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  • 1
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    DataSheet_1.zip
    Frontiers Media SA ; 2023
    In:  Frontiers in Cellular and Infection Microbiology Vol. 13 ( 2023-5-24)
    Details
    In: Frontiers in Cellular and Infection Microbiology, Frontiers Media SA, Vol. 13 ( 2023-5-24)
    Abstract: There has been progressive improvement in immunoinformatics approaches for epitope-based peptide design. Computational-based immune-informatics approaches were applied to identify the epitopes of SARS-CoV-2 to develop vaccines. The accessibility of the SARS-CoV-2 protein surface was analyzed, and hexa-peptide sequences (KTPKYK) were observed having a maximum score of 8.254, located between amino acids 97 and 102, whereas the FSVLAC at amino acids 112 to 117 showed the lowest score of 0.114. The surface flexibility of the target protein ranged from 0.864 to 1.099 having amino acid ranges of 159 to 165 and 118 to 124, respectively, harboring the FCYMHHM and YNGSPSG hepta-peptide sequences. The surface flexibility was predicted, and a 0.864 score was observed from amino acids 159 to 165 with the hepta-peptide (FCYMHHM) sequence. Moreover, the highest score of 1.099 was observed between amino acids 118 and 124 against YNGSPSG. B-cell epitopes and cytotoxic T-lymphocyte (CTL) epitopes were also identified against SARS-CoV-2. In molecular docking analyses, -0.54 to -26.21 kcal/mol global energy was observed against the selected CTL epitopes, exhibiting binding solid energies of -3.33 to -26.36 kcal/mol. Based on optimization, eight epitopes (SEDMLNPNY, GSVGFNIDY, LLEDEFTPF, DYDCVSFCY, GTDLEGNFY, QTFSVLACY, TVNVLAWLY, and TANPKTPKY) showed reliable findings. The study calculated the associated HLA alleles with MHC-I and MHC-II and found that MHC-I epitopes had higher population coverage (0.9019% and 0.5639%) than MHC-II epitopes, which ranged from 58.49% to 34.71% in Italy and China, respectively. The CTL epitopes were docked with antigenic sites and analyzed with MHC-I HLA protein. In addition, virtual screening was conducted using the ZINC database library, which contained 3,447 compounds. The 10 top-ranked scrutinized molecules (ZINC222731806, ZINC077293241, ZINC014880001, ZINC003830427, ZINC030731133, ZINC003932831, ZINC003816514, ZINC004245650, ZINC000057255, and ZINC011592639) exhibited the least binding energy (-8.8 to -7.5 kcal/mol). The molecular dynamics (MD) and immune simulation data suggest that these epitopes could be used to design an effective SARS-CoV-2 vaccine in the form of a peptide-based vaccine. Our identified CTL epitopes have the potential to inhibit SARS-CoV-2 replication.
    Type of Medium: Online Resource
    ISSN: 2235-2988
    URL: Article
    URL: Article
    DOI: 10.3389/fcimb.2023.1134802
    DOI: 10.3389/fcimb.2023.1134802.s001
    Language: Unknown
    Publisher: Frontiers Media SA
    Publication Date: 2023
    detail.hit.zdb_id: 2619676-1
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  • 2
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    Inquiring the inter-relationships amongst grain-filling, grain-yield, and grain-quality of Japonica rice at high latitudes of China
    Frontiers Media SA ; 2022
    In:  Frontiers in Genetics Vol. 13 ( 2022-10-20)
    Details
    In: Frontiers in Genetics, Frontiers Media SA, Vol. 13 ( 2022-10-20)
    Abstract: The widespread impacts of projected global and regional climate change on rice yield have been investigated by different indirect approaches utilizing various simulation models. However, direct approaches to assess the impacts of climatic variabilities on rice growth and development may provide more reliable evidence to evaluate the effects of climate change on rice productivity. Climate change has substantially impacted rice production in the mid-high latitudes of China, especially in Northeast China (NEC). Climatic variabilities occurring in NEC since the 1970s have resulted in an obvious warming trend, which made this region one of the three major rice-growing regions in China. However, the projections of future climate change have indicated the likelihood of more abrupt and irregular climatic changes, posing threats to rice sustainability in this region. Hence, understanding the self-adaptability and identifying adjustive measures to climate variability in high latitudes has practical significance for establishing a sustainable rice system to sustain future food security in China. A well-managed field study under randomized complete block design (RCBD) was conducted in 2017 and 2018 at two study sites in Harbin and Qiqihar, located in Heilongjiang province in NEC. Four different cultivars were evaluated: Longdao-18, Longdao-21 (longer growth duration), Longjing-21, and Suijing-18 (shorter growth duration) to assess the inter-relationships among grain-filling parameters, grain yield and yield components, and grain quality attributes. To better compare the adaptability mechanisms between grain-filling and yield components, the filling phase was divided into three sub-phases (start, middle, and late). The current study evaluated the formation and accumulation of the assimilates in superior and inferior grains during grain-filling, mainly in the middle sub-phase, which accounted for 59.60% of the yield. The grain yields for Suijing-18, Longjing-21, Longdao-21, and Longdao-18 were 8.02%, 12.78%, 17.19%, and 20.53% higher in Harbin than those in Qiqihar, respectively in 2017, with a similar trend observed in 2018. At Harbin, a higher number of productive tillers was noticed in Suijing-18, with averages of 17 and 15 in 2017 and 2018, respectively. The grain-filling parameters of yield analysis showed that the filling duration in Harbin was conducive to increased yield but the low dry weight of inferior grains was a main factor limiting the yield in Qiqihar. The average protein content values in Harbin were significantly higher (8.54% and 9.13%) than those in Qiqihar (8.34% and 9.14%) in 2017 and 2018, respectively. The amylose content was significantly higher in Harbin (20.03% and 22.27%) than those in Qiqihar (14.44% and 14.67%) in 2017 and 2018, respectively. The chalkiness percentage was higher in Qiqihar, indicating that Harbin produced good quality rice. This study provides more direct evidence of the relative changes in rice grain yield due to changes in grain-filling associated with relative changes in environmental components. These self-adaptability mechanisms to climatic variability and the inter-relationships between grain-filling and grain yield underscore the urgent to investigate and explore measures to improve Japonica rice sustainability, with better adaptation to increasing climatic variabilities. These findings may also be a reference for other global rice regions at high latitudes in addressing the impacts of climate change on future rice sustainability.
    Type of Medium: Online Resource
    ISSN: 1664-8021
    URL: Article
    DOI: 10.3389/fgene.2022.988256
    Language: Unknown
    Publisher: Frontiers Media SA
    Publication Date: 2022
    detail.hit.zdb_id: 2606823-0
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  • 3
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    Data_Sheet_1.xlsx
    Frontiers Media SA ; 2021
    In:  Frontiers in Genetics Vol. 12 ( 2021-6-9)
    Details
    In: Frontiers in Genetics, Frontiers Media SA, Vol. 12 ( 2021-6-9)
    Abstract: High-throughput genotyping for functional markers offers an excellent opportunity to effectively practice marker-assisted selection (MAS) while breeding cultivars. We developed kompetitive allele-specific PCR (KASP) assays for genes conferring drought tolerance in common wheat ( Triticum aestivum L.). In total, 11 KASP assays developed in this study and five already reported assays were used for their application in wheat breeding. We investigated alleles at 16 loci associated with drought tolerance among 153 Pakistani hexaploid wheat cultivars released during 1953–2016; 28 diploid wheat accessions (16 for AA and 12 for BB) and 19 tetraploid wheat (AABB) were used to study the evolutionary history of the studied genes. Superior allelic variations of the studied genes were significantly associated with higher grain yield. Favored haplotypes of TaSnRK2.3 -1A, TaSnRK2.3 -1B, TaSnRK2.9 -5A, TaSAP -7B, and TaLTPs -1A predominated in Pakistani wheat germplasm indicating unconscious pyramiding and selection pressure on favorable haplotypes during selection breeding. TaSnRK2.8 -5A, TaDreb -B1, 1-feh w3 , TaPPH -7A, TaMOC -7A, and TaPARG -2A had moderate to low frequencies of favorable haplotype among Pakistani wheat germplasm pointing toward introgression of favorable haplotypes by deploying functional markers in marker-assisted breeding. The KASP assays were compared with gel-based markers for reliability and phenotypically validated among 62 Pakistani wheat cultivars. Association analyses showed that the favorable allelic variations were significantly associated with grain yield-contributing traits. The developed molecular marker toolkit of the genes can be instrumental for the wheat breeding in Pakistan.
    Type of Medium: Online Resource
    ISSN: 1664-8021
    URL: Article
    URL: Article
    DOI: 10.3389/fgene.2021.684702
    DOI: 10.3389/fgene.2021.684702.s001
    Language: Unknown
    Publisher: Frontiers Media SA
    Publication Date: 2021
    detail.hit.zdb_id: 2606823-0
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  • 4
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    Table_2.DOCX
    Frontiers Media SA ; 2023
    In:  Frontiers in Neurology Vol. 14 ( 2023-5-25)
    Details
    In: Frontiers in Neurology, Frontiers Media SA, Vol. 14 ( 2023-5-25)
    Abstract: Intellectual disability (ID) is a clinically and genetically heterogeneous disorder. It drastically affects the learning capabilities of patients and eventually reduces their IQ level below 70. Methods The current genetic study ascertained two consanguineous Pakistani families suffering from autosomal recessive intellectual developmental disorder-5 (MRT5). We have used exome sequencing followed by Sanger sequencing to identify the disease-causing variants. Results and discussion Genetic analysis using whole exome sequencing in these families identified two novel mutations in the NSUN2 (NM_017755.5). Family-A segregated a novel missense variant c.953A & gt;C; p.Tyr318Ser in exon-9 of the NSUN2 . The variant substituted an amino acid Tyr318, highly conserved among different animal species and located in the functional domain of NSUN2 known as “SAM-dependent methyltransferase RsmB/NOP2-type”. Whereas in family B, we identified a novel splice site variant c.97-1G & gt;C that affects the splice acceptor site of NSUN2 . The identified splice variant (c.97-1G & gt;C) was predicted to result in the skipping of exon-2, which would lead to a frameshift followed by a premature stop codon (p. His86Profs * 16). Furthermore, it could result in the termination of translation and synthesis of dysfunctional protein, most likely leading to nonsense-mediated decay. The dynamic consequences of NSUN2 missense variant was further explored together with wildtype through molecular dynamic simulations, which uncovered the disruption of NSUN2 function due to a gain in structural flexibility. The present molecular genetic study further extends the mutational spectrum of NSUN2 to be involved in ID and its genetic heterogeneity in the Pakistani population.
    Type of Medium: Online Resource
    ISSN: 1664-2295
    URL: Article
    URL: Article
    URL: Article
    URL: Article
    URL: Article
    DOI: 10.3389/fneur.2023.1168307
    DOI: 10.3389/fneur.2023.1168307.s001
    DOI: 10.3389/fneur.2023.1168307.s002
    DOI: 10.3389/fneur.2023.1168307.s003
    DOI: 10.3389/fneur.2023.1168307.s004
    Language: Unknown
    Publisher: Frontiers Media SA
    Publication Date: 2023
    detail.hit.zdb_id: 2564214-5
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  • 5
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    Characterization of salt tolerant wheat genotypes by using morpho-physiological, biochemical, and molecular analysis
    Frontiers Media SA ; 2022
    In:  Frontiers in Plant Science Vol. 13 ( 2022-8-22)
    Details
    In: Frontiers in Plant Science, Frontiers Media SA, Vol. 13 ( 2022-8-22)
    Abstract: Food security is facing a major threat from salinity and there is a need to develop salt tolerant crop varieties to ensure that the demand for food from the world’s increasing population is met. Salinity mostly occurs in arid and semi-arid regions. It may cause many adverse physiological effects on plants, i.e., toxic ion accumulation, disturbed osmotic potential, and decreased crop yield. The present study aimed to investigate the morphological, physiological, biochemical, and genetic parameters of wheat genotypes under salt stress. Six wheat genotypes were screened for salt tolerance at the seedling and maturity stage. Seeds were sown at 0 and 150 mM of salinity level. Biochemical traits, i.e., shoot/root fresh and dry weight, chlorophyll a/b and total chlorophyll contents, shoot nitrogen, shoot phosphorus, proline, and carbohydrates were measured. Wheat genotypes showed a significant increase in free amino acids, shoot nitrogen, and total soluble proteins under saline conditions. Higher Na + /K + ratio and free amino acids were estimated under 150 mM NaCl treatment in Pasban-90 and found to be the most salt-tolerant genotype. By contrast, reduced proline, total chlorophyll, and Na + /K + ratio were found in Kohistan-97 marking it to be sensitive to stress. Expression analysis of HKTs genes was performed to validate the results of two contrasting genotypes. The differential expression of HKT2; 1 and HKT2; 3 explained the tissue and genotype specific epigenetic variations. Our findings indicated that these selected genotypes can be further used for molecular studies to find out QTLs/genes related to salinity. This suggests that, in contrasting wheat genotypes, there is a differentially induced defense response to salt stress, indicating a functional correlation between salt stress tolerance and differential expression pattern in wheat.
    Type of Medium: Online Resource
    ISSN: 1664-462X
    URL: Article
    DOI: 10.3389/fpls.2022.956298
    Language: Unknown
    Publisher: Frontiers Media SA
    Publication Date: 2022
    detail.hit.zdb_id: 2687947-5
    detail.hit.zdb_id: 2613694-6
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  • 6
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    Table_3.xlsx
    Frontiers Media SA ; 2024
    In:  Frontiers in Immunology Vol. 15 ( 2024-4-16)
    Details
    In: Frontiers in Immunology, Frontiers Media SA, Vol. 15 ( 2024-4-16)
    Abstract: Haemophilus parainfluenzae is a Gram-negative opportunist pathogen within the mucus of the nose and mouth without significant symptoms and has an ability to cause various infections ranging from ear, eye, and sinus to pneumonia. A concerning development is the increasing resistance of H. parainfluenzae to beta-lactam antibiotics, with the potential to cause dental infections or abscesses. The principal objective of this investigation is to utilize bioinformatics and immuno-informatic methodologies in the development of a candidate multi-epitope Vaccine. The investigation focuses on identifying potential epitopes for both B cells (B lymphocytes) and T cells (helper T lymphocytes and cytotoxic T lymphocytes) based on high non-toxic and non-allergenic characteristics. The selection process involves identifying human leukocyte antigen alleles demonstrating strong associations with recognized antigenic and overlapping epitopes. Notably, the chosen alleles aim to provide coverage for 90% of the global population. Multi-epitope constructs were designed by using suitable linker sequences. To enhance the immunological potential, an adjuvant sequence was incorporated using the EAAAK linker. The final vaccine construct, comprising 344 amino acids, was achieved after the addition of adjuvants and linkers. This multi-epitope Vaccine demonstrates notable antigenicity and possesses favorable physiochemical characteristics. The three-dimensional conformation underwent modeling and refinement, validated through in-silico methods. Additionally, a protein-protein molecular docking analysis was conducted to predict effective binding poses between the multi-epitope Vaccine and the Toll-like receptor 4 protein. The Molecular Dynamics (MD) investigation of the docked TLR4-vaccine complex demonstrated consistent stability over the simulation period, primarily attributed to electrostatic energy. The docked complex displayed minimal deformation and enhanced rigidity in the motion of residues during the dynamic simulation. Furthermore, codon translational optimization and computational cloning was performed to ensure the reliability and proper expression of the multi-Epitope Vaccine. It is crucial to emphasize that despite these computational validations, experimental research in the laboratory is imperative to demonstrate the immunogenicity and protective efficacy of the developed vaccine. This would involve practical assessments to ascertain the real-world effectiveness of the multi-epitope Vaccine.
    Type of Medium: Online Resource
    ISSN: 1664-3224
    URL: Article
    URL: Article
    URL: Article
    URL: Article
    URL: Article
    URL: Article
    DOI: 10.3389/fimmu.2024.1380732
    DOI: 10.3389/fimmu.2024.1380732.s001
    DOI: 10.3389/fimmu.2024.1380732.s002
    DOI: 10.3389/fimmu.2024.1380732.s003
    DOI: 10.3389/fimmu.2024.1380732.s004
    DOI: 10.3389/fimmu.2024.1380732.s005
    Language: Unknown
    Publisher: Frontiers Media SA
    Publication Date: 2024
    detail.hit.zdb_id: 2606827-8
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  • 7
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    Application of silicon and biochar alleviates the adversities of arsenic stress in maize by triggering the morpho-physiological and antioxidant defense mechanisms
    Frontiers Media SA ; 2022
    In:  Frontiers in Environmental Science Vol. 10 ( 2022-10-24)
    Details
    In: Frontiers in Environmental Science, Frontiers Media SA, Vol. 10 ( 2022-10-24)
    Abstract: Arsenic (As) contamination in the soil adversely affects crop productivity, grain quality, and human health. A pot experiment was performed to assess the sole and combined effects of Si and biochar on growth, physiological and antioxidant defense mechanisms, yield, and grain quality of maize. Soil treatments comprised of control (no treatment), As, Si, biochar, Si + biochar, As + Si, As + biochar, and As + Si + biochar placed in a completely randomized design with three replications. As toxicity significantly reduced chlorophyll a (5.18%), chlorophyll b (33.87%), chlorophyll a + b (11.67%), and primary metabolites [soluble protein (54.93%), amino acids (24.85%), total soluble sugars (39.77%), and phenolic contents (25.88%)], while increasing the activities of enzymatic antioxidants such as superoxide dismutase (SOD) by 43.51%, peroxidase (POD) by 47.93%, catalase (CAT) by 47.98%, and ascorbate peroxidase (APX) by 59.02%, as well as that of lipid peroxidation in the leaves of maize. In addition, As contamination reduced the grain yield and yield-related attributes relative to the respective controls. Among the soil applications, the interactive effect of Si and biochar improved maize grain yield (12.12%) by triggering activities of enzymatic antioxidants and proline contents and reducing the H 2 O 2 and MDA contents. The combined application of Si and biochar enhanced the Si contents in shoots of the control and As-contaminated plants, while significantly reducing As concentration in shoots (69%) and grains (142%). In conclusion, the combined application of Si and biochar was found to be a fruitful soil amendment strategy to improve the yield of maize and reduce the toxic limit of As under As-contaminated soil. The results of this study may be useful for the cultivation of food crops under AS-contaminated soils, but before commercial recommendation, more trails are required under field conditions.
    Type of Medium: Online Resource
    ISSN: 2296-665X
    URL: Article
    DOI: 10.3389/fenvs.2022.979049
    Language: Unknown
    Publisher: Frontiers Media SA
    Publication Date: 2022
    detail.hit.zdb_id: 2741535-1
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  • 8
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    New opportunities in plant microbiome engineering for increasing agricultural sustainability under stressful conditions
    Frontiers Media SA ; 2022
    In:  Frontiers in Plant Science Vol. 13 ( 2022-9-15)
    Details
    In: Frontiers in Plant Science, Frontiers Media SA, Vol. 13 ( 2022-9-15)
    Abstract: Plant microbiome (or phytomicrobiome) engineering (PME) is an anticipated untapped alternative strategy that could be exploited for plant growth, health and productivity under different environmental conditions. It has been proven that the phytomicrobiome has crucial contributions to plant health, pathogen control and tolerance under drastic environmental (a)biotic constraints. Consistent with plant health and safety, in this article we address the fundamental role of plant microbiome and its insights in plant health and productivity. We also explore the potential of plant microbiome under environmental restrictions and the proposition of improving microbial functions that can be supportive for better plant growth and production. Understanding the crucial role of plant associated microbial communities, we propose how the associated microbial actions could be enhanced to improve plant growth-promoting mechanisms, with a particular emphasis on plant beneficial fungi. Additionally, we suggest the possible plant strategies to adapt to a harsh environment by manipulating plant microbiomes. However, our current understanding of the microbiome is still in its infancy, and the major perturbations, such as anthropocentric actions, are not fully understood. Therefore, this work highlights the importance of manipulating the beneficial plant microbiome to create more sustainable agriculture, particularly under different environmental stressors.
    Type of Medium: Online Resource
    ISSN: 1664-462X
    URL: Article
    DOI: 10.3389/fpls.2022.899464
    Language: Unknown
    Publisher: Frontiers Media SA
    Publication Date: 2022
    detail.hit.zdb_id: 2687947-5
    detail.hit.zdb_id: 2613694-6
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  • 9
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    Potential Use of Microbial Enzymes for the Conversion of Plastic Waste Into Value-Added Products: A Viable Solution
    Frontiers Media SA ; 2021
    In:  Frontiers in Microbiology Vol. 12 ( 2021-11-30)
    Details
    In: Frontiers in Microbiology, Frontiers Media SA, Vol. 12 ( 2021-11-30)
    Abstract: The widespread use of commercial polymers composed of a mixture of polylactic acid and polyethene terephthalate (PLA-PET) in bottles and other packaging materials has caused a massive environmental crisis. The valorization of these contaminants via cost-effective technologies is urgently needed to achieve a circular economy. The enzymatic hydrolysis of PLA-PET contaminants plays a vital role in environmentally friendly strategies for plastic waste recycling and degradation. In this review, the potential roles of microbial enzymes for solving this critical problem are highlighted. Various enzymes involved in PLA-PET recycling and bioconversion, such as PETase and MHETase produced by Ideonella sakaiensis ; esterases produced by Bacillus and Nocardia ; lipases produced by Thermomyces lanuginosus , Candida antarctica , Triticum aestivum , and Burkholderia spp.; and leaf-branch compost cutinases are critically discussed. Strategies for the utilization of PLA-PET’s carbon content as C1 building blocks were investigated for the production of new plastic monomers and different value-added products, such as cyclic acetals, 1,3-propanediol, and vanillin. The bioconversion of PET-PLA degradation monomers to polyhydroxyalkanoate biopolymers by Pseudomonas and Halomonas strains was addressed in detail. Different solutions to the production of biodegradable plastics from food waste, agricultural residues, and polyhydroxybutyrate (PHB)-accumulating bacteria were discussed. Fuel oil production via PLA-PET thermal pyrolysis and possible hybrid integration techniques for the incorporation of thermostable plastic degradation enzymes for the conversion into fuel oil is explained in detail.
    Type of Medium: Online Resource
    ISSN: 1664-302X
    URL: Article
    DOI: 10.3389/fmicb.2021.777727
    Language: Unknown
    Publisher: Frontiers Media SA
    Publication Date: 2021
    detail.hit.zdb_id: 2587354-4
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  • 10
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    DataSheet1.docx
    Frontiers Media SA ; 2022
    In:  Frontiers in Pharmacology Vol. 13 ( 2022-9-16)
    Details
    In: Frontiers in Pharmacology, Frontiers Media SA, Vol. 13 ( 2022-9-16)
    Abstract: In the past few years, various somatic point mutations of isocitrate dehydrogenase (IDH) encoding genes (IDH1 and IDH2) have been identified in a broad range of cancers, including glioma. Despite the important function of IDH1 in tumorigenesis and its very polymorphic nature, it is not yet clear how different nsSNPs affect the structure and function of IDH1. In the present study, we employed different machine learning algorithms to screen nsSNPs in the IDH1 gene that are highly deleterious. From a total of 207 SNPs, all of the servers classified 80 mutations as deleterious. Among the 80 deleterious mutations, 14 were reported to be highly destabilizing using structure-based prediction methods. Three highly destabilizing mutations G15E, W92G, and I333S were further subjected to molecular docking and simulation validation. The docking results and molecular simulation analysis further displayed variation in dynamics features. The results from molecular docking and binding free energy demonstrated reduced binding of the drug in contrast to the wild type. This, consequently, shows the impact of these deleterious substitutions on the binding of the small molecule. PCA (principal component analysis) and FEL (free energy landscape) analysis revealed that these mutations had caused different arrangements to bind small molecules than the wild type where the total internal motion is decreased, thus consequently producing minimal binding effects. This study is the first extensive in silico analysis of the IDH1 gene that can narrow down the candidate mutations for further validation and targeting for therapeutic purposes.
    Type of Medium: Online Resource
    ISSN: 1663-9812
    URL: Article
    URL: Article
    DOI: 10.3389/fphar.2022.927570
    DOI: 10.3389/fphar.2022.927570.s001
    Language: Unknown
    Publisher: Frontiers Media SA
    Publication Date: 2022
    detail.hit.zdb_id: 2587355-6
    SSG: 15,3
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