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Yadav AK, Murthy TPK, Divyashri G, Prasad N D, Prakash S, Vaishnavi V V, Shukla R, Singh TR. Computational screening of pathogenic missense nsSNPs in heme oxygenase 1 (HMOX1) gene and their structural and functional consequences. J Biomol Struct Dyn 2024; 42:5072-5091. [PMID: 37434323 DOI: 10.1080/07391102.2023.2231553] [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: 03/03/2023] [Accepted: 06/07/2023] [Indexed: 07/13/2023]
Abstract
Heme Oxygenase 1 (HMOX1) is a cytoprotective enzyme, exhibiting the highest activity in the spleen, catalyzing the heme ring breakdown into products of biological significance- biliverdin, CO, and Fe2+. In vascular cells, HMOX1 possesses strong anti-apoptotic, antioxidant, anti-proliferative, anti-inflammatory, and immunomodulatory actions. The majority of these activities are crucial for the prevention of atherogenesis. Single amino acid substitutions in proteins generated by missense non-synonymous single nucleotide polymorphism (nsSNPs) in the protein-encoding regions of genes are potent enough to cause significant medical challenges due to the alteration of protein structure and function. The current study aimed at characterizing and analyzing high-risk nsSNPs associated with the human HMOX1 gene. Preliminary screening of the total available 288 missense SNPs was performed through the lens of deleteriousness and stability prediction tools. Finally, a total of seven nsSNPs (Y58D, A131T, Y134H, F166S, F167S, R183S and M186V) were found to be most deleterious by all tools that are present at highly conserved positions. Molecular dynamics simulations (MDS) analysis explained the mutational effects on the dynamic action of the wild-type and mutant proteins. In a nutshell, R183S (rs749644285) was identified as a highly detrimental mutation that could significantly render the enzymatic activity of HMOX1. The finding of this computational analysis might help subject the experimental confirmatory analysis to characterize the role of nsSNPs in HMOX1.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Arvind Kumar Yadav
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Solan, Himachal Pradesh, India
| | - T P Krishna Murthy
- Department of Biotechnology, Ramaiah Institute of Technology, Bengaluru, Karnataka, India
| | - Gangaraju Divyashri
- Department of Biotechnology, Ramaiah Institute of Technology, Bengaluru, Karnataka, India
| | - Durga Prasad N
- Department of Biotechnology, Ramaiah Institute of Technology, Bengaluru, Karnataka, India
| | - Sriraksha Prakash
- Department of Biotechnology, Ramaiah Institute of Technology, Bengaluru, Karnataka, India
| | - Vijaya Vaishnavi V
- Department of Biotechnology, Ramaiah Institute of Technology, Bengaluru, Karnataka, India
| | - Rohit Shukla
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Solan, Himachal Pradesh, India
| | - Tiratha Raj Singh
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Solan, Himachal Pradesh, India
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Gholami R, Azizi K, Ganjali Koli M. Unveiling the dynamic and thermodynamic interactions of hydrocortisone with β-cyclodextrin and its methylated derivatives through insights from molecular dynamics simulations. Sci Rep 2024; 14:12495. [PMID: 38822025 PMCID: PMC11143220 DOI: 10.1038/s41598-024-63034-7] [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: 04/06/2024] [Accepted: 05/23/2024] [Indexed: 06/02/2024] Open
Abstract
Cyclodextrins (CDs) can enhance the stability and bioavailability of pharmaceutical compounds by encapsulating them within their cavities. This study utilized molecular dynamics simulations to investigate the interaction mechanisms between hydrocortisone (HC) and various methylated CD derivatives. The results reveal that the loading of HC into CD cavities follows different mechanisms depending on the degree and position of methylation. Loading into βCD and 6-MeβCD was more complete, with the hydroxyl groups of HC facing the primary hydroxyl rim (PHR) and the ketone side facing the secondary hydroxyl rim (SHR). In contrast, 2,3-D-MeβCD and 2,6-D-MeβCD showed a different loading mechanism, with the ketone side facing the PHR and the hydroxyl groups facing the SHR. The root mean square fluctuation (RMSF) analysis demonstrated that methylation increases the flexibility of CD heavy atoms, with 3-MeβCD and 2,3-D-MeβCD exhibiting the highest flexibility. However, upon inclusion of HC, 3-MeβCD, 2,3-D-MeβCD, 2-MeβCD, and 6-MeβCD showed a significant reduction in flexibility, suggesting a more rigid structure that effectively retains HC within their cavities. The radial distribution function revealed a significant reduction in the number of water molecules within the innermost layer of the methylated CD cavities, particularly in TMeβCD, indicating a decrease in polarity. The presence of HC led to the release of high-energy water molecules, creating more favorable conditions for HC loading. Conformational analysis showed that methylation caused a partial decrease in the area of the PHR, a significant decrease in the area of the middle rim, and a notable decrease in the area of the SHR. The loading of HC increased the area of the PHR in most derivatives, with the most pronounced increase observed in 2,6-D-MeβCD and 6-MeβCD. The analysis of interaction energies and binding free energies demonstrated that the binding of HC to methylated CD derivatives is thermodynamically more favorable than to βCD, with the strongest association observed for 6-MeβCD, 2-MeβCD, and 2,3-D-MeβCD.
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Affiliation(s)
- Roya Gholami
- Department of Chemistry, University of Kurdistan, Sanandaj, Iran
| | - Khaled Azizi
- Department of Chemistry, University of Kurdistan, Sanandaj, Iran.
- Computational Chemistry Laboratory, Kask Afrand Exire Ltd., Sanandaj, Iran.
| | - Mokhtar Ganjali Koli
- Department of Chemistry, University of Kurdistan, Sanandaj, Iran
- Computational Chemistry Laboratory, Kask Afrand Exire Ltd., Sanandaj, Iran
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3
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Yang Y, Cheng S, Zheng Y, Xue T, Huang JW, Zhang L, Yang Y, Guo RT, Chen CC. Remodeling the polymer-binding cavity to improve the efficacy of PBAT-degrading enzyme. JOURNAL OF HAZARDOUS MATERIALS 2024; 464:132965. [PMID: 37979420 DOI: 10.1016/j.jhazmat.2023.132965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/31/2023] [Accepted: 11/07/2023] [Indexed: 11/20/2023]
Abstract
Poly(butylene adipate-co-terephthalate) (PBAT) is among the most widely applied synthetic polyesters that are utilized in the packaging and agricultural industries, but the accumulation of PBAT wastes has posed a great burden to ecosystems. Using renewable enzymes to decompose PBAT is an eco-friendly solution to tackle this problem. Recently, we demonstrated that cutinase is the most effective PBAT-degrading enzyme and that an engineered cutinase termed TfCut-DM could completely decompose PBAT film to terephthalate (TPA). Here, we report crystal structures of a variant of leaf compost cutinase in complex with soluble fragments of PBAT, including BTa and TaBTa. In the TaBTa complex, one TPA moiety was located at a polymer-binding site distal to the catalytic center that has never been experimentally validated. Intriguingly, the composition of the distal TPA-binding site shows higher diversity relative to the one proximal to the catalytic center in various cutinases. We thus modified the distal TPA-binding site of TfCut-DM and obtained variants that exhibit higher activity. Notably, the time needed to completely degrade the PBAT film to TPA was shortened to within 24 h by TfCut-DM Q132Y (5813 mol per mol protein). Taken together, the structural information regarding the substrate-binding behavior of PBAT-degrading enzymes could be useful guidance for direct enzyme engineering.
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Affiliation(s)
- Yu Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, 430062 Wuhan, People's Republic of China
| | - Shujing Cheng
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, 430062 Wuhan, People's Republic of China
| | - Yingyu Zheng
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, 430062 Wuhan, People's Republic of China
| | - Ting Xue
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, 430062 Wuhan, People's Republic of China
| | - Jian-Wen Huang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, 430062 Wuhan, People's Republic of China
| | - Lilan Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, 430062 Wuhan, People's Republic of China
| | - Yunyun Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, 430062 Wuhan, People's Republic of China
| | - Rey-Ting Guo
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, 430062 Wuhan, People's Republic of China; Department of Immunology and Pathogen Biology, School of Basic Medical Sciences, Hangzhou Normal University, 311121 Hangzhou, People's Republic of China.
| | - Chun-Chi Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, 430062 Wuhan, People's Republic of China; Department of Immunology and Pathogen Biology, School of Basic Medical Sciences, Hangzhou Normal University, 311121 Hangzhou, People's Republic of China.
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Sankarganesh D, Balasundaram A, Doss C GP, Azhwar R, Achiraman S, Archunan G. Mechanistic Insights into the Binding of Boar Salivary Pheromones and Putative Molecule with Receptor Proteins: A Comparative Computational Approach. ACS OMEGA 2024; 9:4986-5001. [PMID: 38313522 PMCID: PMC10831833 DOI: 10.1021/acsomega.3c09211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 12/22/2023] [Accepted: 12/27/2023] [Indexed: 02/06/2024]
Abstract
Precise estrus detection in sows is pivotal in increasing the productivity within the pork industry. Sows in estrus exhibit exclusive behaviors when exposed to either a live boar or the steroid pheromones androstenone and androstenol. Recently, a study employing solid-phase microextraction-gas chromatography-mass spectrometry has identified a novel salivary molecule in boars, known as quinoline. This finding has intriguing implications as a synthetic mixture of androstenone, androstenol, and quinoline induces estrus behaviors in sows. Nevertheless, the precise pheromonal characteristics of quinoline remain elusive. In this study, we validate and compare the binding efficiency of androstenone, androstenol, and quinoline with porcine olfactory receptor proteins (odorant-binding protein [OBP], pheromaxein, salivary lipocalin [SAL], and Von Ebner's gland protein [VEGP]) using molecular docking and molecular dynamics simulations. All protein-ligand complexes demonstrated stability, as evidenced by the root-mean-square deviation (RMSD), root-mean-square fluctuation (RMSF), radius of gyration (Rg), solvent-accessible surface area (SASA), and hydrogen-bond (H-bond) plots. Furthermore, quinoline displayed higher binding efficiency with OBP, measured at -85.456 ± 8.268 kJ/mol, compared to androstenone and androstenol, as determined by molecular mechanics-Poisson-Boltzmann surface area (MM-PBSA) calculations. Conversely, quinoline exhibited a lower binding efficacy when interacting with SAL, pheromaxein, and VEGP compared to androstenone and androstenol. These findings, in part, suggest the binding possibility of quinoline with carrier proteins and warrant further investigation to support the role of quinoline in porcine chemical communication.
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Affiliation(s)
- Devaraj Sankarganesh
- School
of Bio Sciences and Technology, Vellore
Institute of Technology, Vellore 632014, Tamilnadu, India
| | - Ambritha Balasundaram
- School
of Bio Sciences and Technology, Vellore
Institute of Technology, Vellore 632014, Tamilnadu, India
| | - George Priya Doss C
- School
of Bio Sciences and Technology, Vellore
Institute of Technology, Vellore 632014, Tamilnadu, India
| | - Raghunath Azhwar
- Department
of Pediatrics, University of Michigan School
of Medicine, Ann Arbor, Michigan 48109, United States
| | - Shanmugam Achiraman
- Department
of Environmental Biotechnology, Bharathidasan
University, Tiruchirappalli 620024, Tamil Nadu, India
| | - Govindaraju Archunan
- School
of Life Sciences, Marudupandiyar College, Thanjavur 613403, Tamil Nadu, India
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5
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Sudhan M, Janakiraman V, Patil R, Oyouni AAA, Hasan Mufti A, Ahmed SSSJ. Asn215Ser, Ala143Thr, and Arg112Cys variants in α-galactosidase A protein confer stability loss in Fabry's disease. J Biomol Struct Dyn 2023; 41:9840-9849. [PMID: 36420638 DOI: 10.1080/07391102.2022.2148001] [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: 08/18/2022] [Accepted: 11/09/2022] [Indexed: 11/25/2022]
Abstract
Alpha galactosidase A (α-GalA) gene contains nine exons localized at the q-arm of the X chromosome. Generally, an α-GalA enzyme is involved in the removal of galactosyl moieties from the glycoproteins and glycolipids. Dysregulation results in the accumulation of glycoproteins as well as glycolipids in various organs leading to Fabry disease (FD). In this study, we examine the impact of Asn215Ser, Ala143Thr and Arg112Cys variants on the α-GalA protein structure contributing to functional dynamic changes in FD. The seven computational pathogenicity prediction methods were used to predict the effects of these variants on the α-GalA protein. The three-dimensional structure of α-GalA variants was modeled with the Swiss Model and Robetta server and validated using a variety of tools. Then, molecular dynamics (MD) simulation was performed to understand the stability and dynamic behavior of the wild-type and variants structures. Most of our analyzed pathogenicity prediction tools showed that Asn215Ser, Ala143Thr and Arg112Cys variants cause a deleterious effect on the α-GalA protein. Further, MD trajectory analysis showed the destabilizing effect of variants on α-GalA structure based on the root mean square deviation, root mean square fluctuation, solvent accessible surface area, the radius of gyration, hydrogen bond, cluster analysis and PCA analysis. This concludes that the presence of these variants could potentially affect the protein functional process of galactosyl moieties removal which might lead to Fabry disease.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- M Sudhan
- Drug Discovery and Multi-omics Laboratory, Faculty of Allied Health Sciences, Chettinad Hospital and Research Institute, Chettinad Academy of Research and Education, Kelambakkam, India
| | - V Janakiraman
- Drug Discovery and Multi-omics Laboratory, Faculty of Allied Health Sciences, Chettinad Hospital and Research Institute, Chettinad Academy of Research and Education, Kelambakkam, India
| | - Rajesh Patil
- Department of Pharmaceutical Chemistry, Sinhgad College of Pharmacy, Pune, India
| | | | - Ahmad Hasan Mufti
- Medical Genetics Department, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Shiek S S J Ahmed
- Drug Discovery and Multi-omics Laboratory, Faculty of Allied Health Sciences, Chettinad Hospital and Research Institute, Chettinad Academy of Research and Education, Kelambakkam, India
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Adetunji JA, Ogunyemi OM, Gyebi GA, Adewumi AE, Olaiya CO. Atomistic simulations suggest dietary flavonoids from Beta vulgaris (beet) as promising inhibitors of human angiotensin-converting enzyme and 2-alpha-adrenergic receptors in hypertension. BIOINFORMATICS ADVANCES 2023; 3:vbad133. [PMID: 37822725 PMCID: PMC10562952 DOI: 10.1093/bioadv/vbad133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 09/08/2023] [Indexed: 10/13/2023]
Abstract
Motivation Beta vulgaris (beet) is extensively reported for its antihypertensive activity. However, the mechanismunderpinning its antihypertensive activity is not well understood. In this study, we evaluated the in silico interactionsof 70 compounds derived from beta vulgaris against the active sites of angiotensin-converting enzyme (ACE) and alpha-adrenergic receptor (AR). Results Structure-based virtual screening against angiotensin-converting enzyme revealed that, Cochliophilin A (-9.0 Kcal/mol), Miraxanthin (-8.3 Kcal/mol), and quercimeritrin (-9.7 Kcal/mol) had lower docking scores than the reference lisinopril (-7.9 Kcal/mol). These compounds exhibited dual binding tendency as they also ranked top compounds upon screening against adrenergic receptor. The thermodynamic parameters computed from the resulting trajectories obtained from the 100 ns full atomistic molecular dynamics simulation revealed structural stability and conformational flexibility of the ligand-receptor complexes as indicated by the RMSD, RMSF, RoG, SASA, and H-bond calculations. The molecular mechanics with generalized Born and surface area solvation binding energy calculations revealed that the proteins exhibit considerable binding energy with the phytochemicals in a dynamic environment. Furthermore, the hit compounds possess good physicochemical properties and drug-likeness. Overall, cochliophilin and quercimeritrin are promising dual-target directed flavonoids from Beta vulgaris; and are suggested for further experimental and preclinical evaluation. Availability and implementation All data was provided in the manuscript.
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Affiliation(s)
- Joy A Adetunji
- Nutritional and Industrial Biochemistry Laboratory, Department of Biochemistry, Faculty of Basic Medical Sciences, College of Medicine, University of Ibadan, Ibadan 200005, Nigeria
| | - Oludare M Ogunyemi
- Nutritional and Industrial Biochemistry Laboratory, Department of Biochemistry, Faculty of Basic Medical Sciences, College of Medicine, University of Ibadan, Ibadan 200005, Nigeria
| | - Gideon A Gyebi
- Department of Biochemistry, Faculty of Science and Technology, Bingham University, Karu, Nigeria
- Natural Products and Structural (Bio-Chem)-informatics Research Laboratory (NpsBC-Rl), Bingham University, Nasarawa, Nigeria
| | - Anuoluwapo E Adewumi
- Nutritional and Industrial Biochemistry Laboratory, Department of Biochemistry, Faculty of Basic Medical Sciences, College of Medicine, University of Ibadan, Ibadan 200005, Nigeria
| | - Charles O Olaiya
- Nutritional and Industrial Biochemistry Laboratory, Department of Biochemistry, Faculty of Basic Medical Sciences, College of Medicine, University of Ibadan, Ibadan 200005, Nigeria
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Yadav A, Kesharwani A, Chaurasia DK, Katara P. Mining of molecular insights of CYP2A6 and its variants complex with coumarin (CYP2A6*-coumarin) using molecular dynamics simulation. J Biomol Struct Dyn 2023; 41:4081-4092. [PMID: 35427216 DOI: 10.1080/07391102.2022.2062785] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 04/02/2022] [Indexed: 10/18/2022]
Abstract
CYP2A6 is a very important enzyme that plays a crucial role in nicotine compounds and is responsible for the metabolism of more than 3% drugs of total metabolized drugs by the CYP family and reported as one of very important pharmacogenes. CYP2A6 is highly polymorphic in nature and reported with more than 40 variants, most of these variants are SNPs originated and population specific. It has been well observed and reported that the presence of these population-specific non-synonymous SNPs in CYP2A6 alters the rate of drug metabolism and as a functional consequence, drugs produce an abnormal response. Though genomics and pharmacogenomics studies are there, very less is known about the structural effects of these SNPs on molecular-interaction and folding of CYP2A6. To fill the knowledge gap, SNPs based four variants, i.e., CYP2A6*2, CYP2A6*18, CYP2A6*21, and CYP2A6*35, which are frequently reported in the South Asian population, were considered for the study. Coumarin (DB04665), a well reported drug, is considered as a model substance, and the effect of all four variants on 'CYP2A6*-coumarin' complex was studied. MD simulation-based analysis (at 200 ns) was performed and comparative analysis with respect to wild type 'CYP2A6-coumarin' complex was done. Though observation didn't find any global effect on complete complex but found some crucial minor-local alteration in interaction and folding process. It is assumed that the change due to SNPs in the single amino acid did not bring global change in physiochemical properties of CYP2A6* but caused local-trivial changes which are very crucial for its metabolic activity.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Anamika Yadav
- Computational omics Lab, Centre of Bioinformatics, University of Allahabad, Prayagraj, India
| | - Akanksha Kesharwani
- Computational omics Lab, Centre of Bioinformatics, University of Allahabad, Prayagraj, India
- Supercomputing Facility for Bioinformatics and Computational Biology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India
| | - Dheeraj Kumar Chaurasia
- Supercomputing Facility for Bioinformatics and Computational Biology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India
| | - Pramod Katara
- Computational omics Lab, Centre of Bioinformatics, University of Allahabad, Prayagraj, India
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Guo J, Zhao Y, Wu X, Li G, Zhang Y, Song Y, Du Q. Mechanism exploration and prognosis study of Astragali Radix-Spreading hedyotis herb for the treatment of lung adenocarcinoma based on bioinformatics approaches and molecular dynamics simulation. Front Chem 2023; 11:1128671. [PMID: 37065830 PMCID: PMC10090857 DOI: 10.3389/fchem.2023.1128671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 03/17/2023] [Indexed: 03/31/2023] Open
Abstract
Background: Herb pair of Astragali Radix (AR) and Spreading Hedyotis Herb (SH) has been frequently prescribed in clinical for the treatment of lung cancer owing to its favorable efficacy. Yet, the mechanism under the therapeutic effects remained unveiled, which has limited its clinical applications, and new drug development for lung cancer.Methods: The bioactive ingredients of AR and SH were retrieved from the Traditional Chinese Medicine System Pharmacology Database, with the targets of obtained components predicted by Swiss Target Prediction. Genes related to lung adenocarcinoma (LUAD) were acquired from GeneCards, OMIM and CTD databases, with the hub genes of LUAD screened by CTD database. The intersected targets of LUAD and AR-SH were obtained by Venn, with David Database employed to perform Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. Survival analysis of the hub genes of LUAD was carried out using TCGA-LUAD dataset. Molecular docking of core proteins and active ingredients was performed by Auto-Dock Vina software, followed by molecular dynamics simulations of protein-ligand complexes with well-docked conformations.Results: 29 active ingredients were screened out with 422 corresponding targets predicted. It is revealed that AR-SH can act on various targets such as EGFR, MAPK1, and KARS by ursolic acid (UA), Astragaloside IV(ASIV), and Isomucronulatol 7,2′-di-O-glucoside (IDOG) to alleviate the symptoms of LUAD. Biological processes involved are protein phosphorylation, negative regulation of apoptotic process, and pathways involved are endocrine resistance, EGFR tyrosine kinase inhibitor resistance, PI3K-Akt, and HIF-1 pathway. Molecular docking analysis indicated that the binding energy of most of the screened active ingredients to proteins encoded by core genes was less than −5.6 kcal/mol, with some active ingredients showing even lower binding energy to EGFR than Gefitinib. Three ligand-receptor complexes including EGFR-UA, MAPK1-ASIV, and KRAS-IDOG were found to bind relatively stable by molecular dynamics simulation, which was consistent with the results of molecule docking.Conclusion: We suggested that the herb pair of AR-SH can act on targets like EGFR, MAPK1 and KRAS by UA, ASIV and IDOG, to play a vital role in the treatment and the enhancement of prognosis of LUAD.
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Affiliation(s)
- Junfeng Guo
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Yuting Zhao
- Laboratory of Metabolomics and Drug-Induced Liver Injury, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Xuanyu Wu
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Ganggang Li
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Yuwei Zhang
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Yang Song
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
- Correspondence: Yang Song, ; Quanyu Du,
| | - Quanyu Du
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
- Correspondence: Yang Song, ; Quanyu Du,
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9
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Misuan N, Mohamad S, Tubiana T, Yap MKK. Ensemble-based molecular docking and spectrofluorometric analysis of interaction between cytotoxin and tumor necrosis factor receptor 1. J Biomol Struct Dyn 2023; 41:15339-15353. [PMID: 36927291 DOI: 10.1080/07391102.2023.2188945] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 02/28/2023] [Indexed: 03/18/2023]
Abstract
Cytotoxin (CTX) is a three-finger toxin presents predominantly in cobra venom. The functional site of the toxin is located at its three hydrophobic loop tips. Its actual mechanism of cytotoxicity remains inconclusive as few conflicting hypotheses have been proposed in addition to direct cytolytic effects. The present work investigated the interaction between CTX and death receptor families via ensemble-based molecular docking and fluorescence titration analysis. Multiple sequence alignments of different CTX isoforms obtained a conserved CTX sequence. The three-dimensional structure of the conserved CTX was later determined using homology modelling, and its quality was validated. Ensemble-based molecular docking of CTX was performed with different death receptors, such as Fas-ligand and tumor necrosis factor receptor families. Our results showed that tumor necrosis factor receptor 1 (TNFR1) was the best receptor interacting with CTX attributed to the interaction of all three functional loops and evinced with low HADDOCK, Z-score and RMSD value. The interaction between CTX and TNFR1 was also supported by a concentration-dependent reduction of fluorescence intensity with increasing binding affinity. The possible intermolecular interactions between CTX and TNFR1 were Van der Waals forces and hydrogen bonding. Our findings suggest a possibility that CTX triggers apoptosis cell death through non-covalent interactions with TNFR1.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Nurhamimah Misuan
- School of Science, Monash University Malaysia, Bandar Sunway, Malaysia
| | - Saharuddin Mohamad
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
- Centre of Research for Computational Sciences and Informatics for Biology, Bioindustry, Environment, Agriculture and Healthcare (CRYSTAL), University of Malaya, Kuala Lumpur, Malaysia
| | - Thibault Tubiana
- CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, Gif-sur-Yvette, France
| | - Michelle Khai Khun Yap
- School of Science, Monash University Malaysia, Bandar Sunway, Malaysia
- Tropical Medicine and Biology Multidisciplinary Platform, Bandar Sunway, Malaysia
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Kaur A, Gladu EM, Wright KM, Webb JA, Massiah MA. B-box1 Domain of MID1 Interacts with the Ube2D1 E2 Enzyme Differently Than RING E3 Ligases. Biochemistry 2023; 62:1012-1025. [PMID: 36820504 DOI: 10.1021/acs.biochem.2c00693] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
The MID1 TRIM protein is important for ventral midline development in vertebrates, and mutations of its B-box1 domain result in several birth defects. The B-box1 domain of the human MID1 protein binds two zinc atoms and adopt a similar ββα-RING structure. This domain is required for the efficient ubiquitination of protein phosphatase 2A, alpha4, and fused kinase. Considering the structural similarity, the MID1 B-box1 domain exhibits mono-autoubiquitination activity, in contrast to poly-autoubiquitination observed for RING E3 ligases. To understand its mechanism of action, the interaction of the B-box1 domain with Ube2D1 (UbcH5a, E2), a preferred E2 ligase, is investigated. Using isothermal titration calorimetry, the MID1 RING and B-box1 domains were observed to have similar binding affinities with the Ube2D1 protein. However, NMR 15N-1H Heteronuclear Single Quantum Coherence titration, 15N relaxation data, and High Ambiguity Driven protein-protein DOCKing (HADDOCK) calculations show the B-box1 domain binding on a surface distinct from where RING domains bind. The novel binding interaction shows the B-box1 domain partially overlapping the noncovalent Ube2D1 and a ubiquitin binding site that is necessary for poly-autoubiquitination activity. The B-box1 domain also displaces the ubiquitin from the Ube2D1 protein. These studies reveal a novel binding interaction between the zinc-binding ββα-fold B-box1 domain and the Ube2D enzyme family and that this difference in binding, compared to RING E3 ligases, provides a rationale for its auto-monoubiquitination E3 ligase activity.
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Affiliation(s)
- Anupreet Kaur
- Department of Chemistry, George Washington University, 800 22nd St NW, Washington, D.C. 20052, United States
| | - Erin M Gladu
- Department of Chemistry, George Washington University, 800 22nd St NW, Washington, D.C. 20052, United States
| | - Katharine M Wright
- Department of Chemistry, George Washington University, 800 22nd St NW, Washington, D.C. 20052, United States
| | - Jessica A Webb
- Department of Chemistry, George Washington University, 800 22nd St NW, Washington, D.C. 20052, United States
| | - Michael A Massiah
- Department of Chemistry, George Washington University, 800 22nd St NW, Washington, D.C. 20052, United States
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11
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Yousaf M, Fatima D, Amin J, Noureen A, Fatmi MQ. Discovering potential stabilizers for KRAS22RT G-quadruplex DNA: an alternative next generation approach to treat pancreatic cancer. J Biomol Struct Dyn 2023; 41:11957-11968. [PMID: 36729158 DOI: 10.1080/07391102.2023.2174188] [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: 10/17/2022] [Accepted: 12/25/2022] [Indexed: 02/03/2023]
Abstract
KRAS is the signature gene responsible for the occurrence of pancreatic cancer, which is a complex, multifactorial and intractable lethal malignancy. Prevention and treatment of the ailment have always been a key motivation behind the search for new therapeutic drug molecules. G-quadruplexes are non-canonical guanine-rich secondary structures, commonly formed at eukaryotic telomeric ends, oncogenic promotors and G-rich regions of the DNA. These G-quadruplexes play a crucial role in the regulation of gene expression and maintenance of genome integrity, therefore, they are considered as emerging potential therapeutic drug targets. The present study is concerned with the discovery of a potential stabilizer for KRAS22RT G-quadruplex DNA, located in the NHE region of the promotor, while inhibiting the upregulation of KRAS proto-oncogene, as an alternative approach for the treatment of pancreatic cancer. Various chemical libraries have been virtually screened against the targeted G4 structure and 143 compounds showed promising results. However, molecular dynamic studies, ADME and toxicity analyses predicted that three compounds belonging to the class of tetra-substituted phenanthrolines (i.e., 7i, 7j and 7k) can not only effectively stabilize KRAS22RT G4 structure but also have least toxic effects in the in vivo system. Therefore, it is highly recommended to further investigate their effectiveness and efficacy through experimental analysis in laboratory.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Maha Yousaf
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Dua Fatima
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Javaria Amin
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Aqsa Noureen
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
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12
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Dipankar P, Kumar P, Sarangi PP. In silico identification and characterization of small-molecule inhibitors specific to RhoG/Rac1 signaling pathway. J Biomol Struct Dyn 2023; 41:560-580. [PMID: 34877916 DOI: 10.1080/07391102.2021.2009032] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Rho family GTPases serve as molecular switches in numerous cellular processes, and their overexpression is involved in disease conditions. RhoG is one of the less explored Rho GTPases with significant sequential and structural homology with Rac1. Experimental mutations in RhoG (i.e., RhoGG12V and RhoGQ61L) are shown to dysregulate cell migration. Thus, targeting upstream activators of RhoG, such as guanine nucleotide exchange factors (GEFs), maybe an important strategy for inhibiting RhoG activation. In the current study, we have modelled the 3D structure of RhoG with greater accuracy as confirmed through PROCHECK, ProSA, and Verify3D. Our results indicate that 90.4% of residues are in the Ramachandran plots favoured region, with the Z-score of -6.46, and 87.96% of residues had an averaged 3D-1D score ≥0.2. Further, we have evaluated and binding dynamics of ten Rac1 inhibitors to investigate their potential to inhibit RhoG by targeting GEFs binding grooves. To this end, the binding energy of the docked complexes of the wild-type (WT) RhoG and its mutant proteins with inhibitor molecules was calculated using the MM/PBSA method. Our results from docking studies showed that macrolide1 binds efficiently with the GEF site of WT RhoG and the mutants mentioned above. However, an extensive analysis using MD simulations (200 ns) showed that the Rac1 based inhibitor, EHop-016, and NSC23766 might bind with greater affinity to GEF sites of mutants and WT RhoG. Thus, the results from the study indicate that Rac1 inhibitors have the potential for use as therapeutics in conditions involving dysregulation of RhoG.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Pankaj Dipankar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Puneet Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Pranita P Sarangi
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
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13
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Singh MB, Vishvakarma VK, Lal AA, Chandra R, Jain P, Singh P. A comparative study of 5- fluorouracil, doxorubicin, methotrexate, paclitaxel for their inhibition ability for Mpro of nCoV: Molecular docking and molecular dynamics simulations. J INDIAN CHEM SOC 2022. [PMCID: PMC9632266 DOI: 10.1016/j.jics.2022.100790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
A new corona virus (nCoV) is aetiological agent responsible for the viral pneumonia epidemic. Three is no specific therapeutic medicines available for the treatment of this condition and also effective treatment choices are few. In this work author tried to investigate some repurposing drug such as 5- fluorouracil, doxorubicin, methotrexate and paclitaxel against the main protease (Mpro) of nCoV by the computational model. Molecular docking was performed to screen out the best compound and doxorubicin was found to have minimum binding energy −121.89 kcal/mol. To further study, MD simulations were performed at 300 K and the result successfully corroborate the energy obtained by molecular docking. Temperature dependent MD simulation of the best molecule that is doxorubicin obtained from docking result was performed to check the variation in structural changes in Mpro of nCoV at 290 K, 310 K, 320 K and 325 K. It is sound that doxorubicin binds effectively with Mpro of nCoV at 290 K. Further ADME properties of the 5- fluorouracil, doxorubicin, methotrexate and paclitaxel were also evaluated to understand the bioavailability.
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14
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Trang NM, Vinh LB, Thanh NV, Phong NV. Inhibition of PTP1B by isosinensetin, a polymethoxylated flavone isolated from trifoliate orange peel: kinetic studies, molecular docking, and molecular dynamics simulation. CHEMICAL PAPERS 2022. [DOI: 10.1007/s11696-022-02560-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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15
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Shukla PK, Sinha D, Leng AM, Bissell JE, Thatipamula S, Ganguly R, Radmall KS, Skalicky JJ, Shrieve DC, Chandrasekharan MB. Mutations of Rad6 E2 ubiquitin-conjugating enzymes at alanine-126 affect ubiquitination activity and decrease enzyme stability. J Biol Chem 2022; 298:102524. [PMID: 36162503 PMCID: PMC9630792 DOI: 10.1016/j.jbc.2022.102524] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 09/16/2022] [Accepted: 09/17/2022] [Indexed: 11/28/2022] Open
Abstract
Rad6, an E2 ubiquitin-conjugating enzyme conserved from yeast to humans, functions in transcription, genome maintenance, and proteostasis. The contributions of many conserved secondary structures of Rad6 and its human homologs UBE2A and UBE2B to their biological functions are not understood. A mutant RAD6 allele with a missense substitution at alanine-126 (A126) of helix-3 that causes defects in telomeric gene silencing, DNA repair, and protein degradation was reported over 2 decades ago. Here, using a combination of genetics, biochemical, biophysical, and computational approaches, we discovered that helix-3 A126 mutations compromise the ability of Rad6 to ubiquitinate target proteins without disrupting interactions with partner E3 ubiquitin-ligases that are required for their various biological functions in vivo. Explaining the defective in vitro or in vivo ubiquitination activities, molecular dynamics simulations and NMR showed that helix-3 A126 mutations cause local disorder of the catalytic pocket of Rad6 in addition to disorganizing the global structure of the protein to decrease its stability in vivo. We also show that helix-3 A126 mutations deform the structures of UBE2A and UBE2B, the human Rad6 homologs, and compromise the in vitro ubiquitination activity and folding of UBE2B. Providing insights into their ubiquitination defects, we determined helix-3 A126 mutations impair the initial ubiquitin charging and the final discharging steps during substrate ubiquitination by Rad6. In summary, our studies reveal that the conserved helix-3 is a crucial structural constituent that controls the organization of catalytic pockets, enzymatic activities, and biological functions of the Rad6-family E2 ubiquitin-conjugating enzymes.
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Affiliation(s)
- Prakash K Shukla
- Department of Radiation Oncology and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Dhiraj Sinha
- IHU, Aix Marseille University, Marseille, France
| | - Andrew M Leng
- Department of Radiation Oncology and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Jesse E Bissell
- Department of Radiation Oncology and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Shravya Thatipamula
- Department of Radiation Oncology and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Rajarshi Ganguly
- Department of Radiation Oncology and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Kaitlin S Radmall
- Department of Radiation Oncology and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Jack J Skalicky
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Dennis C Shrieve
- Department of Radiation Oncology and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Mahesh B Chandrasekharan
- Department of Radiation Oncology and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA.
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Mahmood TB, Hossan MI, Mahmud S, Shimu MSS, Alam MJ, Bhuyan MMR, Emran TB. Missense mutations in spike protein of SARS‐CoV‐2 delta variant contribute to the alteration in viral structure and interaction with hACE2 receptor. Immun Inflamm Dis 2022; 10:e683. [PMID: 36039645 PMCID: PMC9382871 DOI: 10.1002/iid3.683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 07/17/2022] [Accepted: 07/22/2022] [Indexed: 11/11/2022] Open
Abstract
Introduction Many of the global pandemics threaten human existence over the decades among which coronavirus disease (COVID‐19) is the newest exposure circulating worldwide. The RNA encoded severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) virus is referred as the pivotal agent of this deadly disease that induces respiratory tract infection by interacting host ACE2 receptor with its spike glycoprotein. Rapidly evolving nature of this virus modified into new variants helps in perpetrating immune escape and protection against host defense mechanism. Consequently, a new isolate, delta variant originated from India is spreading perilously at a higher infection rate. Methods In this study, we focused to understand the conformational and functional significance of the missense mutations found in the spike glycoprotein of SARS‐CoV‐2 delta variant performing different computational analysis. Results From physiochemical analysis, we found that the acidic isoelectric point of the virus elevated to basic pH level due to the mutations. The targeted mutations were also found to change the interactive bonding pattern and conformational stability analyzed by the molecular dynamic's simulation. The molecular docking study also revealed that L452R and T478K mutations found in the RBD domain of delta variant spike protein contributed to alter interaction with the host ACE2 receptor. Conclusions Overall, this study provided insightful evidence to understand the morphological and attributive impact of the mutations on SARS‐CoV‐2 delta variant.
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Affiliation(s)
- Tousif Bin Mahmood
- Department of Biotechnology and Genetic Engineering Noakhali Science and Technology University Noakhali Bangladesh
| | - Mohammad Imran Hossan
- Department of Biotechnology and Genetic Engineering Noakhali Science and Technology University Noakhali Bangladesh
| | - Shafi Mahmud
- Department of Genetic Engineering and Biotechnology University of Rajshahi Rajshahi Bangladesh
| | | | - Md. Jahidul Alam
- Department of Applied Chemistry and Chemical Engineering Noakhali Science and Technology University Noakhali Bangladesh
| | - Md. Mahfuzur Rahman Bhuyan
- Department of Biochemistry and Molecular Biology Noakhali Science and Technology University Noakhali Bangladesh
| | - Talha Bin Emran
- Department of Pharmacy BGC Trust University Bangladesh Chittagong Bangladesh
- Department of Pharmacy Faculty of Allied Health Sciences, Daffodil International University Dhaka Bangladesh
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17
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Dey D, Biswas P, Paul P, Mahmud S, Ema TI, Khan AA, Ahmed SZ, Hasan MM, Saikat ASM, Fatema B, Bibi S, Rahman MA, Kim B. Natural flavonoids effectively block the CD81 receptor of hepatocytes and inhibit HCV infection: a computational drug development approach. Mol Divers 2022:10.1007/s11030-022-10491-9. [PMID: 35821161 DOI: 10.1007/s11030-022-10491-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 06/24/2022] [Indexed: 12/15/2022]
Abstract
Hepatitis C virus (HCV) infection is a major public health concern, and almost two million people are infected per year globally. This is occurred by the diverse spectrum of viral genotypes, which are directly associated with chronic liver disease (fibrosis, and cirrhosis). Indeed, the viral genome encodes three principal proteins as sequentially core, E1, and E2. Both E1 and E2 proteins play a crucial role in the attachment of the host system, but E2 plays a more fundamental role in attachment. The researchers have found the "E2-CD81 complex" at the entry site, and therefore, CD81 is the key receptor for HCV entrance in both humans, and chimpanzees. So, the researchers are trying to block the host CD81 receptor and halt the virus entry within the cellular system via plant-derived compounds. Perhaps that is why the current research protocol is designed to perform an in silico analysis of the flavonoid compounds for targeting the tetraspanin CD81 receptor of hepatocytes. To find out the best flavonoid compounds from our library, web-based tools (Swiss ADME, pKCSM), as well as computerized tools like the PyRx, PyMOL, BIOVIA Discovery Studio Visualizer, Ligplot+ V2.2, and YASARA were employed. For molecular docking studies, the flavonoid compounds docked with the targeted CD81 protein, and herein, the best-outperformed compounds are Taxifolin, Myricetin, Puerarin, Quercetin, and (-)-Epicatechin, and outstanding binding affinities are sequentially - 7.5, - 7.9, - 8.2, - 8.4, and - 8.5 kcal/mol, respectively. These compounds have possessed more interactions with the targeted protein. To validate the post docking data, we analyzed both 100 ns molecular dynamic simulation, and MM-PBSA via the YASARA simulator, and finally finds the more significant outcomes. It is concluded that in the future, these compounds may become one of the most important alternative antiviral agents in the fight against HCV infection. It is suggested that further in vivo, and in vitro research studies should be done to support the conclusions of this in silico research workflow.
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Affiliation(s)
- Dipta Dey
- Department of Biochemistry and Molecular Biology, Life Science Faculty, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, 8100, Bangladesh
| | - Partha Biswas
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University of Science and Technology (JUST), Jashore, 7408, Bangladesh.
| | - Priyanka Paul
- Department of Biochemistry and Molecular Biology, Life Science Faculty, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, 8100, Bangladesh
| | - Shafi Mahmud
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, 6204, Bangladesh
| | - Tanzila Ismail Ema
- Department of Biochemistry and Microbiology, North South University, Dhaka, 1229, Bangladesh
| | - Arysha Alif Khan
- Department of Biochemistry and Microbiology, North South University, Dhaka, 1229, Bangladesh
| | - Shahlaa Zernaz Ahmed
- Department of Biochemistry and Microbiology, North South University, Dhaka, 1229, Bangladesh
| | - Mohammad Mehedi Hasan
- Department of Biochemistry and Molecular Biology, Faculty of Life Science, Mawlana Bhashani Science and Technology University, Tangail, Bangladesh
| | - Abu Saim Mohammad Saikat
- Department of Biochemistry and Molecular Biology, Life Science Faculty, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, 8100, Bangladesh
| | - Babry Fatema
- Department of Biochemistry and Molecular Biology, Life Science Faculty, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, 8100, Bangladesh
| | - Shabana Bibi
- Yunnan Herbal Laboratory, College of Ecology and Environmental Sciences, Yunnan University, Kunming, 650091, China
- Department of Biological Sciences, International Islamic University, Islamabad, Pakistan
| | - Md Ataur Rahman
- Global Biotechnology & Biomedical Research Network (GBBRN), Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Islamic University, Kushtia, 7003, Bangladesh
- Department of Pathology, College of Korean Medicine, Kyung Hee University, Seoul, 02447, Korea
- Korean Medicine-Based Drug Repositioning Cancer Research Center, College of Korean Medicine, Kyung Hee University, Seoul, 02447, Korea
| | - Bonglee Kim
- Department of Pathology, College of Korean Medicine, Kyung Hee University, Seoul, 02447, Korea.
- Korean Medicine-Based Drug Repositioning Cancer Research Center, College of Korean Medicine, Kyung Hee University, Seoul, 02447, Korea.
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18
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Saxena S, Murthy TPK, Chandramohan V, Achyuth S, Maansi M, Das P, Sineagha V, Prakash S. In-silico analysis of deleterious single nucleotide polymorphisms of PNMT gene. MOLECULAR SIMULATION 2022. [DOI: 10.1080/08927022.2022.2094922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Sidharth Saxena
- Department of Biotechnology, Ramaiah Institute of Technology, Bengaluru, India
| | | | - Vivek Chandramohan
- Department of Biotechnology, Siddaganga Institute of Technology, Tumakuru, India
| | - Sai Achyuth
- Department of Biotechnology, Ramaiah Institute of Technology, Bengaluru, India
| | - M. Maansi
- Department of Biotechnology, Ramaiah Institute of Technology, Bengaluru, India
| | - Papiya Das
- Department of Biotechnology, Ramaiah Institute of Technology, Bengaluru, India
| | - V. Sineagha
- Department of Biotechnology, Ramaiah Institute of Technology, Bengaluru, India
| | - Sriraksha Prakash
- Department of Biotechnology, Ramaiah Institute of Technology, Bengaluru, India
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19
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Qu Y, Davey K, Sun Y, Middelberg A, Bi J. Engineered Design of the E-Helix Structure on Ferritin Nanoparticles. ACS APPLIED BIO MATERIALS 2022; 5:3167-3179. [PMID: 35770389 DOI: 10.1021/acsabm.2c00154] [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: 11/30/2022]
Abstract
Insertion of an immunogenic epitope at the C-terminus of ferritin has shown the potential to produce a stable and efficacious vaccine. There is however limited understanding of how C-terminus insertion affects ferritin protein stability. The E-helix at the C-terminus has attracted interest because there are contradictory reports as to whether it has a role in protein stabilization. Here, we report, for the first time, combining molecular dynamics simulation (MDS) with experiment to engineer the design of the E-helix at the C-terminus of engineered human ferritin heavy chain (F1) inserted with Epstein-Barr nuclear antigen 1 (EBNA1, E1) and flexible linker (L3) residues (to afford F1L3E1). Hot spots on the E-helix of the C-terminus were predicted by MDS at aa 167 (Glu) and aa 171 (Asp). Five (5) variants of F1L3E1 were constructed by considering hot spots and alteration of electrostatic or hydrophobic interfaces, namely, (1) C1, hot spots substituted with noncharged residue Gln; (2) C2, hot spots substituted with positively charged residue Arg; (3) C3, hydrophobic residues substituted with the most hydrophobic residues Val and Ile; (4) C4, hydrophobic residues substituted with the most hydrophilic residues Gln and Asn; and (5) C5, a heptad repeat structure in the E-helix disrupted by substituting "a" and "d" heptad residues with noncharged polar residue Gln. It was found that the E-helix is essential to maintain integrated protein stability and that changing the hydrophobic interface (C3 and C4) had more significant effects on protein folding and stability than changing the electrostatic interface (C1 and C2). It was confirmed by both MDS and experiment that variants C1, C2, and C5 were able to fold to form stable conformational structures with protein surface hydrophobicity similar to that of F1L3E1. However, they are less thermally stable than F1L3E1. Significant changes in hydrophobicity drove significant protein aggregation for variants C3 and C4. It is concluded that the molecular design of the C-terminus in engineered ferritin, especially the E-helix, is important to ensure the epitope-based chimeric vaccine is safe (aggregate free) and efficacious.
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Affiliation(s)
- Yiran Qu
- School of Chemical Engineering and Advanced Materials, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Kenneth Davey
- School of Chemical Engineering and Advanced Materials, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Yan Sun
- Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of the Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Anton Middelberg
- Division of Research and Innovation, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Jingxiu Bi
- School of Chemical Engineering and Advanced Materials, The University of Adelaide, Adelaide, SA 5005, Australia
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20
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Kharrat M, Triki CC, Alila-Fersi O, Jallouli O, Khemakham B, Mallouli S, Maalej M, Ammar M, Frikha F, Kamoun F, Fakhfakh F. Combined in Silico Prediction Methods, Molecular Dynamic Simulation, and Molecular Docking of FOXG1 Missense Mutations: Effect on FoxG1 Structure and Its Interactions with DNA and Bmi-1 Protein. J Mol Neurosci 2022; 72:1695-1705. [PMID: 35654936 DOI: 10.1007/s12031-022-02032-8] [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] [Received: 03/16/2022] [Accepted: 05/23/2022] [Indexed: 11/28/2022]
Abstract
FoxG1 encoded by FOXG1 gene is a transcriptional factor interacting with the DNA of targeted genes as well as with several proteins to regulate the forebrain development. Mutations in the FOXG1 gene have been shown to cause a wide spectrum of brain disorders, including the congenital variant of Rett syndrome. In this study, the direct sequencing of FOXG1 gene revealed a novel c.645C > A (F215L) variant in the patient P1 and a de novo known one c.755G > A (G252D) in the patient P2. To investigate the putative impact of FOXG1 missense variants, a computational pipeline by the application of in silico prediction methods, molecular dynamic simulation, and molecular docking approaches was used. Bioinformatics analysis and molecular dynamics simulation have demonstrated that F215L and G252D variants found in the DNA binding domain are highly deleterious mutations that may cause the protein structure destabilization. On the other hand, molecular docking revealed that F215L mutant is likely to have a great impact on destabilizing the protein structure and the disruption of the Bmi-1 binding site quite significantly. Regarding G252D mutation, it seems to abolish the ability of FoxG1 to bind DNA target, affecting the transcriptional regulation of targeted genes. Our study highlights the usefulness of combined computational approaches, molecular dynamic simulation, and molecular docking for a better understanding of the dysfunctional effects of FOXG1 missense mutations and their role in the etiopathogenesis as well as in the genotype-phenotype correlation.
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Affiliation(s)
- Marwa Kharrat
- Laboratory of Molecular and Functional Genetics, Faculty of Science, Sfax University, Sfax, Tunisia.
| | - Chahnez Charfi Triki
- Child Neurology Department, Hedi Chaker Hospital, Sfax, Tunisia.,Research Laboratory (LR19ES15), Sfax Medical School, Sfax University, Sfax, Tunisia
| | - Olfa Alila-Fersi
- Laboratory of Molecular and Functional Genetics, Faculty of Science, Sfax University, Sfax, Tunisia
| | - Olfa Jallouli
- Child Neurology Department, Hedi Chaker Hospital, Sfax, Tunisia.,Research Laboratory (LR19ES15), Sfax Medical School, Sfax University, Sfax, Tunisia
| | - Bassem Khemakham
- Laboratory of Plant Biotechnology, Faculty of Sciences of Sfax, Sfax University, Sfax, Tunisia
| | - Salma Mallouli
- Child Neurology Department, Hedi Chaker Hospital, Sfax, Tunisia.,Research Laboratory (LR19ES15), Sfax Medical School, Sfax University, Sfax, Tunisia
| | - Marwa Maalej
- Laboratory of Molecular and Functional Genetics, Faculty of Science, Sfax University, Sfax, Tunisia
| | - Marwa Ammar
- Laboratory of Molecular and Functional Genetics, Faculty of Science, Sfax University, Sfax, Tunisia
| | - Fakher Frikha
- Laboratory of Molecular and Cellular Screening Processes, Center of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Fatma Kamoun
- Child Neurology Department, Hedi Chaker Hospital, Sfax, Tunisia.,Research Laboratory (LR19ES15), Sfax Medical School, Sfax University, Sfax, Tunisia
| | - Faiza Fakhfakh
- Laboratory of Molecular and Functional Genetics, Faculty of Science, Sfax University, Sfax, Tunisia.
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21
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Ferdausi N, Islam S, Rimti FH, Quayum ST, Arshad EM, Ibnat A, Islam T, Arefin A, Ema TI, Biswas P, Dey D, Azad SA. Point-specific interactions of isovitexin with the neighboring amino acid residues of the hACE2 receptor as a targeted therapeutic agent in suppressing the SARS-CoV-2 influx mechanism. J Adv Vet Anim Res 2022; 9:230-240. [PMID: 35891654 PMCID: PMC9298103 DOI: 10.5455/javar.2022.i588] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 04/12/2022] [Accepted: 04/14/2022] [Indexed: 12/02/2022] Open
Abstract
Objective: Despite the development of several vaccines against severe acute respiratory syndrome coronavirus-2, the need for an additional prophylactic agent is evident. In recent in silico studies, isovitexin exhibited a higher binding affinity against the human angiotensin converting-enzyme 2 (hACE2) receptor than existing antiviral drugs. The research aimed to find out the point specificity of isovitexin for the hACE2 receptor and to assess its therapeutic potential, depending on the stability of the isovitexin–hACE2 complex. Materials and Methods: The pharmacokinetic profile of isovitexin was analyzed. The crystal structure of the hACE2 receptor and the ligand isovitexin were docked to form a ligand–protein complex following molecular optimization. To determine the isovitexin–hACE2 complex stability, their binding affinity, hydrogen bonding, and hydrophobic interactions were studied. Lastly, the root mean square deviation (RMSD), root mean square fluctuation, solvent accessible surface area, molecular surface area, radius of gyration (Rg), polar surface area, and principal component analysis values were found by simulating the complex with molecular dynamic (MD). Results: The predicted Lethal dose50 for isovitexin was 2.56 mol/kg, with an acceptable maximum tolerated dose and no hepatotoxicity or AMES toxicity. Interactions with the amino acid residues Thr371, Asp367, Glu406, Pro346, His345, Phe274, Tyr515, Glu375, Thr347, Glu402, and His374 of the hACE2 protein were required for the high binding affinity and specificity of isovitexin. Based on what was learned from the MD simulation, the hACE2 receptor-blocking properties of isovitexin were looked at. Conclusions: Isovitexin is a phytochemical with a reasonable bioactivity and safety profile for use in humans, and it can potentially be used as a hACE2-specific therapeutic to inhibit COVID-19 infection.
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Affiliation(s)
- Nourin Ferdausi
- Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - Samarth Islam
- Department of Biochemistry and Microbiology, North South University, Dhaka, Bangladesh
| | - Fahmida Hoque Rimti
- Bachelor of Medicine and Surgery, Chittagong Medical College, Chittagong, Bangladesh
| | - Syeda Tasnim Quayum
- Department of Biochemistry and Microbiology, North South University, Dhaka, Bangladesh
| | - Efat Muhammad Arshad
- Department of Biochemistry and Microbiology, North South University, Dhaka, Bangladesh
| | - Aashian Ibnat
- Department of Pharmaceutical Sciences, North South University, Dhaka, Bangladesh
| | - Tamnia Islam
- Wolfson Institute for Biomedical Research, Division of Medicine, University College London, London, United Kingdom.,Immunoinformatics and Vaccinomics Research Unit, RPG Interface Lab, Jashore, Bangladesh
| | - Adittya Arefin
- Wolfson Institute for Biomedical Research, Division of Medicine, University College London, London, United Kingdom.,Immunoinformatics and Vaccinomics Research Unit, RPG Interface Lab, Jashore, Bangladesh
| | - Tanzila Ismail Ema
- Department of Biochemistry and Microbiology, North South University, Dhaka, Bangladesh.,Immunoinformatics and Vaccinomics Research Unit, RPG Interface Lab, Jashore, Bangladesh
| | - Partha Biswas
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, Bangladesh.,Immunoinformatics and Vaccinomics Research Unit, RPG Interface Lab, Jashore, Bangladesh
| | - Dipta Dey
- Department of Biochemistry and Molecular Biology, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, Bangladesh.,Immunoinformatics and Vaccinomics Research Unit, RPG Interface Lab, Jashore, Bangladesh
| | - Salauddin Al Azad
- Fermentation Engineering Major, School of Biotechnology, Jiangnan University, Wuxi, PR China.,Immunoinformatics and Vaccinomics Research Unit, RPG Interface Lab, Jashore, Bangladesh
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22
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Evaluation of Cyc 1 protein stability in Acidithiobacillus ferrooxidans bacterium after E121D mutation by molecular dynamics simulation to improve electron transfer. JOURNAL OF MICROBIOLOGY (SEOUL, KOREA) 2022; 60:526-532. [PMID: 35286603 DOI: 10.1007/s12275-022-1645-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/12/2022] [Accepted: 01/13/2022] [Indexed: 10/18/2022]
Abstract
Cyc1 (Cytochrome c552) is a protein in the electron transport chain of the Acidithiobacillus ferrooxidans (Af) bacteria which obtain their energy from oxidation Fe2+ to Fe3+. The electrons are directed through Cyc2, RCY (rusticyanin), Cyc1 and Cox aa3 proteins to O2. Cyc1 protein consists of two chains, A and B. In the present study, a novel mutation (E121D) in the A chain of Cyc1 protein was selected due to electron receiving from Histidine 143 of RCY. Then, the changes performed in the E121D mutant were evaluated by MD simulations analyzes. Cyc1 and RCY proteins were docked by a Patchdock server. By E121D mutation, the connection between Zn 1388 of chain B and aspartate 121 of chain A weaken. Asp 121 gets farther from Zn 1388. Therefore, the aspartate gets closer to Cu 1156 of the RCY leading to the higher stability of the RCY/Cyc1 complex. Further, an acidic residue (Glu121) becomes a more acidic residue (Asp121) and improves the electron transfer to Cyc1 protein. The results of RMSF analysis showed further ligand flexibility in mutation. This leads to fluctuation of the active site and increases redox potential at the mutation point and the speed of electron transfer. This study also predicts that in all respiratory chain proteins, electrons probably enter the first active site via glutamate and exit histidine in the second active site of each respiratory chain protein.
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Maurya SK, Mishra R. Molecular docking studies of natural immunomodulators indicate their interactions with the CD40L of CD40/CD40L pathway and CSF1R kinase domain of microglia. J Mol Model 2022; 28:101. [PMID: 35325302 DOI: 10.1007/s00894-022-05084-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 03/08/2022] [Indexed: 10/18/2022]
Abstract
Natural products have proved beneficial in reducing neuroinflammation in neurological diseases. Their impacts have also been associated with the activities of microglia, responsible for brain-specific immunity. Recent studies have shown the involvement of the number of microglia-specific proteins in the regulation of brain-specific immunity. However, molecular targets of natural products and their mechanism of interaction with microglia-specific proteins are elusive. Since the genetic signature of microglia offers many potential targets for drug discovery, molecular docking followed by molecular dynamics (MD) simulations of cluster of differentiation 40 ligand (CD40L) and colony-stimulating factor 1 receptor (CSF1R) kinase domain protein with some known neuro-immunomodulators (Curcumin, Cannabidiol, Ginsenoside Rg1, Resveratrol, and Sulforaphane) has been evaluated. Curcumin and cannabidiol were observed likely to modulate CD40L and expression of cytokines and entry of inflammatory cells. Resveratrol and cannabidiol may affect the CSF1R kinase domain and activation of microglia. Our finding suggests that curcumin, cannabidiol, and resveratrol may serve specific drug ligands in regulating microglia-mediated brain immunity.
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Affiliation(s)
- Shashank Kumar Maurya
- Department of Zoology, Ramjas College, University of Delhi, 110007, Delhi, India.,Department of Zoology, School of Sciences, Cluster University of Jammu, 180001, Jammu, India.,Biochemistry and Molecular Biology Laboratory, Department of Zoology, Banaras Hindu University, 221005, Varanasi, India
| | - Rajnikant Mishra
- Biochemistry and Molecular Biology Laboratory, Department of Zoology, Banaras Hindu University, 221005, Varanasi, India.
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24
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Nipun TS, Ema TI, Mia MAR, Hossen MS, Arshe FA, Ahmed SZ, Masud A, Taheya FF, Khan AA, Haque F, Azad SA, Al Hasibuzzaman M, Tanbir M, Anis S, Akter S, Mily SJ, Dey D. Active site-specific quantum tunneling of hACE2 receptor to assess its complexing poses with selective bioactive compounds in co-suppressing SARS-CoV-2 influx and subsequent cardiac injury. J Adv Vet Anim Res 2022; 8:540-556. [PMID: 35106293 PMCID: PMC8757663 DOI: 10.5455/javar.2021.h544] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 09/01/2021] [Accepted: 09/04/2021] [Indexed: 12/16/2022] Open
Abstract
Objective: This research aims to study the target specificity of selective bioactive compounds in complexing with the human angiotensin-converting enzyme (hACE2) receptor to impede the severe acute respiratory syndrome coronavirus 2 influx mechanism resulting in cardiac injury and depending on the receptor’s active site properties and quantum tunneling. Materials and Methods: A library of 120 phytochemical ligands was prepared, from which 5 were selected considering their absorption, distribution, metabolism, and excretion (ADMET) and quantitative structure–activity relationship (QSAR) profiles. The protein active sites and belonging quantum tunnels were defined to conduct supramolecular docking of the aforementioned ligands. The hydrogen bond formation and hydrophobic interactions between the ligand–receptor complexes were studied following the molecular docking steps. A comprehensive molecular dynamic simulation (MDS) was conducted for each of the ligand–receptor complexes to figure out the values – root mean square deviation (RMSD) (Å), root mean square fluctuation (RMSF) (Å), H-bonds, Cα, solvent accessible surface area (SASA) (Å2), molecular surface area (MolSA) (Å2), Rg (nm), and polar surface area (PSA) (Å). Finally, computational programming and algorithms were used to interpret the dynamic simulation outputs into their graphical quantitative forms. Results: ADMET and QSAR profiles revealed that the most active candidates from the library to be used were apigenin, isovitexin, piperolactam A, and quercetin as test ligands, whereas serpentine as the control. Based on the binding affinities of supramolecular docking and the parameters of molecular dynamic simulation, the strength of the test ligands can be classified as isovitexin > quercetin > piperolactam A > apigenin when complexed with the hACE2 receptor. Surprisingly, serpentine showed lower affinity (−8.6 kcal/mol) than that of isovitexin (−9.9 kcal/mol) and quercetin (−8.9 kcal/mol). The MDS analysis revealed all ligands except isovitexin having a value lower than 2.5 Ǻ. All the test ligands exhibited acceptable fluctuation ranges of RMSD (Å), RMSF (Å), H-bonds, Cα, SASA (Å2), MolSA (Å2), Rg (nm), and PSA (Å) values. Conclusion: Considering each of the parameters of molecular optimization, docking, and dynamic simulation interventions, all of the test ligands can be suggested as potential targeted drugs in blocking the hACE2 receptor.
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Affiliation(s)
- Tanzina Sharmin Nipun
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, International Islamic University Malaysia, Kuantan, Malaysia
| | - Tanzila Ismail Ema
- Department of Biochemistry and Microbiology, North South University, Dhaka, Bangladesh
| | - Md Abdur Rashid Mia
- Department of Pharmaceutical Technology, Faculty of Pharmacy, International Islamic University Malaysia, Kuantan, Malaysia
| | - Md Saddam Hossen
- Microbiology Major, Faculty of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, PR China
| | - Farzana Alam Arshe
- Department of Biochemistry and Microbiology, North South University, Dhaka, Bangladesh
| | - Shahlaa Zernaz Ahmed
- Department of Biochemistry and Microbiology, North South University, Dhaka, Bangladesh
| | - Afsana Masud
- Department of Biochemistry and Microbiology, North South University, Dhaka, Bangladesh
| | - Fatiha Faheem Taheya
- Department of Biochemistry and Microbiology, North South University, Dhaka, Bangladesh
| | - Arysha Alif Khan
- Department of Biochemistry and Microbiology, North South University, Dhaka, Bangladesh
| | - Fauzia Haque
- Department of Biochemistry and Microbiology, North South University, Dhaka, Bangladesh
| | - Salauddin Al Azad
- Fermentation Engineering Major, School of Biotechnology, Jiangnan University, Wuxi, PR China
| | | | - Mohammad Tanbir
- Department of Biochemistry and Microbiology, North South University, Dhaka, Bangladesh
| | - Samin Anis
- Chattogram Maa-O-Shishu Hospital Medical College, University of Chittagong, Chattogram, Bangladesh
| | - Sharmin Akter
- Department of Genetics and Plant Breeding, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
| | | | - Dipta Dey
- Department of Biochemistry and Molecular Biology, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalgonj, Bangladesh
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25
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Caseinolytic Proteins (Clp) in the Genus Klebsiella: Special Focus on ClpK. Molecules 2021; 27:molecules27010200. [PMID: 35011428 PMCID: PMC8746953 DOI: 10.3390/molecules27010200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 11/15/2021] [Accepted: 12/15/2021] [Indexed: 11/16/2022] Open
Abstract
Caseinolytic proteins (Clp), which are present in both prokaryotes and eukaryotes, play a major role in cell protein quality control and survival of bacteria in harsh environmental conditions. Recently, a member of this protein family, ClpK was identified in a pathogenic strain of Klebsiella pneumoniae which was responsible for nosocomial infections. ClpK is linked to the thermal stress survival of this pathogen. The genome wide analysis of Clp proteins in Klebsiella spp. indicates that ClpK is present in only 34% of the investigated strains. This suggests that the uptake of the clpk gene is selective and may only be taken up by a pathogen that needs to survive harsh environmental conditions. In silico analyses and molecular dynamic simulations show that ClpK is mainly α-helical and is highly dynamic. ClpK was successfully expressed and purified to homogeneity using affinity and anion exchange chromatography. Biophysical characterization of ClpK showed that it is predominantly alpha-helical, and this is in agreement with in silico analysis of the protein structure. Furthermore, the purified protein is biologically active and hydrolyses ATP in a concentration- dependent manner.
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26
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Arefin A, Ismail Ema T, Islam T, Hossen S, Islam T, Al Azad S, Uddin Badal N, Islam A, Biswas P, Alam NU, Islam E, Anjum M, Masud A, Kamran S, Rahman A, Kumar Paul P. Target specificity of selective bioactive compounds in blocking α-dystroglycan receptor to suppress Lassa virus infection: an in silico approach. J Biomed Res 2021; 35:459-473. [PMID: 34857680 PMCID: PMC8637655 DOI: 10.7555/jbr.35.20210111] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Lassa hemorrhagic fever, caused by Lassa mammarenavirus (LASV) infection, accumulates up to 5000 deaths every year. Currently, there is no vaccine available to combat this disease. In this study, a library of 200 bioactive compounds was virtually screened to study their drug-likeness with the capacity to block the α-dystroglycan (α-DG) receptor and prevent LASV influx. Following rigorous absorption, distribution, metabolism, and excretion (ADME) and quantitative structure-activity relationship (QSAR) profiling, molecular docking was conducted with the top ligands against the α-DG receptor. The compounds chrysin, reticuline, and 3-caffeoylshikimic acid emerged as the top three ligands in terms of binding affinity. Post-docking analysis revealed that interactions with Arg76, Asn224, Ser259, and Lys302 amino acid residues of the receptor protein were important for the optimum binding affinity of ligands. Molecular dynamics simulation was performed comprehensively to study the stability of the protein-ligand complexes. In-depth assessment of root-mean-square deviation (RMSD), root mean square fluctuation (RMSF), polar surface area (PSA), B-Factor, radius of gyration (Rg), solvent accessible surface area (SASA), and molecular surface area (MolSA) values of the protein-ligand complexes affirmed that the candidates with the best binding affinity formed the most stable protein-ligand complexes. To authenticate the potentialities of the ligands as target-specific drugs, an in vivo study is underway in real time as the continuation of the research.
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Affiliation(s)
- Adittya Arefin
- Wolfson Institute for Biomedical Research, Division of Medicine, University College London, London WC1E6AE, UK
| | - Tanzila Ismail Ema
- Department of Biochemistry and Microbiology, North South University, Dhaka 1229, Bangladesh
| | - Tamnia Islam
- Wolfson Institute for Biomedical Research, Division of Medicine, University College London, London WC1E6AE, UK
| | - Saddam Hossen
- Faculty of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, Zhejiang 310018, China
| | - Tariqul Islam
- Faculty of Pharmacy, International Islamic University Malaysia, Kuantan, Pahang 25200, Malaysia
| | - Salauddin Al Azad
- School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Nasir Uddin Badal
- Department of Biomedical Technology, Tampere University, Tampere 33014, Finland
| | - Aminul Islam
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore 7408, Bangladesh
| | - Partha Biswas
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore 7408, Bangladesh
| | - Nafee Ul Alam
- Faculty of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, Zhejiang 310018, China
| | - Enayetul Islam
- Department of Genetic Engineering and Biotechnology, University of Chittagong, Chittagong 4331, Bangladesh
| | - Maliha Anjum
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore 7408, Bangladesh
| | - Afsana Masud
- Department of Biochemistry and Microbiology, North South University, Dhaka 1229, Bangladesh
| | - Shaikh Kamran
- Applied Statistics and Data Science, Jahangirnagar University, Dhaka 1342, Bangladesh
| | - Ahsab Rahman
- Department of Mathematics and Natural Sciences, Brac University, Dhaka 1212, Bangladesh
| | - Parag Kumar Paul
- Department of Electrical and Electronic Engineering, United International University, Dhaka 1212, Bangladesh
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27
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Mukherjee SK, Mukherjee M, Mishra PP. Impact of Mutation on the Structural Stability and the Conformational Landscape of Inhibitor-Resistant TEM β-Lactamase: A High-Performance Molecular Dynamics Simulation Study. J Phys Chem B 2021; 125:11188-11196. [PMID: 34609140 DOI: 10.1021/acs.jpcb.1c05988] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Gain-of-function mutations and structural adjustment toward β-lactamase inhibitors in the TEM-type β-lactamases among the uropathogenic E. coli (UPEC) culminate in treatment complications and demands detailed investigation. In this study, uncharacterized amino acid substitutions, M69L/I84V/W165G/V184A/V262I/N276S, in inhibitor-resistant TEM (IRT) β-lactamase isolated from clinical UPEC were subjected to extensive molecular dynamics (EMD) simulations for 100 ns to estimate parameters such as root-mean-square deviation (RMSD), root-mean-square fluctuation (RMSF), the radius of gyration (Rg), contour plot (Rg/RMSD), secondary structure element (SSE), etc. Residue interaction networks, principal component analysis (PCA), and correlation heatmaps were generated to predict the relation between functionally important atomic motions to uncover the structural stability of the mutants. To avoid the false positive conclusion of the simulation study, we performed three identically parameterize replicas of 100 ns each. Alterations in hydrophobic interactions resulted in conformation changes exhibited as comparable residue interaction networks. Besides, PCA and porcupine plot analysis based on the ensemble of structure from molecular dynamics trajectories revealed the collective atomic motions of the IRT variants that impart structural flexibility to their active site loop. This study conducted on IRT mutants that delineate intricate protein motions contributes to their stability and folding, which is an absolute necessity for designing candidate molecules owing to the clinical threat of emerging resistance against potent β-lactam antibiotics.
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Affiliation(s)
- Sandip K Mukherjee
- Department of Biochemistry and Medical Biotechnology, Calcutta School of Tropical Medicine, 108, Chittaranjan Ave, Kolkata, West Bengal 700073, India
| | - Mandira Mukherjee
- Department of Biochemistry and Medical Biotechnology, Calcutta School of Tropical Medicine, 108, Chittaranjan Ave, Kolkata, West Bengal 700073, India
| | - Padmaja P Mishra
- Chemical Science Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, West Bengal 700064, India.,Homi Bhaba National Institute, Anushaktinagar, Mumbai, Maharashtra 400094, India
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28
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Wu X, Wen B, Lin L, Shi W, Li D, Cheng Y, Xu LY, Li EM, Dong G. New insights into the function of Fascin in actin bundling: A combined theoretical and experimental study. Int J Biochem Cell Biol 2021; 139:106056. [PMID: 34390855 DOI: 10.1016/j.biocel.2021.106056] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 08/04/2021] [Accepted: 08/07/2021] [Indexed: 02/05/2023]
Abstract
Fascin, one of actin bundling proteins, plays an important role in the cross-linking of actin filaments (F-actin). Phosphorylation of Fascin is an important posttranslational modification to affect its structure and function. For example, a phosphomimetic mutation of Fascin-S39D decrease its bundling ability with F-actin significantly. In this paper, we studied the actin-bundling activity of Fascin by using molecular dynamics (MD) simulations and biochemical methods. All single-site mutations from serine/threonine to aspartic acid were mimicked by MD simulations. For five mutants (S146D, S156D, S218D, T239D and S259D), the mutated residues in domain 2 of Fascin were found to form salt-bridge interactions with an adjacent residue, indicating that mutations of these residues could potentially reduce actin-bundling activity. Further, F-actin-bundling assays and immunofluorescence technique showed S146D and T239D to have a strong effect on Fascin bundling with F-actin. Finally, we show that single-site mutations do not change the general shape of Fascin, but local structures near the mutated residues in Fascin-S146D and T239D become unstable, thereby affecting the ability of Fascin to bind with F-actin. These findings suggest that targeting domain 2 of Fascin would be very useful for the drug design. In addition, our study indicates that MD simulation is a useful method to screening which residues on Fascin are important.
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Affiliation(s)
- Xiaodong Wu
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, 515041, PR China
| | - Bing Wen
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, 515041, PR China
| | - Lirui Lin
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, 515041, PR China; Medical Informatics Research Center, Shantou University Medical College, Shantou, 515041, PR China
| | - Wenqi Shi
- Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou, 515041, PR China; Cancer Research Center, Shantou University Medical College, Shantou, 515041, PR China
| | - Dajia Li
- Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou, 515041, PR China; Cancer Research Center, Shantou University Medical College, Shantou, 515041, PR China
| | - Yinwei Cheng
- Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou, 515041, PR China; Cancer Research Center, Shantou University Medical College, Shantou, 515041, PR China
| | - Li-Yan Xu
- Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou, 515041, PR China; Cancer Research Center, Shantou University Medical College, Shantou, 515041, PR China.
| | - En-Min Li
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, 515041, PR China; Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou, 515041, PR China.
| | - Geng Dong
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, 515041, PR China; Medical Informatics Research Center, Shantou University Medical College, Shantou, 515041, PR China.
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29
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Wargasetia TL, Ratnawati H, Widodo N, Widyananda MH. Bioinformatics Study of Sea Cucumber Peptides as Antibreast Cancer Through Inhibiting the Activity of Overexpressed Protein (EGFR, PI3K, AKT1, and CDK4). Cancer Inform 2021; 20:11769351211031864. [PMID: 34345161 PMCID: PMC8283226 DOI: 10.1177/11769351211031864] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 06/22/2021] [Indexed: 12/28/2022] Open
Abstract
Breast cancer is the most common type of cancer in women globally. The overexpressed proteins, including EGFR, PI3K, AKT1, and CDK4, have a role in the growth of breast cancer cells. The 3D peptide structure of sea cucumber Cucumaria frondosa was modeled and then docked with EGFR, PI3K, AKT1, and CDK4 proteins using AutoDock Vina software. The docking result, which has the best binding affinity value, is continued with molecular dynamics simulation. The docking results showed that all peptides bind to the active sites of the four proteins. WPPNYQW and YDWRF peptides bind to proteins with lower binding affinity values than positive controls. The four proteins were in a stable state when complexed with the WPPNYQW peptide, which was seen from the RMSD and RMSF value. PI3K-YDWRF and AKT1-YDWRF complexes are stable, characterized by high RMSD values and increased volatility in several amino acids. WPPNYQW peptide has high potential as an antibreast cancer agent because it binds to the active sites of the four proteins with low binding affinity values and stable interactions. Meanwhile, the YDWRF peptide interacts with the four proteins with low binding affinity values, but the interaction is only stable on PI3K and AKT1 proteins.
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Affiliation(s)
| | - Hana Ratnawati
- Faculty of Medicine, Maranatha Christian University, Bandung, Indonesia
| | - Nashi Widodo
- Biology Department, Faculty of Mathematics and Natural Sciences, The University of Brawijaya, Malang, Indonesia
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30
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Singh AK, Burada PS, Roy A. Biomolecular response to hour-long ultralow field microwave radiation: An effective coarse-grained model simulation. Phys Rev E 2021; 103:042416. [PMID: 34005990 DOI: 10.1103/physreve.103.042416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 03/16/2021] [Indexed: 11/07/2022]
Abstract
Various electronic devices, which we commonly use, radiate microwaves. Such external perturbation influences the functionality of biomolecules. In an ultralow field, the cumulative response of a molecule is expected only over a time scale of hours. To study the structural dynamics of biomolecules over hours, we adopt a simple methodology for constructing the coarse-grained structure of the protein molecule and solve the Langevin equation under different working potentials. In this approach, each amino acid residue of a biomolecule is mapped onto a number of beads, a few for the backbone, and few for the side chain, depending on the complexity of its chemical structure. We choose the force field in such a way that the dynamics of the protein molecule in the presence of ultralow radiation field of microvolt/nm could be followed over the time frame of 2 h. We apply the model to describe a biomolecule, hen egg white lysozyme, and simulate its structural evolution under ultralow strength electromagnetic radiation. The simulation revealed the finer structural details, like the extent of exposure of bioactive residues and the state of the secondary structures of the molecule, further confirmed from spectroscopic measurements [details are available in Phys. Rev. E 97, 052416 (2018)10.1103/PhysRevE.97.052416 and briefly described here]. Though tested for a specific system, the model is quite general. We believe that it harnesses the potential in studying the structural dynamics of any biopolymer under external perturbation over an extended time scale.
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Affiliation(s)
- Anang Kumar Singh
- Department of Physics, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal 721302, India
| | - P S Burada
- Department of Physics, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal 721302, India
| | - Anushree Roy
- Department of Physics, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal 721302, India
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Shah S, Chaple D, Arora S, Yende S, Moharir K, Lohiya G. Exploring the active constituents of Oroxylum indicum in intervention of novel coronavirus (COVID-19) based on molecular docking method. NETWORK MODELING AND ANALYSIS IN HEALTH INFORMATICS AND BIOINFORMATICS 2021; 10:8. [PMID: 33585155 PMCID: PMC7865104 DOI: 10.1007/s13721-020-00279-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 11/24/2020] [Accepted: 12/15/2020] [Indexed: 12/31/2022]
Abstract
The severe acute respiratory syndrome COVID-19 declared a global pandemic by WHO has become the present wellbeing worry to the whole world. There is an emergent need to search for possible medications. We report in this study a molecular docking study of eighteen Oroxylum indicum molecules with the main protease (Mpro) responsible for the replication of SARS-CoV-2 virus. The outcome of their molecular simulation and ADMET properties reveal four potential inhibitors of the enzyme (Baicalein-7-O-diglucoside, Chrysin-7-O-glucuronide, Oroxindin and Scutellarein) with preference of ligand Chrysin-7-O-glucuronide that has the second highest binding energy (- 8.6 kcal/mol) and fully obeys the Lipinski's rule of five. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13721-020-00279-y.
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Affiliation(s)
- Sapan Shah
- Department of Pharmaceutical Chemistry, Priyadarshini J. L. College of Pharmacy, Hingna Road, Nagpur, Maharashtra 440016 India
| | - Dinesh Chaple
- Department of Pharmaceutical Chemistry, Priyadarshini J. L. College of Pharmacy, Hingna Road, Nagpur, Maharashtra 440016 India
| | - Sumit Arora
- Pharmacognosy and Phytochemistry Division, Gurunanak College of Pharmacy, Nari, Nagpur, Maharashtra 440026 India
| | - Subhash Yende
- Pharmacology Department, Gurunanak College of Pharmacy, Nari, Nagpur, Maharashtra 440026 India
| | - Keshav Moharir
- Pharmaceutics Department, Gurunanak College of Pharmacy, Nari, Nagpur, Maharashtra 440026 India
| | - Govind Lohiya
- Pharmaceutics Department, Gurunanak College of Pharmacy, Nari, Nagpur, Maharashtra 440026 India
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Duran T, Minatovicz B, Bai J, Shin D, Mohammadiarani H, Chaudhuri B. Molecular Dynamics Simulation to Uncover the Mechanisms of Protein Instability During Freezing. J Pharm Sci 2021; 110:2457-2471. [PMID: 33421436 DOI: 10.1016/j.xphs.2021.01.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 12/07/2020] [Accepted: 01/03/2021] [Indexed: 11/19/2022]
Abstract
Freezing is a common process applied in the pharmaceutical industry to store and transport biotherapeutics. Herewith, multi-scale molecular dynamics simulations of Lactate dehydrogenase (LDH) protein in phosphate buffer with/without ice formation performed to uncover the still poorly understood mechanisms and molecular details of protein destabilization upon freezing. Both fast and slow ice growing conditions were simulated at 243 K from one or two-side of the simulation box, respectively. The rate of ice formation at all-atom simulations was crucial to LDH stability, as faster freezing rates resulted in enhanced structural stability maintained by a higher number of intramolecular hydrogen bonds, less flexible protein's residues, lower solvent accessibility and greater structural compactness. Further, protein aggregation investigated by coarse-grained simulations was verified to be initiated by extended protein structures and retained by electrostatic interactions of the salt bridges between charged residues and hydrogen bonds between polar residues of the protein. Lastly, the study of free energy of dissociation through steered molecular dynamics simulation revealed LDH was destabilized by the solvation of the hydrophobic core and the loss of hydrophobic interactions. For the first time, experimentally validated molecular simulations revealed the detailed mechanisms of LDH destabilization upon ice formation and cryoconcentration of solutes.
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Affiliation(s)
- Tibo Duran
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, CT, 06269, USA
| | - Bruna Minatovicz
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, CT, 06269, USA
| | - Jun Bai
- Department of Computer Sciences and Engineering, University of Connecticut, Storrs, CT, 06269, USA
| | - Dongkwan Shin
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, CT, 06269, USA
| | - Hossein Mohammadiarani
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, CT, 06269, USA
| | - Bodhisattwa Chaudhuri
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, CT, 06269, USA; Institute of Material Sciences (IMS), University of Connecticut, Storrs, CT, USA; Department of Chemical & Biomolecular Engineering, University of Connecticut, Storrs, CT 06269, USA.
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Ghaderi S, Bozorgmehr MR, Ahmadi M, Tarahomjoo S. Identification of Conformational B-cell Epitopes in Diphtheria Toxin at Varying Temperatures Using Molecular Dynamics Simulations. ARCHIVES OF RAZI INSTITUTE 2021; 75:427-437. [PMID: 33403838 PMCID: PMC8410147 DOI: 10.22092/ari.2019.127251.1377] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 09/15/2019] [Indexed: 09/30/2022]
Abstract
The changes in temperature levels can potentially affect the toxins in terms of stability and immunological properties via alteration of their structures. Diphtheria Toxin (DT) is highly considered by scientists since its mechanism of action is similar to those of most bacterial toxins, such as botulinum, tetanus, and anthrax. The protection of conformational B-cell epitopes is critically important in the process of diphtheria vaccine production. This study aimed to evaluate the conformational changes of the DT structure at three different temperature levels (27˚C, 37˚C, and 47˚C) using molecular dynamic simulations. Secondary structures were analyzed in YASARA software. According to the results, significant decreases were observed in percentages of the β-sheets, turns, and the helices of the DT structure at 47˚C in comparison with those at 27˚C and 37˚C. Furthermore, the tertiary structure of the DT was compared at different temperatures using the contact map. Accordingly, the results showed that the root-mean-square deviation of the DT structure increased upon temperature rising. In addition, amino acids D68, G128, G171, C186, and K534-S535 at 27˚C and 37˚C, as well as amino acids G26, P38, S291, T267, H384, A356, and V518 at 47˚C showed higher root mean square fluctuation values. The finding demonstrated that the stability of the DT structure decreased at high temperature (47˚C). The solvent-accessible surface area diagram showed that the hydrophobicity of the DT structure increased via temperature rising, and the amino acid residues belonging to B-cell epitopes extended through increasing temperature. However, B-cell epitopes belonging to the junction region of chains A and B were only present at 37˚C. The results of this study are expected to be applicable for determining a suitable temperature level for the production process of the diphtheria vaccine.
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Affiliation(s)
- S Ghaderi
- Division of Central Laboratory, Department of Biotechnology, Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - M R Bozorgmehr
- Department of Chemistry, Mashhad Branch, Islamic Azad University, Mashhad, Iran
| | - M Ahmadi
- Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
- Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Sh Tarahomjoo
- Division of Genomics and Genetic Engineering, Department of Biotechnology, Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
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Wang H, Song L, Zhou T, Zeng C, Jia Y, Zhao Y. A computational study of Tat-CDK9-Cyclin binding dynamics and its implication in transcription-dependent HIV latency. Phys Chem Chem Phys 2020; 22:25474-25482. [PMID: 33043947 DOI: 10.1039/d0cp03662e] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
HIV is a virus that attacks the T cells. HIV may either actively replicate or become latent within host cells for years. Since HIV uses its own protein Tat to hijack the host CDK9-Cyclin complex for transcription, Tat is implicated in transcription-dependent HIV latency. To quantify the impact of Tat binding, we propose a computational framework to probe the dynamics of the CDK9-Cyclin interface and the ATP pocket reorganization upon binding by different Tat mutants. Specifically, we focus on mutations at three Tat residues P10, W11, and N12 that are known to interact directly with CDK9 based on the crystal structure of the Tat-CDK9-Cyclin complex. Our molecular dynamics simulations show that the CDK9-Cyclin interface becomes slightly weaker for P10S and W11R mutants but tighter for the K12N mutant. Furthermore, the side chain orientation of residue K48 in the ATP pocket of CDK9 is similar to the inactive state in P10S and W11R simulations, but similar to the active state in K12N simulations. These are consistent with some existing but puzzling observations of latency for these mutants. This framework may hence help gain a better understanding of the role of Tat in the transcription-dependent HIV latency establishment.
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Affiliation(s)
- Huiwen Wang
- Institute of Biophysics and Department of Physics, Central China Normal University, Wuhan 430079, China.
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35
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Wang H, Qiu J, Liu H, Xu Y, Jia Y, Zhao Y. HKPocket: human kinase pocket database for drug design. BMC Bioinformatics 2019; 20:617. [PMID: 31783725 PMCID: PMC6884818 DOI: 10.1186/s12859-019-3254-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 11/15/2019] [Indexed: 01/06/2023] Open
Abstract
Background The kinase pocket structural information is important for drug discovery targeting cancer or other diseases. Although some kinase sequence, structure or drug databases have been developed, the databases cannot be directly used in the kinase drug study. Therefore, a comprehensive database of human kinase protein pockets is urgently needed to be developed. Results Here, we have developed HKPocket, a comprehensive Human Kinase Pocket database. This database provides sequence, structure, hydrophilic-hydrophobic, critical interactions, and druggability information including 1717 pockets from 255 kinases. We further divided these pockets into 91 pocket clusters using structural and position features in each kinase group. The pocket structural information would be useful for preliminary drug screening. Then, the potential drugs can be further selected and optimized by analyzing the sequence conservation, critical interactions, and hydrophobicity of identified drug pockets. HKPocket also provides online visualization and pse files of all identified pockets. Conclusion The HKPocket database would be helpful for drug screening and optimization. Besides, drugs targeting the non-catalytic pockets would cause fewer side effects. HKPocket is available at http://zhaoserver.com.cn/HKPocket/HKPocket.html.
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Affiliation(s)
- Huiwen Wang
- Department of Physics, Central China Normal University, Wuhan, 430079, China
| | - Jiadi Qiu
- Department of Physics, Central China Normal University, Wuhan, 430079, China
| | - Haoquan Liu
- Department of Physics, Central China Normal University, Wuhan, 430079, China
| | - Ying Xu
- Department of Physics, Central China Normal University, Wuhan, 430079, China
| | - Ya Jia
- Department of Physics, Central China Normal University, Wuhan, 430079, China
| | - Yunjie Zhao
- Department of Physics, Central China Normal University, Wuhan, 430079, China.
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Osire T, Yang T, Xu M, Zhang X, Li X, Niyomukiza S, Rao Z. Lys-Arg mutation improved the thermostability of Bacillus cereus neutral protease through increased residue interactions. World J Microbiol Biotechnol 2019; 35:173. [PMID: 31673794 DOI: 10.1007/s11274-019-2751-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Accepted: 10/18/2019] [Indexed: 11/26/2022]
Abstract
Neutral proteases have broad application as additives in modern laundry detergents and therefore, thermostability is an integral parameter for effective production of protein crystals. To improve thermostability, the contribution of individual residues of Bacillus cereus neutral protease was examined by site-directed mutagenesis. The Lys11Arg and Lys211Arg mutants clearly possessed improved thermostabilities (Tm were 63 and 61 °C respectively) compared to the wild-type (Tm was 60 °C). MD simulations further revealed that the mutants had low RMSD and RMSF values compared to wild-type BCN indicating increased stability of the protein structure. Lys11Arg mutant particularly possessed the lowest RMSD values due to increased residue interactions, which resulted in enhanced thermostability. The mutants also displayed strong stability to most inhibitors, organic solvents and surfactants after incubation for 1 h. This study demonstrated Lys-Arg mutation enhanced thermostability of BCN and thus provides insight for engineering stabilizing mutations with improved thermostability for related proteins.
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Affiliation(s)
- Tolbert Osire
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 LiHu Boulevard, Wuxi, 214122, Jiangsu, China
| | - Taowei Yang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 LiHu Boulevard, Wuxi, 214122, Jiangsu, China.
| | - Meijuan Xu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 LiHu Boulevard, Wuxi, 214122, Jiangsu, China
| | - Xian Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 LiHu Boulevard, Wuxi, 214122, Jiangsu, China
| | - Xu Li
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 LiHu Boulevard, Wuxi, 214122, Jiangsu, China
| | - Samuel Niyomukiza
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 LiHu Boulevard, Wuxi, 214122, Jiangsu, China
| | - Zhiming Rao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 LiHu Boulevard, Wuxi, 214122, Jiangsu, China.
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37
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Wang K, Jian Y, Wang H, Zeng C, Zhao Y. RBind: computational network method to predict RNA binding sites. Bioinformatics 2019; 34:3131-3136. [PMID: 29718097 DOI: 10.1093/bioinformatics/bty345] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 04/24/2018] [Indexed: 12/21/2022] Open
Abstract
Motivation Non-coding RNA molecules play essential roles by interacting with other molecules to perform various biological functions. However, it is difficult to determine RNA structures due to their flexibility. At present, the number of experimentally solved RNA-ligand and RNA-protein structures is still insufficient. Therefore, binding sites prediction of non-coding RNA is required to understand their functions. Results Current RNA binding site prediction algorithms produce many false positive nucleotides that are distance away from the binding sites. Here, we present a network approach, RBind, to predict the RNA binding sites. We benchmarked RBind in RNA-ligand and RNA-protein datasets. The average accuracy of 0.82 in RNA-ligand and 0.63 in RNA-protein testing showed that this network strategy has a reliable accuracy for binding sites prediction. Availability and implementation The codes and datasets are available at https://zhaolab.com.cn/RBind. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Kaili Wang
- Institute of Biophysics and Department of Physics, Central China Normal University, Wuhan, China
| | - Yiren Jian
- Department of Physics, The George Washington University, Washington, DC, USA
| | - Huiwen Wang
- Institute of Biophysics and Department of Physics, Central China Normal University, Wuhan, China
| | - Chen Zeng
- Institute of Biophysics and Department of Physics, Central China Normal University, Wuhan, China.,Department of Physics, The George Washington University, Washington, DC, USA
| | - Yunjie Zhao
- Institute of Biophysics and Department of Physics, Central China Normal University, Wuhan, China
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38
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Roy U. Structure and Function of an Inflammatory Cytokine, Interleukin-2, Analyzed Using the Bioinformatic Approach. Protein J 2019; 38:525-536. [PMID: 31006082 DOI: 10.1007/s10930-019-09833-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The inflammatory cytokine, interleukin-2 (IL-2), is an important regulator of cellular functions. This relatively less studied member of the interleukin protein family is responsible for multiple immuno-modulatory and immuno-stimulatory tasks, like T cell activation, triggering of natural killer cells, inflammation, as well as proliferation and progression of autoimmune diseases and cancers. In this communication we report the temporally variant structural aspects of the IL-2 ligand and its receptor interfaces, based on the available crystal structures. The intended goal of this effort is to generate simulated results that could potentially aid the designs of novel structure based therapeutics.
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Affiliation(s)
- Urmi Roy
- Department of Chemistry & Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY, 13699-5820, USA.
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39
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40
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Wright KM, Du H, Massiah MA. Structural and functional observations of the P151L MID1 mutation reveal alpha4 plays a significant role in X-linked Opitz Syndrome. FEBS J 2017; 284:2183-2193. [PMID: 28548391 DOI: 10.1111/febs.14121] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 05/16/2017] [Accepted: 05/24/2017] [Indexed: 12/20/2022]
Abstract
Mutations of human MID1 are associated with X-linked Opitz G Syndrome (XLOS), which is characterized by midline birth defects. XLOS-observed mutations within the MID1 B-box1 domain are associated with cleft lip/palate, wide-spaced eyes and hyperspadias. Three of the four XLOS-observed mutations in the B-box1 domain results in unfolding but the structural and functional effects of the P151L mutation is not characterized. Here, we demonstrate that the P151L mutation does not disrupt the overall tertiary structure of the B-box1 domain and the adjacent domains. In fact, MID1 E3 ligase activity is slightly enhanced. However, the P151L mutation disrupted the ability of MID1 to catalyze the poly-ubiquitination of alpha4, a novel regulator of PP2A. This observation is consistent with results observed with the other three structure-destabilizing B-box1 mutations in targeting alpha4 but not PP2A. Alpha4 is shown to bind and sequester the catalytic subunit of PP2A and protect it from MID1-mediated ubiquitination and as a result, an increase in alpha4 can contribute to an increase in PP2A, playing a greater role in midline development during embryogenesis.
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Affiliation(s)
- Katharine M Wright
- Department of Chemistry and Center of Biomolecular Science, George Washington University, DC, USA
| | - Haijuan Du
- Department of Chemistry and Center of Biomolecular Science, George Washington University, DC, USA
| | - Michael A Massiah
- Department of Chemistry and Center of Biomolecular Science, George Washington University, DC, USA
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41
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Zhao Y, Jian Y, Liu Z, Liu H, Liu Q, Chen C, Li Z, Wang L, Huang HH, Zeng C. Network Analysis Reveals the Recognition Mechanism for Dimer Formation of Bulb-type Lectins. Sci Rep 2017; 7:2876. [PMID: 28588265 PMCID: PMC5460271 DOI: 10.1038/s41598-017-03003-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 04/20/2017] [Indexed: 12/26/2022] Open
Abstract
The bulb-type lectins are proteins consist of three sequential beta-sheet subdomains that bind to specific carbohydrates to perform certain biological functions. The active states of most bulb-type lectins are dimeric and it is thus important to elucidate the short- and long-range recognition mechanism for this dimer formation. To do so, we perform comparative sequence analysis for the single- and double-domain bulb-type lectins abundant in plant genomes. In contrast to the dimer complex of two single-domain lectins formed via protein-protein interactions, the double-domain lectin fuses two single-domain proteins into one protein with a short linker and requires only short-range interactions because its two single domains are always in close proximity. Sequence analysis demonstrates that the highly variable but coevolving polar residues at the interface of dimeric bulb-type lectins are largely absent in the double-domain bulb-type lectins. Moreover, network analysis on bulb-type lectin proteins show that these same polar residues have high closeness scores and thus serve as hubs with strong connections to all other residues. Taken together, we propose a potential mechanism for this lectin complex formation where coevolving polar residues of high closeness are responsible for long-range recognition.
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Affiliation(s)
- Yunjie Zhao
- Institute of Biophysics and Department of Physics, Central China Normal University, Wuhan, 430079, China.,Department of Physics, The George Washington University, Washington, DC, 20052, USA
| | - Yiren Jian
- Department of Physics, The George Washington University, Washington, DC, 20052, USA
| | - Zhichao Liu
- Department of Physics, The George Washington University, Washington, DC, 20052, USA
| | - Hang Liu
- Department of Electrical and Computer Engineering, The George Washington University, Washington, DC, 20052, USA
| | - Qin Liu
- School of Life Sciences, Jianghan University, Wuhan, 430056, China
| | - Chanyou Chen
- School of Life Sciences, Jianghan University, Wuhan, 430056, China
| | - Zhangyong Li
- Research Center of Biomedical Engineering, Chongqing University of Posts and Telecommunications, Chongqing, 400065, China
| | - Lu Wang
- Research Center of Biomedical Engineering, Chongqing University of Posts and Telecommunications, Chongqing, 400065, China
| | - H Howie Huang
- Department of Electrical and Computer Engineering, The George Washington University, Washington, DC, 20052, USA
| | - Chen Zeng
- Research Center of Biomedical Engineering, Chongqing University of Posts and Telecommunications, Chongqing, 400065, China. .,Department of Physics, The George Washington University, Washington, DC, 20052, USA. .,School of Life Sciences, Jianghan University, Wuhan, 430056, China.
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