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K C Y, Pal S, Nitz TJ, Wild C, Gaur R. Construction of a HIV-1 subtype C 3D model using homology modeling and in-silico docking, molecular dynamics simulation, and MM-GBSA calculation of second-generation HIV-1 maturation inhibitor(s). J Biomol Struct Dyn 2024; 42:7150-7159. [PMID: 37489057 DOI: 10.1080/07391102.2023.2238079] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 07/13/2023] [Indexed: 07/26/2023]
Abstract
Maturation inhibitors (MIs) efficiently block HIV-1 maturation by inhibiting the cleavage of the capsid protein and spacer peptide 1 (CA-SP1) leading to the production of immature and non-infectious virus particles. We have previously reported that second-generation MIs were more potent than bevirimat (BVM) against HIV-1 subtype C. In-silico studies on interaction of with BVM and their analogs have been limited to HIV-1 subtype B(5I4T) due to lack of an available 3D structure for HIV-1 subtype C virus. In our current study, we have developed a 3D model of HIV-1C Gag CA-SP1 region using protein homology modeling with HIV-1 subtype B(514T) as a template. The HIV-1 C homology model generated was extensively validated using several online tools and served as a template to perform molecular docking studies with eight well-characterized MIs. The docked complex of HIV-1C and all nine MIs was subjected to molecular dynamics simulation for 100 ns using AMBER and binding free energy calculations were done using MM-GBSA. Based on our data, CV8611 exhibited highest binding energy of -6.5 Kcal/mol among all BVM analogs. CV8611 formed strong interactions with Gly222 and Met235 of HIV-1C Gag CA-SP1 during MD simulation and remained intact. The root mean square deviation and root mean square fluctuation values of the complex were stable during the simulations. Our study is the first to report construction and validation of 3D model for the HIV-1C Gag CA-SP1, which could serve as a crucial tool in the structure-aided design of novel and broadly acting maturation inhibitors.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Yuvraj K C
- Faculty of Life Sciences and Biotechnology, South Asian University, New Delhi, India
| | - Sapna Pal
- Bioinformatics centre, National Institute of Immunology, New Delhi, India
| | - T J Nitz
- DFH Pharma, Gaithersburg, MD, USA
| | | | - Ritu Gaur
- Faculty of Life Sciences and Biotechnology, South Asian University, New Delhi, India
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2
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Raut B, Upadhyaya SR, Bashyal J, Parajuli N. In Silico and In Vitro Analyses to Repurpose Quercetin as a Human Pancreatic α-Amylase Inhibitor. ACS OMEGA 2023; 8:43617-43631. [PMID: 38027372 PMCID: PMC10666247 DOI: 10.1021/acsomega.3c05082] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 10/20/2023] [Accepted: 10/27/2023] [Indexed: 12/01/2023]
Abstract
Human pancreatic α-amylase (HPA), situated at the apex of the starch digestion hierarchy, is an attractive therapeutic approach to precisely regulate blood glucose levels, thereby efficiently managing diabetes. Polyphenols offer a natural and multifaceted approach to moderate postprandial sugar spikes, with their slight modulation in carbohydrate digestion and potential secondary benefits, such as antioxidant and anti-inflammatory effects. Taking into consideration the unfavorable side effects of currently available commercial medications, we aimed to study a library of polyphenols attributed to their remarkable antidiabetic properties and screened the most potent HPA inhibitor via a comprehensive in silico study encompassing molecular docking, molecular mechanics with generalized Born and surface area solvation (MM/GBSA) calculation, molecular dynamics (MD) simulation, density functional theory (DFT) study, and pharmacokinetic properties followed by an in vitro assay. Significant hydrogen bonding with the catalytic triad residues of HPA, prominent MM/GBSA binding energy of -27.03 kcal/mol, and the stable nature of the protein-ligand complex with regard to 100 ns MD simulation screened quercetin as the best HPA inhibitor. Additionally, quercetin showed strong reactivity in the substrate-binding pocket of HPA and exhibited favorable pharmacokinetic properties with a considerable inhibitory concentration (IC50) of 57.37 ± 0.9 μg/mL against α-amylase. This study holds prospects for HPA inhibition and suggests quercetin as an approach to therapy for diabetes; however, it is imperative to conduct further research.
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Affiliation(s)
- Bimal
K. Raut
- Central Department of Chemistry, Tribhuvan University, Kirtipur 44600, Kathmandu, Nepal
| | - Siddha Raj Upadhyaya
- Central Department of Chemistry, Tribhuvan University, Kirtipur 44600, Kathmandu, Nepal
| | - Jyoti Bashyal
- Central Department of Chemistry, Tribhuvan University, Kirtipur 44600, Kathmandu, Nepal
| | - Niranjan Parajuli
- Central Department of Chemistry, Tribhuvan University, Kirtipur 44600, Kathmandu, Nepal
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3
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Seal S, Chakraborty T, Polley S, Paul D, Banerjee N, Sinha D, Dutta A, Chatterjee S, Sau K, Ghosh Dastidar S, Sau S. Modeling and monitoring the effects of three partly conserved Ile residues in the dimerization domain of a Mip-like virulence factor from Escherichia coli. J Biomol Struct Dyn 2023:1-14. [PMID: 37902555 DOI: 10.1080/07391102.2023.2274978] [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: 04/05/2023] [Accepted: 10/18/2023] [Indexed: 10/31/2023]
Abstract
FKBP22, an Escherichia coli-made peptidyl-prolyl cis-trans isomerase, has shown considerable homology with Mip-like virulence factors. While the C-terminal domain of this enzyme is used for executing catalytic function and binding inhibitor, the N-terminal domain is employed for its dimerization. To precisely determine the underlying factors of FKBP22 dimerization, its structural model, developed using a suitable template, was carefully inspected. The data show that the dimeric FKBP22, like dimeric Mip proteins, has a V-like shape. Further, it dimerizes using 40 amino acid residues including Ile 9, Ile 17, Ile 42, and Ile 65. All of the above Ile residues except Ile 9 are partly conserved in the Mip-like proteins. To confirm the roles of the partly conserved Ile residues, three FKBP22 mutants, constructed by substituting them with an Ala residue, were studied as well. The results together indicate that Ile 65 has little role in maintaining the dimeric state or enzymatic activity of FKBP22. Conversely, both Ile 17 and Ile 42 are essential for preserving the structure, enzymatic activity, and dimerization ability of FKBP22. Ile 42 in particular looks more essential to FKBP22. However, none of these two Ile residues is required for binding the cognate inhibitor. Additional computational studies also indicated the change of V-shape and the dimeric state of FKBP22 due to the Ala substitution at position 42. The ways Ile 17 and Ile 42 protect the structure, function, and dimerization of FKBP22 have been discussed at length.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Soham Seal
- Department of Biological Sciences, Bose Institute, Kolkata, India
| | | | - Soumitra Polley
- Department of Biological Sciences, Bose Institute, Kolkata, India
| | - Debarati Paul
- Department of Biological Sciences, Bose Institute, Kolkata, India
| | | | - Debasmita Sinha
- Department of Biological Sciences, Bose Institute, Kolkata, India
| | - Anindya Dutta
- Department of Biological Sciences, Bose Institute, Kolkata, India
| | | | - Keya Sau
- Department of Biotechnology, Haldia Institute of Technology, Haldia, India
| | | | - Subrata Sau
- Department of Biological Sciences, Bose Institute, Kolkata, India
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4
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Gharemirshamloo FR, Majumder R, Kumar S U, Doss C GP, Bamdad K, Frootan F, Un C. Effects of the pathological E200K mutation on human prion protein: A computational screening and molecular dynamics approach. J Cell Biochem 2023; 124:254-265. [PMID: 36565210 DOI: 10.1002/jcb.30359] [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: 10/10/2022] [Revised: 12/06/2022] [Accepted: 12/08/2022] [Indexed: 12/25/2022]
Abstract
The human prion protein gene (PRNP) is mapped to the short arm of chromosome 20 (20pter-12). Prion disease is associated with mutations in the prion protein-encoding gene sequence. Earlier studies found that the mutation G127V in the PRNP increases protein stability. In contrast, the mutation E200K, which has the highest mutation rate in the prion protein, causes Creutzfeldt-Jakob disease (CJD) in humans and induces protein aggregation. We aimed to identify the structural mechanisms of E200k and G127V mutations causing CJD. We used a variety of bioinformatic algorithms, including SIFT, PolyPhen, I-Mutant, PhD-SNP, and SNP& GO, to predict the association of the E200K mutation with prion disease. MD simulation is performed, and graphs for root mean square deviation, root mean square fluctuation, radius of gyration, DSSP, principal component analysis, porcupine, and free energy landscape are generated to confirm and prove the stability of the wild-type and mutant protein structures. The protein is analyzed for aggregation, and the results indicate more fluctuations in the protein structure during the simulation owing to the E200K mutation; however, the G127V mutation makes the protein structure stable against aggregation during the simulation.
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Affiliation(s)
| | - Ranabir Majumder
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Udhaya Kumar S
- Department of Integrative Biology, Laboratory of Integrative Genomics, School of Bio Sciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, India
| | - George Priya Doss C
- Department of Integrative Biology, Laboratory of Integrative Genomics, School of Bio Sciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, India
| | - Kourosh Bamdad
- Department of Biology, Payame Noor University, Tehran, Iran
| | - Fateme Frootan
- Institute of Agricultural Biotechnology, National Institute of Genetic Engineering & Biotechnology (NIGEB), Tehran, Iran
| | - Cemal Un
- Department of Biology, Division of Molecular Biology, Ege University, Izmir, Turkey
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5
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Yasmin T. In silico comprehensive analysis of coding and non-coding SNPs in human mTOR protein. PLoS One 2022; 17:e0270919. [PMID: 35788771 PMCID: PMC9255762 DOI: 10.1371/journal.pone.0270919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 06/17/2022] [Indexed: 11/21/2022] Open
Abstract
The mammalian/mechanistic target of rapamycin (mTOR) protein is an important growth regulator and has been linked with multiple diseases including cancer and diabetes. Non-synonymous mutations of this gene have already been found in patients with renal clear cell carcinoma, melanoma, and acute lymphoid leukemia among many others. Such mutations can potentially affect a protein’s structure and hence its functions. In this study, therefore, the most deleterious SNPs of mTOR protein have been determined to identify potential biomarkers for various disease treatments. The aim is to generate a structured dataset of the mTOR gene’s SNPs that may prove to be an asset for the identification and treatment of multiple diseases associated with the target gene. Both sequence and structure-based approaches were adopted and a wide variety of bioinformatics tools were applied to analyze the SNPs of mTOR protein. In total 11 nsSNPs have been filtered out of 2178 nsSNPs along with two non-coding variations. All of the nsSNPs were found to destabilize the protein structure and disrupt its function. While R619C, A1513D, and T1977R mutations were shown to alter C alpha distances and bond angles of the mTOR protein, L509Q, R619C and N2043S were predicted to disrupt the mTOR protein’s interaction with NBS1 protein and FKBP1A/rapamycin complex. In addition, one of the non-coding SNPs was shown to alter miRNA binding sites. Characterizing nsSNPs and non-coding SNPs and their harmful effects on a protein’s structure and functions will enable researchers to understand the critical impact of mutations on the molecular mechanisms of various diseases. This will ultimately lead to the identification of potential targets for disease diagnosis and therapeutic interventions.
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Affiliation(s)
- Tahirah Yasmin
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
- * E-mail:
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6
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High-Risk Polymorphisms Associated with the Molecular Function of Human HMGCR Gene Infer the Inhibition of Cholesterol Biosynthesis. BIOMED RESEARCH INTERNATIONAL 2022; 2022:4558867. [PMID: 35707384 PMCID: PMC9192228 DOI: 10.1155/2022/4558867] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 05/13/2022] [Indexed: 11/17/2022]
Abstract
HMG-CoA reductase or HMGCR (3-hydroxy-3-methylglutaryl-CoA reductase) is a rate-limiting enzyme involved in cholesterol biosynthesis. HMGCR plays an important role in the possible occurrence of hypercholesterolemia leading to atherosclerosis and coronary heart disease. This enzyme is a major target for cholesterol-lowering drugs such as "statin" which blocks the synthesis of mevalonate, a precursor for cholesterol biosynthesis. This study is aimed at characterizing deleterious mutations and classifying functional single nucleotide polymorphisms (SNPs) of the HMGCR gene through analysis of functional and structural evaluation, domain association, solvent accessibility, and energy minimization studies. The functional and characterization tools such as SIFT, PolyPhen, SNPs and GO, Panther, I-Mutant, and Pfam along with programming were employed to explore all the available SNPs in the HMGCR gene in the database. Among 6815 SNP entries from different databases, approximately 388 SNPs were found to be missense. Analysis showed that seven missense SNPs are more likely to have deleterious effects. A tertiary model of the mutant protein was constructed to determine the functional and structural effects of the HMGCR mutation. In addition, the location of the mutations suggests that they may have deleterious effects because most of the mutations are residing in the functional domain of the protein. The findings from the analysis predicted that rs147043821 and rs193026499 missense SNPs could cause significant structural and functional instability in the mutated proteins of the HMGCR gene. The findings of the current study will likely be useful in future efforts to uncover the mechanism and cause of hypercholesterolemia. In addition, the identified SNPs of HMGCR gene could set up a strong foundation for further therapeutic discovery.
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Pradhan D, Biswasroy P, Sahu DK, Ghosh G, Rath G. Isolation and structure elucidation of a steroidal moiety from Withania somnifera and in silico evaluation of antimalarial efficacy against artemisinin resistance Plasmodium falciparum kelch 13 protein. J Biomol Struct Dyn 2022:1-14. [PMID: 35585777 DOI: 10.1080/07391102.2022.2077448] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
According to the 2021 Malaria report, 241 million clinical episodes with 627000 deaths penalty was estimated across the worldwide. However, mutation in the propeller domain of Plasmodium falciparum kelch 13 protein resulted in longer parasite clearance time following an artemisinin-based treatment and had a greater survival rate of ring-stage parasites even after a brief exposure to a high dose of artesunate. Clinical manifestations become more complex and worse with the emerging trend of drug resistance against artemisinin derivatives and the poor effectiveness of malaria vaccination drive. Steroidal lactone (withanolide) moiety (C-28) isolated from methanolic leaf extract Withania somnifera show a greater affinity towards Pfkelch 13 protein in comparison to the artemisinin derivatives (artesunate, artemether). The isolated compound was characterized to be withaferin A with a percentage yield of 29.01% w/w in chloroform fraction, 1.75% w/w in methanolic extract, and 0.29% w/w in raw leaf powder. Structure-based analysis shows that withaferin A (docking score -8.253, -9.802) has a higher affinity for two distinct binding pockets I and II of the Plasmodium falciparum kelch 13 protein than artesunate (docking score -4.470, -3.656). Further, Gibbs binding free energy signifies thermodynamic stability of the docked complex of withaferin A (-43.25, -43.76 Kcal/mol) in comparison to artesunate docked complex (-8.49, -5.75 Kcal/mol). The pharmacokinetic profile of withaferin A shows more drug-likeness characteristics without violating Jorgensen's rule of three, and Lipinski's rule of five. Hence above experimental findings suggest withaferin A could be a suitable therapeutic adjunct for preclinical evaluation of antimalarial potentiality in artemisinin-resistant malaria.
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Affiliation(s)
- Deepak Pradhan
- School of Pharmaceutical Sciences, Siksha O Anusandhan (Deemed to be University), Bhubaneswar, India
| | - Prativa Biswasroy
- School of Pharmaceutical Sciences, Siksha O Anusandhan (Deemed to be University), Bhubaneswar, India
| | - Dipak Kumar Sahu
- School of Pharmaceutical Sciences, Siksha O Anusandhan (Deemed to be University), Bhubaneswar, India
| | - Goutam Ghosh
- School of Pharmaceutical Sciences, Siksha O Anusandhan (Deemed to be University), Bhubaneswar, India
| | - Goutam Rath
- School of Pharmaceutical Sciences, Siksha O Anusandhan (Deemed to be University), Bhubaneswar, India
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8
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Vyas B, Bhowmik R, Akhter M, Ahmad FJ. Identification, analysis of deleterious SNPs of the human GSR gene and their effects on the structure and functions of associated proteins and other diseases. Sci Rep 2022; 12:5474. [PMID: 35361806 PMCID: PMC8971378 DOI: 10.1038/s41598-022-09295-6] [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: 11/02/2021] [Accepted: 03/08/2022] [Indexed: 11/27/2022] Open
Abstract
Hereditary glutathione reductase deficiency, caused by mutations of the GSR gene, is an autosomal recessive disorder characterized by decreased glutathione disulfide (GSSG) reduction activity and increased thermal instability. This study implemented computational analysis to screen the most likely mutation that might be associated with hereditary glutathione reductase deficiency and other diseases. Using ten online computational tools, the study revealed four nsSNPs among the 17 nsSNPs identified as most deleterious and disease associated. Structural analyses and evolutionary confirmation study of native and mutant GSR proteins using the HOPE project and ConSruf. HOPE revealed more flexibility in the native GSR structure than in the mutant structure. The mutation in GSR might be responsible for changes in the structural conformation and function of the GSR protein and might also play a significant role in inducing hereditary glutathione reductase deficiency. LD and haplotype studies of the gene revealed that the identified variations rs2978663 and rs8190955 may be responsible for obstructive heart defects (OHDs) and hereditary anemia, respectively. These interethnic differences in the frequencies of SNPs and haplotypes might help explain the unpredictability that has been reported in association studies and can contribute to predicting the pharmacokinetics and pharmacodynamics of drugs that make use of GSR.
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Affiliation(s)
- Bharti Vyas
- School of Interdisciplinary Studies, Jamia Hamdard, New Delhi, India
| | - Ratul Bhowmik
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, 110062, India
| | - Mymoona Akhter
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, 110062, India.
| | - Farhan Jalees Ahmad
- School of Interdisciplinary Studies, Jamia Hamdard, New Delhi, India.,Department of Pharmaceutical Chemistry, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, 110062, India
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Polymeric biocompatible iron oxide nanoparticles labeled with peptides for imaging in ovarian cancer. Biosci Rep 2022; 42:230723. [PMID: 35103283 PMCID: PMC8837818 DOI: 10.1042/bsr20212622] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 01/11/2022] [Accepted: 01/26/2022] [Indexed: 11/17/2022] Open
Abstract
Compared with other nanomaterials, surface-modified iron oxide nanoparticles (IONPs) have gained attraction for cancer therapy applications due to its low toxicity, and long retention time. An innocuous targeting strategy was developed by generation of fluorescein isothiocyanate (FITC)-labeled peptide (growth factor domain (GFD) and somatomedin B domain (SMB)) functionalized, chitosan-coated IONPs (IONPs/C). It can be used to target urokinase plasminogen activator receptor (uPAR), which is a surface biomarker, in ovarian cancer. Binding affinity between uPAR and peptides (GFD and SMB) were revealed by in-silico docking studies. The biophysical characterizations of IONPs, IONPs/C, and IONPs/C/GFD-FITC or SMB-FITC nanoprobes were assessed via Vibrating Sample Magnetometer (VSM), Transmission Electron Microscopy (TEM), Dynamic Light Scattering (DLS), and Fourier Transform Infrared Spectroscopy (FT-IR). Prussian Blue staining, fluorescence spectroscopy, and fluorescence imaging were performed to confirm the targeting of nanoprobes with the surface receptor uPAR. The combination of IONPs/C/GFD+SMB showed efficient targeting of uPAR in the tumor microenvironment, and thus can be implemented as a molecular magnetic nanoprobe for cancer cell imaging and targeting.
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Lim SW, Tan KJ, Azuraidi OM, Sathiya M, Lim EC, Lai KS, Yap WS, Afizan NARNM. Functional and structural analysis of non-synonymous single nucleotide polymorphisms (nsSNPs) in the MYB oncoproteins associated with human cancer. Sci Rep 2021; 11:24206. [PMID: 34921182 PMCID: PMC8683427 DOI: 10.1038/s41598-021-03624-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 11/26/2021] [Indexed: 12/17/2022] Open
Abstract
MYB proteins are highly conserved DNA-binding domains (DBD) and mutations in MYB oncoproteins have been reported to cause aberrant and augmented cancer progression. Identification of MYB molecular biomarkers predictive of cancer progression can be used for improving cancer management. To address this, a biomarker discovery pipeline was employed in investigating deleterious non-synonymous single nucleotide polymorphisms (nsSNPs) in predicting damaging and potential alterations on the properties of proteins. The nsSNP of the MYB family; MYB, MYBL1, and MYBL2 was extracted from the NCBI database. Five in silico tools (PROVEAN, SIFT, PolyPhen-2, SNPs&GO and PhD-SNP) were utilized to investigate the outcomes of nsSNPs. A total of 45 nsSNPs were predicted as high-risk and damaging, and were subjected to PMut and I-Mutant 2.0 for protein stability analysis. This resulted in 32 nsSNPs with decreased stability with a DDG score lower than - 0.5, indicating damaging effect. G111S, N183S, G122S, and S178C located within the helix-turn-helix (HTH) domain were predicted to be conserved, further posttranslational modifications and 3-D protein analysis indicated these nsSNPs to shift DNA-binding specificity of the protein thus altering the protein function. Findings from this study would help in the field of pharmacogenomic and cancer therapy towards better intervention and management of cancer.
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Affiliation(s)
- Shu Wen Lim
- Faculty of Applied Sciences, UCSI University, No. 1, Jalan Menara Gading UCSI Height, 56000, Cheras, Kuala Lumpur, Malaysia
| | - Kennet JunKai Tan
- Faculty of Applied Sciences, UCSI University, No. 1, Jalan Menara Gading UCSI Height, 56000, Cheras, Kuala Lumpur, Malaysia
| | - Osman Mohd Azuraidi
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, 43400, Serdang, Selangor, Malaysia
| | - Maran Sathiya
- School of Pharmacy, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor, Malaysia
| | - Ee Chen Lim
- Faculty of Applied Sciences, UCSI University, No. 1, Jalan Menara Gading UCSI Height, 56000, Cheras, Kuala Lumpur, Malaysia
| | - Kok Song Lai
- Health Sciences Division, Abu Dhabi Women's College, Higher Colleges of Technology, 41012, Abu Dhabi, United Arab Emirates
| | - Wai-Sum Yap
- Faculty of Applied Sciences, UCSI University, No. 1, Jalan Menara Gading UCSI Height, 56000, Cheras, Kuala Lumpur, Malaysia.
| | - Nik Abd Rahman Nik Mohd Afizan
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, 43400, Serdang, Selangor, Malaysia.
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11
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Integrative Bioinformatics approaches to therapeutic gene target selection in various cancers for Nitroglycerin. Sci Rep 2021; 11:22036. [PMID: 34764329 PMCID: PMC8586365 DOI: 10.1038/s41598-021-01508-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 07/27/2021] [Indexed: 12/30/2022] Open
Abstract
Integrative Bioinformatics analysis helps to explore various mechanisms of Nitroglycerin activity in different types of cancers and help predict target genes through which Nitroglycerin affect cancers. Many publicly available databases and tools were used for our study. First step in this study is identification of Interconnected Genes. Using Pubchem and SwissTargetPrediction Direct Target Genes (activator, inhibitor, agonist and suppressor) of Nitroglycerin were identified. PPI network was constructed to identify different types of cancers that the 12 direct target genes affected and the Closeness Coefficient of the direct target genes so identified. Pathway analysis was performed to ascertain biomolecules functions for the direct target genes using CluePedia App. Mutation Analysis revealed Mutated Genes and types of cancers that are affected by the mutated genes. While the PPI network construction revealed the types of cancer that are affected by 12 target genes this step reveals the types of cancers affected by mutated cancers only. Only mutated genes were chosen for further study. These mutated genes were input into STRING to perform NW Analysis. NW Analysis revealed Interconnected Genes within the mutated genes as identified above. Second Step in this study is to predict and identify Upregulated and Downregulated genes. Data Sets for the identified cancers from the above procedure were obtained from GEO Database. DEG Analysis on the above Data sets was performed to predict Upregulated and Downregulated genes. A comparison of interconnected genes identified in step 1 with Upregulated and Downregulated genes obtained in step 2 revealed Co-Expressed Genes among Interconnected Genes. NW Analysis using STRING was performed on Co-Expressed Genes to ascertain Closeness Coefficient of Co-Expressed genes. Gene Ontology was performed on Co-Expressed Genes to ascertain their Functions. Pathway Analysis was performed on Co-Expressed Genes to identify the Types of Cancers that are influenced by co-expressed genes. The four types of cancers identified in Mutation analysis in step 1 were the same as the ones that were identified in this pathway analysis. This further corroborates the 4 types of cancers identified in Mutation analysis. Survival Analysis was done on the co-expressed genes as identified above using Survexpress. BIOMARKERS for Nitroglycerin were identified for four types of cancers through Survival Analysis. The four types of cancers are Bladder cancer, Endometrial cancer, Melanoma and Non-small cell lung cancer.
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12
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Rahman MM, Junaid M, Hosen SMZ, Mostafa M, Liu L, Benkendorff K. Mollusc-Derived Brominated Indoles for the Selective Inhibition of Cyclooxygenase: A Computational Expedition. Molecules 2021; 26:molecules26216538. [PMID: 34770946 PMCID: PMC8587571 DOI: 10.3390/molecules26216538] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/25/2021] [Accepted: 10/25/2021] [Indexed: 11/16/2022] Open
Abstract
Inflammation plays an important role in different chronic diseases. Brominated indoles derived from the Australian marine mollusk Dicathais orbita (D. orbita) are of interest for their anti-inflammatory properties. This study evaluates the binding mechanism and potentiality of several brominated indoles (tyrindoxyl sulfate, tyrindoleninone, 6-bromoisatin, and 6,6′-dibromoindirubin) against inflammatory mediators cyclooxygenases-1/2 (COX-1/2) using molecular docking, followed by molecular dynamics simulation, along with physicochemical, drug-likeness, pharmacokinetic (pk), and toxicokinetic (tk) properties. Molecular docking identified that these indole compounds are anchored, with the main amino acid residues, positioned in the binding pocket of the COX-1/2, required for selective inhibition. Moreover, the molecular dynamics simulation based on root mean square deviation (RMSD), radius of gyration (Rg), solvent accessible surface area (SASA), and root mean square fluctuation (RMSF) analyses showed that these natural brominated molecules transit rapidly to a progressive constant configuration during binding with COX-1/2 and seem to accomplish a consistent dynamic behavior by maintaining conformational stability and compactness. The results were comparable to the Food and Drug Administration (FDA)-approved selective COX inhibitor, aspirin. Furthermore, the free energy of binding for the compounds assessed by molecular mechanics–Poisson–Boltzmann surface area (MM–PBSA) confirmed the binding capacity of indoles towards COX-1/2, with suitable binding energy values except for the polar precursor tyrindoxyl sulfate (with COX-1). The physicochemical and drug-likeness analysis showed zero violations of Lipinski’s rule, and the compounds are predicted to have excellent pharmacokinetic profiles. These indoles are projected to be non-mutagenic and free from hepatotoxicity, with no inhibition of human ether-a-go–go gene (hERG) I inhibitors, and the oral acute toxicity LD50 in rats is predicted to be similar or lower than aspirin. Overall, this work has identified a plausible mechanism for selective COX inhibition by natural marine indoles as potential therapeutic candidates for the mitigation of inflammation.
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Affiliation(s)
- Md. Mominur Rahman
- Marine Ecology Research Centre, Faculty of Science and Engineering, Southern Cross University, Lismore, NSW 2480, Australia;
| | - Md. Junaid
- Molecular Modeling Drug-design and Discovery Laboratory, Pharmacology Research Division, BCSIR Laboratories Chattogram, Bangladesh Council of Scientific and Industrial Research, Chattogram 4217, Bangladesh; (M.J.); (S.M.Z.H.); (M.M.)
| | - S. M. Zahid Hosen
- Molecular Modeling Drug-design and Discovery Laboratory, Pharmacology Research Division, BCSIR Laboratories Chattogram, Bangladesh Council of Scientific and Industrial Research, Chattogram 4217, Bangladesh; (M.J.); (S.M.Z.H.); (M.M.)
- Pancreatic Research Group, South Western Sydney Clinical School, and Ingham Institute for AppliedMedical Research, Faculty of Medicine, University of New South Wales, Sydney, NSW 2052, Australia
| | - Mohammad Mostafa
- Molecular Modeling Drug-design and Discovery Laboratory, Pharmacology Research Division, BCSIR Laboratories Chattogram, Bangladesh Council of Scientific and Industrial Research, Chattogram 4217, Bangladesh; (M.J.); (S.M.Z.H.); (M.M.)
| | - Lei Liu
- Southern Cross Plant Science, Faculty of Science and Engineering, Southern Cross University, Lismore, NSW 2480, Australia;
| | - Kirsten Benkendorff
- Marine Ecology Research Centre, Faculty of Science and Engineering, Southern Cross University, Lismore, NSW 2480, Australia;
- National Marine Science Centre, Faculty of Science and Engineering, Southern Cross University, Coffs Harbour, NSW 2450, Australia
- Correspondence:
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13
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Khoruddin NA, Noorizhab MN, Teh LK, Mohd Yusof FZ, Salleh MZ. Pathogenic nsSNPs that increase the risks of cancers among the Orang Asli and Malays. Sci Rep 2021; 11:16158. [PMID: 34373545 PMCID: PMC8352870 DOI: 10.1038/s41598-021-95618-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Accepted: 07/26/2021] [Indexed: 02/07/2023] Open
Abstract
Single-nucleotide polymorphisms (SNPs) are the most common genetic variations for various complex human diseases, including cancers. Genome-wide association studies (GWAS) have identified numerous SNPs that increase cancer risks, such as breast cancer, colorectal cancer, and leukemia. These SNPs were cataloged for scientific use. However, GWAS are often conducted on certain populations in which the Orang Asli and Malays were not included. Therefore, we have developed a bioinformatic pipeline to mine the whole-genome sequence databases of the Orang Asli and Malays to determine the presence of pathogenic SNPs that might increase the risks of cancers among them. Five different in silico tools, SIFT, PROVEAN, Poly-Phen-2, Condel, and PANTHER, were used to predict and assess the functional impacts of the SNPs. Out of the 80 cancer-related nsSNPs from the GWAS dataset, 52 nsSNPs were found among the Orang Asli and Malays. They were further analyzed using the bioinformatic pipeline to identify the pathogenic variants. Three nsSNPs; rs1126809 (TYR), rs10936600 (LRRC34), and rs757978 (FARP2), were found as the most damaging cancer pathogenic variants. These mutations alter the protein interface and change the allosteric sites of the respective proteins. As TYR, LRRC34, and FARP2 genes play important roles in numerous cellular processes such as cell proliferation, differentiation, growth, and cell survival; therefore, any impairment on the protein function could be involved in the development of cancer. rs1126809, rs10936600, and rs757978 are the important pathogenic variants that increase the risks of cancers among the Orang Asli and Malays. The roles and impacts of these variants in cancers will require further investigations using in vitro cancer models.
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Affiliation(s)
- Nurul Ain Khoruddin
- Integrative Pharmacogenomics Institute (iPROMISE), Universiti Teknologi MARA (UiTM), Selangor Branch, Puncak Alam Campus, 42300, Puncak Alam, Selangor, Malaysia
- Faculty of Applied Sciences, Universiti Teknologi MARA (UiTM), Shah Alam Campus, Selangor, Malaysia
| | - Mohd NurFakhruzzaman Noorizhab
- Integrative Pharmacogenomics Institute (iPROMISE), Universiti Teknologi MARA (UiTM), Selangor Branch, Puncak Alam Campus, 42300, Puncak Alam, Selangor, Malaysia
- Faculty of Pharmacy, Universiti Teknologi MARA (UiTM), Selangor Branch, Puncak Alam Campus, 42300, Puncak Alam, Selangor, Malaysia
| | - Lay Kek Teh
- Integrative Pharmacogenomics Institute (iPROMISE), Universiti Teknologi MARA (UiTM), Selangor Branch, Puncak Alam Campus, 42300, Puncak Alam, Selangor, Malaysia
- Faculty of Pharmacy, Universiti Teknologi MARA (UiTM), Selangor Branch, Puncak Alam Campus, 42300, Puncak Alam, Selangor, Malaysia
| | - Farida Zuraina Mohd Yusof
- Integrative Pharmacogenomics Institute (iPROMISE), Universiti Teknologi MARA (UiTM), Selangor Branch, Puncak Alam Campus, 42300, Puncak Alam, Selangor, Malaysia
- Faculty of Applied Sciences, Universiti Teknologi MARA (UiTM), Shah Alam Campus, Selangor, Malaysia
| | - Mohd Zaki Salleh
- Integrative Pharmacogenomics Institute (iPROMISE), Universiti Teknologi MARA (UiTM), Selangor Branch, Puncak Alam Campus, 42300, Puncak Alam, Selangor, Malaysia.
- Faculty of Pharmacy, Universiti Teknologi MARA (UiTM), Selangor Branch, Puncak Alam Campus, 42300, Puncak Alam, Selangor, Malaysia.
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14
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Ezaj MMA, Junaid M, Akter Y, Nahrin A, Siddika A, Afrose SS, Nayeem SMA, Haque MS, Moni MA, Hosen SMZ. Whole proteome screening and identification of potential epitopes of SARS-CoV-2 for vaccine design-an immunoinformatic, molecular docking and molecular dynamics simulation accelerated robust strategy. J Biomol Struct Dyn 2021; 40:6477-6502. [PMID: 33586620 DOI: 10.1080/07391102.2021.1886171] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the most cryptic pandemic outbreak of the 21st century, has gripped more than 1.8 million people to death and infected almost eighty six million. As it is a new variant of SARS, there is no approved drug or vaccine available against this virus. This study aims to predict some promising cytotoxic T lymphocyte epitopes in the SARS-CoV-2 proteome utilizing immunoinformatic approaches. Firstly, we identified 21 epitopes from 7 different proteins of SARS-CoV-2 inducing immune response and checked for allergenicity and conservancy. Based on these factors, we selected the top three epitopes, namely KAYNVTQAF, ATSRTLSYY, and LTALRLCAY showing functional interactions with the maximum number of MHC alleles and no allergenicity. Secondly, the 3D model of selected epitopes and HLA-A*29:02 were built and Molecular Docking simulation was performed. Most interestingly, the best two epitopes predicted by docking are part of two different structural proteins of SARS-CoV-2, namely Membrane Glycoprotein (ATSRTLSYY) and Nucleocapsid Phosphoprotein (KAYNVTQAF), which are generally target of choice for vaccine designing. Upon Molecular Docking, interactions between selected epitopes and HLA-A*29:02 were further validated by 50 ns Molecular Dynamics (MD) simulation. Analysis of RMSD, Rg, SASA, number of hydrogen bonds, RMSF, MM-PBSA, PCA, and DCCM from MD suggested that ATSRTLSYY is the most stable and promising epitope than KAYNVTQAF epitope. Moreover, we also identified B-cell epitopes for each of the antigenic proteins of SARS CoV-2. Findings of our work will be a good resource for wet lab experiments and will lessen the timeline for vaccine construction.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Md Muzahid Ahmed Ezaj
- Department of Genetic Engineering and Biotechnology, University of Chittagong, Chattogram, Bangladesh.,Reverse Vaccinology Research Division, Advanced Bioinformatics, Computational Biology and Data Science Laboratory, Chattogram, Bangladesh
| | - Md Junaid
- Reverse Vaccinology Research Division, Advanced Bioinformatics, Computational Biology and Data Science Laboratory, Chattogram, Bangladesh.,Molecular Modeling Drug-design and Discovery Laboratory, Pharmacology Research Division, BCSIR Laboratories Chattogram, Bangladesh Council of Scientific and Industrial Research, Chattogram, Bangladesh
| | - Yeasmin Akter
- Reverse Vaccinology Research Division, Advanced Bioinformatics, Computational Biology and Data Science Laboratory, Chattogram, Bangladesh.,Department of Biotechnology & Genetic Engineering, Noakhali Science & Technology University, Noakhali, Bangladesh
| | - Afsana Nahrin
- Department of Pharmacy, University of Science and Technology Chittagong, Chattogram, Bangladesh
| | - Aysha Siddika
- Reverse Vaccinology Research Division, Advanced Bioinformatics, Computational Biology and Data Science Laboratory, Chattogram, Bangladesh.,Department of Chemistry, University of Chittagong, Chattogram, Bangladesh
| | - Syeda Samira Afrose
- Reverse Vaccinology Research Division, Advanced Bioinformatics, Computational Biology and Data Science Laboratory, Chattogram, Bangladesh.,Department of Chemistry, University of Chittagong, Chattogram, Bangladesh
| | - S M Abdul Nayeem
- Reverse Vaccinology Research Division, Advanced Bioinformatics, Computational Biology and Data Science Laboratory, Chattogram, Bangladesh.,Department of Chemistry, University of Chittagong, Chattogram, Bangladesh
| | - Md Sajedul Haque
- Department of Chemistry, University of Chittagong, Chattogram, Bangladesh
| | - Mohammad Ali Moni
- WHO Collaborating Centre on eHealth, UNSW Digital Health, School of Public Health and Community Medicine, Faculty of Medicine, UNSW Sydney, Sydney, NSW, Australia
| | - S M Zahid Hosen
- Molecular Modeling Drug-design and Discovery Laboratory, Pharmacology Research Division, BCSIR Laboratories Chattogram, Bangladesh Council of Scientific and Industrial Research, Chattogram, Bangladesh.,Pancreatic Research Group, South Western Sydney Clinical School, and Ingham Institute for Applied Medical Research, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
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15
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S UK, R B, D TK, Doss CGP, Zayed H. Mutational landscape of K-Ras substitutions at 12th position-a systematic molecular dynamics approach. J Biomol Struct Dyn 2020; 40:1571-1585. [PMID: 33034275 DOI: 10.1080/07391102.2020.1830177] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
K-Ras is a small GTPase and acts as a molecular switch by recruiting GEFs and GAPs, and alternates between the inert GDP-bound and the dynamic GTP-bound forms. The amino acid at position 12 of K-Ras is a hot spot for oncogenic mutations (G12A, G12C, G12D, G12R, G12S, and G12V), disturbing the active fold of the protein, leading to cancer development. This study aimed to investigate the potential conformational changes induced by these oncogenic mutations at the 12th position, impairing GAP-mediated GTP hydrolysis. Comprehensive computational tools (iStable, FoldX, SNPeffect, DynaMut, and CUPSAT) were used to evaluate the effect of these six mutations on the stability of wild type K-Ras protein. The docking of GTP with K-Ras was carried out using AutoDock4.2, followed by molecular dynamics simulations. Furthermore, on comparison of binding energies between the wild type K-Ras and the six mutants, we have demonstrated that the G12A and G12V mutants exhibited the strongest binding efficiency compared to the other four mutants. Trajectory analyses of these mutations revealed that G12A encountered the least deviation, fluctuation, intermolecular H-bonds, and compactness compared to the wildtype, which was supported by the lower Gibbs free energy value. Our study investigates the molecular dynamics simulations of the mutant K-Ras forms at the 12th position, which expects to provide insights about the molecular mechanisms involved in cancer development, and may serve as a platform for targeted therapies against cancer. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Udhaya Kumar S
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Bithia R
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Thirumal Kumar D
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - C George Priya Doss
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Hatem Zayed
- Department of Biomedical Sciences, College of Health and Sciences, Qatar University, Doha, Qatar
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16
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Singh A, Thakur M, Singh SK, Sharma LK, Chandra K. Exploring the effect of nsSNPs in human YPEL3 gene in cellular senescence. Sci Rep 2020; 10:15301. [PMID: 32943700 PMCID: PMC7498449 DOI: 10.1038/s41598-020-72333-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Accepted: 08/28/2020] [Indexed: 12/19/2022] Open
Abstract
YPEL3 that induces cellular senescence in both normal and tumour cells of humans may show altered expression under the influence of incidental mutations. In this study, we proposed the first structure of Native YPEL3 protein and its five possible deleterious mutants—V40M, C61Y, G98R, G108S, and A131T and predicted their deleterious effects to alter stability, flexibility and conformational changes in the protein. The MD simulation (RMSD, RMSF, Rg, h-bond and SASA) analysis revealed that the variants V40M, G98R and G108S increased the flexibility in protein, and variant V40M imparted more compactness to the protein.. In general, variants attributed changes in the native conformation and structure of the YPEL3 protein which might affect the native function of cellular senescence. The study provides opportunities for health professionals and practitioners in formulating précised medicines to effectively cure various cancers. We propose in-vitro or in-vivo studies should consider these reported nsSNPs while examining any malfunction in the YPEL3 protein.
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Affiliation(s)
- Abhishek Singh
- Zoological Survey of India, New Alipore, Kolkata, 700053, India.
| | - Mukesh Thakur
- Zoological Survey of India, New Alipore, Kolkata, 700053, India.
| | | | | | - Kailash Chandra
- Zoological Survey of India, New Alipore, Kolkata, 700053, India
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17
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Alzahrani FA, Ahmed F, Sharma M, Rehan M, Mahfuz M, Baeshen MN, Hawsawi Y, Almatrafi A, Alsagaby SA, Kamal MA, Warsi MK, Choudhry H, Jamal MS. Investigating the pathogenic SNPs in BLM helicase and their biological consequences by computational approach. Sci Rep 2020; 10:12377. [PMID: 32704157 PMCID: PMC7378827 DOI: 10.1038/s41598-020-69033-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 07/06/2020] [Indexed: 12/15/2022] Open
Abstract
The BLM helicase protein plays a vital role in DNA replication and the maintenance of genomic integrity. Variation in the BLM helicase gene resulted in defects in the DNA repair mechanism and was reported to be associated with Bloom syndrome (BS) and cancer. Despite extensive investigation of helicase proteins in humans, no attempt has previously been made to comprehensively analyse the single nucleotide polymorphism (SNPs) of the BLM gene. In this study, a comprehensive analysis of SNPs on the BLM gene was performed to identify, characterize and validate the pathogenic SNPs using computational approaches. We obtained SNP data from the dbSNP database version 150 and mapped these data to the genomic coordinates of the "NM_000057.3" transcript expressing BLM helicase (P54132). There were 607 SNPs mapped to missense, 29 SNPs mapped to nonsense, and 19 SNPs mapped to 3'-UTR regions. Initially, we used many consensus tools of SIFT, PROVEAN, Condel, and PolyPhen-2, which together increased the accuracy of prediction and identified 18 highly pathogenic non-synonymous SNPs (nsSNPs) out of 607 SNPs. Subsequently, these 18 high-confidence pathogenic nsSNPs were analysed for BLM protein stability, structure-function relationships and disease associations using various bioinformatics tools. These 18 mutants of the BLM protein along with the native protein were further investigated using molecular dynamics simulations to examine the structural consequences of the mutations, which might reveal their malfunction and contribution to disease. In addition, 28 SNPs were predicted as "stop gained" nonsense SNPs and one SNP was predicted as "start lost". Two SNPs in the 3'UTR were found to abolish miRNA binding and thus may enhance the expression of BLM. Interestingly, we found that BLM mRNA overexpression is associated with different types of cancers. Further investigation showed that the dysregulation of BLM is associated with poor overall survival (OS) for lung and gastric cancer patients and hence led to the conclusion that BLM has the potential to be used as an important prognostic marker for the detection of lung and gastric cancer.
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Affiliation(s)
- Faisal A Alzahrani
- Department of Biochemistry, Faculty of Science, Stem Cells Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
- Aston Medical Research Institute, Aston Medical School, Aston University, Birmingham, B4 7ET, UK
| | - Firoz Ahmed
- Department of Biochemistry, College of Science, University of Jeddah, Jeddah, 21589, Saudi Arabia.
- University of Jeddah Centre for Scientific and Medical Research (UJ-CSMR), University of Jeddah, Jeddah, 21589, Saudi Arabia.
| | - Monika Sharma
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER), Mohali, India
| | - Mohd Rehan
- King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Maryam Mahfuz
- Department of Computer Science, Jamia Millia Islamia, New Delhi, Delhi, India
| | - Mohammed N Baeshen
- Department of Biology, College of Science, University of Jeddah, Jeddah, 21589, Saudi Arabia
| | - Yousef Hawsawi
- Department of Genetics, Research Center, King Faisal Specialist Hospital, and Research Center, MBC-03, PO Box 3354, Riyadh, 11211, Saudi Arabia
| | - Ahmed Almatrafi
- Department of Biology, Faculty of Science, University of Taibah, Medinah, Saudi Arabia
| | - Suliman Abdallah Alsagaby
- Department of Medical Laboratories, Central Biosciences Research Laboratories, College of Science in Al Zulfi, Majmaah University, Al Majma'ah, Saudi Arabia
| | - Mohammad Azhar Kamal
- Department of Biochemistry, College of Science, University of Jeddah, Jeddah, 21589, Saudi Arabia
- University of Jeddah Centre for Scientific and Medical Research (UJ-CSMR), University of Jeddah, Jeddah, 21589, Saudi Arabia
| | - Mohiuddin Khan Warsi
- Department of Biochemistry, College of Science, University of Jeddah, Jeddah, 21589, Saudi Arabia
- University of Jeddah Centre for Scientific and Medical Research (UJ-CSMR), University of Jeddah, Jeddah, 21589, Saudi Arabia
| | - Hani Choudhry
- Department of Biochemistry, Cancer Metabolism and Epigenetic Unit, Faculty of Science, Cancer and Mutagenesis Unit, King Fahd Center for Medical Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mohammad Sarwar Jamal
- King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia.
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.
- Integrative Biosciences Center, Wayne State University, Detroit, MI, 48202, USA.
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18
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Chatterjee S, Salimi A, Lee JY. Insights into amyotrophic lateral sclerosis linked Pro525Arg mutation in the fused in sarcoma protein through in silico analysis and molecular dynamics simulation. J Biomol Struct Dyn 2020; 39:5963-5976. [DOI: 10.1080/07391102.2020.1794967] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
| | - Abbas Salimi
- Department of Chemistry, Sungkyunkwan University, Suwon, Korea
| | - Jin Yong Lee
- Department of Chemistry, Sungkyunkwan University, Suwon, Korea
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19
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Rohini K, Ramanathan K, Shanthi V. Multi-Dimensional Screening Strategy for Drug Repurposing with Statistical Framework—A New Road to Influenza Drug discovery. Cell Biochem Biophys 2019; 77:319-333. [DOI: 10.1007/s12013-019-00887-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Accepted: 09/16/2019] [Indexed: 12/17/2022]
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20
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Mallick B, Sharma AR, Lee SS, Chakraborty C. Understanding the molecular interaction of human argonaute-2 and miR-20a complex: A molecular dynamics approach. J Cell Biochem 2019; 120:19915-19924. [PMID: 31318096 DOI: 10.1002/jcb.29300] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 06/18/2019] [Indexed: 12/16/2022]
Abstract
Argonaute-2 (AGO2), a member of the Argonaute family, is the only member possessing catalytic and RNA silencing activity. In here, a molecular dynamics (MDs) simulation was performed using the crystal structure of human AGO2 protein complex with miR-20a. miR-20a is involved with various kind of biological process like heart and lung development, oncogenic process, etc. In precise, MD simulation was carried out with AGO2 protein complex with wild type, two mutant sites and four mutant sites in guided microRNA (miRNA). It has been noted that root-mean-square deviation (RMSD) of atomic positions of nucleic acid for wild type and two mutant sites guided miRNA has the same pattern of fluctuations, which stabilizes around 0.27 nm after 2 ns. Cα atom of AGO2 protein in the complex shows that this complex with wild type and two mutant site mutation duplex has a stable RMSD value after 20 ns, ranging between 0.14 and 0.21 nm. From the root-mean-square fluctuation (RMSF), we observed an increased pattern of fluctuations for the atoms of four mutant complex of AGO2-miR-20a complex. This increased RMSF of non-mutated nucleic acids is contributed by U-A bond breaking at the site of the nucleotide of U2 of guided miRNA, as observed from the duplex structure taken at different time steps of the simulation. Superimposed structure of the miRNA-mRNA duplex for the three complexes depicts that the three miRNA-mRNA duplexes are stable during the simulation. Current work demonstrates the possible correlations between the conformational changes of this AGO2-miR-20a duplex structure and the interactions of different atoms.
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Affiliation(s)
- Bidyut Mallick
- Departments of Physics, Galgotias College of Engineering and Technology, Greater Noida, India
| | - Ashish Ranjan Sharma
- Institute for Skeletal Aging & Orthopedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon, Gangwon-Do, Republic of Korea
| | - Sang-Soo Lee
- Institute for Skeletal Aging & Orthopedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon, Gangwon-Do, Republic of Korea
| | - Chiranjib Chakraborty
- Institute for Skeletal Aging & Orthopedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon, Gangwon-Do, Republic of Korea.,Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Kolkata, West Bengal, India
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21
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Gopalakrishnan C, Al-Subaie AM, N N, Yeh HY, Tayubi IA, Kamaraj B. Prioritization of SNPs in y+LAT-1 culpable of Lysinuric protein intolerance and their mutational impacts using protein-protein docking and molecular dynamics simulation studies. J Cell Biochem 2019; 120:18496-18508. [PMID: 31211457 DOI: 10.1002/jcb.29172] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 05/21/2019] [Accepted: 05/23/2019] [Indexed: 12/18/2022]
Abstract
Lysinuric protein intolerance (LPI) is a rare, yet inimical, genetic disorder characterized by the paucity of essential dibasic amino acids in the cells. Amino acid transporter y+LAT-1 interacts with 4F2 cell-surface antigen heavy chain to transport the required dibasic amino acids. Mutation in y+LAT-1 is rumored to cause LPI. However, the underlying pathological mechanism is unknown, and, in this analysis, we investigate the impact of point mutation in y+LAT-1's interaction with 4F2 cell-surface antigen heavy chain in causing LPI. Using an efficient and extensive computational pipeline, we have isolated M50K and L334R single-nucleotide polymorphisms to be the most deleterious mutations in y+LAT-1s. Docking of mutant y+LAT-1 with 4F2 cell-surface antigen heavy chain showed decreased interaction compared with native y+LAT-1. Further, molecular dynamic simulation analysis reveals that the protein molecules increase in size, become more flexible, and alter their secondary structure upon mutation. We believe that these conformational changes because of mutation could be the reason for decreased interaction with 4F2 cell-surface antigen heavy chain causing LPI. Our analysis gives pathological insights about LPI and helps researchers to better understand the disease mechanism and develop an effective treatment strategy.
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Affiliation(s)
| | - Abeer Mohammed Al-Subaie
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Nagasundaram N
- School of Humanities, Nanyang Technological University, Singapore
| | - Hui-Yuan Yeh
- School of Humanities, Nanyang Technological University, Singapore
| | - Iftikhar Alam Tayubi
- Faculty of Computing and Information Technology, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Balu Kamaraj
- Department of Neuroscience Technology, Imam Abdulrahman Bin Faisal University, Jubail, Saudi Arabia
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22
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John A, Sivashanmugam M, Natarajan SK, Umashankar V. Computational modeling of novel inhibitory peptides targeting proteoglycan like region of carbonic anhydrase IX and in vitro validation in HeLa cells. J Biomol Struct Dyn 2019; 38:1995-2006. [PMID: 31146646 DOI: 10.1080/07391102.2019.1623075] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Carbonic anhydrase IX (CAIX) is a tumour-associated, hypoxia-induced, membrane-bound metallo-enzyme which catalyzes the reversible hydration of carbon dioxide (CO2) to bicarbonate (HCO3-) and proton (H+) ions. Over expression of CAIX is observed in cancers of colon, lung, kidney, breast, etc. CAIX plays a vital role in maintaining favourable intracellular pH for tumour cell growth and extracellular acidification which in-turn leads to drug resistance and spread of factors influencing tumour invasion. The N-terminal proteoglycan (PG) - like fragment of CAIX is unique to this isoform and is considered as potential druggable hotspot. Recently, M75 monoclonal antibody targeting the LPGEEDLPG epitope of PG like region has been proposed to reduce cellular adhesion in cancer cells. LPGEEDLPG fragment in complex with M75 has been crystallized and it serves as a strong base for development of peptide inhibitors based on interacting interfaces. Thus, in this study, an in-depth analysis of intermolecular interactions in LPGEEDLPG-M75 complex was carried out by implementing extensive molecular dynamics simulations, binding free energy calculations so as to infer the major determinant fragments of M75 that can be used as peptide inhibitors targeting PG region. Based on these analyses, 3 peptides (Pep1, Pep2 and Pep3) were synthesized and validated by in vitro assays involving cytotoxicity assessment, CAIX inhibition analysis through Direct and Indirect functional assays, and inhibition of Cell adhesion in HeLa cells. The results reveal Pep1 to be a promising inhibitor as it could efficiently modulate CAIX mediated pH homeostasis and cell adhesion in cancer cells.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Arun John
- Centre for Bioinformatics, Kamalnayan Bajaj Institute for Research in Vision and Ophthalmology, Vision Research Foundation, Sankara Nethralaya, Chennai, India.,School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, India
| | - Muthukumaran Sivashanmugam
- Centre for Bioinformatics, Kamalnayan Bajaj Institute for Research in Vision and Ophthalmology, Vision Research Foundation, Sankara Nethralaya, Chennai, India
| | - Sulochana Konerirajapuram Natarajan
- R.S. Mehta Jain Department of Biochemistry and Cell Biology, Kamalnayan Bajaj Institute for Research in Vision and Ophthalmology, Vision Research Foundation, Sankara Nethralaya, Chennai, India
| | - Vetrivel Umashankar
- Centre for Bioinformatics, Kamalnayan Bajaj Institute for Research in Vision and Ophthalmology, Vision Research Foundation, Sankara Nethralaya, Chennai, India
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23
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Zhang B, Wu Q, Xu R, Hu X, Sun Y, Wang Q, Ju F, Ren S, Zhang C, Qi F, Ma Q, Wang Z, Zhou YL. The promising novel biomarkers and candidate small molecule drugs in lower-grade glioma: Evidence from bioinformatics analysis of high-throughput data. J Cell Biochem 2019; 120:15106-15118. [PMID: 31020692 DOI: 10.1002/jcb.28773] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2018] [Revised: 03/21/2019] [Accepted: 04/01/2019] [Indexed: 01/12/2023]
Abstract
Overall survival of patients with low-grade glioma (LGG) has shown no significant improvement over the past 30 years, with survival averaging approximately 7 years. This study aimed to identify novel promising biomarkers of LGG and reveal its potential molecular mechanisms by integrated bioinformatics analysis. The microarray datasets of GSE68848 and GSE4290 were selected from GEO database for integrated analysis. In total, 293 overlapping differentially expressed genes (DEGs) were detected using the limma package. One hundred and eighty-eight nodes with 603 interactions were obtained from the establishment of protein-protein interaction (PPI) network. Functional and signaling pathway enriched were significantly correlated with the synapse and calcium signaling pathway, respectively. Module analysis revealed eight hub genes with high connectivity, which included CHRM1, DLG2, GABRD, GRIN1, HTR2A, KCNJ3, KCNJ9, and NUSAP1, and they were markedly correlated with patients' prognosis. The mining of the Gene Expression Profiling Interactive Analysis database and qPCR further confirmed the abnormal expression of these key genes with their prognostic value in LGG. We eventually predicted the 20 most vital small molecule drugs, which potentially reverse the carcinogenic state of LGG, as per the CMap (connectivity map) database and these DEGs, and MS-275 (enrichment score = -0.939) was considered as the most promising small molecule to treat LGG. In conclusion, our study provided eight reliable novel molecular biomarkers for diagnosis, prognosis prediction, and treatment targets for LGG. These conclusions will contribute to a better comprehension of molecular mechanisms fundamental to LGG occurrence and progression, and providing new insights for future development of genomic individualized treatment in LGG.
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Affiliation(s)
- Bo Zhang
- Medical School, Nantong University, Nantong, P.R. China.,The Hand Surgery Research Center, Department of Hand Surgery, Affiliated Hospital of Nantong University, Nantong, P.R. China
| | - Qiong Wu
- Medical School, Nantong University, Nantong, P.R. China.,The Hand Surgery Research Center, Department of Hand Surgery, Affiliated Hospital of Nantong University, Nantong, P.R. China
| | - Ran Xu
- Medical School, Nantong University, Nantong, P.R. China
| | - Xinyi Hu
- Department of Medicine, Nantong University Xinling college, Nantong, Jiangsu, P.R. China
| | - Yidan Sun
- Department of Oncology, First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, P.R. China
| | - Qiuhong Wang
- The Hand Surgery Research Center, Department of Hand Surgery, Affiliated Hospital of Nantong University, Nantong, P.R. China
| | - Fei Ju
- The Hand Surgery Research Center, Department of Hand Surgery, Affiliated Hospital of Nantong University, Nantong, P.R. China
| | - Shiqi Ren
- Department of Medicine, Nantong University Xinling college, Nantong, Jiangsu, P.R. China
| | - Chenlin Zhang
- Department of Spine, Wuxi Hospital Affiliated to Nanjing University of Chinese Medicine, Wuxi, P.R. China
| | - Fuwei Qi
- Department of Anesthesiology, The First People's Hospital of Taicang City, Taicang Affiliated Hospital of Soochow University, Suzhou, P.R. China
| | - Qianqian Ma
- Emergency office, Wuxi Center for Disease Control and Prevention, Wuxi, P.R. China
| | - Ziheng Wang
- The Hand Surgery Research Center, Department of Hand Surgery, Affiliated Hospital of Nantong University, Nantong, P.R. China
| | - You Lang Zhou
- The Hand Surgery Research Center, Department of Hand Surgery, Affiliated Hospital of Nantong University, Nantong, P.R. China
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24
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Agrahari AK, Doss GPC, Siva R, Magesh R, Zayed H. Molecular insights of the G2019S substitution in LRRK2 kinase domain associated with Parkinson's disease: A molecular dynamics simulation approach. J Theor Biol 2019; 469:163-171. [PMID: 30844370 DOI: 10.1016/j.jtbi.2019.03.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 02/15/2019] [Accepted: 03/01/2019] [Indexed: 12/19/2022]
Abstract
The G2019S substitution in the Leucine-rich repeat kinase 2 (LRRK2) is significantly associated with Parkinson's disease (PD). This substitution was identified in both familial and sporadic forms of PD with a higher frequency. Few computational studies have reported the impact of G2019S substitution on inhibitors of the kinase domain of LRRK2. However, no computational study deeply investigated the possible impact of the G2019S substitution on the kinase domain in its Apo conformation. Therefore, in this study, we used 200 ns molecular dynamic simulation using the GROMACS 5.1.4 package software to investigate the impact of the G2019S substitution on the structure of the kinase domain of LRRK2. Our results indicate that the G2019S substitution affects the dynamics and stability of LRRK2 by decreasing the flexibility and increasing the compactness of the kinase domain and showing its tendency to be in an active conformation for long time interval because of the high energy barrier between active and inactive conformation. This study predicts the molecular pathogenicity mechanism of the G2019S on patients with PD and provides a potential platform for developing therapeutics for patients with PD that harbor this amino acid substitution.
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Affiliation(s)
- Ashish Kumar Agrahari
- Department of Integrative Biology, School of Biosciences and Technology, VIT, Vellore, Tamil Nadu 632014, India
| | - George Priya C Doss
- Department of Integrative Biology, School of Biosciences and Technology, VIT, Vellore, Tamil Nadu 632014, India.
| | - R Siva
- Department of Integrative Biology, School of Biosciences and Technology, VIT, Vellore, Tamil Nadu 632014, India
| | - R Magesh
- Department of Biotechnology, Sri Ramachandra Institute of Higher Education and Research (SRIHER), Deemed to be University (DU), Porur, Chennai, 600116, India
| | - Hatem Zayed
- Department of Biomedical Sciences, College of Health and Sciences, Qatar University, Doha, Qatar.
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25
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Tu Y, Fan G, Xi H, Zeng T, Sun H, Cai X, Kong W. Identification of candidate aberrantly methylated and differentially expressed genes in thyroid cancer. J Cell Biochem 2018; 119:8797-8806. [PMID: 30069928 PMCID: PMC6220990 DOI: 10.1002/jcb.27129] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 05/07/2018] [Indexed: 12/24/2022]
Abstract
Aberrant methylation of DNA sequences plays a criticle role in finding novel aberrantly methylated genes and pathways in thyroid cancer (THCA). This study aimed to integrate three cohorts profile datasets to find novel aberrantly methylated genes and pathways in THCA. Data of gene expression profiling microarrays (GSE33630 and GSE65144) and gene methylation profiling microarrays (GSE51090) were downloaded from the Gene Expression Omnibus database. Aberrantly methylated and differentially expressed genes were sorted and pathways were analyzed. Functional and enrichment analyses of selected genes were performed using the String database. A protein‐protein interaction network was constructed using the Cytoscape software, and module analysis was performed using Molecular Complex detection. In total, we identified 12 hypomethylation/high‐expression genes and 30 hypermethylation/low‐expression genes at the screening step and, finally, found 6 mostly changed hub genes including PPARGC1A, CREBBP, EP300, CD44, SPP1, and MMP9. Pathway analysis showed that aberrantly methylated differentially expressed genes were mainly associated with the thyroid hormone signaling pathway, AMP‐activated protein kinase (AMPK) signaling pathway, and cell cycle process in THCA. After validation in the Cancer Genome Atlas database, the methylation and expression status of hub genes was significantly altered and the same with our results. Taken together, we identified novel aberrantly methylated genes and pathways in THCA, which could improve our understanding of the cause and underlying molecular events, and these candidate genes could serve as aberrant methylation‐based biomarkers for precise diagnosis and treatment of THCA.
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Affiliation(s)
- Yaqin Tu
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Guorun Fan
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Hongli Xi
- Department of Clinical laboratory, Cancer Center of Guangzhou Medical University, Guangzhou, China
| | - Tianshu Zeng
- Department of Endocrinology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Haiying Sun
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Xiong Cai
- Department of Hepatobiliary Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Wen Kong
- Department of Endocrinology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
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26
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P S, Ebrahimi EA, Ghazala SA, D TK, R S, Priya Doss C G, Zayed H. Structural analysis of missense mutations in galactokinase 1 (GALK1) leading to galactosemia type-2. J Cell Biochem 2018; 119:7585-7598. [PMID: 29893426 DOI: 10.1002/jcb.27097] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 04/26/2018] [Indexed: 12/27/2022]
Abstract
Galactosemia type 2 is an autosomal recessive disorder characterized by the deficiency of galactokinase (GALK) enzyme due to missense mutations in GALK1 gene, which is associated with various manifestations such as hyper galactosemia and formation of cataracts. GALK enzyme catalyzes the adenosine triphosphate (ATP)-dependent phosphorylation of α-d-galactose to galactose-1-phosphate. We searched 4 different literature databases (Google Scholar, PubMed, PubMed Central, and Science Direct) and 3 gene-variant databases (Online Mendelian Inheritance in Man, Human Gene Mutation Database, and UniProt) to collect all the reported missense mutations associated with GALK deficiency. Our search strategy yielded 32 missense mutations. We used several computational tools (pathogenicity and stability, biophysical characterization, and physiochemical analyses) to prioritize the most significant mutations for further analyses. On the basis of the pathogenicity and stability predictions, 3 mutations (P28T, A198V, and L139P) were chosen to be tested further for physicochemical characterization, molecular docking, and simulation analyses. Molecular docking analysis revealed a decrease in interaction between the protein and ATP in all the 3 mutations, and molecular dynamic simulations of 50 ns showed a loss of stability and compactness in the mutant proteins. As the next step, comparative physicochemical changes of the native and the mutant proteins were carried out using essential dynamics. Overall, P28T and A198V were predicted to alter the structure and function of GALK protein when compared to the mutant L139P. This study demonstrates the power of computational analysis in variant classification and interpretation and provides a platform for developing targeted therapeutics.
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Affiliation(s)
- Sneha P
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, India
| | - Elaheh Ahmad Ebrahimi
- Department of Biomedical Sciences, College of Health Sciences, Qatar University, Doha, Qatar
| | - Sara Ahmed Ghazala
- Department of Biomedical Sciences, College of Health Sciences, Qatar University, Doha, Qatar
| | - Thirumal Kumar D
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, India
| | - Siva R
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, India
| | - George Priya Doss C
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, India
| | - Hatem Zayed
- Department of Biomedical Sciences, College of Health Sciences, Qatar University, Doha, Qatar
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27
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Raghuraman P, Sudandiradoss C. R516Q mutation in Melanoma differentiation-associated protein 5 (MDA5) and its pathogenic role towards rare Singleton-Merten syndrome; a signature associated molecular dynamics study. J Biomol Struct Dyn 2018; 37:750-765. [DOI: 10.1080/07391102.2018.1439770] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- P. Raghuraman
- Department of Biotechnology, School of Bioscience and Technology, VIT University, Vellore 632014, India
| | - C. Sudandiradoss
- Department of Biotechnology, School of Bioscience and Technology, VIT University, Vellore 632014, India
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28
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Balaraman S, Ramalingam R. The structural and functional reliability of Circulins of
Chassalia parvifolia
for peptide therapeutic scaffolding. J Cell Biochem 2018; 119:3999-4008. [DOI: 10.1002/jcb.26557] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 11/30/2017] [Indexed: 02/06/2023]
Affiliation(s)
- Senthilkumar Balaraman
- Bioinformatics Division, School of Bio Sciences and TechnologyVellore Institute of Technology UniversityVelloreTamil NaduIndia
| | - Rajasekaran Ramalingam
- Bioinformatics Division, School of Bio Sciences and TechnologyVellore Institute of Technology UniversityVelloreTamil NaduIndia
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29
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Senthilkumar B, Meshach Paul D, Srinivasan E, Rajasekaran R. Structural Stability Among Hybrid Antimicrobial Peptide Cecropin A(1–8)–Magainin 2(1–12) and Its Analogues: A Computational Approach. J CLUST SCI 2017. [DOI: 10.1007/s10876-017-1240-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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30
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Gromicho M, Oliveira Santos M, Pinto A, Pronto-Laborinho A, De Carvalho M. Young-onset rapidly progressive ALS associated with heterozygous FUS mutation. Amyotroph Lateral Scler Frontotemporal Degener 2017; 18:451-453. [PMID: 28288521 DOI: 10.1080/21678421.2017.1299762] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We report a 36-years-old Cape Verdean man who presented with respiratory insufficiency due to rapidly progressive sporadic amyotrophic lateral sclerosis (ALS), in whom FUS mutation c.1551C > G (p.Hist517Gln) in heterozygosity was identified, a finding previously described as non-pathogenic. The only previous report on this mutation was in a family from Cape Verde in which four members developed ALS; all were homozygous for the mutation. This case shows that this FUS mutation presents a highly variable penetrance and expressivity.
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Affiliation(s)
- Marta Gromicho
- a Instituto de Medicina Molecular and Instituto de Fisiologia, Faculdade de Medicina, Universidade de Lisboa , Lisbon , Portugal and
| | - Miguel Oliveira Santos
- a Instituto de Medicina Molecular and Instituto de Fisiologia, Faculdade de Medicina, Universidade de Lisboa , Lisbon , Portugal and.,b Department of Neurosciences and Mental Health , Hospital de Santa Maria - CHLN , Lisbon , Portugal
| | - Anabela Pinto
- a Instituto de Medicina Molecular and Instituto de Fisiologia, Faculdade de Medicina, Universidade de Lisboa , Lisbon , Portugal and.,b Department of Neurosciences and Mental Health , Hospital de Santa Maria - CHLN , Lisbon , Portugal
| | - Ana Pronto-Laborinho
- a Instituto de Medicina Molecular and Instituto de Fisiologia, Faculdade de Medicina, Universidade de Lisboa , Lisbon , Portugal and
| | - Mamede De Carvalho
- a Instituto de Medicina Molecular and Instituto de Fisiologia, Faculdade de Medicina, Universidade de Lisboa , Lisbon , Portugal and.,b Department of Neurosciences and Mental Health , Hospital de Santa Maria - CHLN , Lisbon , Portugal
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31
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D. K, Ramireddy S, P. R, C. S. Expediting dynamics approach to understand the influence of 14-3-3ζ causing metastatic cancer through the interaction of YAP1 and β-TRCP. MOLECULAR BIOSYSTEMS 2017; 13:1981-1992. [DOI: 10.1039/c7mb00271h] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The 14-3-3ζ protein acts as a molecular switch in regulating the TGF-β pathway, which alters from a tumor suppressor in the early stage of breast cancer to a promoter of metastasis in the late stage.
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Affiliation(s)
- Kamalesh D.
- Department of Integrative Biology
- School of Biosciences and Technology
- VIT University
- Vellore
- India
| | - Sriroopreddy Ramireddy
- Department of Biotechnology
- School of Biosciences and Technology
- VIT University
- Vellore
- India
| | - Raguraman P.
- Department of Biotechnology
- School of Biosciences and Technology
- VIT University
- Vellore
- India
| | - Sudandiradoss C.
- Department of Biotechnology
- School of Biosciences and Technology
- VIT University
- Vellore
- India
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32
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Raghuraman P, Jesu Jaya Sudan R, Lesitha Jeeva Kumari J, Sudandiradoss C. Casting the critical regions in nucleotide binding oligomerization domain 2 protein: a signature mediated structural dynamics approach. J Biomol Struct Dyn 2016; 35:3297-3315. [PMID: 27790943 DOI: 10.1080/07391102.2016.1254116] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Nucleotide binding oligomerization domain 2 (NOD2), a protein involved in the first line defence mechanism has a pivotal role in innate immunity. Impaired function of this protein is implicated in disorders such as Blau syndrome and Crohn's disease. Since an altered function is linked to protein's structure, we framed a systematic strategy to interpret the structure-function relationship of the protein. Initiated with mutation-based pattern prediction and identified a distant ortholog (DO) of NOD2 from which the intra-residue interaction network was elucidated. The network was used to identify hotspots that serve as critical points to maintain the stable architecture of the protein. Structural comparison of NOD2 domains with a DO revealed the minimal number of intra-protein interactions required by the protein to maintain the structural fold. In addition, the conventional molecular dynamics simulation emphasized the conformational transitions at hot spot residues between native NOD2 domains and its respective mutants (G116R, R42W and R54A) structures. The analysis of intra-protein interactions globally and the displacement of residues locally around the mutational site revealed loss of several critical bonds and residues vital for the protein's function. Conclusively we report, about 10 residues in leucine-rich repeat, 13 residues in NOD and 6 residues in CARD domain are required by the NOD2 to maintain its function. This protocol will help the researchers to achieve for more prospective studies to attest druggable site utility in discovering novel drug candidates.
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Affiliation(s)
- P Raghuraman
- a Department of Biotechnology , School of Bioscience and Technology, VIT University , Vellore 632301 , India
| | - R Jesu Jaya Sudan
- a Department of Biotechnology , School of Bioscience and Technology, VIT University , Vellore 632301 , India
| | - J Lesitha Jeeva Kumari
- a Department of Biotechnology , School of Bioscience and Technology, VIT University , Vellore 632301 , India
| | - C Sudandiradoss
- a Department of Biotechnology , School of Bioscience and Technology, VIT University , Vellore 632301 , India
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33
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Yu H, Li H, Zhang J, Liu G. Influence of MDM2 polymorphisms on squamous cell carcinoma susceptibility: a meta-analysis. Onco Targets Ther 2016; 9:6211-6224. [PMID: 27785069 PMCID: PMC5067019 DOI: 10.2147/ott.s113417] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
PURPOSE Controversial associations between single-nucleotide polymorphisms (rs2279744, rs937283, rs3730485) of the MDM2 gene and the etiology of squamous cell carcinomas (SCCs) have been reported. This merits further comprehensive assessment. MATERIALS AND METHODS We systematically reviewed the available data and conducted an updated meta-analysis to evaluate the genetic effect of MDM2 polymorphisms in SCC susceptibility, using Stata/SE 12.0 software. RESULTS After screening, 7,987 SCC cases and 12,954 controls from 26 eligible case-control studies were enrolled. Overall, compared with the control group, a significantly increased SCC risk was observed for the MDM2 rs2279744 polymorphism in the Asian population (test of association: odds ratio [OR] 1.12, P=0.027 for G vs T; OR 1.26, P=0.016 for GG vs TT; OR 1.25, P<0.001 for GG vs TT + TG; and OR 1.08, P=0.023 for carrier G vs T). In subgroup analysis by SCC type, a similarly increased esophageal SCC risk was detected (OR 1.19, P<0.001 for G vs T; OR 1.46, P<0.001 for GG vs TT; and OR 1.48, P=0.005 for GG vs TT + TG). Furthermore, MDM2-TP53 double mutation was statistically associated with increased SCC susceptibility overall (OR 1.52, P=0.001), especially in the Asian population (OR 1.49, P=0.022). However, no significant difference between the control and case groups was obtained for MDM2 rs937283 or rs3730485 under any genetic model (all P>0.05). CONCLUSION Our results highlight a positive association between the GG genotype of MDM2 rs2279744 polymorphism and an increased risk of esophageal SCC in the Asian population, which needs to be clarified by more large-scale studies.
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Affiliation(s)
- Huanxin Yu
- Department of Otorhinolaryngology Head and Neck Surgery, Tianjin Huanhu Hospital, Tianjin, People's Republic of China
| | - Haiyan Li
- Department of Otorhinolaryngology Head and Neck Surgery, Tianjin Huanhu Hospital, Tianjin, People's Republic of China
| | - Jinling Zhang
- Department of Otorhinolaryngology Head and Neck Surgery, Tianjin Huanhu Hospital, Tianjin, People's Republic of China
| | - Gang Liu
- Department of Otorhinolaryngology Head and Neck Surgery, Tianjin Huanhu Hospital, Tianjin, People's Republic of China
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34
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Senthilkumar B, Rajasekaran R. In Silico Template Selection of Short Antimicrobial Peptide Viscotoxin for Improving Its Antimicrobial Efficiency in Development of Potential Therapeutic Drugs. Appl Biochem Biotechnol 2016; 181:898-913. [PMID: 27696138 DOI: 10.1007/s12010-016-2257-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 09/19/2016] [Indexed: 12/22/2022]
Abstract
Rapid increase in antibiotic resistance has posed a worldwide threat, due to increased mortality, morbidity, and expenditure caused by antibiotic-resistant microbes. Recent development of the antimicrobial peptides like viscotoxin (Vt) has been successfully comprehended as a substitute for classical antibiotics. A structurally stable peptide, Vt can enhance antimicrobial property and can be used for various developmental purposes. Thus, structural stability among the antimicrobial peptides, Vt A1 (3C8P), A2 (1JMN), A3 (1ED0), B (1JMP), and C (1ORL) of Viscus album was computationally analyzed. In specific, the static confirmation of VtA3 showed high number of intramolecular interactions, along with an increase in hydrophobicity than others comparatively. Further, conformational sampling was used to analyze various geometrical parameters such as root mean square deviation, root mean square fluctuation, radius of gyration, and ovality which also revealed the structural stability of VtA3. Moreover, the statistically validated contours of surface area, lipophilicity, and distance constraints of disulfide bonds also supported the priority of VtA3 with respect to stability. Finally, the functional activity of peptides was accessed by computing their free energy of membrane association and membrane interactions, which defined VtA3 as functionally stable. Currently, peptide-based antibiotics and nanoparticles have attracted the pharmaceutical industries for their potential therapeutic applications. Thereby, it is proposed that viscotoxin A3 (1ED0) could be used as a preeminent template for scaffolding potentially efficient antimicrobial peptide-based drugs and nanomaterials in future.
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Affiliation(s)
- B Senthilkumar
- Department of Biotechnology, School of Bio Sciences and Technology, VIT University, Vellore, Tamil Nadu, 632014, India
| | - R Rajasekaran
- Department of Biotechnology, School of Bio Sciences and Technology, VIT University, Vellore, Tamil Nadu, 632014, India.
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35
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Rajendran V, Gopalakrishnan C, Purohit R. Impact of point mutation P29S in RAC1 on tumorigenesis. Tumour Biol 2016; 37:15293-15304. [DOI: 10.1007/s13277-016-5329-y] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 09/06/2016] [Indexed: 01/07/2023] Open
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36
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Basharat Z, Messaoudi A, Ruba S, Yasmin A. NQO1 rs1800566 polymorph is more prone to NOx induced lung injury: Endorsing deleterious functionality through informatics approach. Gene 2016; 591:14-20. [DOI: 10.1016/j.gene.2016.06.048] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Revised: 06/12/2016] [Accepted: 06/23/2016] [Indexed: 02/06/2023]
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37
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Meshach Paul D, Rajasekaran R. In silico approach to explore the disruption in the molecular mechanism of human hyaluronidase 1 by mutant E268K that directs Natowicz syndrome. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2016; 46:157-169. [PMID: 27424109 DOI: 10.1007/s00249-016-1151-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 06/02/2016] [Accepted: 07/01/2016] [Indexed: 01/27/2023]
Abstract
Natowicz syndrome (mucopolysaccharidoses type 9) is a lysosomal storage disorder caused by deficient or defective human hyaluronidase 1. The disorder is not well studied at the molecular level. Therefore, a new in silico approach was proposed to study the molecular basis on which one clinically observed mutation, Glu268Lys, results in a defective enzyme. The native and mutant structures were subjected to comparative analyses using a conformational sampling approach for geometrical variables viz, RMSF, RMSD, and Ramachandran plot. In addition, the strength of a Cys207-Cys221 disulfide bond and electrostatic interaction between Arg265 and Asp206 were studied, as they are known to be involved in the catalytic activity of the enzyme. Native and mutant E268K showed statistically significant variations with p < 0.05 in RMSD, Ramachandran plot, strengths of disulfide bond, and electrostatic interactions. Further, single model analysis showed variations between native and mutant structures in terms of intra-protein interactions, hydrogen bond dilution, secondary structure, and dihedral angles. Docking analysis predicted the mutant to have a less favorable substrate binding energy compared to the native protein. Additionally, steered MD analysis indicated that the substrate should have more affinity to the native than mutant enzymes. The observed changes theoretically explain the less favorable binding energy of substrate towards mutant E268K, thereby providing a structural basis for its reduced catalytic activity. Hence, our study provides a basis for understanding the disruption in the molecular mechanism of human hyaluronidase 1 by mutation E268K, which may prove useful for the development of synthetic chaperones as a treatment option for Natowicz syndrome.
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Affiliation(s)
- D Meshach Paul
- Computational Biology Lab, Department of Biotechnology, School of Bio Sciences and Technology, VIT University, Vellore, 632014, Tamil Nadu, India
| | - R Rajasekaran
- Computational Biology Lab, Department of Biotechnology, School of Bio Sciences and Technology, VIT University, Vellore, 632014, Tamil Nadu, India.
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38
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Krebs BB, De Mesquita JF. Amyotrophic Lateral Sclerosis Type 20 - In Silico Analysis and Molecular Dynamics Simulation of hnRNPA1. PLoS One 2016; 11:e0158939. [PMID: 27414033 PMCID: PMC4945010 DOI: 10.1371/journal.pone.0158939] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 06/24/2016] [Indexed: 12/13/2022] Open
Abstract
Amyotrophic Lateral Sclerosis (ALS) is a fatal neurodegenerative disease that affects the upper and lower motor neurons. 5-10% of cases are genetically inherited, including ALS type 20, which is caused by mutations in the hnRNPA1 gene. The goals of this work are to analyze the effects of non-synonymous single nucleotide polymorphisms (nsSNPs) on hnRNPA1 protein function, to model the complete tridimensional structure of the protein using computational methods and to assess structural and functional differences between the wild type and its variants through Molecular Dynamics simulations. nsSNP, PhD-SNP, Polyphen2, SIFT, SNAP, SNPs&GO, SNPeffect and PROVEAN were used to predict the functional effects of nsSNPs. Ab initio modeling of hnRNPA1 was made using Rosetta and refined using KoBaMIN. The structure was validated by PROCHECK, Rampage, ERRAT, Verify3D, ProSA and Qmean. TM-align was used for the structural alignment. FoldIndex, DICHOT, ELM, D2P2, Disopred and DisEMBL were used to predict disordered regions within the protein. Amino acid conservation analysis was assessed by Consurf, and the molecular dynamics simulations were performed using GROMACS. Mutations D314V and D314N were predicted to increase amyloid propensity, and predicted as deleterious by at least three algorithms, while mutation N73S was predicted as neutral by all the algorithms. D314N and D314V occur in a highly conserved amino acid. The Molecular Dynamics results indicate that all mutations increase protein stability when compared to the wild type. Mutants D314N and N319S showed higher overall dimensions and accessible surface when compared to the wild type. The flexibility level of the C-terminal residues of hnRNPA1 is affected by all mutations, which may affect protein function, especially regarding the protein ability to interact with other proteins.
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Affiliation(s)
- Bruna Baumgarten Krebs
- Laboratory of Bioinformatics and Computational Biology, Department of Genetics and Molecular Biology, Federal University of Rio de Janeiro State (UNIRIO), Rio de Janeiro, Brazil
| | - Joelma Freire De Mesquita
- Laboratory of Bioinformatics and Computational Biology, Department of Genetics and Molecular Biology, Federal University of Rio de Janeiro State (UNIRIO), Rio de Janeiro, Brazil
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Kalsi N, Gopalakrishnan C, Rajendran V, Purohit R. Biophysical aspect of phosphatidylinositol 3-kinase and role of oncogenic mutants (E542K & E545K). J Biomol Struct Dyn 2016; 34:2711-2721. [DOI: 10.1080/07391102.2015.1127774] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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Behera AK, Chandra I, Cherian SS. Molecular dynamics simulation of the effects of single (S221P) and double (S221P and K216E) mutations in the hemagglutinin protein of influenza A H5N1 virus: a study on host receptor specificity. J Biomol Struct Dyn 2015; 34:2054-67. [DOI: 10.1080/07391102.2015.1106341] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Abhisek Kumar Behera
- Bioinformatics and Data Management Group, National Institute of Virology, 20-A, Dr. Ambedkar Road, Post Box No. 11, Pune 411001, Maharashtra, India
| | - Ishwar Chandra
- Bioinformatics and Data Management Group, National Institute of Virology, 20-A, Dr. Ambedkar Road, Post Box No. 11, Pune 411001, Maharashtra, India
| | - Sarah S. Cherian
- Bioinformatics and Data Management Group, National Institute of Virology, 20-A, Dr. Ambedkar Road, Post Box No. 11, Pune 411001, Maharashtra, India
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King A, Troakes C, Smith B, Nolan M, Curran O, Vance C, Shaw CE, Al-Sarraj S. ALS-FUS pathology revisited: singleton FUS mutations and an unusual case with both a FUS and TARDBP mutation. Acta Neuropathol Commun 2015; 3:62. [PMID: 26452761 PMCID: PMC4600255 DOI: 10.1186/s40478-015-0235-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 08/25/2015] [Indexed: 12/12/2022] Open
Abstract
Introduction Mutations in the FUS gene have been shown to be a rare cause of amyotrophic lateral sclerosis (ALS-FUS) and whilst well documented clinically and genetically there have been relatively few neuropathological studies.Recent work suggested a possible correlation between pathological features such as frequency of basophilic inclusions in neurons and rate of clinical decline, other studies have revealed a discrepancy between the upper motor neuron features detected clinically and the associated pathology. The purpose of this study was to describe the pathological features associated with more recently discovered FUS mutations and reinvestigate those with well recognised mutations in an attempt to correlate the pathology with mutation and/or clinical phenotype. The brains and spinal cords of seven cases of ALS-FUS were examined neuropathologically, including cases with the newly described p.K510E mutation and a case with both a known p.P525L mutation in the FUS gene and a truncating p.Y374X mutation in the TARDBP gene. Results The neuropathology in all cases revealed basophilic and FUS inclusions in the cord. The density and type of inclusions varied markedly between cases, but did not allow a clear correlation with clinical progression. Only one case showed significant motor cortical pathology despite the upper motor neuron clinical features being evident in 4 patients. The case with both a FUS and TARDBP mutation revealed FUS positive inclusions but no TDP-43 pathology. Instead there were unusual p62 positive, FUS negative neuronal and glial inclusions as well as dot-like neurites. Conclusions The study confirms cases of ALS-FUS to be mainly a lower motor neuron disease and to have pathology that does not appear to neatly correlate with clinical features or genetics. Furthermore, the case with both a FUS and TARDBP mutation reveals an intriguing pathological profile which at least in part involves a very unusual staining pattern for the ubiquitin-binding protein p62.
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Computational investigation of molecular mechanism and neuropathological implications in Huntington disease. Mol Cell Biochem 2015; 409:1-11. [DOI: 10.1007/s11010-015-2462-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 05/23/2015] [Indexed: 12/31/2022]
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Structure and Function of p53-DNA Complexes with Inactivation and Rescue Mutations: A Molecular Dynamics Simulation Study. PLoS One 2015; 10:e0134638. [PMID: 26244575 PMCID: PMC4526489 DOI: 10.1371/journal.pone.0134638] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 07/10/2015] [Indexed: 01/10/2023] Open
Abstract
The tumor suppressor protein p53 can lose its function upon DNA-contact mutations (R273C and R273H) in the core DNA-binding domain. The activity can be restored by second-site suppressor or rescue mutations (R273C_T284R, R273H_T284R, and R273H_S240R). In this paper, we elucidate the structural and functional consequence of p53 proteins upon DNA-contact mutations and rescue mutations and the underlying mechanisms at the atomic level by means of molecular dynamics simulations. Furthermore, we also apply the docking approach to investigate the binding phenomena between the p53 protein and DNA upon DNA-contact mutations and rescue mutations. This study clearly illustrates that, due to DNA-contact mutants, the p53 structure loses its stability and becomes more rigid than the native protein. This structural loss might affect the p53-DNA interaction and leads to inhibition of the cancer suppression. Rescue mutants (R273C_T284R, R273H_T284R and R273H_S240R) can restore the functional activity of the p53 protein upon DNA-contact mutations and show a good interaction between the p53 protein and a DNA molecule, which may lead to reactivate the cancer suppression function. Understanding the effects of p53 cancer and rescue mutations at the molecular level will be helpful for designing drugs for p53 associated cancer diseases. These drugs should be designed so that they can help to inhibit the abnormal function of the p53 protein and to reactivate the p53 function (cell apoptosis) to treat human cancer.
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Polley S, Chakravarty D, Chakrabarti G, Chattopadhyaya R, Sau S. Proline substitutions in a Mip-like peptidyl-prolyl cis-trans isomerase severely affect its structure, stability, shape and activity. BIOCHIMIE OPEN 2015; 1:28-39. [PMID: 29632827 PMCID: PMC5889476 DOI: 10.1016/j.biopen.2015.07.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 07/12/2015] [Indexed: 01/28/2023]
Abstract
FKBP22, an Escherichia coli-specific peptidyl-prolyl cis-trans isomerase, shows substantial homology with the Mip-like virulence factors. Mip-like proteins are homodimeric and possess a V-shaped conformation. Their N-terminal domains form dimers, whereas their C-terminal domains bind protein/peptide substrates and distinct inhibitors such as rapamycin and FK506. Interestingly, the two domains of the Mip-like proteins are separated by a lengthy, protease-susceptible α-helix. To delineate the structural requirement of this domain-connecting region in Mip-like proteins, we have investigated a recombinant FKBP22 (rFKBP22) and its three point mutants I65P, V72P and A82P using different probes. Each mutant harbors a Pro substitution mutation at a distinct location in the hinge region. We report that the three mutants are not only different from each other but also different from rFKBP22 in structure and activity. Unlike rFKBP22, the three mutants were unfolded by a non-two state mechanism in the presence of urea. In addition, the stabilities of the mutants, particularly I65P and V72P, differed considerably from that of rFKBP22. Conversely, the rapamycin binding affinity of no mutant was different from that of rFKBP22. Of the mutants, I65P showed the highest levels of structural/functional loss and dissociated partly in solution. Our computational study indicated a severe collapse of the V-shape in I65P due to the anomalous movement of its C-terminal domains. The α-helical nature of the domain-connecting region is, therefore, critical for the Mip-like proteins.
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Key Words
- A82P, a FKBP22/rFKBP22 derivative harboring a Ala to Pro change at position 82 in the helix α3
- CTD, C-terminal domain of FKBP22
- FKBP22, a PPIase from Escherichia coli
- Helix α3
- I65P, a FKBP22/rFKBP22 variant carrying a Ile to Pro replacement at position 65 in the helix α3
- Mip, macrophage infectivity potentiator
- Mutation
- NTD, N-terminal domain of FKBP22
- PPIase, peptidyl-prolyl cis-trans isomerase
- Peptidyl-prolyl cis-trans isomerase
- Stability
- Structure
- TUGE, transverse urea gradient gel electrophoresis
- V72P, a FKBP22/rFKBP22 variant with a Val to Pro substitution at position 72 in the helix α3
- rFKBP22, a polyhistidine-tagged FKBP22
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Affiliation(s)
- Soumitra Polley
- Department of Biochemistry, Bose Institute, P-1/12, CIT Scheme VII M, Kolkata 700054, West Bengal, India
| | - Devlina Chakravarty
- Department of Biochemistry, Bose Institute, P-1/12, CIT Scheme VII M, Kolkata 700054, West Bengal, India
| | - Gopal Chakrabarti
- Dr. B.C. Guha Centre for Genetic Engineering, University of Calcutta, Ballygunge Circular Road, Kolkata 700019, West Bengal, India
| | - Rajagopal Chattopadhyaya
- Department of Biochemistry, Bose Institute, P-1/12, CIT Scheme VII M, Kolkata 700054, West Bengal, India
| | - Subrata Sau
- Department of Biochemistry, Bose Institute, P-1/12, CIT Scheme VII M, Kolkata 700054, West Bengal, India
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A Novel Mutation of SMAD3 Identified in a Chinese Family with Aneurysms-Osteoarthritis Syndrome. BIOMED RESEARCH INTERNATIONAL 2015. [PMID: 26221609 PMCID: PMC4499615 DOI: 10.1155/2015/968135] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Aneurysms-osteoarthritis syndrome (AOS) is a recently delineated autosomal dominant disorder characterized by aneurysms, dissections, and tortuosity throughout the arterial tree in association with early onset osteoarthritis, mild craniofacial features, and skeletal and cutaneous anomalies. Previous studies have demonstrated that mutations in SMAD3, a key regulator of TGF-β signal transduction, contribute to AOS. Here, we investigated a family of three generations affected by AOS. A novel SMAD3 mutation, c.266G>A (p.C89Y), was identified and cosegregated with the affected individuals in this family. Our finding expands the mutation spectrum of SMAD3 gene and further strengthens the connection between the presence of aneurysms-osteoarthritis phenotype and SMAD3 mutations, which facilitates the understanding of the genotype-phenotype correlation of AOS.
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