 Enya-Cho, Izumo, 693-8501, Japan
| | - Atsushi Nagai
- Department of Neurology, Faculty of Medicine, Shimane University, 89-1 Enya-Cho, Izumo, 693-8501, Japan.
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Shibly AZ, Sheikh AM, Michikawa M, Tabassum S, Azad AK, Zhou X, Zhang Y, Yano S, Nagai A. Correction: Shibly et al. Analysis of Cerebral Small Vessel Changes in AD Model Mice. Biomedicines 2023, 11, 50. Biomedicines 2024; 12:104. [PMID: 38255328 PMCID: PMC10807687 DOI: 10.3390/biomedicines12010104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 12/20/2023] [Indexed: 01/24/2024] Open
Abstract
In the original publication [...].
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Affiliation(s)
- Abu Zaffar Shibly
- Department of Neurology, Faculty of Medicine, Shimane University, 89-1 Enya-cho, Izumo 693-8501, Japan; (A.Z.S.); (A.K.A.); (X.Z.); (Y.Z.)
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Santosh, Tangail 1902, Bangladesh
| | - Abdullah Md. Sheikh
- Department of Laboratory Medicine, Faculty of Medicine, Shimane University, 89-1 Enya-cho, Izumo 693-8501, Japan; (A.M.S.); (S.T.); (S.Y.)
| | - Makoto Michikawa
- Department of Biochemistry, Graduate School of Medical Sciences, Nagoya City University, Nagoya 467-8601, Japan;
| | - Shatera Tabassum
- Department of Laboratory Medicine, Faculty of Medicine, Shimane University, 89-1 Enya-cho, Izumo 693-8501, Japan; (A.M.S.); (S.T.); (S.Y.)
| | - Abul Kalam Azad
- Department of Neurology, Faculty of Medicine, Shimane University, 89-1 Enya-cho, Izumo 693-8501, Japan; (A.Z.S.); (A.K.A.); (X.Z.); (Y.Z.)
| | - Xiaojing Zhou
- Department of Neurology, Faculty of Medicine, Shimane University, 89-1 Enya-cho, Izumo 693-8501, Japan; (A.Z.S.); (A.K.A.); (X.Z.); (Y.Z.)
| | - Yuchi Zhang
- Department of Neurology, Faculty of Medicine, Shimane University, 89-1 Enya-cho, Izumo 693-8501, Japan; (A.Z.S.); (A.K.A.); (X.Z.); (Y.Z.)
| | - Shozo Yano
- Department of Laboratory Medicine, Faculty of Medicine, Shimane University, 89-1 Enya-cho, Izumo 693-8501, Japan; (A.M.S.); (S.T.); (S.Y.)
| | - Atsushi Nagai
- Department of Neurology, Faculty of Medicine, Shimane University, 89-1 Enya-cho, Izumo 693-8501, Japan; (A.Z.S.); (A.K.A.); (X.Z.); (Y.Z.)
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Bappy SS, Haque Asim MM, Ahasan MM, Ahsan A, Sultana S, Khanam R, Shibly AZ, Kabir Y. Virus-induced host cell metabolic alteration. Rev Med Virol 2024; 34:e2505. [PMID: 38282396 DOI: 10.1002/rmv.2505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 11/16/2023] [Accepted: 12/17/2023] [Indexed: 01/30/2024]
Abstract
Viruses change the host cell metabolism to produce infectious particles and create optimal conditions for replication and reproduction. Numerous host cell pathways have been modified to ensure available biomolecules and sufficient energy. Metabolomics studies conducted over the past decade have revealed that eukaryotic viruses alter the metabolism of their host cells on a large scale. Modifying pathways like glycolysis, fatty acid synthesis and glutaminolysis could provide potential energy for virus multiplication. Thus, almost every virus has a unique metabolic signature and a different relationship between the viral life cycle and the individual metabolic processes. There are enormous research in virus induced metabolic reprogramming of host cells that is being conducted through numerous approaches using different vaccine candidates and antiviral drug substances. This review provides an overview of viral interference to different metabolic pathways and improved monitoring in this area will open up new ways for more effective antiviral therapies and combating virus induced oncogenesis.
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Affiliation(s)
| | | | | | - Asif Ahsan
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Tangail, Bangladesh
| | - Sorna Sultana
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Tangail, Bangladesh
| | - Roksana Khanam
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Tangail, Bangladesh
| | - Abu Zaffar Shibly
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Tangail, Bangladesh
| | - Yearul Kabir
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
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Bhuiya J, Notsu Y, Kobayashi H, Shibly AZ, Sheikh AM, Okazaki R, Yamaguchi K, Nagai A, Nabika T, Abe T, Yamasaki M, Isomura M, Yano S. Neither Trimethylamine-N-Oxide nor Trimethyllysine Is Associated with Atherosclerosis: A Cross-Sectional Study in Older Japanese Adults. Nutrients 2023; 15:nu15030759. [PMID: 36771464 PMCID: PMC9921512 DOI: 10.3390/nu15030759] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 01/26/2023] [Accepted: 01/29/2023] [Indexed: 02/05/2023] Open
Abstract
Recent evidence suggests that trimethylamine-N-oxide (TMAO), a metabolite of L-carnitine and choline, is linked to atherosclerosis and cardiovascular diseases. As TMAO content is very high in fish, we raised the following question: why do Japanese people, who consume lots of fish, show a low risk of atherosclerosis? To address this question, we investigated the effects of TMAO and other L-carnitine-related metabolites on carotid intima-media thickness (IMT). Participants were recruited from a small island and a mountainous region. Plasma L-carnitine, γ-butyrobetaine (γBB), TMAO, trimethyllysine (TML), eicosapentaenoic acid (EPA), and docosahexaenoic acid (DHA) levels were measured using liquid or gas chromatography-mass spectrometry. Plasma L-carnitine concentration was higher in men than in women. TMAO and TML were significantly higher in the residents of the island than in the mountainous people. In multiple linear regression analyses in all participants, TML showed a significant inverse association with max-IMT and plaque score (PS), whereas TMAO did not show any associations. In women, L-carnitine was positively associated with max-IMT and PS. TMAO was correlated with both EPA and DHA levels, implying that fish is a major dietary source of TMAO in Japanese people. Our study found that plasma TMAO was not an apparent risk factor for atherosclerosis in elderly Japanese people, whereas a low level of TML might be a potential risk. L-carnitine may be a marker for atherosclerosis in women.
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Affiliation(s)
- Jubo Bhuiya
- Department of Laboratory Medicine, Faculty of Medicine, Shimane University, 89-1 Enya-cho, Izumo City 693-8501, Japan
| | - Yoshitomo Notsu
- Department of Laboratory Medicine, Faculty of Medicine, Shimane University, 89-1 Enya-cho, Izumo City 693-8501, Japan
- Metabolizumo Project, Faculty of Medicine, Shimane University, 89-1 Enya-cho, Izumo City 693-8501, Japan
| | - Hironori Kobayashi
- Department of Laboratory Medicine, Faculty of Medicine, Shimane University, 89-1 Enya-cho, Izumo City 693-8501, Japan
- Metabolizumo Project, Faculty of Medicine, Shimane University, 89-1 Enya-cho, Izumo City 693-8501, Japan
| | - Abu Zaffar Shibly
- Department of Neurology, Faculty of Medicine, Shimane University, 89-1 Enya-cho, Izumo City 693-8501, Japan
| | - Abdullah Md. Sheikh
- Department of Laboratory Medicine, Faculty of Medicine, Shimane University, 89-1 Enya-cho, Izumo City 693-8501, Japan
| | - Ryota Okazaki
- Department of Laboratory Medicine, Faculty of Medicine, Shimane University, 89-1 Enya-cho, Izumo City 693-8501, Japan
| | - Kazuto Yamaguchi
- Department of Cardiology, Faculty of Medicine, Shimane University, 89-1 Enya-cho, Izumo City 693-8501, Japan
| | - Atsushi Nagai
- Department of Neurology, Faculty of Medicine, Shimane University, 89-1 Enya-cho, Izumo City 693-8501, Japan
| | - Toru Nabika
- Metabolizumo Project, Faculty of Medicine, Shimane University, 89-1 Enya-cho, Izumo City 693-8501, Japan
- Center for Community-Based Healthcare Research and Education (CoHRE), Shimane University, 89-1 Enya-cho, Izumo City 693-8501, Japan
| | - Takafumi Abe
- Center for Community-Based Healthcare Research and Education (CoHRE), Shimane University, 89-1 Enya-cho, Izumo City 693-8501, Japan
| | - Masayuki Yamasaki
- Center for Community-Based Healthcare Research and Education (CoHRE), Shimane University, 89-1 Enya-cho, Izumo City 693-8501, Japan
| | - Minoru Isomura
- Center for Community-Based Healthcare Research and Education (CoHRE), Shimane University, 89-1 Enya-cho, Izumo City 693-8501, Japan
| | - Shozo Yano
- Department of Laboratory Medicine, Faculty of Medicine, Shimane University, 89-1 Enya-cho, Izumo City 693-8501, Japan
- Center for Community-Based Healthcare Research and Education (CoHRE), Shimane University, 89-1 Enya-cho, Izumo City 693-8501, Japan
- Correspondence: ; Tel.: +81-0853-20-2312; Fax: +81-0853-20-2409
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Shibly AZ, Sheikh AM, Michikawa M, Tabassum S, Azad AK, Zhou X, Zhang Y, Yano S, Nagai A. Analysis of Cerebral Small Vessel Changes in AD Model Mice. Biomedicines 2022; 11:50. [PMID: 36672558 PMCID: PMC9855388 DOI: 10.3390/biomedicines11010050] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/19/2022] [Accepted: 12/21/2022] [Indexed: 12/28/2022] Open
Abstract
Amyloid β (Aβ) peptide is deposited in the brains of sporadic Alzheimer's disease (AD) due to impaired vessel-dependent clearance. To understand the mechanisms, we investigated time-dependent cerebrovascular changes in AD model mice. Cerebrovascular and other pathological changes were analyzed in AD model mice (J20 strain) aging from 2 to 9 months by immunostaining. At 2 months, Aβ was only intraneuronal, whereas vessels were positive from 3 months in J20 mice. Compared to wild-type (WT), vessel density was increased at 2 months but decreased at 9 months in J20 mice, claudin-5 levels were decreased, and vascular endothelial growth factor (VEGF) levels were increased in the cortex and hippocampus of J20 mice brain at all time points. Albumin extravasation was evident from 3 months in J20 brains. Collagen 4 was increased at 2 and 3 months. Aquaporin 4 was spread beyond the vessels starting from 3 months in J20, which was restricted around the vessel in wild-type mice. In conclusion, the study showed that an early decrease in claudin-5 was associated with VEGF expression, indicating dysfunction of the blood-brain barrier. Decreased claudin-5 might cause the leakage of blood constituents into the parenchyma that alters astrocyte polarity and its functions.
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Affiliation(s)
- Abu Zaffar Shibly
- Department of Neurology, Faculty of Medicine, Shimane University, 89-1 Enya-cho, Izumo 693-8501, Japan; (A.Z.S.); (A.K.A.); (X.Z.); (Y.Z.)
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Santosh, Tangail 1902, Bangladesh
| | - Abdullah Md. Sheikh
- Department of Laboratory Medicine, Faculty of Medicine, Shimane University, 89-1 Enya-cho, Izumo 693-8501, Japan; (A.M.S.); (S.T.); (S.Y.)
| | - Makoto Michikawa
- Department of Biochemistry, Graduate School of Medical Sciences, Nagoya City University, Nagoya 467-8601, Japan;
| | - Shatera Tabassum
- Department of Laboratory Medicine, Faculty of Medicine, Shimane University, 89-1 Enya-cho, Izumo 693-8501, Japan; (A.M.S.); (S.T.); (S.Y.)
| | - Abul Kalam Azad
- Department of Neurology, Faculty of Medicine, Shimane University, 89-1 Enya-cho, Izumo 693-8501, Japan; (A.Z.S.); (A.K.A.); (X.Z.); (Y.Z.)
| | - Xiaojing Zhou
- Department of Neurology, Faculty of Medicine, Shimane University, 89-1 Enya-cho, Izumo 693-8501, Japan; (A.Z.S.); (A.K.A.); (X.Z.); (Y.Z.)
| | - Yuchi Zhang
- Department of Neurology, Faculty of Medicine, Shimane University, 89-1 Enya-cho, Izumo 693-8501, Japan; (A.Z.S.); (A.K.A.); (X.Z.); (Y.Z.)
| | - Shozo Yano
- Department of Laboratory Medicine, Faculty of Medicine, Shimane University, 89-1 Enya-cho, Izumo 693-8501, Japan; (A.M.S.); (S.T.); (S.Y.)
| | - Atsushi Nagai
- Department of Neurology, Faculty of Medicine, Shimane University, 89-1 Enya-cho, Izumo 693-8501, Japan; (A.Z.S.); (A.K.A.); (X.Z.); (Y.Z.)
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Azad AK, Sheikh AM, Haque MA, Osago H, Sakai H, Shibly AZ, Yano S, Michikawa M, Hossain S, Tabassum S, A. G, Zhou X, Zhang Y, Nagai A. Time-Dependent Analysis of Plasmalogens in the Hippocampus of an Alzheimer's Disease Mouse Model: A Role of Ethanolamine Plasmalogen. Brain Sci 2021; 11:1603. [PMID: 34942905 PMCID: PMC8699479 DOI: 10.3390/brainsci11121603] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 11/23/2021] [Accepted: 11/29/2021] [Indexed: 12/26/2022] Open
Abstract
Plasmalogens are alkenyl-acyl glycerophospholipids and decreased in post-mortem Alzheimer's disease (AD) brains. The aim of this study is to investigate the time-dependent changes of plasmalogens in the hippocampus of an AD model mouse (J20). Plasmalogen levels at 3, 6, 9, 12 and 15 months were analyzed by liquid-chromatography-targeted-multiplexed-selected-reaction-monitoring-tandem-mass-spectrometry (LC-SRM/MS). Reactive oxygen species (ROS) levels were evaluated using dichlorofluorescein diacetate (DCF-DA). Plasmalogen synthesizing enzyme glycerone-phosphate O-acyltransferase (GNPAT) and late endosome marker Rab7 levels were quantified by Western blotting. GNPAT localization, changes of neuronal and glial cell numbers were evaluated by immunostaining. Compared to wild-type mice (WT), total plasmalogen-ethanolamine, but not plasmalogen-choline levels, were increased at 9 months and subsequently decreased at 15 months in J20 mice. A principal component analysis of plasmalogen-ethanolamine species could separate WT and J20 mice both at 9 and 15 months. Both GNPAT and Rab7 protein were increased in J20 mice at 9 months, whereas GNPAT was decreased at 15 months. ROS levels were increased in J20 mice except for 9 months. Our results suggest that increased plasmalogen-ethanolamine could counteract ROS levels and contribute to the phagocytosis process in J20 mice at 9 months. Such results might indicate a transient protective response of plasmalogen-ethanolamine in AD conditions.
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Affiliation(s)
- Abul Kalam Azad
- Department of Neurology, Faculty of Medicine, Shimane University, Izumo 693-8501, Japan; (A.K.A.); (A.Z.S.); (G.A.); (X.Z.); (Y.Z.)
- Department of Microbiology, Jagannath University, Dhaka 1100, Bangladesh
| | - Abdullah Md. Sheikh
- Department of Laboratory Medicine, Faculty of Medicine, Shimane University, Izumo 693-8501, Japan; (A.M.S.); (M.A.H.); (S.Y.); (S.T.)
| | - Md. Ahsanul Haque
- Department of Laboratory Medicine, Faculty of Medicine, Shimane University, Izumo 693-8501, Japan; (A.M.S.); (M.A.H.); (S.Y.); (S.T.)
- Department of Pharmacy, University of Asia Pacific, Dhaka 1205, Bangladesh
| | - Harumi Osago
- Department of Biochemistry, Faculty of Medicine, Shimane University, Izumo 693-8501, Japan;
| | - Hiromichi Sakai
- Department of Biosignaling and Radioisotope Experiment, Faculty of Medicine, Shimane University, Izumo 693-8501, Japan;
| | - Abu Zaffar Shibly
- Department of Neurology, Faculty of Medicine, Shimane University, Izumo 693-8501, Japan; (A.K.A.); (A.Z.S.); (G.A.); (X.Z.); (Y.Z.)
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Tangail 1902, Bangladesh
| | - Shozo Yano
- Department of Laboratory Medicine, Faculty of Medicine, Shimane University, Izumo 693-8501, Japan; (A.M.S.); (M.A.H.); (S.Y.); (S.T.)
| | - Makoto Michikawa
- Department of Biochemistry, Graduate School of Medical Sciences, Nagoya City University, Nagoya 467-8601, Japan;
| | - Shahdat Hossain
- Department of Biochemistry and Molecular Biology, Jahangirnagar University, Dhaka 1342, Bangladesh;
| | - Shatera Tabassum
- Department of Laboratory Medicine, Faculty of Medicine, Shimane University, Izumo 693-8501, Japan; (A.M.S.); (M.A.H.); (S.Y.); (S.T.)
| | - Garu A.
- Department of Neurology, Faculty of Medicine, Shimane University, Izumo 693-8501, Japan; (A.K.A.); (A.Z.S.); (G.A.); (X.Z.); (Y.Z.)
| | - Xiaojing Zhou
- Department of Neurology, Faculty of Medicine, Shimane University, Izumo 693-8501, Japan; (A.K.A.); (A.Z.S.); (G.A.); (X.Z.); (Y.Z.)
| | - Yuchi Zhang
- Department of Neurology, Faculty of Medicine, Shimane University, Izumo 693-8501, Japan; (A.K.A.); (A.Z.S.); (G.A.); (X.Z.); (Y.Z.)
| | - Atsushi Nagai
- Department of Neurology, Faculty of Medicine, Shimane University, Izumo 693-8501, Japan; (A.K.A.); (A.Z.S.); (G.A.); (X.Z.); (Y.Z.)
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Bappy SS, Shibly AZ, Sultana S, Mohiuddin AKM, Kabir Y. Designing potential siRNA molecule for the nucleocapsid(N) gene silencing of different SARS-CoV-2 strains of Bangladesh: Computational approach. Comput Biol Chem 2021; 92:107486. [PMID: 33984653 PMCID: PMC8099544 DOI: 10.1016/j.compbiolchem.2021.107486] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 03/18/2021] [Accepted: 04/08/2021] [Indexed: 02/08/2023]
Abstract
SARS-CoV-2 is a single-stranded RNA (+) virus first identified in China and then became an ongoing global outbreak. In most cases, it is fatal in humans due to respiratory malfunction. Extensive researches are going to find an effective therapeutic technique for the treatment of SARS-CoV-2 infected individuals. In this study, we attempted to design a siRNA molecule to silence the most suitable nucleocapsid(N) gene of SARS-CoV-2, which play a major role during viral pathogenesis, replication, encapsidation and RNA packaging. At first, 270 complete N gene sequences of different strains in Bangladesh of these viruses were retrieved from the NCBI database. Different computational methods were used to design siRNA molecules. A siRNA molecule was built against these strains using the SiDirect 2.0 server. Using Mfold and the OligoCalc server, the siRNA molecule was tested for its secondary structure and GC material. The Clustal Omega tool was employed to evaluate any off-target harmony of the planned siRNA molecule. Herein, we proposed a duplex siRNA molecule that does not fit any off-target sequences for the gene silencing of SARS-CoV-2. To treat SARS-CoV-2 infections, currently, any effective therapy is not available. Our engineered siRNA molecule could give an alternative therapeutic approach against various sequenced SARS-CoV-2 strains in Bangladesh.
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Affiliation(s)
- Syed Shahariar Bappy
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Santosh, Tangail, 1902, Bangladesh; Research and Development, Incepta Vaccine Ltd, Zirabo, Savar, Dhaka, 1341, Bangladesh
| | - Abu Zaffar Shibly
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Santosh, Tangail, 1902, Bangladesh
| | - Sorna Sultana
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Santosh, Tangail, 1902, Bangladesh
| | - A K M Mohiuddin
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Santosh, Tangail, 1902, Bangladesh
| | - Yearul Kabir
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, 1000, Bangladesh.
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Rahman MM, Ahmed P, Kar A, Sakib N, Shibly AZ, Zohora FT, Hasan MN. Prevalence, Antimicrobial Resistance, and Pathogenic Potential of Enterotoxigenic and Enteropathogenic Escherichia coli Associated with Acute Diarrheal Patients in Tangail, Bangladesh. Foodborne Pathog Dis 2020; 17:434-439. [DOI: 10.1089/fpd.2019.2741] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Md Masuder Rahman
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Tangail, Bangladesh
| | - Parvez Ahmed
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Tangail, Bangladesh
| | - Antora Kar
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Tangail, Bangladesh
| | - Nazmus Sakib
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Tangail, Bangladesh
| | - Abu Zaffar Shibly
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Tangail, Bangladesh
| | - Fatama Tous Zohora
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Tangail, Bangladesh
| | - Md Nazmul Hasan
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, Bangladesh
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Bappy SS, Sultana S, Adhikari J, Mahmud S, Khan MA, Kibria KMK, Rahman MM, Shibly AZ. Extensive immunoinformatics study for the prediction of novel peptide-based epitope vaccine with docking confirmation against envelope protein of Chikungunya virus: a computational biology approach. J Biomol Struct Dyn 2020; 39:1139-1154. [PMID: 32037968 DOI: 10.1080/07391102.2020.1726815] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Chikungunya virus (CHIKV) instigating Chikungunya fever is a global infective menace resulting in high fever, weakened joint-muscle pain, and brain inflammation. Inaccessibility and unavailability of effective drugs have led us to an uncertain arena when it comes to providing proper medical treatment to the affected people. In this study, authentic encroachment has been made concerning the peptide-based epitope vaccine designing against CHIKV. A Proteome-wide search was performed to locate a conserved portion among the accessible viral outer membrane proteins which showcase a remarkable immune response using specific immunoinformatics and docking simulation tools. Primarily, the most probable immunogenic envelope glycoproteins E1 and E2 were identified from the UniProt database depending on their antigenicity scores. Subsequently, we selected two distinctive sequences "SEDVYANTQLVLQRP" and "IMLLYPDHPTLLSYR" in both E1 and E2 glycoproteins respectively. These two sequences identified as the most potent T and B cell epitope-based peptides as they interacted with 6 and 7 HLA-I and 5 HLA-II molecules with an extremely low IC50 score that was verified by molecular docking. Moreover, the sequences possess no allergenicity and are certainly located outside the transmembrane region. In addition, the sequences exhibited 88.46% and 100.00% Conservancy, covering high population coverage of 89.49% to 94.74% and 60.51% to 88.87% respectively in endemic countries. The identified peptide SEDVYANTQLVLQRP and IMLLYPDHPTLLSYR can be utilized next for the development of peptide-based epitope vaccine contrary to CHIKV, so further documentations and experimentations like Antigen testing, Antigen production, Clinical trials are needed to prove the validity of it. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Syed Shahariar Bappy
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Tangail, Bangladesh
| | - Sorna Sultana
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Tangail, Bangladesh
| | - Juthi Adhikari
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Tangail, Bangladesh
| | - Shafi Mahmud
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | - Md Arif Khan
- Department of Biotechnology and Genetic Engineering, University of Development Alternative, Dhaka, Bangladesh.,Bio-Bio-1 Research Foundation, Sangskriti Bikash Kendra Bhaban, Dhaka, Bangladesh
| | - K M Kaderi Kibria
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Tangail, Bangladesh
| | - Md Masuder Rahman
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Tangail, Bangladesh
| | - Abu Zaffar Shibly
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Tangail, Bangladesh
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Hossain MU, Omar TM, Oany AR, Kibria KMK, Shibly AZ, Moniruzzaman M, Ali SR, Islam MM. Design of peptide-based epitope vaccine and further binding site scrutiny led to groundswell in drug discovery against Lassa virus. 3 Biotech 2018; 8:81. [PMID: 29430345 DOI: 10.1007/s13205-018-1106-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 01/07/2018] [Indexed: 10/18/2022] Open
Abstract
Lassa virus (LASV) is responsible for an acute viral hemorrhagic fever known as Lassa fever. Sequence analyses of LASV proteome identified the most immunogenic protein that led to predict both T-cell and B-cell epitopes and further target and binding site depiction could allow novel drug findings for drug discovery field against this virus. To induce both humoral and cell-mediated immunity peptide sequence SSNLYKGVY, conserved region 41-49 amino acids were found as the most potential B-cell and T-cell epitopes, respectively. The peptide sequence might intermingle with 17 HLA-I and 16 HLA-II molecules, also cover 49.15-96.82% population coverage within the common people of different countries where Lassa virus is endemic. To ensure the binding affinity to both HLA-I and HLA-II molecules were employed in docking simulation with suggested epitope sequence. Further the predicted 3D structure of the most immunogenic protein was analyzed to reveal out the binding site for the drug design against Lassa Virus. Herein, sequence analyses of proteome identified the most immunogenic protein that led to predict both T-cell and B-cell epitopes and further target and binding site depiction could allow novel drug findings for drug discovery field against this virus.
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Sayed MA, Alam MA, Islam MS, Ali MT, Ullah ME, Shibly AZ, Ali MA, Hasan-Olive MM. Leonurus sibiricus L. (honeyweed): A review of its phytochemistry and pharmacology. Asian Pac J Trop Biomed 2016. [DOI: 10.1016/j.apjtb.2016.10.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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Uzzal Hossain M, Zaffar Shibly A, Md Omar T, Tous Zohora F, Sara Santona U, Hossain MJ, Hosen Khoka MS, Ara Keya C, Salimullah M. Towards finding the linkage between metabolic and age-related disorders using semantic gene data network analysis. Bioinformation 2016; 12:22-7. [PMID: 27212841 PMCID: PMC4857462 DOI: 10.6026/97320630012022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2015] [Accepted: 01/07/2016] [Indexed: 11/23/2022] Open
Abstract
A metabolic disorder (MD) occurs when the metabolic process is disturbed. This process is carried out by thousands of enzymes
participating in numerous inter-dependent metabolic pathways. Critical biochemical reactions that involve the processing and
transportation of carbohydrates, proteins and lipids are affected in metabolic diseases. Therefore, it is of interest to identify the
common pathways of metabolic disorders by building protein-protein interactions (PPI) for network analysis. The molecular
network linkages between MD and age related diseases (ARD) are intriguing. Hence, we created networks of protein-protein
interactions that are related with MD and ARD using relevant known data in the public domain. The network analysis identified
known MD associated proteins and predicted genes and or its products of ARD in common pathways. The genes in the common
pathways were isolated from the network and further analyzed for their co-localization and shared domains. Thus, a model
hypothesis is proposed using interaction networks that are linked between MD and ARD. This data even if less conclusive finds
application in understanding the molecular mechanism of known diseases in relation to observed molecular events
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Affiliation(s)
- Mohammad Uzzal Hossain
- Department of Biotechnology and Genetic Engineering, Life Science Faculty, Mawlana Bhashani Science and Technology University, Santosh, Tangail 1902, Bangladesh
| | - Abu Zaffar Shibly
- Department of Biotechnology and Genetic Engineering, Life Science Faculty, Mawlana Bhashani Science and Technology University, Santosh, Tangail 1902, Bangladesh
| | - Taimur Md Omar
- Department of Biotechnology and Genetic Engineering, Life Science Faculty, Mawlana Bhashani Science and Technology University, Santosh, Tangail 1902, Bangladesh
| | - Fatama Tous Zohora
- Department of Biotechnology and Genetic Engineering, Life Science Faculty, Mawlana Bhashani Science and Technology University, Santosh, Tangail 1902, Bangladesh
| | - Umme Sara Santona
- Department of Biotechnology and Genetic Engineering, Life Science Faculty, Mawlana Bhashani Science and Technology University, Santosh, Tangail 1902, Bangladesh
| | - Md Jakir Hossain
- Department of Biotechnology and Genetic Engineering, Life Science Faculty, Mawlana Bhashani Science and Technology University, Santosh, Tangail 1902, Bangladesh
| | - Md Sadek Hosen Khoka
- Department of Biotechnology and Genetic Engineering, Life Science Faculty, Mawlana Bhashani Science and Technology University, Santosh, Tangail 1902, Bangladesh
| | - Chaman Ara Keya
- Department of Biology and Chemistry, North south University, Bashundhara, Dhaka 1229, Bangladesh
| | - Md Salimullah
- Molecular Biotechnology Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka 1349, Bangladesh
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