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Sierra A, Miron VE, Paolicelli RC, Ransohoff RM. Microglia in Health and Diseases: Integrative Hubs of the Central Nervous System (CNS). Cold Spring Harb Perspect Biol 2024; 16:a041366. [PMID: 38438189 PMCID: PMC11293550 DOI: 10.1101/cshperspect.a041366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2024]
Abstract
Microglia are usually referred to as "the innate immune cells of the brain," "the resident macrophages of the central nervous system" (CNS), or "CNS parenchymal macrophages." These labels allude to their inherent immune function, related to their macrophage lineage. However, beyond their classic innate immune responses, microglia also play physiological roles crucial for proper brain development and maintenance of adult brain homeostasis. Microglia sense both external and local stimuli through a variety of surface receptors. Thus, they might serve as integrative hubs at the interface between the external environment and the CNS, able to decode, filter, and buffer cues from outside, with the aim of preserving and maintaining brain homeostasis. In this perspective, we will cast a critical look at how these multiple microglial functions are acquired and coordinated, and we will speculate on their impact on human brain physiology and pathology.
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Affiliation(s)
- Amanda Sierra
- Achucarro Basque Center for Neuroscience, Glial Cell Biology Laboratory, Science Park of UPV/EHU, E-48940 Leioa, Bizkaia, Spain
- Department of Biochemistry and Molecular Biology, University of the Basque Country EHU/UPV, 48940 Leioa, Spain
- Ikerbasque Foundation, Bilbao 48009, Spain
| | - Veronique E Miron
- BARLO Multiple Sclerosis Centre, Keenan Research Centre for Biomedical Science at St. Michael's Hospital, Toronto M5B 1T8, Canada
- Department of Immunology, University of Toronto, Toronto M5S 1A8, Canada
- UK Dementia Research Institute at the University of Edinburgh, Edinburgh BioQuarter, Edinburgh EH16 4TJ, United Kingdom
| | - Rosa C Paolicelli
- Department of Biomedical Sciences, Faculty of Biology and Medicine, University of Lausanne, CH-1005 Lausanne, Switzerland
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Wang M, Bo Z, Zhang C, Guo M, Wu Y, Zhang X. Deciphering the Genetic Variation: A Comparative Analysis of Parental and Attenuated Strains of the QXL87 Vaccine for Infectious Bronchitis. Animals (Basel) 2024; 14:1784. [PMID: 38929403 PMCID: PMC11200882 DOI: 10.3390/ani14121784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 06/05/2024] [Accepted: 06/11/2024] [Indexed: 06/28/2024] Open
Abstract
The QXL87 live attenuated vaccine strain for infectious bronchitis represents the first approved QX type (GI-19 lineage) vaccine in China. This strain was derived from the parental strain CK/CH/JS/2010/12 through continuous passage in SPF chicken embryos. To elucidate the molecular mechanism behind its attenuation, whole-genome sequencing was conducted on both the parental and attenuated strains. Analysis revealed 145 nucleotide mutations in the attenuated strain, leading to 48 amino acid mutations in various proteins, including Nsp2 (26), Nsp3 (14), Nsp4 (1), S (4), 3a (1), E (1), and N (1). Additionally, a frameshift mutation caused by a single base insertion in the ORFX resulted in a six-amino-acid extension. Subsequent comparison of post-translational modification sites, protein structure, and protein-protein binding sites between the parental and attenuated strains identified three potential virulence genes: Nsp2, Nsp3, and S. The amino acid mutations in these proteins not only altered their conformation but also affected the distribution of post-translational modification sites and protein-protein interaction sites. Furthermore, three potential functional mutation sites-P106S, A352T, and L472F, all located in the Nsp2 protein-were identified through PROVEAN, PolyPhen, and I-Mutant. Overall, our findings suggest that Nsp2, Nsp3, and S proteins may play a role in modulating IBV pathogenicity, with a particular focus on the significance of the Nsp2 protein. This study contributes to our understanding of the molecular mechanisms underlying IBV attenuation and holds promise for the development of safer live attenuated IBV vaccines using reverse genetic approaches.
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Affiliation(s)
- Mengmeng Wang
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (M.W.); (Z.B.); (C.Z.); (M.G.)
| | - Zongyi Bo
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (M.W.); (Z.B.); (C.Z.); (M.G.)
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
| | - Chengcheng Zhang
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (M.W.); (Z.B.); (C.Z.); (M.G.)
| | - Mengjiao Guo
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (M.W.); (Z.B.); (C.Z.); (M.G.)
| | - Yantao Wu
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (M.W.); (Z.B.); (C.Z.); (M.G.)
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
| | - Xiaorong Zhang
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (M.W.); (Z.B.); (C.Z.); (M.G.)
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3
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Nelson RB, Rose KN, Menniti FS, Zorn SH. Hiding in plain sight: Do recruited dendritic cells surround amyloid plaques in Alzheimer's disease? Biochem Pharmacol 2024:116258. [PMID: 38705533 DOI: 10.1016/j.bcp.2024.116258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 04/18/2024] [Accepted: 05/02/2024] [Indexed: 05/07/2024]
Abstract
Over the past decade, human genome-wide association and expression studies have strongly implicated dysregulation of the innate immune system in the pathogenesis of Alzheimer's disease (AD). Single cell mRNA sequencing studies have identified innate immune cell subtypes that are minimally present in normal healthy brain, but whose numbers greatly increase in association with AD pathology. These AD pathology-associated immune cells are putatively the locus for the immune-related AD risk. While the prevailing view is that these immune cells arise from transformation of resident brain microglia, studies across several decades and using multiple techniques and strategies suggest instead that the pathology-associated immune cells are bone-marrow derived hematopoietic cells that are recruited into brain. We critically review this translational literature, emphasizing the strengths and limitations of techniques used to address recruitment and the experimental designs employed. We conclude that the aggregate evidence points toward recruitment into brain of innate immune cells of the myeloid dendritic cell lineage. Recruitment of dendritic cells and their role in AD pathogenesis has broad implications for our understanding of the etiology and pathobiology of AD that impact the strategies to develop new, immune system-targeted therapeutics for this devastating disease.
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Affiliation(s)
- Robert B Nelson
- MindImmune Therapeutics, Inc., Kingston, RI; George and Anne Ryan Institute for Neuroscience, University of Rhode Island, Kingston, RI; Dept of Biomedical and Pharmaceutical Sciences, University of Rhode Island, Kingston, RI.
| | - Kenneth N Rose
- MindImmune Therapeutics, Inc., Kingston, RI; Dept of Biomedical and Pharmaceutical Sciences, University of Rhode Island, Kingston, RI
| | - Frank S Menniti
- MindImmune Therapeutics, Inc., Kingston, RI; George and Anne Ryan Institute for Neuroscience, University of Rhode Island, Kingston, RI; Dept of Biomedical and Pharmaceutical Sciences, University of Rhode Island, Kingston, RI
| | - Stevin H Zorn
- MindImmune Therapeutics, Inc., Kingston, RI; George and Anne Ryan Institute for Neuroscience, University of Rhode Island, Kingston, RI; Dept of Biomedical and Pharmaceutical Sciences, University of Rhode Island, Kingston, RI
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4
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Swain PS, Panda S, Pati S, Dehury B. Computational saturation mutagenesis to explore the effect of pathogenic mutations on extra-cellular domains of TREM2 associated with Alzheimer's and Nasu-Hakola disease. J Mol Model 2023; 29:360. [PMID: 37924367 DOI: 10.1007/s00894-023-05770-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 10/25/2023] [Indexed: 11/06/2023]
Abstract
CONTEXT The specialised family of triggering receptors expressed on myeloid cells (TREMs) plays a pivotal role in causing neurodegenerative disorders and activating microglial anti-inflammatory responses. Nasu-Hakola disease (NHD), a rare autosomal recessive disorder, has been associated with mutations in TREM2, which is also responsible for raising the risk of Alzheimer's disease (AD). Herein, we have made an endeavour to differentiate the confirmed pathogenic variants in TREM2 extra-cellular domain (ECD) linked with NHD and AD using mutation-induced fold stability change (∆∆G), with the computation of 12distinct structure-based methods through saturation mutagenesis. Correlation analysis between relative solvent accessibility (RSA) and ∆∆G expresses the discrete distributive behaviour of mutants associated with TREM2 in AD (R2 = 0.061) and NHD (R2 = 0.601). Our findings put an emphasis on W50 and V126 as major players in maintaining V-like domain in TREM2. Interestingly, we discern that both of them interact with a common residue Y108, which is dissolved upon mutation. This Y108 could have structural or functional role for TREM2 which can be an ideal candidate for further study. Furthermore, the residual interaction network highlights the importance of R47 and R62 in maintaining the CDR loops that are crucial for ligand binding. Future studies using biophysical characterisation of ligand interactions in TREM2-ECD would be helpful for the development of novel therapeutics for AD and NHD. METHODS ConSurf algorithm and ENDscript were used to determine the position and conservation of each residue in the wild-type ECD of TREM2. The mutation-induced fold stability change (∆∆G) of confirmed pathogenic mutants associated with NHD and AD was estimated using 12 state-of-the-art structure-based protein stability tools. Furthermore, we also computed the effect of random mutation on these sites using computational saturation mutagenesis. Linear regression analysis was performed using mutants ∆∆G and RSA through GraphPad software. In addition, a comprehensive non-bonded residual interaction network (RIN) of wild type and its mutants of TREM2-ECD was enumerated using RING3.0.
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Affiliation(s)
- Preety Sthutika Swain
- Bioinformatics Division, ICMR-Regional Medical Research Centre, Nalco Square, Chandrasekharpur, Bhubaneswar, 751023, Odisha, India
| | - Sunita Panda
- Mycology Laboratory, ICMR-Regional Medical Research Centre, Nalco Square, Chandrasekharpur, Bhubaneswar, 751023, Odisha, India
| | - Sanghamitra Pati
- Bioinformatics Division, ICMR-Regional Medical Research Centre, Nalco Square, Chandrasekharpur, Bhubaneswar, 751023, Odisha, India.
| | - Budheswar Dehury
- Bioinformatics Division, ICMR-Regional Medical Research Centre, Nalco Square, Chandrasekharpur, Bhubaneswar, 751023, Odisha, India.
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Filipello F, You SF, Mirfakhar FS, Mahali S, Bollman B, Acquarone M, Korvatska O, Marsh JA, Sivaraman A, Martinez R, Cantoni C, De Feo L, Ghezzi L, Minaya MA, Renganathan A, Cashikar AG, Satoh JI, Beatty W, Iyer AK, Cella M, Raskind WH, Piccio L, Karch CM. Defects in lysosomal function and lipid metabolism in human microglia harboring a TREM2 loss of function mutation. Acta Neuropathol 2023; 145:749-772. [PMID: 37115208 PMCID: PMC10175346 DOI: 10.1007/s00401-023-02568-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 03/29/2023] [Accepted: 03/30/2023] [Indexed: 04/29/2023]
Abstract
TREM2 is an innate immune receptor expressed by microglia in the adult brain. Genetic variation in the TREM2 gene has been implicated in risk for Alzheimer's disease and frontotemporal dementia, while homozygous TREM2 mutations cause a rare leukodystrophy, Nasu-Hakola disease (NHD). Despite extensive investigation, the role of TREM2 in NHD pathogenesis remains poorly understood. Here, we investigate the mechanisms by which a homozygous stop-gain TREM2 mutation (p.Q33X) contributes to NHD. Induced pluripotent stem cell (iPSC)-derived microglia (iMGLs) were generated from two NHD families: three homozygous TREM2 p.Q33X mutation carriers (termed NHD), two heterozygous mutation carriers, one related non-carrier, and two unrelated non-carriers. Transcriptomic and biochemical analyses revealed that iMGLs from NHD patients exhibited lysosomal dysfunction, downregulation of cholesterol genes, and reduced lipid droplets compared to controls. Also, NHD iMGLs displayed defective activation and HLA antigen presentation. This defective activation and lipid droplet content were restored by enhancing lysosomal biogenesis through mTOR-dependent and independent pathways. Alteration in lysosomal gene expression, such as decreased expression of genes implicated in lysosomal acidification (ATP6AP2) and chaperone mediated autophagy (LAMP2), together with reduction in lipid droplets were also observed in post-mortem brain tissues from NHD patients, thus closely recapitulating in vivo the phenotype observed in iMGLs in vitro. Our study provides the first cellular and molecular evidence that the TREM2 p.Q33X mutation in microglia leads to defects in lysosomal function and that compounds targeting lysosomal biogenesis restore a number of NHD microglial defects. A better understanding of how microglial lipid metabolism and lysosomal machinery are altered in NHD and how these defects impact microglia activation may provide new insights into mechanisms underlying NHD and other neurodegenerative diseases.
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Affiliation(s)
- Fabia Filipello
- Department of Psychiatry, Washington University in St Louis, St Louis, MO, USA
| | - Shih-Feng You
- Department of Psychiatry, Washington University in St Louis, St Louis, MO, USA
| | | | - Sidhartha Mahali
- Department of Psychiatry, Washington University in St Louis, St Louis, MO, USA
| | - Bryan Bollman
- Department of Neurology, Washington University in St Louis, St Louis, MO, USA
| | - Mariana Acquarone
- Department of Psychiatry, Washington University in St Louis, St Louis, MO, USA
| | - Olena Korvatska
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, USA
| | - Jacob A Marsh
- Department of Psychiatry, Washington University in St Louis, St Louis, MO, USA
| | - Anirudh Sivaraman
- Department of Psychiatry, Washington University in St Louis, St Louis, MO, USA
| | - Rita Martinez
- Department of Psychiatry, Washington University in St Louis, St Louis, MO, USA
| | - Claudia Cantoni
- Department of Neurology, Washington University in St Louis, St Louis, MO, USA
| | - Luca De Feo
- Department of Neurology, Washington University in St Louis, St Louis, MO, USA
| | - Laura Ghezzi
- Department of Neurology, Washington University in St Louis, St Louis, MO, USA
| | - Miguel A Minaya
- Department of Psychiatry, Washington University in St Louis, St Louis, MO, USA
| | - Arun Renganathan
- Department of Psychiatry, Washington University in St Louis, St Louis, MO, USA
| | - Anil G Cashikar
- Department of Psychiatry, Washington University in St Louis, St Louis, MO, USA
| | - Jun-Ichi Satoh
- Department of Bioinformatics and Molecular Neuropathology, Meiji Pharmaceutical University, Tokyo, Japan
| | - Wandy Beatty
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Abhirami K Iyer
- Department of Psychiatry, Washington University in St Louis, St Louis, MO, USA
| | - Marina Cella
- Department Of Pathology and Immunology, Washington University in St Louis, St Louis, MO, USA
| | - Wendy H Raskind
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, USA
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA, USA
| | - Laura Piccio
- Department of Neurology, Washington University in St Louis, St Louis, MO, USA.
- Charles Perkins Centre and Brain and Mind Centre, School of Medical Sciences (Neuroscience), University of Sydney, Sydney, NSW, Australia.
- School of Medical Sciences, Brain and Mind Centre, University of Sydney, 94 Mallett St, Camperdown, Sydney, NSW, 2050, Australia.
| | - Celeste M Karch
- Department of Psychiatry, Washington University in St Louis, St Louis, MO, USA.
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Unveiling the Potentiality of Shikonin Derivatives Inhibiting SARS-CoV-2 Main Protease by Molecular Dynamic Simulation Studies. Int J Mol Sci 2023; 24:ijms24043100. [PMID: 36834524 PMCID: PMC9963214 DOI: 10.3390/ijms24043100] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 01/13/2023] [Accepted: 01/28/2023] [Indexed: 02/09/2023] Open
Abstract
Shikonin, a phytochemical present in the roots of Lithospermum erythrorhizon, is well-known for its broad-spectrum activity against cancer, oxidative stress, inflammation, viruses, and anti-COVID-19 agents. A recent report based on a crystallographic study revealed a distinct conformation of shikonin binding to the SARS-CoV-2 main protease (Mpro), suggesting the possibility of designing potential inhibitors based on shikonin derivatives. The present study aimed to identify potential shikonin derivatives targeting the Mpro of COVID-19 by using molecular docking and molecular dynamics simulations. A total of 20 shikonin derivatives were screened, of which few derivatives showed higher binding affinity than shikonin. Following the MM-GBSA binding energy calculations using the docked structures, four derivatives were retained with the highest binding energy and subjected to molecular dynamics simulation. Molecular dynamics simulation studies suggested that alpha-methyl-n-butyl shikonin, beta-hydroxyisovaleryl shikonin, and lithospermidin-B interacted with two conserved residues, His41 and Cys145, through multiple bonding in the catalytic sites. This suggests that these residues may effectively suppress SARS-CoV-2 progression by inhibiting Mpro. Taken together, the present in silico study concluded that shikonin derivatives may play an influential role in Mpro inhibition.
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Seyedi SH, Alhagh MS, Ahmadizad M, Ardalan N, Hosseininezhadian Koushki E, Farshadfar C, Amjadi B. Structural screening into the recognition of a potent inhibitor against non-structural protein 16: a molecular simulation to inhibit SARS-CoV-2 infection. J Biomol Struct Dyn 2022; 40:14115-14130. [PMID: 34762019 DOI: 10.1080/07391102.2021.2001374] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
COVID-19 infection is caused by endemic crown infection (SARS-CoV-2) and is associated with lung damage and severe immune response. Non-Structural Proteins are the central components of coronaviral transcription and replication machinery in SARS-CoV-2 and also stimulate mRNA cap methylation to avoid the immune response. Non-Structural Protein 16 (NSP16) is one of the primary targets for the drug discovery of coronaviruses. Discovering an effective inhibitor against the NSP16 in comparison with Sinefungin was the main purpose of this investigation. Binding free-energy calculations, computational methods of molecular dynamics, docking, and virtual screening were utilized in this study. The ZINC and PubChem databases were applied to screen some chemical compounds regarding Sinefungin as a control inhibitor. Based on structural similarity to Sinefungin, 355 structures were obtained from the mentioned databases. Subsequently, this set of compounds were monitored by AutoDock Vina software, and ultimately the potent inhibitor (PUBCHEM512713) was chosen. At the next stage, molecular dynamics were carried out by GROMACS software to evaluate the potential elected compounds in a simulated environment and in a timescale of 100 nanoseconds. MM-PBSA investigation exhibited that the value of binding free energy for PUBCHEM512713 (-30.829 kJ.mol-1) is more potent than Sinefungin (-11.941 kJ.mol-1). Furthermore, the results of ADME analysis illustrated that the pharmacokinetics, drug-likeness, and lipophilicity parameters of PUBCHEM512713 are admissible for human utilization. Finally, our data suggested that PUBCHEM512713 is an effective drug candidate for inhibiting the NSP16 and is suitable for in vitro and in vivo studies.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Seyed Hamid Seyedi
- Department of Biochemistry, Science and Research Branch, Islamic Azad University, Sanandaj, Iran
| | - Mohammad Shakib Alhagh
- Department of Microbiology, Faculty of Medicine, Kurdistan University of Medical Sciences, Sanandaj, Iran
| | - Mehran Ahmadizad
- Department of Biochemistry, Science and Research Branch, Islamic Azad University, Sanandaj, Iran
| | - Noeman Ardalan
- Department of Microbiology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | | | - Chiako Farshadfar
- Department of Biochemistry, Science and Research Branch, Islamic Azad University, Sanandaj, Iran
| | - Barzan Amjadi
- Department of Biochemistry, Science and Research Branch, Islamic Azad University, Sanandaj, Iran
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Ali MC, Khatun MS, Jahan SI, Das R, Munni YA, Rahman MM, Dash R. In silico design of epitope-based peptide vaccine against non-typhoidal Salmonella through immunoinformatic approaches. J Biomol Struct Dyn 2022; 40:10696-10714. [PMID: 36529187 DOI: 10.1080/07391102.2021.1947381] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Non-typhoidal Salmonella (NTS) is one of the leading bacterial causes of many invasive human infections with a high antibiotic resistance profile. With this concern, the current study aimed to design an effective epitope-based peptide vaccine against NTS species as a successive and substitutive protective measure of invasive NTS disease. To design rationally, the current study considered a comprehensive in silico workflow combination of both immunoinformatics and molecular modeling approaches, including molecular docking and molecular dynamics (MD) simulation. We identified the two most promising T cell epitopes KVLYGIFAI and YGIFAITAL, and three B cell epitopes AAPVQVGEAAGS, TGGGDGSNT, and TGGGDGSNTGTTTT, in the outer membrane of NTS. Using these epitopes, a multiepitope vaccine was subsequently constructed along with appropriate adjuvant and linkers, which showed a good binding affinity and stability with toll-like receptor 2 (TLR2) in both molecular docking and MD simulation. Furthermore, in silico immune simulation described a strong immune response with a high number of antibodies, interferon-γ, and activated B and T cells. This study collectively suggests that predicted vaccine constructs could be considered potential vaccine candidates against common NTS species.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Md Chayan Ali
- Department of Biotechnology & Genetic Engineering, Faculty of Biological Sciences, Islamic University, Kushtia, Bangladesh
| | - Mst Shanzeda Khatun
- Department of Biotechnology & Genetic Engineering, Faculty of Biological Sciences, Islamic University, Kushtia, Bangladesh
| | - Sultana Israt Jahan
- Department of Biotechnology & Genetic Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Raju Das
- Department of Physiology, Dongguk University College of Medicine, Gyeongju, Republic of Korea
| | - Yeasmin Akter Munni
- Department of Anatomy, Dongguk University College of Medicine, Gyeongju, Republic of Korea
| | - Md Mafizur Rahman
- Department of Biotechnology & Genetic Engineering, Faculty of Biological Sciences, Islamic University, Kushtia, Bangladesh
| | - Raju Dash
- Department of Anatomy, Dongguk University College of Medicine, Gyeongju, Republic of Korea
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Berdyński M, Ludwiczak J, Barczak A, Barcikowska-Kotowicz M, Kuźma-Kozakiewicz M, Dunin-Horkawicz S, Żekanowski C, Borzemska B. TREM2 Gene Compound Heterozygosity in Neurodegenerative Disorders. J Alzheimers Dis 2022; 89:1211-1219. [PMID: 36031890 DOI: 10.3233/jad-220210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND Homozygous variants of the TREM2 and TYROBP genes have been shown to be causative for multiple bone cysts and neurodegeneration leading to progressive dementia (NHD, Nasu-Hakola disease). OBJECTIVE To determine if biallelic variants of these genes and/or oligogenic inheritance could be responsible for a wider spectrum of neurodegenerative conditions. METHODS We analyzed 52 genes associated with neurodegenerative disorders using targeted next generation sequencing in a selected group of 29 patients (n = 14 Alzheimer's disease, n = 8 frontotemporal dementia, n = 7 amyotrophic lateral sclerosis) carrying diverse already determined rare variants in exon 2 of TREM2. Molecular modeling was used to get an insight into the potential effects of the mutation. RESULTS We identified a novel mutation c.401_406delinsTCTAT; p.(Asp134Valfs*55) in exon 3 of TREM2 in an Alzheimer's disease patient also carrying the p.Arg62His TREM2 variant. Molecular modeling revealed that the identified mutation prevents anchoring of the TREM2 protein in the membrane, leaving the core of the Ig-like domain intact. CONCLUSION Our results expand the spectrum of neurodegenerative diseases, where the carriers of biallelic mutations in TREM2 have been described for Alzheimer's disease, and highlight the impact of variant burden in other genes on phenotypic heterogeneity.
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Affiliation(s)
- Mariusz Berdyński
- Department of Neurogenetics and Functional Genomics, Mossakowski Medical Research Institute, Polish Academy of Sciences, Warsaw, Poland
| | - Jan Ludwiczak
- Laboratory of Structural Bioinformatics, Centre of New Technologies, University of Warsaw, Warsaw, Poland.,Laboratory of Bioinformatics, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Anna Barczak
- Rare Diseases Research Platform, Mossakowski Medical Research Institute, Polish Academy of Sciences, Warsaw, Poland
| | | | - Magdalena Kuźma-Kozakiewicz
- Neurodegenerative Diseases Research Group, Medical University of Warsaw, Warsaw, Poland.,Department of Neurology, Medical University of Warsaw, Warsaw, Poland
| | - Stanisław Dunin-Horkawicz
- Laboratory of Structural Bioinformatics, Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Cezary Żekanowski
- Department of Neurogenetics and Functional Genomics, Mossakowski Medical Research Institute, Polish Academy of Sciences, Warsaw, Poland
| | - Beata Borzemska
- Department of Neurogenetics and Functional Genomics, Mossakowski Medical Research Institute, Polish Academy of Sciences, Warsaw, Poland
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10
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Ahmed S, Ali MC, Ruma RA, Mahmud S, Paul GK, Saleh MA, Alshahrani MM, Obaidullah AJ, Biswas SK, Rahman MM, Rahman MM, Islam MR. Molecular Docking and Dynamics Simulation of Natural Compounds from Betel Leaves ( Piper betle L.) for Investigating the Potential Inhibition of Alpha-Amylase and Alpha-Glucosidase of Type 2 Diabetes. Molecules 2022; 27:molecules27144526. [PMID: 35889399 PMCID: PMC9316265 DOI: 10.3390/molecules27144526] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 07/06/2022] [Accepted: 07/07/2022] [Indexed: 11/16/2022] Open
Abstract
Piper betle L. is widely distributed and commonly used medicinally important herb. It can also be used as a medication for type 2 diabetes patients. In this study, compounds of P. betle were screened to investigate the inhibitory action of alpha-amylase and alpha-glucosidase against type 2 diabetes through molecular docking, molecular dynamics simulation, and ADMET (absorption, distribution, metabolism, excretion, and toxicity) analysis. The molecule apigenin-7-O-glucoside showed the highest binding affinity among 123 (one hundred twenty-three) tested compounds. This compound simultaneously bound with the two-target proteins alpha-amylase and alpha-glucosidase, with high molecular mechanics-generalized born surface area (MM/GBSA) values (ΔG Bind = -45.02 kcal mol-1 for alpha-amylase and -38.288 for alpha-glucosidase) compared with control inhibitor acarbose, which had binding affinities of -36.796 kcal mol-1 for alpha-amylase and -29.622 kcal mol-1 for alpha-glucosidase. The apigenin-7-O-glucoside was revealed to be the most stable molecule with the highest binding free energy through molecular dynamics simulation, indicating that it could compete with the inhibitors' native ligand. Based on ADMET analysis, this phytochemical exhibited a wide range of physicochemical, pharmacokinetic, and drug-like qualities and had no significant side effects, making them prospective drug candidates for type 2 diabetes. Additional in vitro, in vivo, and clinical investigations are needed to determine the precise efficacy of drugs.
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Affiliation(s)
- Sabbir Ahmed
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Islamic University, Kushtia 7003, Bangladesh; (S.A.); (M.C.A.); (R.A.R.); (S.K.B.); (M.M.R.); (M.R.I.)
| | - Md Chayan Ali
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Islamic University, Kushtia 7003, Bangladesh; (S.A.); (M.C.A.); (R.A.R.); (S.K.B.); (M.M.R.); (M.R.I.)
| | - Rumana Akter Ruma
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Islamic University, Kushtia 7003, Bangladesh; (S.A.); (M.C.A.); (R.A.R.); (S.K.B.); (M.M.R.); (M.R.I.)
| | - Shafi Mahmud
- Division of Genome Sciences and Cancer, The John Curtin School of Medical Research and The Shine-Dalgarno Centre for RNA Innovation, The Australian National University, Canberra, ACT 2601, Australia;
| | - Gobindo Kumar Paul
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh; (G.K.P.); (M.A.S.)
| | - Md Abu Saleh
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh; (G.K.P.); (M.A.S.)
| | - Mohammed Merae Alshahrani
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, Najran University, Najran 61441, Saudi Arabia;
| | - Ahmad J. Obaidullah
- Drug Exploration and Development Chair (DEDC), Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia;
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Sudhangshu Kumar Biswas
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Islamic University, Kushtia 7003, Bangladesh; (S.A.); (M.C.A.); (R.A.R.); (S.K.B.); (M.M.R.); (M.R.I.)
| | - Md Mafizur Rahman
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Islamic University, Kushtia 7003, Bangladesh; (S.A.); (M.C.A.); (R.A.R.); (S.K.B.); (M.M.R.); (M.R.I.)
- Correspondence:
| | - Md Mizanur Rahman
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Islamic University, Kushtia 7003, Bangladesh; (S.A.); (M.C.A.); (R.A.R.); (S.K.B.); (M.M.R.); (M.R.I.)
| | - Md Rezuanul Islam
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Islamic University, Kushtia 7003, Bangladesh; (S.A.); (M.C.A.); (R.A.R.); (S.K.B.); (M.M.R.); (M.R.I.)
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11
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Dash R, Munni YA, Mitra S, Choi HJ, Jahan SI, Chowdhury A, Jang TJ, Moon IS. Dynamic insights into the effects of nonsynonymous polymorphisms (nsSNPs) on loss of TREM2 function. Sci Rep 2022; 12:9378. [PMID: 35672339 PMCID: PMC9174165 DOI: 10.1038/s41598-022-13120-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 05/16/2022] [Indexed: 11/09/2022] Open
Abstract
Single nucleotide variations in Triggering Receptor Expressed on Myeloid Cells 2 (TREM2) are associated with many neurodegenerative diseases, including Nasu-Hakola disease (NHD), frontotemporal dementia (FTD), and late-onset Alzheimer's disease because they disrupt ligand binding to the extracellular domain of TREM2. However, the effects of nonsynonymous single nucleotide polymorphisms (nsSNPs) in TREM2 on disease progression remain unknown. In this study, we identified several high-risk nsSNPs in the TREM2 gene using various deleterious SNP predicting algorithms and analyzed their destabilizing effects on the ligand recognizing region of the TREM2 immunoglobulin (Ig) domain by molecular dynamics (MD) simulation. Cumulative prediction by all tools employed suggested the three most deleterious nsSNPs involved in loss of TREM2 function are rs549402254 (W50S), rs749358844 (R52C), and rs1409131974 (D104G). MD simulation showed that these three variants cause substantial structural alterations and conformational remodeling of the apical loops of the TREM2 Ig domain, which is responsible for ligand recognition. Detailed analysis revealed that these variants substantially increased distances between apical loops and induced conformation remodeling by changing inter-loop nonbonded contacts. Moreover, all nsSNPs changed the electrostatic potentials near the putative ligand-interacting region (PLIR), which suggested they might reduce specificity or loss of binding affinity for TREM2 ligands. Overall, this study identifies three potential high-risk nsSNPs in the TREM2 gene. We propose further studies on the molecular mechanisms responsible for loss of TREM2 function and the associations between TREM2 nsSNPs and neurodegenerative diseases.
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Affiliation(s)
- Raju Dash
- Department of Anatomy, Dongguk University College of Medicine, Gyeongju, 38066, Republic of Korea
| | - Yeasmin Akter Munni
- Department of Anatomy, Dongguk University College of Medicine, Gyeongju, 38066, Republic of Korea
| | - Sarmistha Mitra
- Department of Anatomy, Dongguk University College of Medicine, Gyeongju, 38066, Republic of Korea
| | - Ho Jin Choi
- Department of Anatomy, Dongguk University College of Medicine, Gyeongju, 38066, Republic of Korea
| | - Sultana Israt Jahan
- Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University, Noakhali, 3814, Bangladesh
| | - Apusi Chowdhury
- Department of Pharmaceutical Science, North-South University, Dhaka, 1229, Bangladesh
| | - Tae Jung Jang
- Department of Pathology, Dongguk University College of Medicine, Gyeongju, 38066, Republic of Korea
| | - Il Soo Moon
- Department of Anatomy, Dongguk University College of Medicine, Gyeongju, 38066, Republic of Korea.
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12
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Structural Consequence of Non-Synonymous Single-Nucleotide Variants in the N-Terminal Domain of LIS1. Int J Mol Sci 2022; 23:ijms23063109. [PMID: 35328531 PMCID: PMC8955593 DOI: 10.3390/ijms23063109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 03/10/2022] [Accepted: 03/11/2022] [Indexed: 02/04/2023] Open
Abstract
Disruptive neuronal migration during early brain development causes severe brain malformation. Characterized by mislocalization of cortical neurons, this condition is a result of the loss of function of migration regulating genes. One known neuronal migration disorder is lissencephaly (LIS), which is caused by deletions or mutations of the LIS1 (PAFAH1B1) gene that has been implicated in regulating the microtubule motor protein cytoplasmic dynein. Although this class of diseases has recently received considerable attention, the roles of non-synonymous polymorphisms (nsSNPs) in LIS1 on lissencephaly progression remain elusive. Therefore, the present study employed combined bioinformatics and molecular modeling approach to identify potential damaging nsSNPs in the LIS1 gene and provide atomic insight into their roles in LIS1 loss of function. Using this approach, we identified three high-risk nsSNPs, including rs121434486 (F31S), rs587784254 (W55R), and rs757993270 (W55L) in the LIS1 gene, which are located on the N-terminal domain of LIS1. Molecular dynamics simulation highlighted that all variants decreased helical conformation, increased the intermonomeric distance, and thus disrupted intermonomeric contacts in the LIS1 dimer. Furthermore, the presence of variants also caused a loss of positive electrostatic potential and reduced dimer binding potential. Since self-dimerization is an essential aspect of LIS1 to recruit interacting partners, thus these variants are associated with the loss of LIS1 functions. As a corollary, these findings may further provide critical insights on the roles of LIS1 variants in brain malformation.
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13
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The emerging role of triggering receptor expressed on myeloid cell-2 in malignant tumor. Cent Eur J Immunol 2022; 47:373-381. [PMID: 36817396 PMCID: PMC9901261 DOI: 10.5114/ceji.2022.124387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 12/14/2022] [Indexed: 02/05/2023] Open
Abstract
Triggering receptor expressed on myeloid cell-2 (TREM2) is a transmembrane receptor which is specifically expressed on myeloid cells. To date, TREM2 has been confirmed as a key factor in many pathologies, such as Alzheimer's disease, obesity-related metabolic syndrome, fatty liver and atherosclerosis. However, the role of TREM2 in tumors remains poorly understood. TREM2 is highly expressed in more than 200 primary and metastatic tumors, a feature that makes TREM2 a potential clinical target for tumor immunotherapy. The tumor microenvironment (TME) is the "soil" which tumors survive on and exhibits immunosuppressive characteristics. During the development of a tumor, TME will secrete various chemotactic factors to recruit myeloid cells. It is clear now that cancer progression and metastasis depend on the interactions between cancer cells and myeloid cell infiltration in TME. As an important receptor involved in inflammatory suppression signaling pathways, TREM2 may play an important role in immune escape by the tumor. Recently, several studies have illustrated that TREM2 expressed on tumor infiltrated myeloid cells acts as a crucial regulator of the antitumor immune response. In this review, we systematically summarize recent publications about the latest advances in knowledge of TREM2 in cancer, especially focusing on its role in tumor associated myeloid cells and tumor immunotherapy.
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14
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Lary CW, Rosen CJ, Kiel DP. Osteoporosis and Dementia: Establishing a Link. J Bone Miner Res 2021; 36:2103-2105. [PMID: 34515377 PMCID: PMC8595864 DOI: 10.1002/jbmr.4431] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 08/29/2021] [Indexed: 12/17/2022]
Affiliation(s)
| | | | - Douglas P Kiel
- Hinda and Arthur Marcus Institute for Aging Research, Hebrew SeniorLife, Boston, MA, USA.,Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA
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15
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Dash R, Mitra S, Munni YA, Choi HJ, Ali MC, Barua L, Jang TJ, Moon IS. Computational Insights into the Deleterious Impacts of Missense Variants on N-Acetyl-d-glucosamine Kinase Structure and Function. Int J Mol Sci 2021; 22:8048. [PMID: 34360815 PMCID: PMC8347710 DOI: 10.3390/ijms22158048] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 07/05/2021] [Accepted: 07/22/2021] [Indexed: 12/11/2022] Open
Abstract
An enzyme of the mammalian amino-sugar metabolism pathway, N-acetylglucosamine kinase (NAGK), that synthesizes N-acetylglucosamine (GlcNAc)-6-phosphate, is reported to promote dynein functions during mitosis, axonal and dendritic growth, cell migration, and selective autophagy, which all are unrelated to its enzyme activity. As non-enzymatic structural functions can be altered by genetic variation, we made an effort in this study aimed at deciphering the pathological effect of nonsynonymous single-nucleotide polymorphisms (nsSNPs) in NAGK gene. An integrated computational approach, including molecular dynamics (MD) simulation and protein-protein docking simulation, was used to identify the damaging nsSNPs and their detailed structural and functional consequences. The analysis revealed the four most damaging variants (G11R, G32R, G120E, and A156D), which are highly conserved and functional, positioned in both small (G11R and G32R) and large (G120E and A156D) domains of NAGK. G11R is located in the ATP binding region, while variants present in the large domain (G120E and A156D) were found to induce substantial alterations in the structural organizations of both domains, including the ATP and substrate binding sites. Furthermore, all variants were found to reduce binding energy between NAGK and dynein subunit DYNLRB1, as revealed by protein-protein docking and MM-GBSA binding energy calculation supporting their deleteriousness on non-canonical function. We hope these findings will direct future studies to gain more insight into the role of these variants in the loss of NAGK function and their role in neurodevelopmental disorders.
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Affiliation(s)
- Raju Dash
- Department of Anatomy, Dongguk University College of Medicine, Gyeongju 38066, Korea; (R.D.); (S.M.); (Y.A.M.); (H.J.C.)
| | - Sarmistha Mitra
- Department of Anatomy, Dongguk University College of Medicine, Gyeongju 38066, Korea; (R.D.); (S.M.); (Y.A.M.); (H.J.C.)
| | - Yeasmin Akter Munni
- Department of Anatomy, Dongguk University College of Medicine, Gyeongju 38066, Korea; (R.D.); (S.M.); (Y.A.M.); (H.J.C.)
| | - Ho Jin Choi
- Department of Anatomy, Dongguk University College of Medicine, Gyeongju 38066, Korea; (R.D.); (S.M.); (Y.A.M.); (H.J.C.)
| | - Md. Chayan Ali
- Department of Biotechnology & Genetic Engineering, Faculty of Biological Sciences, Islamic University, Kushtia 7003, Bangladesh;
| | - Largess Barua
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong 4381, Bangladesh;
| | - Tae Jung Jang
- Department of Pathology, Dongguk University College of Medicine, Gyeongju 38066, Korea;
| | - Il Soo Moon
- Department of Anatomy, Dongguk University College of Medicine, Gyeongju 38066, Korea; (R.D.); (S.M.); (Y.A.M.); (H.J.C.)
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16
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Noorbakhsh A, Hosseininezhadian Koushki E, Farshadfar C, Ardalan N. Designing a natural inhibitor against human kynurenine aminotransferase type II and a comparison with PF-04859989: a computational effort against schizophrenia. J Biomol Struct Dyn 2021; 40:7038-7051. [PMID: 33645449 DOI: 10.1080/07391102.2021.1893817] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The Kynurenine aminotransferase II (KATII) enzyme has an essential role in L-kynurenine transmission to kynurenic acid (KYNA). High concentration of kynurenic acid associates with schizophrenia and some neurocognitive disorders. Decreasing KYNA production via inhibiting KATII would be an effective method for treating and understanding the related central nervous system (CNS) diseases. This study aimed to discover a potent inhibitor against human KATII (hKATII) in comparison with PF-04859989. We utilized the computational methods of molecular dynamics, virtual screening, docking, and binding free-energy calculations. Initially, the 58722 compounds from three drug libraries, including IBS library, DrugBank library, and Analyticon library, were obtained. At the next stage, these sets of compounds were screened by AutoDock Vina software, and a potent inhibitor (ZINC35466084) was selected. Following the screening, molecular dynamics simulations for both ZINC35466084 and PF-04859989 were performed by GROMACS software. MM-PBSA analysis showed that the amount of binding free energy for ZINC35466084 (-61.26 KJ mol-1) is more potent than PF-04859989 (-43.14 KJ mol-1). Furthermore, the ADME analysis results revealed that the pharmacokinetic parameters of ZINC35466084 are acceptable for human use. Eventually, our data demonstrated that ZINC35466084 is suitable for hKATII inhibition, and it is an appropriate candidate for further studies in the laboratory. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Akbar Noorbakhsh
- Department of Biochemistry, Science and Research Branch, Islamic Azad University, Sanandaj, Iran
| | - Elnaz Hosseininezhadian Koushki
- Nano Drug Delivery Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Chiako Farshadfar
- Department of Biochemistry, Science and Research Branch, Islamic Azad University, Sanandaj, Iran
| | - Noeman Ardalan
- Department of Microbiology, Science and Research Branch, Islamic Azad University, Tehran, Iran
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17
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Islam MA, Choi HJ, Dash R, Sharif SR, Oktaviani DF, Seog DH, Moon IS. N-Acetyl- D-Glucosamine Kinase Interacts with NudC and Lis1 in Dynein Motor Complex and Promotes Cell Migration. Int J Mol Sci 2020; 22:ijms22010129. [PMID: 33374456 PMCID: PMC7795690 DOI: 10.3390/ijms22010129] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 12/17/2020] [Accepted: 12/20/2020] [Indexed: 12/18/2022] Open
Abstract
Recently, we showed that N-acetylglucosamine kinase (NAGK), an enzyme of amino sugar metabolism, interacts with dynein light chain roadblock type 1 (DYNLRB1) and promotes the functions of dynein motor. Here, we report that NAGK interacts with nuclear distribution protein C (NudC) and lissencephaly 1 (Lis1) in the dynein complex. Yeast two-hybrid assays, pull-down assays, immunocytochemistry, and proximity ligation assays revealed NAGK-NudC-Lis1-dynein complexes around nuclei, at the leading poles of migrating HEK293T cells, and at the tips of migratory processes of cultured rat neuroblast cells. The exogenous expression of red fluorescent protein (RFP)-tagged NAGK accelerated HEK293T cell migration during in vitro wound-healing assays and of neurons during in vitro neurosphere migration and in utero electroporation assays, whereas NAGK knockdown by short hairpin RNA (shRNA) delayed migration. Finally, a small NAGK peptide derived from the NudC interacting domain in in silico molecular docking analysis retarded the migrations of HEK293T and SH-SY5Y cells. These data indicate a functional interaction between NAGK and dynein-NudC-Lis1 complex at the nuclear envelope is required for the regulation of cell migration.
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Affiliation(s)
- Md. Ariful Islam
- Department of Anatomy, Dongguk University College of Medicine, Gyeongju 38066, Korea; (M.A.I.); (H.J.C.); (R.D.); (S.R.S.); (D.F.O.)
| | - Ho Jin Choi
- Department of Anatomy, Dongguk University College of Medicine, Gyeongju 38066, Korea; (M.A.I.); (H.J.C.); (R.D.); (S.R.S.); (D.F.O.)
| | - Raju Dash
- Department of Anatomy, Dongguk University College of Medicine, Gyeongju 38066, Korea; (M.A.I.); (H.J.C.); (R.D.); (S.R.S.); (D.F.O.)
| | - Syeda Ridita Sharif
- Department of Anatomy, Dongguk University College of Medicine, Gyeongju 38066, Korea; (M.A.I.); (H.J.C.); (R.D.); (S.R.S.); (D.F.O.)
| | - Diyah Fatimah Oktaviani
- Department of Anatomy, Dongguk University College of Medicine, Gyeongju 38066, Korea; (M.A.I.); (H.J.C.); (R.D.); (S.R.S.); (D.F.O.)
| | - Dae-Hyun Seog
- Department of Biochemistry, Dementia and Neurodegenerative Disease Research Center, Inje University College of Medicine, Busan 47392, Korea;
| | - Il Soo Moon
- Department of Anatomy, Dongguk University College of Medicine, Gyeongju 38066, Korea; (M.A.I.); (H.J.C.); (R.D.); (S.R.S.); (D.F.O.)
- Dongguk Medical Institute, Dongguk University College of Medicine, Gyeongju 38066, Korea
- Correspondence: ; Tel.: +82-54-770-2414; Fax: +82-54-770-2447
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18
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Munni YA, Ali MC, Selsi NJ, Sultana M, Hossen M, Bipasha TH, Rahman M, Uddin MN, Hosen SMZ, Dash R. Molecular simulation studies to reveal the binding mechanisms of shikonin derivatives inhibiting VEGFR-2 kinase. Comput Biol Chem 2020; 90:107414. [PMID: 33191109 DOI: 10.1016/j.compbiolchem.2020.107414] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 10/17/2020] [Accepted: 10/29/2020] [Indexed: 12/20/2022]
Abstract
Traditional vascular endothelial growth factor receptor 2 (VEGFR-2) inhibitors can manage angiogenesis; however, severe toxicity and resistance limit their long-term applications in clinical therapy. Shikonin (SHK) and its derivatives could be promising to inhibit the VEGFR-2 mediated angiogenesis, as they are reported to bind in the catalytic kinase domain with low affinity. However, the detailed molecular insights and binding dynamics of these natural inhibitors are unknown, which is crucial for potential SHK based lead design. Therefore, the present study employed molecular modeling and simulations techniques to get insight into the binding behaviors of SHK and its two derivates, β-hydroxyisovalerylshikonin (β-HIVS) and acetylshikonin (ACS). Here the intermolecular interactions between protein and ligands were studied by induced fit docking approach, which were further evaluated by treating QM/MM (quantum mechanics/molecular mechanics) and molecular dynamics (MD) simulation. The result showed that the naphthazarin ring of the SHK derivates is vital for strong binding to the catalytic domain; however, the binding stability can be modulated by the side chain modification. Because of having electrostatic potential, this ring makes essential interactions with the DFG (Asp1046 and Phe1047) motif and also allows interacting with the allosteric binding site. Taken together, the studies will advance our knowledge and scope for the development of new selective VEGFR-2 inhibitors based on SHK and its analogs.
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Affiliation(s)
- Yeasmin Akter Munni
- Department of Anatomy, Dongguk University College of Medicine, Gyeongju, 38066, Republic of Korea.
| | - Md Chayan Ali
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Islamic University, Kushtia, 7003, Bangladesh.
| | - Nusrat Jahan Selsi
- Department of Pharmacy, University of Science & Technology, Chittagong, 4202, Bangladesh.
| | - Marium Sultana
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong, 4381, Bangladesh.
| | - Md Hossen
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong, 4381, Bangladesh.
| | - Tanjiba Harun Bipasha
- Department of Pharmacy, University of Science & Technology, Chittagong, 4202, Bangladesh.
| | - Mahbubur Rahman
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong, 4381, Bangladesh.
| | - Md Nazim Uddin
- Department of Pharmacy, Southern University Bangladesh, Chittagong, 4000, Bangladesh.
| | - S M Zahid Hosen
- Pancreatic Research Group, South Western Sydney Clinical School, University of New South Wales, and Ingham Institute for Applied Medical Research, Liverpool, NSW, 2170, Australia.
| | - Raju Dash
- Department of Anatomy, Dongguk University College of Medicine, Gyeongju, 38066, Republic of Korea.
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19
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Nayarisseri A, Khandelwal R, Madhavi M, Selvaraj C, Panwar U, Sharma K, Hussain T, Singh SK. Shape-based Machine Learning Models for the Potential Novel COVID-19 Protease Inhibitors Assisted by Molecular Dynamics Simulation. Curr Top Med Chem 2020; 20:2146-2167. [PMID: 32621718 DOI: 10.2174/1568026620666200704135327] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 03/20/2020] [Accepted: 04/25/2020] [Indexed: 12/17/2022]
Abstract
BACKGROUND The vast geographical expansion of novel coronavirus and an increasing number of COVID-19 affected cases have overwhelmed health and public health services. Artificial Intelligence (AI) and Machine Learning (ML) algorithms have extended their major role in tracking disease patterns, and in identifying possible treatments. OBJECTIVE This study aims to identify potential COVID-19 protease inhibitors through shape-based Machine Learning assisted by Molecular Docking and Molecular Dynamics simulations. METHODS 31 Repurposed compounds have been selected targeting the main coronavirus protease (6LU7) and a machine learning approach was employed to generate shape-based molecules starting from the 3D shape to the pharmacophoric features of their seed compound. Ligand-Receptor Docking was performed with Optimized Potential for Liquid Simulations (OPLS) algorithms to identify highaffinity compounds from the list of selected candidates for 6LU7, which were subjected to Molecular Dynamic Simulations followed by ADMET studies and other analyses. RESULTS Shape-based Machine learning reported remdesivir, valrubicin, aprepitant, and fulvestrant as the best therapeutic agents with the highest affinity for the target protein. Among the best shape-based compounds, a novel compound identified was not indexed in any chemical databases (PubChem, Zinc, or ChEMBL). Hence, the novel compound was named 'nCorv-EMBS'. Further, toxicity analysis showed nCorv-EMBS to be suitable for further consideration as the main protease inhibitor in COVID-19. CONCLUSION Effective ACE-II, GAK, AAK1, and protease 3C blockers can serve as a novel therapeutic approach to block the binding and attachment of the main COVID-19 protease (PDB ID: 6LU7) to the host cell and thus inhibit the infection at AT2 receptors in the lung. The novel compound nCorv- EMBS herein proposed stands as a promising inhibitor to be evaluated further for COVID-19 treatment.
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Affiliation(s)
- Anuraj Nayarisseri
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore-452010, Madhya Pradesh, India,Bioinformatics Research Laboratory, LeGene Biosciences Pvt Ltd., Mahalakshmi Nagar, Indore-452010, Madhya
Pradesh, India,Research Chair for Biomedical Applications of Nanomaterials, Biochemistry Department, College of Science, King
Saud University, Riyadh, Saudi Arabia,Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi-630 003, Tamil Nadu, India
| | - Ravina Khandelwal
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore-452010, Madhya Pradesh, India
| | - Maddala Madhavi
- Department of Zoology, Nizam College, Osmania University, Hyderabad-500001, Telangana State, India
| | - Chandrabose Selvaraj
- Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi-630 003, Tamil Nadu, India
| | - Umesh Panwar
- Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi-630 003, Tamil Nadu, India
| | - Khushboo Sharma
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore-452010, Madhya Pradesh, India
| | - Tajamul Hussain
- Center of Excellence in Biotechnology Research, College of Science, King Saud University, Riyadh, Saudi Arabia,Research Chair for Biomedical Applications of Nanomaterials, Biochemistry Department, College of Science, King
Saud University, Riyadh, Saudi Arabia
| | - Sanjeev Kumar Singh
- Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi-630 003, Tamil Nadu, India
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20
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Computational SNP Analysis and Molecular Simulation Revealed the Most Deleterious Missense Variants in the NBD1 Domain of Human ABCA1 Transporter. Int J Mol Sci 2020; 21:ijms21207606. [PMID: 33066695 PMCID: PMC7589834 DOI: 10.3390/ijms21207606] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 10/12/2020] [Accepted: 10/12/2020] [Indexed: 12/12/2022] Open
Abstract
The ATP-binding cassette transporter A1 (ABCA1) is a membrane-bound exporter protein involved in regulating serum HDL level by exporting cholesterol and phospholipids to load up in lipid-poor ApoA-I and ApoE, which allows the formation of nascent HDL. Mutations in the ABCA1 gene, when presents in both alleles, disrupt the canonical function of ABCA1, which associates with many disorders related to lipid transport. Although many studies have reported the phenotypic effects of a large number of ABCA1 variants, the pathological effect of non-synonymous polymorphisms (nsSNPs) in ABCA1 remains elusive. Therefore, aiming at exploring the structural and functional consequences of nsSNPs in ABCA1, in this study, we employed an integrated computational approach consisting of nine well-known in silico tools to identify damaging SNPs and molecular dynamics (MD) simulation to get insights into the magnitudes of the damaging effects. In silico tools revealed four nsSNPs as being most deleterious, where the two SNPs (G1050V and S1067C) are identified as the highly conserved and functional disrupting mutations located in the NBD1 domain. MD simulation suggested that both SNPs, G1050V and S1067C, changed the overall structural flexibility and dynamics of NBD1, and induced substantial alteration in the structural organization of ATP binding site. Taken together, these findings direct future studies to get more insights into the role of these variants in the loss of the ABCA1 function.
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Positron Emission Tomography in the Inflamed Cerebellum: Addressing Novel Targets among G Protein-Coupled Receptors and Immune Receptors. Pharmaceutics 2020; 12:pharmaceutics12100925. [PMID: 32998351 PMCID: PMC7601272 DOI: 10.3390/pharmaceutics12100925] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 09/17/2020] [Accepted: 09/25/2020] [Indexed: 01/12/2023] Open
Abstract
Inflammatory processes preceding clinical manifestation of brain diseases are moving increasingly into the focus of positron emission tomographic (PET) investigations. A key role in inflammation and as a target of PET imaging efforts is attributed to microglia. Cerebellar microglia, with a predominant ameboid and activated subtype, is of special interest also regarding improved and changing knowledge on functional involvement of the cerebellum in mental activities in addition to its regulatory role in motor function. The present contribution considers small molecule ligands as potential PET tools for the visualization of several receptors recognized to be overexpressed in microglia and which can potentially serve as indicators of inflammatory processes in the cerebellum. The sphingosine 1 phosphate receptor 1 (S1P1), neuropeptide Y receptor 2 (NPY2) and purinoceptor Y12 (P2Y12) cannabinoid receptors and the chemokine receptor CX3CR1 as G-protein-coupled receptors and the ionotropic purinoceptor P2X7 provide structures with rather classical binding behavior, while the immune receptor for advanced glycation end products (RAGE) and the triggering receptor expressed on myeloid cells 2 (TREM2) might depend for instance on further accessory proteins. Improvement in differentiation between microglial functional subtypes in comparison to the presently used 18 kDa translocator protein ligands as well as of the knowledge on the role of polymorphisms are special challenges in such developments.
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Ripon MKH, Lee H, Dash R, Choi HJ, Oktaviani DF, Moon IS, Haque MN. N-acetyl-D-glucosamine kinase binds dynein light chain roadblock 1 and promotes protein aggregate clearance. Cell Death Dis 2020; 11:619. [PMID: 32796833 PMCID: PMC7427805 DOI: 10.1038/s41419-020-02862-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 06/30/2020] [Accepted: 07/03/2020] [Indexed: 12/18/2022]
Abstract
Emerging evidence indicates that neurodegenerative diseases (NDs) result from a failure to clear toxic protein aggregates rather than from their generation. We previously showed N-acetylglucosamine kinase (NAGK) promotes dynein functionality and suggested this might promote aggregate removal and effectively address proteinopathies. Here, we report NAGK interacts with dynein light chain roadblock type 1 (DYNLRB1) and efficiently suppresses mutant huntingtin (mHtt) (Q74) and α-synuclein (α-syn) A53T aggregation in mouse brain cells. A kinase-inactive NAGKD107A also efficiently cleared Q74 aggregates. Yeast two-hybrid selection and in silico protein-protein docking analysis showed the small domain of NAGK (NAGK-DS) binds to the C-terminal of DYNLRB1. Furthermore, a small peptide derived from NAGK-DS interfered with Q74 clearance. We propose binding of NAGK-DS to DYNLRB1 'pushes up' the tail of dynein light chain and confers momentum for inactive phi- to active open-dynein transition.
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Affiliation(s)
- Md Kamal Hossain Ripon
- Department of Anatomy, Dongguk Medical Institute, Dongguk University College of Medicine, Gyeongju, 38066, Republic of Korea
- Department of Pharmacy, Mawlana Bhashani Science and Technology University, Tangail, 1902, Bangladesh
| | - HyunSook Lee
- Section of Neuroscience, Dongguk Medical Institute, Dongguk University College of Medicine, Gyeongju, 38066, Republic of Korea
| | - Raju Dash
- Department of Anatomy, Dongguk Medical Institute, Dongguk University College of Medicine, Gyeongju, 38066, Republic of Korea
| | - Ho Jin Choi
- Department of Anatomy, Dongguk Medical Institute, Dongguk University College of Medicine, Gyeongju, 38066, Republic of Korea
| | - Diyah Fatimah Oktaviani
- Department of Anatomy, Dongguk Medical Institute, Dongguk University College of Medicine, Gyeongju, 38066, Republic of Korea
| | - Il Soo Moon
- Department of Anatomy, Dongguk Medical Institute, Dongguk University College of Medicine, Gyeongju, 38066, Republic of Korea.
- Section of Neuroscience, Dongguk Medical Institute, Dongguk University College of Medicine, Gyeongju, 38066, Republic of Korea.
| | - Md Nazmul Haque
- Dongguk Medical Institute, Dongguk University College of Medicine, Gyeongju, 38066, Republic of Korea
- Department of Fisheries Biology and Genetics, Patuakhali Science and Technology University, Patuakhali, 8602, Bangladesh
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