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Article ; Online: Unveiling clinically significant PPARγ mutations for thiazolidinedione treatment responsiveness through atomistic simulations.

Shahrear, Sazzad / Islam, Abul Bashar Mir Md Khademul

International journal of biological macromolecules

2023 Volume 253, Issue Pt 4, Page(s) 126990

Abstract: In Type 2 diabetes, increased insulin sensitivity is induced by thiazolidinedione activation of the peroxisome proliferator-activated receptor gamma (PPARγ). Recent data indicate a relationship between SNPs in PPARγ and poor drug response. Therefore, ... ...

Abstract	In Type 2 diabetes, increased insulin sensitivity is induced by thiazolidinedione activation of the peroxisome proliferator-activated receptor gamma (PPARγ). Recent data indicate a relationship between SNPs in PPARγ and poor drug response. Therefore, understanding the pathogenic consequences of mutations in PPARγ-mediated protein-drug interactions will be prima-facie for establishing personalized medicine. The PPARG gene has 197 missense SNPs, 22 of which were determined to be both deleterious and destabilizing, employing in silico approaches. Molecular docking analysis suggested that the mutation influenced the binding energy of at least seven of the variants. The mutant R316H was identified as the most damaging and deleterious from the observed results. For a better understanding of the dynamic variation upon mutation at the atomic level, molecular dynamics simulations of the wild-type and R316H mutant PPARγ structure were performed. The analysis indicates that the mutation increased protein structural compactness while decreasing flexibility. The reduced dynamics in the mutant structure was further validated by principal component analysis. This mechanistic evaluation of the PPARγ protein variants provides insight into the relationship between genetic variation and interindividual variability of drug responsiveness and will facilitate the future studies for the development of tailored treatment regime for precision medicine.
MeSH term(s)	Humans ; PPAR gamma/metabolism ; Diabetes Mellitus, Type 2 ; Molecular Docking Simulation ; Thiazolidinediones/pharmacology ; Mutation
Chemical Substances	PPAR gamma ; 2,4-thiazolidinedione (AA68LXK93C) ; Thiazolidinediones
Language	English
Publishing date	2023-09-21
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	282732-3
ISSN	1879-0003 ; 0141-8130
ISSN (online)	1879-0003
ISSN	0141-8130
DOI	10.1016/j.ijbiomac.2023.126990
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Article ; Online: Association between DPP6 gene rs10260404 polymorphism and increased risk of sporadic amyotrophic lateral sclerosis (sALS): a meta-analysis.

Miah, Mohammad Mohasin / Zinnia, Maliha Afroj / Tabassum, Nuzhat / Islam, Abul Bashar Mir Md Khademul

Neurological sciences : official journal of the Italian Neurological Society and of the Italian Society of Clinical Neurophysiology

2024

Abstract: Background: Sporadic amyotrophic lateral sclerosis (sALS) is a severe neurodegenerative disease characterized by continuous diminution of motor neurons in the brain and spinal cord. Earlier studies indicated that the DPP6 gene variant has a role in the ... ...

Abstract	Background: Sporadic amyotrophic lateral sclerosis (sALS) is a severe neurodegenerative disease characterized by continuous diminution of motor neurons in the brain and spinal cord. Earlier studies indicated that the DPP6 gene variant has a role in the development of sALS. This meta-analysis was designed to uncover the role of rs10260404 polymorphism of the DPP6 gene and its association with sALS. Methods: All case-control articles published prior to October 2022 on the association between DPP6 (rs10260404) polymorphism and sALS risk were systematically extracted from different databases which include PubMed, PubMed Central, and Google Scholar. Overall odds ratios (ORs) and "95% confidence intervals (CIs)" were summarized for various genetic models. Subgroup and heterogeneity assessments were performed. Egger's and "Begg's tests were applied to evaluate publication bias. Trial sequential analysis (TSA) and false-positive report probability (FPRP) were performed. Results: Nine case-control studies containing 4202 sALS cases and 4444 healthy controls were included in the meta-analysis. A significant association of the DPP6 (rs10260404) variant with an increased sALS risk in overall pooled subjects under allelic model [C allele vs. T allele, OR = 1.149, 95% CI (1.010-1.307), p-value = 0.035], dominant model [CC + CT vs. TT, OR = 1.165, 95% CI (1.067-1.273), p-value = 0.001], and homozygote comparison [CC vs. TT, OR = 1.421, 95% CI (1.003-2.011), p-value = 0.048] were observed. Moreover, in subgroup analysis by nationality, remarkable associations were detected in Dutch, Irish, American, and Swedish under allelic, dominant, and homozygote models. Additionally, stratification analysis by ethnicity exhibited an association with sALS risk among Caucasians and Americans under different genetic models. Interestingly, none of the models found any significant association with Asians. Conclusion: The present meta-analysis indicates that DPP6 (rs10260404) polymorphism could be a candidate risk factor for sALS predisposition.
Language	English
Publishing date	2024-02-21
Publishing country	Italy
Document type	Journal Article
ZDB-ID	2016546-8
ISSN	1590-3478 ; 1590-1874
ISSN (online)	1590-3478
ISSN	1590-1874
DOI	10.1007/s10072-024-07401-2
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Article: Functional Analysis of Hypothetical Proteins of

Shahrear, Sazzad / Afroj Zinnia, Maliha / Sany, Md Rabi Us / Islam, Abul Bashar Mir Md Khademul

Bioinformatics and biology insights

2022 Volume 16, Page(s) 11779322221136002

Abstract: ... Vibrio ... ...

Abstract	Vibrio parahaemolyticus
Language	English
Publishing date	2022-11-09
Publishing country	United States
Document type	Journal Article
ZDB-ID	2423808-9
ISSN	1177-9322
ISSN	1177-9322
DOI	10.1177/11779322221136002
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Article: Functional Annotation of Hypothetical Proteins From the

Dey, Supantha / Shahrear, Sazzad / Afroj Zinnia, Maliha / Tajwar, Ahnaf / Islam, Abul Bashar Mir Md Khademul

Bioinformatics and biology insights

2022 Volume 16, Page(s) 11779322221115535

Abstract: Enterobacter ... ...

Abstract	Enterobacter cloacae
Language	English
Publishing date	2022-08-06
Publishing country	United States
Document type	Journal Article
ZDB-ID	2423808-9
ISSN	1177-9322
ISSN	1177-9322
DOI	10.1177/11779322221115535
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Article ; Online: Modeling of MT. P495, an mRNA-based vaccine against the phosphate-binding protein PstS1 of Mycobacterium tuberculosis.

Shahrear, Sazzad / Islam, Abul Bashar Mir Md Khademul

Molecular diversity

2022 Volume 27, Issue 4, Page(s) 1613–1632

Abstract: Tuberculosis (TB) is a contagious disease that predominantly affects the lungs, but can also spread to other organs via the bloodstream. TB affects about one-fourth population of the world. With age, the effectiveness of Bacillus Calmette-Guérin (BCG), ... ...

Abstract	Tuberculosis (TB) is a contagious disease that predominantly affects the lungs, but can also spread to other organs via the bloodstream. TB affects about one-fourth population of the world. With age, the effectiveness of Bacillus Calmette-Guérin (BCG), the only authorized TB vaccine, decreases. In the quest for a prophylactic and immunotherapeutic vaccine, in this study, a hypothetical mRNA vaccine is delineated, named MT. P495, implementing in silico and immunoinformatics approaches to evaluate key aspects and immunogenic epitopes across the PstS1, a highly conserved periplasmic protein of Mycobacterium tuberculosis (Mtb). PstS1 elicited the potential to generate 99.9% population coverage worldwide. The presence of T- and B-cell epitopes across the PstS1 protein were validated using several computational prediction tools. Molecular docking and dynamics simulation confirmed stable epitope-allele interaction. Immune cell response to the antigen clearance rate was verified by the in silico analysis of immune simulation. Codon optimization confirmed the efficient translation of the mRNA in the host cell. With Toll-like receptors, the vaccine exhibited stable and strong interactions. Findings suggest that the MT. P495 vaccine probably will elicit specific immune responses against Mtb. This mRNA vaccine model is a ready source for further wet-lab validation to confirm the efficacy of this proposed vaccine candidate.
MeSH term(s)	Humans ; Mycobacterium tuberculosis ; Molecular Docking Simulation ; Phosphate-Binding Proteins ; Tuberculosis/prevention & control ; Epitopes ; mRNA Vaccines
Chemical Substances	Phosphate-Binding Proteins ; Epitopes
Language	English
Publishing date	2022-08-25
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	1376507-3
ISSN	1573-501X ; 1381-1991
ISSN (online)	1573-501X
ISSN	1381-1991
DOI	10.1007/s11030-022-10515-4
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Article ; Online: Modeling mRNA-based vaccine YFV.E1988 against yellow fever virus E-protein using immuno-informatics and reverse vaccinology approach.

Khan, Nabiha Tasneem / Zinnia, Maliha Afroj / Islam, Abul Bashar Mir Md Khademul

Journal of biomolecular structure & dynamics

2022 Volume 41, Issue 5, Page(s) 1617–1638

Abstract: To surmount constraints of live-attenuated vaccines we ... ...

Abstract	To surmount constraints of live-attenuated vaccines we have
MeSH term(s)	Humans ; Yellow fever virus ; Epitopes, B-Lymphocyte ; Molecular Docking Simulation ; Vaccines, Attenuated ; Vaccinology/methods ; Epitopes, T-Lymphocyte ; Molecular Dynamics Simulation ; Vaccines, Subunit ; Computational Biology
Chemical Substances	Epitopes, B-Lymphocyte ; Vaccines, Attenuated ; Epitopes, T-Lymphocyte ; Vaccines, Subunit
Language	English
Publishing date	2022-01-07
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2021.2024253
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Article ; Online: Fenugreek steroidal saponins hinder osteoclastogenic bone resorption by targeting CSF-1R which diminishes the RANKL/OPG ratio.

Zinnia, Maliha Afroj / Khademul Islam, Abul Bashar Mir Md

International journal of biological macromolecules

2021 Volume 186, Page(s) 351–364

Abstract: Osteoporosis is skeletal fragility caused by the excessive bone resorption due to osteoclastogenesis. But current drugs are less bioavailable and possess higher toxicity. Our study was conducted to identify safe oral bioavailable drugs from Fenugreek ... ...

Abstract	Osteoporosis is skeletal fragility caused by the excessive bone resorption due to osteoclastogenesis. But current drugs are less bioavailable and possess higher toxicity. Our study was conducted to identify safe oral bioavailable drugs from Fenugreek steroidal saponins and to delineate underlying mechanism of them to lower the osteoclastogenic bone resorption. We observed higher molecular docked binding affinities in finally selected eight hit compounds within the range of -11.0 to -10.1 kcal/mol which was greater than currently used drugs. Molecular Dynamics simulation with Root Mean Square Deviation (RMSD), Root Mean Square Fluctuation (RMSF), Solvent Accessible Surface Area (SASA) and Gyration trajectory projection reinforced the stability of the protein-ligand complexes. Pharmacokinetics analysis confirmed bioavailability of seven compounds out of eight, and drug likeliness and bioavailability profile evaluation indicated that they all are eligible to be developed as a potent oral inhibitor of CSF-1R. By literature mining knowledge-driven analysis, RNAseq data and Molecular Dynamics Simulation, we proposed that, the hit derivatives block the CSF-1/CSF-1R induced phosphorylation signaling pathway in both osteoclast and osteoblast resulting in hindrance of RANK expression and formation of Reactive oxygen species (ROS) in osteoclast and osteoblast respectively, thus declines the RANKL/OPG ratio, lowering the osteoclast survival, proliferation and differentiation.
MeSH term(s)	Administration, Oral ; Biological Availability ; Bone Density Conservation Agents/administration & dosage ; Bone Density Conservation Agents/isolation & purification ; Bone Density Conservation Agents/pharmacokinetics ; Bone Density Conservation Agents/pharmacology ; Databases, Genetic ; Humans ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Molecular Structure ; Osteoblasts/drug effects ; Osteoblasts/metabolism ; Osteoblasts/pathology ; Osteoclasts/drug effects ; Osteoclasts/metabolism ; Osteoclasts/pathology ; Osteoporosis/metabolism ; Osteoporosis/pathology ; Osteoporosis/prevention & control ; Osteoprotegerin/metabolism ; Plant Extracts/administration & dosage ; Plant Extracts/isolation & purification ; Plant Extracts/pharmacokinetics ; Plant Extracts/pharmacology ; RANK Ligand/metabolism ; Receptors, Granulocyte-Macrophage Colony-Stimulating Factor/antagonists & inhibitors ; Receptors, Granulocyte-Macrophage Colony-Stimulating Factor/metabolism ; Saponins/administration & dosage ; Saponins/isolation & purification ; Saponins/pharmacokinetics ; Saponins/pharmacology ; Signal Transduction ; Structure-Activity Relationship ; Trigonella/chemistry
Chemical Substances	Bone Density Conservation Agents ; CSF1R protein, human ; Osteoprotegerin ; Plant Extracts ; RANK Ligand ; Receptors, Granulocyte-Macrophage Colony-Stimulating Factor ; Saponins ; TNFRSF11B protein, human ; TNFSF11 protein, human
Language	English
Publishing date	2021-07-01
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	282732-3
ISSN	1879-0003 ; 0141-8130
ISSN (online)	1879-0003
ISSN	0141-8130
DOI	10.1016/j.ijbiomac.2021.06.197
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Article: SARS-CoV-2 mutations altering regulatory properties: Deciphering host's and virus's perspectives.

Islam, Abul Bashar Mir Md Khademul / Khan, Md Abdullah-Al-Kamran

Gene reports

2021 Volume 24, Page(s) 101236

Abstract: Since the first recorded case of the SARS-CoV-2, it has acquired several mutations in its genome while spreading throughout the globe. In this study, we investigated the significance of these mutations by analyzing the host miRNA binding and virus's ... ...

Abstract	Since the first recorded case of the SARS-CoV-2, it has acquired several mutations in its genome while spreading throughout the globe. In this study, we investigated the significance of these mutations by analyzing the host miRNA binding and virus's internal ribosome entry site (IRES). Strikingly, we observed that due to the acquired mutations, five host miRNAs lost their affinity for targeting the viral genome, and another five can target the mutated viral genome. Moreover, functional enrichment analysis suggests that targets of both of these miRNAs might be involved in various host immune signaling pathways. Remarkably, we detected that three particular mutations in the IRES can disrupt its secondary structure which can consequently make the virus less functional. These results could be valuable in exploring the functional importance of the mutations of SARS-CoV-2 and could provide novel insights into the differences observed different parts of the world.
Language	English
Publishing date	2021-06-11
Publishing country	United States
Document type	Journal Article
ISSN	2452-0144
ISSN	2452-0144
DOI	10.1016/j.genrep.2021.101236
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Article: SARS-CoV-2 Proteins Exploit Host's Genetic and Epigenetic Mediators for the Annexation of Key Host Signaling Pathways.

Khan, Md Abdullah-Al-Kamran / Islam, Abul Bashar Mir Md Khademul

Frontiers in molecular biosciences

2021 Volume 7, Page(s) 598583

Abstract: The constant rise of the death toll and cases of COVID-19 has made this pandemic a serious threat to human civilization. Understanding of host-SARS-CoV-2 interaction in viral pathogenesis is still in its infancy. In this study, we utilized a blend of ... ...

Abstract	The constant rise of the death toll and cases of COVID-19 has made this pandemic a serious threat to human civilization. Understanding of host-SARS-CoV-2 interaction in viral pathogenesis is still in its infancy. In this study, we utilized a blend of computational and knowledgebase approaches to model the putative virus-host interplay in host signaling pathways by integrating the experimentally validated host interactome proteins and differentially expressed host genes in SARS-CoV-2 infection. While searching for the pathways in which viral proteins interact with host proteins, we discovered various antiviral immune response pathways such as hypoxia-inducible factor 1 (HIF-1) signaling, autophagy, retinoic acid-inducible gene I (RIG-I) signaling, Toll-like receptor signaling, fatty acid oxidation/degradation, and IL-17 signaling. All these pathways can be either hijacked or suppressed by the viral proteins, leading to improved viral survival and life cycle. Aberration in pathways such as HIF-1 signaling and relaxin signaling in the lungs suggests the pathogenic lung pathophysiology in COVID-19. From enrichment analysis, it was evident that the deregulated genes in SARS-CoV-2 infection might also be involved in heart development, kidney development, and AGE-RAGE signaling pathway in diabetic complications. Anomalies in these pathways might suggest the increased vulnerability of COVID-19 patients with comorbidities. Moreover, we noticed several presumed infection-induced differentially expressed transcription factors and epigenetic factors, such as miRNAs and several histone modifiers, which can modulate different immune signaling pathways, helping both host and virus. Our modeling suggests that SARS-CoV-2 integrates its proteins in different immune signaling pathways and other cellular signaling pathways for developing efficient immune evasion mechanisms while leading the host to a more complicated disease condition. Our findings would help in designing more targeted therapeutic interventions against SARS-CoV-2.
Language	English
Publishing date	2021-01-27
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2814330-9
ISSN	2296-889X
ISSN	2296-889X
DOI	10.3389/fmolb.2020.598583
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Article ; Online: Immunoinformatics guided modeling of CCHF_GN728, an mRNA-based universal vaccine against Crimean-Congo hemorrhagic fever virus.

Shahrear, Sazzad / Islam, Abul Bashar Mir Md Khademul

Computers in biology and medicine

2021 Volume 140, Page(s) 105098

Abstract: The Crimean-Congo hemorrhagic fever virus (CCHFV) is a lethal human pathogen belonging to the Nairoviridae family that causes Crimean-Congo hemorrhagic fever (CCHF), a tick-borne infection with an alarming mortality rate of up to 80%. CCHFV is the most ... ...

Abstract	The Crimean-Congo hemorrhagic fever virus (CCHFV) is a lethal human pathogen belonging to the Nairoviridae family that causes Crimean-Congo hemorrhagic fever (CCHF), a tick-borne infection with an alarming mortality rate of up to 80%. CCHFV is the most widespread tick-borne virus with the potential to trigger a pandemic. To date, no vaccines or therapeutics for CCHF have been authorized. In this study, we implemented immunoinformatics approach for developing CCHF_GN728, a universal mRNA-based multi-epitope vaccine against CCHFV. Glycoprotein precursor (GPC) and nucleoprotein (NP) from the virus were selected and screened for potential immunogenic T- and B-cell epitopes. Our developed antigen exhibited the potential to generate 99.95% population coverage worldwide. Stable epitope-allele interaction was confirmed using molecular docking and dynamics simulation. In silico immune simulation corroborated immune cell response to antigen clearance rate. Optimized codons ensured efficient expression of the mRNA in the host cell. The vaccine exhibited stable and strong interactions with the Toll-like receptors. Our findings suggest that the CCHF_GN728 vaccine will trigger specific anti-CCHFV immune responses. Our model is ready for wet-lab experimentation to assess the efficacy of this putative vaccine candidate.
Language	English
Publishing date	2021-12-02
Publishing country	United States
Document type	Journal Article
ZDB-ID	127557-4
ISSN	1879-0534 ; 0010-4825
ISSN (online)	1879-0534
ISSN	0010-4825
DOI	10.1016/j.compbiomed.2021.105098
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