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Dehury B, Tang N, Blundell TL, Kepp KP. Structure and dynamics of γ-secretase with presenilin 2 compared to presenilin 1. RSC Adv 2019; 9:20901-20916. [PMID: 35515530 PMCID: PMC9065803 DOI: 10.1039/c9ra02623a] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 06/27/2019] [Indexed: 12/12/2022] Open
Abstract
Severe early-onset familial Alzheimer's disease (FAD) is caused by more than 200 different mutations in the genes coding for presenilin, the catalytic subunit of the 4-subunit protease complex γ-secretase, which cleaves the C99 fragment of the amyloid precursor protein (APP) to produce Aβ peptides. γ-Secretase exists with either of two homologues, PS1 and PS2. All cryo-electron microscopic structures and computational work has so far focused on γ-secretase with PS1, yet PS2 mutations also cause FAD. A central question is thus whether there are structural and dynamic differences between PS1 and PS2. To address this question, we use the cryo-electron microscopic data for PS1 to develop the first structural and dynamic model of PS2-γ-secretase in the catalytically relevant mature membrane-bound state at ambient temperature, equilibrated by three independent 500 ns molecular dynamics simulations. We find that the characteristic nicastrin extra-cellular domain breathing mode and major movements in the cytosolic loop between TM6 and TM7 occur in both PS2- and PS1-γ-secretase. The overall structures and conformational states are similar, suggesting similar catalytic activities. However, at the sequence level, charge-controlled membrane-anchoring is extracellular for PS1 and intracellular for PS2, which suggests different subcellular locations. The tilt angles of the TM2, TM6, TM7 and TM9 helices differ in the two forms of γ-secretase, suggesting that the two proteins have somewhat different substrate processing and channel sizes. Our MD simulations consistently indicated that PS2 retains several water molecules near the catalytic site at the bilayer, as required for catalysis. The possible reasons for the differences of PS1 and PS2 are discussed in relation to their location and function.
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Affiliation(s)
- Budheswar Dehury
- Department of Chemistry, Technical University of Denmark DK-2800 Kongens Lyngby Denmark +045 45252409
| | - Ning Tang
- Department of Chemistry, Technical University of Denmark DK-2800 Kongens Lyngby Denmark +045 45252409
| | - Tom L Blundell
- Department of Biochemistry, University of Cambridge Cambridge CB2 1GA UK
| | - Kasper P Kepp
- Department of Chemistry, Technical University of Denmark DK-2800 Kongens Lyngby Denmark +045 45252409
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Qi L, Gao C, Feng F, Zhang T, Yao Y, Wang X, Liu C, Li J, Li J, Sun C. MicroRNAs associated with lung squamous cell carcinoma: New prognostic biomarkers and therapeutic targets. J Cell Biochem 2019; 120:18956-18966. [PMID: 31241205 DOI: 10.1002/jcb.29216] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 05/31/2019] [Indexed: 12/24/2022]
Affiliation(s)
- Lingyu Qi
- College of First Clinical MedicineShandong University of Traditional Chinese Medicine Jinan Shandong PR China
| | - Chundi Gao
- College of First Clinical MedicineShandong University of Traditional Chinese Medicine Jinan Shandong PR China
| | - Fubin Feng
- Department of OncologyWeifang Traditional Chinese Hospital Weifang Shandong PR China
| | - Tingting Zhang
- College of Traditional Chinese MedicineShandong University of Traditional Chinese Medicine Jinan Shandong PR China
| | - Yan Yao
- Clinical Medical CollegesWeifang Medical University Weifang Shandong PR China
| | - Xue Wang
- College of Basic MedicineQingdao University Qingdao Shandong PR China
| | - Cun Liu
- College of Traditional Chinese MedicineShandong University of Traditional Chinese Medicine Jinan Shandong PR China
| | - Jia Li
- Clinical Medical CollegesWeifang Medical University Weifang Shandong PR China
| | - Jie Li
- College of First Clinical MedicineShandong University of Traditional Chinese Medicine Jinan Shandong PR China
| | - Changgang Sun
- Department of OncologyAffiliated Hospital of Weifang Medical University Weifang Shandong PR China
- Department of OncologyAffiliated Hospital of Shandong University of Traditional Chinese Medicine Jinan Shandong PR China
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53
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Bhardwaj V, Purohit R. Computational investigation on effect of mutations in PCNA resulting in structural perturbations and inhibition of mismatch repair pathway. J Biomol Struct Dyn 2019; 38:1963-1974. [PMID: 31138032 DOI: 10.1080/07391102.2019.1621210] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
From bacteria to mammals, DNA mismatch repair (MMR) pathway plays an essential role in eliminating mismatched nucleotides and insertion-deletion mismatches during the process of DNA replication. Among many of the proteins which participate in the mismatch repair process, proliferating cell nuclear antigen (PCNA) remains the principal conductor at the replication fork. The pol30-201 and pol30-204 are the two mutated alleles which encode for C22Y and C81R mutant forms of PCNA proteins. We performed long term molecular dynamics (MD) simulations analysis (0.8 μs) to understand the dynamic behavior and alterations in the structure of wild type and mutated forms of PCNA at the atomic level. We observed changes in the structural characteristics like length, radius, rise per residue of alpha helices in both the mutated forms of PCNA. Apart from it, disfigurement of the charge distribution which effects binding with the dsDNA due to mutant C22Y and other structural perturbations were also seen in regions significant for the formation of a biologically active trimeric form of PCNA due to mutant C81R. Our analysis of native and mutated forms of PCNA provides an insight into the essential structural and functional features required for proper and well-coordinated DNA mismatch repair process and consequences of the mutation leading to an impaired process of MMR. These structural characteristics are fundamental for the MMR process and hence our analysis likely contributes to or presents the novel mechanism involved in the process of MMR.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Vijay Bhardwaj
- Structural Bioinformatics Lab, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, India.,Biotechnology division, CSIR-IHBT, Palampur, India
| | - Rituraj Purohit
- Structural Bioinformatics Lab, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, India.,Biotechnology division, CSIR-IHBT, Palampur, India.,Academy of Scientific & Innovative Research (AcSIR), CSIR-IHBT Campus, Palampur, India
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54
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Naqvi AAT, Alajmi MF, Rehman T, Hussain A, Hassan I. Effects of Pro1266Leu mutation on structure and function of glycoprotein Ib binding domain of von Willebrand factor. J Cell Biochem 2019; 120:17847-17857. [PMID: 31135071 DOI: 10.1002/jcb.29052] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 04/26/2019] [Accepted: 04/30/2019] [Indexed: 02/06/2023]
Abstract
Glycoprotein Ibα (GpIbα) binding ability of A1 domain of von Willebrand factor (vWF) facilitates platelet adhesion that plays a crucial role in maintaining hemostasis and thrombosis at the site of vascular damage. There are both "loss as well as gain of function" mutations observed in this domain. Naturally occurring "gain of function" mutations leave self-activating impacts on the A1 domain which turns the normal binding to characteristic constitutive binding with GPIbα. These "gain of function" mutations are associated with the von Willebrand disease type 2B. In recent years, studies focused on understanding the mechanism and conformational patterns attached to these phenomena have been conducted, but the conformational pathways leading to such binding patterns are poorly understood as of now. To obtain a microscopic picture of such events for the better understanding of pathways, we used molecular dynamics (MD) simulations along with principal component analysis and normal mode analysis to study the effects of Pro1266Leu (Pro503Leu in structural context) mutation on the structure and function of A1 domain of vWF. MD simulations have provided atomic-level details of intermolecular motions as a function of time to understand the dynamic behavior of A1 domain of vWF. Comparative analysis of the trajectories obtained from MD simulations of both the wild type and Pro503Leu mutant suggesting appreciable conformational changes in the structure of mutant which might provide a basis for assuming the "gain of function" effects of these mutations on the A1 domain of vWF, resulting in the constitutive binding with GpIbα.
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Affiliation(s)
- Ahmad Abu Turab Naqvi
- Center for Interdisciplinary Research in Basic Science, Jamia Millia Islamia, Jamia Nagar, New Delhi, India
| | - Mohamed F Alajmi
- Department of Pharmacognosy College of Pharmacy, King Saud University, Riyadh, KSA
| | - Tabish Rehman
- Department of Pharmacognosy College of Pharmacy, King Saud University, Riyadh, KSA
| | - Afzal Hussain
- Department of Pharmacognosy College of Pharmacy, King Saud University, Riyadh, KSA
| | - Imtaiyaz Hassan
- Center for Interdisciplinary Research in Basic Science, Jamia Millia Islamia, Jamia Nagar, New Delhi, India
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55
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Pradhan SK, Singh NR, Dehury B, Panda D, Modi MK, Thatoi H. Insights into the mode of flavin mononucleotide binding and catalytic mechanism of bacterial chromate reductases: A molecular dynamics simulation study. J Cell Biochem 2019; 120:16990-17005. [PMID: 31131470 DOI: 10.1002/jcb.28960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 02/04/2019] [Accepted: 02/14/2019] [Indexed: 11/09/2022]
Abstract
Enzymes from natural sources protect the environment via complex biological mechanisms, which aid in reductive immobilization of toxic metals including chromium. Nevertheless, progress was being made in elucidating high-resolution crystal structures of reductases and their binding with flavin mononucleotide (FMN) to understand the underlying mechanism of chromate reduction. Therefore, herein, we employed molecular dynamics (MD) simulations, principal component analysis (PCA), and binding free energy calculations to understand the dynamics behavior of these enzymes with FMN. Six representative chromate reductases in monomeric and dimeric forms were selected to study the mode, dynamics, and energetic component that drive the FMN binding process. As evidenced by MD simulation, FMN prefers to bind the cervix formed between the catalytic domain surrounded by strong conserved hydrogen bonding, electrostatic, and hydrophobic contacts. The slight movement and reorientation of FMN resulted in breakage of some crucial H-bonds and other nonbonded contacts, which were well compensated with newly formed H-bonds, electrostatic, and hydrophobic interactions. The critical residues aiding in tight anchoring of FMN within dimer were found to be strongly conserved in the bacterial system. The molecular mechanics combined with the Poisson-Boltzmann surface area binding free energy of the monomer portrayed that the van der Waals and electrostatic energy contribute significantly to the total free energy, where, the polar solvation energy opposes the binding of FMN. The proposed proximity relationships between enzyme and FMN binding site presented in this study will open up better avenues to engineer enzymes with optimized chromate reductase activity for sustainable bioremediation of heavy metals.
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Affiliation(s)
- Sukanta Kumar Pradhan
- Department of Bioinformatics, Odisha University of Agriculture and Technology, Bhubaneswar, Odisha, India.,Department of Biotechnology, School of Life Sciences, Ravenshaw University, Cuttack, Odisha, India
| | - Nihar Ranjan Singh
- Department of Botany, School of Life Sciences, Ravenshaw University, Cuttack, Odisha, India
| | - Budheswar Dehury
- Biomedical Informatics Centre, Regional Medical Research Centre (ICMR), Nalco Square, Chandrasekharpur, Bhubaneswar, Odisha, India.,Department of Chemistry, Technical University of Denmark, DK-2800 Kgs, Lyngby
| | - Debashis Panda
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
| | - Mahendra Kumar Modi
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
| | - Hrudayanath Thatoi
- Department of Biotechnology, North Orissa University, Sriram Chandra Vihar, Takatpur, Baripada, Odisha, India
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56
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Yao Y, Liu R, Gao C, Zhang T, Qi L, Liu G, Zhang W, Wang X, Li J, Li J, Sun C. Identification of prognostic biomarkers for breast cancer based on miRNA and mRNA co-expression network. J Cell Biochem 2019; 120:15378-15388. [PMID: 31037764 DOI: 10.1002/jcb.28805] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 01/28/2019] [Accepted: 01/30/2019] [Indexed: 12/31/2022]
Abstract
PURPOSE Breast cancer (BC) remains a serious health threat for women due to its high incidence and the trend of rejuvenation. Accumulating evidence has highlighted that microRNAs (miRNAs) and messenger RNAs (mRNAs) could play important roles in various biological processes involved in the pathogenesis of BC. The present study aimed to identify potential prognostic biomarkers associated with BC. METHODS Here, original gene expression profiles of patients with BC was downloaded from The Cancer Genome Atlas (TCGA) database. TargetScan, miRDB, and miRTarBase databases were used to predict the target genes of prognostic-related differentially expressed miRNAs (DEMs). Subsequently, functional enrichment analysis and topological analysis were performed on the overlaps of target genes and differentially expressed mRNAs (DEGs), and Kaplan-Meier analysis was used to predict prognosis-related target genes to identify prognostic biomarkers. RESULTS A total of 218 DEMs and 2222 DEGs were extracted in which eight miRNAs were associated with prognosis, and 278 target DEGs were screened out incorporated into functional enrichment analysis and protein-protein interaction network visualization studies. Additionally, five hub genes (CXCL12, IGF1, LEF1, MMP1, and RACGAP1) were observed as potential biomarkers for BC prognosis through survival analysis. CONCLUSION We performed a distinctive correlation analysis of miRNA-mRNA in BC patients, and identified eight miRNAs and five hub genes may be effective biomarkers for the prognosis of BC patients.
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Affiliation(s)
- Yan Yao
- Clinical Medical Colleges, Weifang Medical University, Weifang, Shandong, People's Republic of China
| | - Ruijuan Liu
- Department of Oncology, Weifang Traditional Chinese Hospital, Weifang, Shandong, People's Republic of China
| | - Chundi Gao
- College of First Clinical Medicine, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, People's Republic of China
| | - Tingting Zhang
- College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, People's Republic of China
| | - Lingyu Qi
- College of First Clinical Medicine, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, People's Republic of China
| | - Gongxi Liu
- Department of Oncology, Weifang Traditional Chinese Hospital, Weifang, Shandong, People's Republic of China
| | - Wenfeng Zhang
- Clinical Medical Colleges, Weifang Medical University, Weifang, Shandong, People's Republic of China
| | - Xue Wang
- Medical Colleges, Qingdao University, Qingdao, Shandong, People's Republic of China
| | - Jie Li
- College of First Clinical Medicine, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, People's Republic of China
| | - Jia Li
- Clinical Medical Colleges, Weifang Medical University, Weifang, Shandong, People's Republic of China
| | - Changgang Sun
- Department of Oncology, Affiliated Hospital of Weifang Medical University, Weifang, Shandong, People's Republic of China.,Department of Oncology, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, Shandong, People's Republic of China
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57
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Manhas A, Patel D, Lone MY, Jha PC. Identification of natural compound inhibitors against PfDXR: A hybrid structure-based molecular modeling approach and molecular dynamics simulation studies. J Cell Biochem 2019; 120:14531-14543. [PMID: 30994966 DOI: 10.1002/jcb.28714] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 01/18/2019] [Accepted: 01/24/2019] [Indexed: 12/30/2022]
Abstract
In the present contribution, multicomplex-based pharmacophore studies were carried out on the structural proteome of Plasmodium falciparum 1-deoxy-D-xylulose-5-phosphate reductoisomerase. Among the constructed models, a representative model with complementary features, accountable for the inhibition was used as a primary filter for the screening of database molecules. Auxiliary evaluations of the screened molecules were performed via drug-likeness and molecular docking studies. Subsequently, the stability of the docked inhibitors was envisioned by molecular dynamics simulations, principle component analysis, and molecular mechanics-Poisson-Boltzmann surface area-based free binding energy calculations. The stability assessment of the hits was done by comparing with the reference (beta-substituted fosmidomycin analog, LC5) to prioritize more potent candidates. All the complexes showed stable dynamic behavior while three of them displayed higher binding free energy compared with the reference. The work resulted in the identification of the compounds with diverse scaffolds, which could be used as initial leads for the design of novel PfDXR inhibitors.
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Affiliation(s)
- Anu Manhas
- School of Chemical Sciences, Central University of Gujarat, Gandhinagar, Gujarat, India
| | - Dhaval Patel
- Department of Bioinformatics and Stśructural Biology, Indian Institute of Advanced Research, Gujarat, India
| | - Mohsin Y Lone
- School of Chemical Sciences, Central University of Gujarat, Gandhinagar, Gujarat, India.,Department of Chemistry, Indian Institute of Technology, Gandhinagar, Gujarat, India
| | - Prakash C Jha
- Centre for Applied Chemistry, Central University of Gujarat, Gandhinagar, Gujarat, India
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58
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Zhang X, Gao C, Liu L, Zhou C, Liu C, Li J, Zhuang J, Sun C. DNA methylation‐based diagnostic and prognostic biomarkers of nonsmoking lung adenocarcinoma patients. J Cell Biochem 2019; 120:13520-13530. [PMID: 30920015 DOI: 10.1002/jcb.28627] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Revised: 01/25/2019] [Accepted: 01/28/2019] [Indexed: 12/12/2022]
Affiliation(s)
- Xiaoming Zhang
- College of Traditional Chinese Medicine Shandong University of Traditional Chinese Medicine Jinan Shandong PR China
| | - Chundi Gao
- College of First Clinical Medicine Shandong University of Traditional Chinese Medicine Jinan Shandong PR China
| | - Lijuan Liu
- Department of Traditional Chinese Medicine Oncology Weifang Traditional Chinese Hospital Weifang Shandong PR China
- Department of Oncology Affiliated Hospital of Weifang Medical University Weifang Shandong PR China
| | - Chao Zhou
- Department of Traditional Chinese Medicine Oncology Weifang Traditional Chinese Hospital Weifang Shandong PR China
- Department of Oncology Affiliated Hospital of Weifang Medical University Weifang Shandong PR China
| | - Cun Liu
- College of First Clinical Medicine Shandong University of Traditional Chinese Medicine Jinan Shandong PR China
| | - Jia Li
- School of Clinical Medicine Weifang Medical University Weifang Shandong PR China
| | - Jing Zhuang
- Department of Traditional Chinese Medicine Oncology Weifang Traditional Chinese Hospital Weifang Shandong PR China
- Department of Oncology Affiliated Hospital of Weifang Medical University Weifang Shandong PR China
| | - Changgang Sun
- Department of Oncology Affiliated Hospital of Weifang Medical University Weifang Shandong PR China
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59
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Lokhande KB, Nagar S, Swamy KV. Molecular interaction studies of Deguelin and its derivatives with Cyclin D1 and Cyclin E in cancer cell signaling pathway: The computational approach. Sci Rep 2019; 9:1778. [PMID: 30741976 PMCID: PMC6370771 DOI: 10.1038/s41598-018-38332-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 11/19/2018] [Indexed: 11/09/2022] Open
Abstract
Deguelin is a major active ingredient and principal component in several plants and it is a potential molecule to target proteins of cancer cell signaling pathway. As a complex natural extract, deguelin interacts with various molecular targets to exert its anti-tumor properties at nanomolar level. It induces cell apoptosis by blocking anti-apoptotic pathways, while inhibiting tumor cell multiplication and malignant transformation through p27-cyclin-E-pRb-E2F1- cell cycle control and HIF-1alphaVEGF antiangiogenic pathways. In silico studies of deguelin and its derivatives is performed to explore interactions with Cyclin D1 and Cyclin E to understand the molecular insights of derivatives with the receptors. Deguelin and its derivatives are minimized by Avogadro to achieve stable conformation. All docking simulation are performed with AutoDockVina and virtual screening of docked ligands are carried out based on binding energy and number of hydrogen bonds. Molecular dynamics (MD) and Simulation of Cyclin D1 and Cyclin E1 is performed for 100 ns and stable conformation is obtained at 78 ns and 19 ns respectively. Ligands thus obtained from docking studies may be probable target to inhibit cancer cell signaling pathways.
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Affiliation(s)
- Kiran Bharat Lokhande
- Bioinformatics Research Laboratory, Dr. D. Y. Patil Biotechnology and Bioinformatics Institute, Dr. D. Y. Patil Vidyapeeth, Pune, 411033, India
| | - Shuchi Nagar
- Bioinformatics Research Laboratory, Dr. D. Y. Patil Biotechnology and Bioinformatics Institute, Dr. D. Y. Patil Vidyapeeth, Pune, 411033, India
| | - K Venkateswara Swamy
- Bioinformatics Research Laboratory, Dr. D. Y. Patil Biotechnology and Bioinformatics Institute, Dr. D. Y. Patil Vidyapeeth, Pune, 411033, India.
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Rawat K, Shard A, Jadhav M, Gandhi M, Anand P, Purohit R, Padwad Y, Sinha AK. Styryl-cinnamate hybrid inhibits glioma by alleviating translation, bioenergetics and other key cellular responses leading to apoptosis. Exp Cell Res 2019; 375:11-21. [PMID: 30513337 DOI: 10.1016/j.yexcr.2018.11.015] [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: 05/08/2018] [Revised: 10/27/2018] [Accepted: 11/19/2018] [Indexed: 10/27/2022]
Abstract
Gliomas are lethal and aggressive form of brain tumors with resistance to conventional radiation and cytotoxic chemotherapies; inviting continuous efforts for drug discovery and drug delivery. Interestingly, small molecule hybrids are one such pharmacophore that continues to capture interest owing to their pluripotent medicinal effects. Accordingly, we earlier reported synthesis of potent Styryl-cinnamate hybrids (analogues of Salvianolic acid F) along with its plausible mode of action (MOA). We explored iTRAQ-LC/MS-MS technique to deduce differentially expressed landscape of native & phospho-proteins in treated glioma cells. Based on this, Protein-Protein Interactome (PPI) was looked into by employing computational tools and further validated in vitro. We hereby report that the Styryl-cinnamate hybrid, an analogue of natural Salvianolic acid F, alters key regulatory proteins involved in translation, cytoskeleton development, bioenergetics, DNA repair, angiogenesis and ubiquitination. Cell cycle analysis dictates arrest at G0/G1 stage along with reduced levels of cyclin D; involved in G1 progression. We discovered that Styryl-cinnamate hybrid targets glioma by intrinsically triggering metabolite-mediated stress. Various oncological circuits alleviated by the potential drug candidate strongly supports the role of such pharmacophores as anticancer drugs. Although, further analysis of SC hybrid in treating xenografts or solid tumors is yet to be explored but their candidature has gained huge impetus through this study. This study equips us better in understanding the shift in proteomic landscape after treating glioma cells with SC hybrid. It also allows us to elicit molecular targets of this potential drug before progressing to preclinical studies.
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Affiliation(s)
- Kiran Rawat
- Pharmacology and Toxicology Laboratory, Food and Nutraceuticals Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, 176061 H.P., India; Academy of Scientific and Innovative Research (AcSIR), CSIR, Institute of Himalayan Bioresource Technology, Palampur, 176061 H.P., India
| | - Amit Shard
- Natural Product Chemistry and Process Development Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, 176061 H.P., India
| | - Manali Jadhav
- SAIF, Indian Institute of Technology, Bombay 400076, Maharashtra, India
| | - Mayuri Gandhi
- SAIF, Indian Institute of Technology, Bombay 400076, Maharashtra, India
| | - Prince Anand
- Pharmacology and Toxicology Laboratory, Food and Nutraceuticals Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, 176061 H.P., India; Academy of Scientific and Innovative Research (AcSIR), CSIR, Institute of Himalayan Bioresource Technology, Palampur, 176061 H.P., India
| | - Rituraj Purohit
- Division of Biotechnology, CSIR-Institute of Himalayan Bioresource Technology, Palampur, 176061 H.P., India
| | - Yogendra Padwad
- Pharmacology and Toxicology Laboratory, Food and Nutraceuticals Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, 176061 H.P., India; Academy of Scientific and Innovative Research (AcSIR), CSIR, Institute of Himalayan Bioresource Technology, Palampur, 176061 H.P., India.
| | - Arun K Sinha
- Natural Product Chemistry and Process Development Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, 176061 H.P., India; Medicinal & Process Chemistry, CSIR-Central Drug Research Institute, Lucknow, 226031 U.P., India.
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61
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Sneha P, Zenith TU, Abu Habib US, Evangeline J, Thirumal Kumar D, George Priya Doss C, Siva R, Zayed H. Impact of missense mutations in survival motor neuron protein (SMN1) leading to Spinal Muscular Atrophy (SMA): A computational approach. Metab Brain Dis 2018; 33:1823-1834. [PMID: 30006696 DOI: 10.1007/s11011-018-0285-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 06/29/2018] [Indexed: 12/12/2022]
Abstract
Spinal muscular atrophy (SMA) is a neuromuscular disorder caused by the mutations in survival motor neuron 1 gene (SMN1). The molecular pathology of missense mutations in SMN1 is not thoroughly investigated so far. Therefore, we collected all missense mutations in the SMN1 protein, using all possible search terms, from three databases (PubMed, PMC and Google Scholar). All missense mutations were subjected to in silico pathogenicity, conservation, and stability analysis tools. We used statistical analysis as a QC measure for validating the specificity and accuracy of these tools. PolyPhen-2 demonstrated the highest specificity and accuracy. While PolyPhen-1 showed the highest sensitivity; overall, PolyPhen2 showed better measures in comparison to other in silico tools. Three mutations (D44V, Y272C, and Y277C) were identified as the most pathogenic and destabilizing. Further, we compared the physiochemical properties of the native and the mutant amino acids and observed loss of H-bonds and aromatic stacking upon the cysteine to tyrosine substitution, which led to the loss of aromatic rings and may reduce protein stability. The three mutations were further subjected to Molecular Dynamics Simulation (MDS) analysis using GROMACS to understand the structural changes. The Y272C and Y277C mutants exhibited maximum deviation pattern from the native protein as compared to D44V mutant. Further MDS analysis predicted changes in the stability that may have been contributed due to the loss of hydrogen bonds as observed in intramolecular hydrogen bond analysis and physiochemical analysis. A loss of function/structural impact was found to be severe in the case of Y272C and Y277C mutants in comparison to D44V mutation. Correlating the results from in silico predictions, physiochemical analysis, and MDS, we were able to observe a loss of stability in all the three mutants. This combinatorial approach could serve as a platform for variant interpretation and drug design for spinal muscular dystrophy resulting from missense mutations.
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Affiliation(s)
- P Sneha
- School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India
| | - Tanzila U Zenith
- College of Health Sciences, Department of Biomedical Sciences, Qatar University, Doha, Qatar
| | - Ummay Salma Abu Habib
- College of Health Sciences, Department of Biomedical Sciences, Qatar University, Doha, Qatar
| | - Judith Evangeline
- School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India
| | - D Thirumal Kumar
- School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India
| | - C George Priya Doss
- School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India.
| | - R Siva
- School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India
| | - Hatem Zayed
- College of Health Sciences, Department of Biomedical Sciences, Qatar University, Doha, Qatar.
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Gao C, Zhou C, Zhuang J, Liu L, Wei J, Liu C, Li H, Sun C. Identification of key candidate genes and miRNA‑mRNA target pairs in chronic lymphocytic leukemia by integrated bioinformatics analysis. Mol Med Rep 2018; 19:362-374. [PMID: 30431072 PMCID: PMC6297738 DOI: 10.3892/mmr.2018.9636] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 10/08/2018] [Indexed: 12/12/2022] Open
Abstract
Chronic lymphocytic leukemia (CLL) is a malignant clonal proliferative disorder of B cells. Inhibition of cell apoptosis and cell cycle arrest are the main pathological causes of this disease, but its molecular mechanism requires further investigation. The purpose of the present study was to identify biomarkers for the early diagnosis and treatment of CLL, and to explore the molecular mechanisms of CLL progression. A total of 488 differentially expressed genes (DEGs) and 32 differentially expressed microRNAs (miRNAs; DEMs) for CLL were identified by analyzing the gene chips GSE22529, GSE39411 and GSE62137. Functional and pathway enrichment analyses of DEGs demonstrated that DEGs were mainly involved in transcriptional dysregulation and multiple signaling pathways, such as the nuclear factor‑κB and mitogen‑activated protein kinase signaling pathways. In addition, Cytoscape software was used to visualize the protein‑protein interactions of these DEGs in order to identify hub genes, which could be used as biomarkers for the early diagnosis and treatment of CLL. Cytoscape software was also used to analyze the association between the predicted target mRNAs of DEMs and DEGs and increase knowledge about the miRNA‑mRNA regulatory network associated with the progression of CLL. Taken together, the present study provided a bioinformatics basis for advancing our understanding of the pathogenesis of CLL by identifying differentially expressed hub genes, miRNA‑mRNA target pairs and molecular pathways. In addition, hub genes may be used as novel biomarkers for the diagnosis of CLL and to guide the selection of CLL drug combinations.
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Affiliation(s)
- Chundi Gao
- College of First Clinical Medicine, Shandong University of Traditional Chinese Medicine, Jinan, Shandong 250014, P.R. China
| | - Chao Zhou
- Cancer Center, Weifang Traditional Chinese Hospital, Weifang, Shandong 261000, P.R. China
| | - Jing Zhuang
- Cancer Center, Weifang Traditional Chinese Hospital, Weifang, Shandong 261000, P.R. China
| | - Lijuan Liu
- Cancer Center, Weifang Traditional Chinese Hospital, Weifang, Shandong 261000, P.R. China
| | - Junyu Wei
- Cancer Center, Weifang Traditional Chinese Hospital, Weifang, Shandong 261000, P.R. China
| | - Cun Liu
- College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, Shandong 250014, P.R. China
| | - Huayao Li
- College of First Clinical Medicine, Shandong University of Traditional Chinese Medicine, Jinan, Shandong 250014, P.R. China
| | - Changgang Sun
- Cancer Center, Weifang Traditional Chinese Hospital, Weifang, Shandong 261000, P.R. China
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63
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Bayel Secinti B, Tatar G, Taskin Tok T. Determination of potential selective inhibitors for ROCKI and ROCKII isoforms with molecular modeling techniques: structure based docking, ADMET and molecular dynamics simulation. J Biomol Struct Dyn 2018; 37:2457-2463. [DOI: 10.1080/07391102.2018.1491420] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Burcu Bayel Secinti
- Department of Bioinformatics and Computational Biology, Gaziantep University, Institute of Health Sciences, Gaziantep, Turkey
| | - Gizem Tatar
- Department of Bioinformatics and Computational Biology, Gaziantep University, Institute of Health Sciences, Gaziantep, Turkey
| | - Tugba Taskin Tok
- Faculty of Arts and Sciences, Department of Chemistry, Gaziantep University, Gaziantep, TurkeyCommunicated by Ramaswamy H. Sarma
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64
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Ganesan P, Ramalingam R. Investigation of structural stability and functionality of homodimeric gramicidin towards peptide‐based drug: a molecular simulation approach. J Cell Biochem 2018; 120:4903-4911. [DOI: 10.1002/jcb.27765] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 09/06/2018] [Indexed: 12/17/2022]
Affiliation(s)
- Pavithrra Ganesan
- Bioinformatics Lab, Department of Biotechnology, School of Biosciences and Technology Vellore Institute of Technology (VIT) Vellore India
| | - Rajasekaran Ramalingam
- Bioinformatics Lab, Department of Biotechnology, School of Biosciences and Technology Vellore Institute of Technology (VIT) Vellore India
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65
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Kataria A, Singh J, Kundu B. Identification and validation of
l
‐asparaginase as a potential metabolic target against
Mycobacterium tuberculosis. J Cell Biochem 2018; 120:143-154. [DOI: 10.1002/jcb.27169] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 05/18/2018] [Indexed: 12/15/2022]
Affiliation(s)
- Arti Kataria
- Kusuma School of Biological Sciences Indian Institute of Technology Delhi New Delhi India
| | - Jasdeep Singh
- Kusuma School of Biological Sciences Indian Institute of Technology Delhi New Delhi India
| | - Bishwajit Kundu
- Kusuma School of Biological Sciences Indian Institute of Technology Delhi New Delhi India
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66
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The variation of mitochondrial NADH dehydrogenase subunit 4 (mtND4) and molecular dynamics simulation of SNPs among Iranian women with breast cancer. J Mol Graph Model 2018; 85:242-249. [PMID: 30227369 DOI: 10.1016/j.jmgm.2018.08.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2018] [Revised: 07/31/2018] [Accepted: 08/20/2018] [Indexed: 01/20/2023]
Abstract
Breast cancer is the second cause of death among women all around the world. One out of every eight women is diagnosed with breast cancer in Iran. There are many reasons for cancer, one of which is the mutations in the mitochondrial genome observed in most breast cancer studies. However, the aim of this study is to evaluate the genetic region of NADH dehydrogenase subunit 4 in patients with breast cancer. First, the genomic DNA was extracted from a tissue. The NADH dehydrogenase subunit 4 coding region was amplified by PCR, and then the SSCP was sequenced. After that, the molecular dynamics were employed. The association between the mutations and the prognostic factors such as ER, PR, HER-2, and age were statistically examined. The sequence of the ND4 area was determined in 24 suspected patients, and 15 nucleotide changes were reported. The role of this variations was investigated by in-silico. The harmful mutations were predicted based on some servers. The molecular dynamics results showed that there is a significant relationship between the mutant protein and the changes in the structural conformation. Our results showed that the mutation in the ND4 area plays an important role in developing breast cancer. So, it can be concluded that the mitochondrial NADH dehydrogenase analysis may help to detect breast cancer in the early stages.
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67
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Tu J, Song LT, Liu RR, Zhai HL, Wang J, Zhang XY. Molecular inhibitory mechanism study on the potent inhibitor brigatinib against four crizotinib‐resistant ALK mutations. J Cell Biochem 2018; 120:562-574. [DOI: 10.1002/jcb.27412] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 07/10/2018] [Indexed: 01/04/2023]
Affiliation(s)
- Jing Tu
- College of Chemistry & Chemical Engineering, Lanzhou University Lanzhou China
| | - Li Ting Song
- College of Chemistry & Chemical Engineering, Lanzhou University Lanzhou China
| | - Rui Rui Liu
- College of Chemistry & Chemical Engineering, Lanzhou University Lanzhou China
| | - Hong Lin Zhai
- College of Chemistry & Chemical Engineering, Lanzhou University Lanzhou China
| | - Juan Wang
- College of Chemistry & Chemical Engineering, Lanzhou University Lanzhou China
| | - Xiao Yun Zhang
- College of Chemistry & Chemical Engineering, Lanzhou University Lanzhou China
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68
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Manhas A, Patel A, Lone MY, Jha PK, Jha PC. Identification of
Pf
ENR inhibitors: A hybrid structure‐based approach in conjunction with molecular dynamics simulations. J Cell Biochem 2018; 119:8490-8500. [DOI: 10.1002/jcb.27075] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 04/26/2018] [Indexed: 01/31/2023]
Affiliation(s)
- Anu Manhas
- School of Chemical Sciences Central University of Gujarat Gandhinagar Gujarat India
| | - Anjali Patel
- Department of Physics M. S. University of Baroda Vadodara Gujarat India
| | - Mohsin Y. Lone
- School of Chemical Sciences Central University of Gujarat Gandhinagar Gujarat India
- Department of Chemistry Indian Institute of Technology Gandhinagar Gujarat India
| | - Prafulla K. Jha
- Department of Physics M. S. University of Baroda Vadodara Gujarat India
| | - Prakash C. Jha
- Centre for Applied Chemistry Central University of Gujarat Gandhinagar Gujarat India
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69
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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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70
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Targeting Outer Membrane Protein Component AdeC for the Discovery of Efflux Pump Inhibitor against AdeABC Efflux Pump of Multidrug Resistant Acinetobacter baumannii. Cell Biochem Biophys 2018; 76:391-400. [PMID: 29926429 DOI: 10.1007/s12013-018-0846-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 06/07/2018] [Indexed: 01/19/2023]
Abstract
The structure and functioning of multidrug efflux systems provide us with a better understanding of the transport of various antibiotics, thus giving a path for the discovery of effective compounds for combating the multidrug resistance in Acinetobacter baumannii. In the present study, a number of computational techniques have been used to search for an inhibitor for the RND efflux pump, AdeABC, of A. baumannii targeting specifically its outermost component, i.e., AdeC. We have prepared the three-dimensional structure for AdeC using MODELLER v9.16 and identified its active binding site using SiteMap. Using high-throughput virtual screening, we identified compounds from a large library of biogenic compounds on the basis of their effective interaction at the binding site of AdeC. The validation of docking step was performed by plotting ROC curve (enrichment calculations). The docked complexes were further analyzed for their binding free energies by molecular mechanics using Generalized Born model and Solvent Accessibility (MMGBSA). The molecular dynamics simulation was performed for AdeC-ZINC77257599 complex using GROMACS. The present rational drug designing, molecular mechanics and molecular dynamics data provided an inhibitor, i.e, ZINC77257599 [(3R,4Z,6E,8E)-3-hydroxy-2,2,4-trimethyl-10-oxazol-5-yl-deca-4,6,8-trienamide], for the outer membrane protein component (AdeC) of efflux pump AdeABC of A. baumannii.
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71
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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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72
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Gao C, Zhou C, Zhuang J, Liu L, Liu C, Li H, Liu G, Wei J, Sun C. MicroRNA expression in cervical cancer: Novel diagnostic and prognostic biomarkers. J Cell Biochem 2018; 119:7080-7090. [PMID: 29737570 DOI: 10.1002/jcb.27029] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 04/06/2018] [Indexed: 12/31/2022]
Abstract
Growing evidence has shown that a large number of miRNAs are abnormally expressed in cervical cancer (CC) tissues and play irreplaceable roles in tumorigenesis, progression, and metastasis. This study aimed to identify new biomarkers and pivotal genes associated with CC prognosis through comprehensive bioinformatics analysis. At first, the data of gene expression microarray (GSE30656) was downloaded from GEO database and differential miRNAs were obtained. Additionally, 4 miRNAs associated with the survival time of patients with CC were screened through TCGA differential data analysis, Kaplan-Meier, and Landmark analysis. Among them, the low expression of miR-188 and high expression of miR-223 correlated with the short survival of CC patients, while the down-regulation of miR-99a and miR-125b was closely related to the 5-year survival rate of patients. Then, based on the correspondence between the differentially expressed genes (DEGs) in CC from the TCGA data and the 4 miRNAs target genes, 58 target genes were screened to perform the analysis of function enrichment and the visualization of protein-protein interaction (PPI) networks. The seven pivotal genes of the PPI network as the target genes of four miRNAs related to prognosis, they were directly or indirectly involved in the development of CC. In this study, based on high-throughput data mining, differentially expressed miRNAs and related target genes were analyzed to provide an effective bioinformatics basis for further understanding of the pathogenesis and prognosis of CC. And the results may be a promising biomarker for the early screening of high-risk populations and early diagnosis of cervical cancer.
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Affiliation(s)
- Chundi Gao
- College of First Clinical Medicine, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, P. R. China
| | - Chao Zhou
- Departmen of Oncology, Weifang Traditional Chinese Hospital, Weifang, Shandong, P. R. China.,Department of Oncology, Affiliated Hospital of Weifang Medical University, Weifang, Shandong, P. R. China
| | - Jing Zhuang
- Departmen of Oncology, Weifang Traditional Chinese Hospital, Weifang, Shandong, P. R. China.,Department of Oncology, Affiliated Hospital of Weifang Medical University, Weifang, Shandong, P. R. China
| | - Lijuan Liu
- Departmen of Oncology, Weifang Traditional Chinese Hospital, Weifang, Shandong, P. R. China.,Department of Oncology, Affiliated Hospital of Weifang Medical University, Weifang, Shandong, P. R. China
| | - Cun Liu
- College of First Clinical Medicine, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, P. R. China
| | - Huayao Li
- College of First Clinical Medicine, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, P. R. China
| | - Gongxi Liu
- Departmen of Oncology, Weifang Traditional Chinese Hospital, Weifang, Shandong, P. R. China.,Department of Oncology, Affiliated Hospital of Weifang Medical University, Weifang, Shandong, P. R. China
| | - Junyu Wei
- Departmen of Oncology, Weifang Traditional Chinese Hospital, Weifang, Shandong, P. R. China.,Department of Oncology, Affiliated Hospital of Weifang Medical University, Weifang, Shandong, P. R. China
| | - Changgang Sun
- Department of Oncology, Affiliated Hospital of Weifang Medical University, Weifang, Shandong, P. R. China
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73
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Singh P, Dass JFP. Nearly neutral evolution in IFNL3 gene retains the immune function to detect and clear the viral infection in HCV. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2018; 140:107-116. [PMID: 29746888 DOI: 10.1016/j.pbiomolbio.2018.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 04/24/2018] [Accepted: 05/05/2018] [Indexed: 02/07/2023]
Abstract
IFNL3 gene plays a crucial role in immune defense against viruses. It induces the interferon stimulated genes (ISGs) with antiviral properties by activating the JAK-STAT pathway. In this study, we investigated the evolutionary force involved in shaping the IFNL3 gene to perform its downstream function as a regulatory gene in HCV clearance. We have selected 25 IFNL3 coding sequences with human gene as a reference sequence and constructed a phylogeny. Furthermore, rate of variation, substitution saturation test, phylogenetic informativeness and differential selection were also analysed. The codon evolution result suggests that nearly neutral mutation is the key pattern in shaping the IFNL3 evolution. The results were validated by subjecting the human IFNL3 protein variants to that of the native through a molecular dynamics simulation study. The molecular dynamics simulation clearly depicts the negative impact on the reported variants in human IFNL3 protein. However, these detrimental mutations (R157Q and R157W) were shown to be negatively selected in the evolutionary study of the mammals. Hence, the variation revealed a mild impact on the IFNL3 function and may be removed from the population through negative selection due to its high functional constraints. In a nutshell, our study may contribute the overall evidence in phylotyping and structural transformation that takes place in the non-synonymous substitutions of IFNL3 protein. Substantially, our obtained theoretical knowledge will lay the path to extend the experimental validation in HCV clearance.
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Affiliation(s)
- Pratichi Singh
- Department of Integrative Biology, School of Biosciences and Technology, VIT University, Vellore, Tamil Nadu 632014, India
| | - J Febin Prabhu Dass
- Department of Integrative Biology, School of Biosciences and Technology, VIT University, Vellore, Tamil Nadu 632014, India.
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74
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Juritz EI, Bascur JP, Almonacid DE, González-Nilo FD. Novel Insights for Inhibiting Mutant Heterodimer IDH1 wt-R132H in Cancer: An In-Silico Approach. Mol Diagn Ther 2018; 22:369-380. [PMID: 29651790 DOI: 10.1007/s40291-018-0331-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
BACKGROUND Isocitrate dehydrogenase 1 (IDH1) is a dimeric enzyme responsible for supplying the cell's nicotinamide adenine dinucleotide phosphate (NADPH) reserves via dehydrogenation of isocitrate (ICT) and reduction of NADP+. Mutations in position R132 trigger cancer by enabling IDH1 to produce D-2-hydroxyglutarate (2-HG) and reduce inhibition by ICT. Mutant IDH1 can be found as a homodimer or a heterodimer. OBJECTIVE We propose a novel strategy to inhibit IDH1 R132 variants as a means not to decrease the concentration of 2-HG but to provoke a cytotoxic effect, as the cell malignancy at this point no longer depends on 2-HG. We aim to inhibit the activity of the mutant heterodimer to block the wild-type subunit. Limiting the NADPH reserves in a cancerous cell will enhance its susceptibility to the oxidative stress provoked by chemotherapy. METHODS We performed a virtual screening using all US FDA-approved drugs to replicate the loss of inhibition of mutant IDH1 by ICT. We characterized our results based on molecular interactions and correlated them with the described phenotypes. RESULTS We replicated the loss of inhibition by ICT in mutant IDH1. We identified 20 drugs with the potential to inhibit the heterodimeric isoform. Six of them are used in cancer treatment. CONCLUSIONS We present 20 FDA-approved drugs with the potential to inhibit IDH1 wild-type activity in mutated cells. We believe this work may provide important insights into current and new approaches to dealing with IDH1 mutations. In addition, it may be used as a basis for additional studies centered on drugs presenting differential sensitivities to different IDH1 isoforms.
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Affiliation(s)
- Ezequiel Iván Juritz
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andrés Bello, 8370146, Santiago, Chile.
| | - Juan Pablo Bascur
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andrés Bello, 8370146, Santiago, Chile
| | - Daniel Eduardo Almonacid
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andrés Bello, 8370146, Santiago, Chile.,uBiome, Inc., San Francisco, CA, USA
| | - Fernando Danilo González-Nilo
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andrés Bello, 8370146, Santiago, Chile.,Centro Interdisciplinario de Neurociencia de Valparaíso, Facultad de Ciencias, Universidad de Valparaíso, 2366103, Valparaíso, Chile
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75
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Karunakaran R, Srikumar PS. A molecular dynamics approach to explore the structural characterization of cataract causing mutation R58H on human γD crystallin. Mol Cell Biochem 2018. [PMID: 29532225 DOI: 10.1007/s11010-018-3342-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The crystallins are a family of monomeric proteins present in the mammalian lens and mutations in these proteins cause various forms of cataracts. The aim of our current study is to emphasize the structural characterization of aggregation propensity of mutation R58H on γD crystallin using molecular dynamics (MD) approach. MD result revealed that difference in the sequence level display a wide variation in the backbone atomic position, and thus exhibits rigid conformational dynamics. Changes in the flexibility of residues favoured to increase the number of intra-molecular hydrogen bonds in mutant R58H. Moreover, notable changes in the hydrogen bonding interaction resulted to cause the misfolding of mutant R58H by introducing α-helix. Principal component analysis (PCA) result suggested that mutant R58H showed unusual conformational dynamics along the two principal components when compared to the wild-type (WT)-γD crystallin. In a nutshell, the increased surface hydrophobicity could be the cause of self-aggregation of mutant R58H leading to aculeiform cataract.
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Affiliation(s)
- Rohini Karunakaran
- Unit of Biochemistry, Faculty of Medicine, AIMST University, Semeling, Bedong, Kedah, Malaysia.
| | - P S Srikumar
- Unit of Psychiatry, Faculty of Medicine, AIMST University, Bedong, Malaysia
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76
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Xing M, Akowuah GA, Gautam V, Gaurav A. Structure-based design of selective phosphodiesterase 4B inhibitors based on ginger phenolic compounds. J Biomol Struct Dyn 2017; 35:2910-2924. [PMID: 27608741 DOI: 10.1080/07391102.2016.1234417] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 09/05/2016] [Indexed: 01/02/2023]
Abstract
Phosphodiesterase 4 (PDE4) has been established as a drug target for inflammatory diseases of respiratory tract like asthma and chronic obstructive pulmonary disease. The selective inhibitors of PDE4B, a subtype of PDE4, are devoid of adverse effects like nausea and vomiting commonly associated with non-selective PDE4B inhibitors. This makes the development of PDE4B subtype selective inhibitors a desirable research goal. Thus, in the present study, molecular docking, molecular dynamic simulations and binding free energy were performed to explore potential selective PDE4B inhibitors based on ginger phenolic compounds. The results of docking studies indicate that some of the ginger phenolic compounds demonstrate higher selective PDE4B inhibition than existing selective PDE4B inhibitors. Additionally, 6-gingerol showed the highest PDE4B inhibitory activity as well as selectivity. The comparison of binding mode of PDE4B/6-gingerol and PDE4D/6-gingerol complexes revealed that 6-gingerol formed additional hydrogen bond and hydrophobic interactions with active site and control region 3 (CR3) residues in PDE4B, which were primarily responsible for its PDE4B selectivity. The results of binding free energy demonstrated that electrostatic energy is the primary factor in elucidating the mechanism of PDE4B inhibition by 6-gingerol. Dynamic cross-correlation studies also supported the results of docking and molecular dynamics simulation. Finally, a small library of molecules were designed based on the identified structural features, majority of designed molecules showed higher PDE4B selectivity than 6-gingerol. These results provide important structural features for designing new selective PDE4B inhibitors as anti-inflammatory drugs and promising candidates for synthesis and pre-clinical pharmacological investigations.
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Affiliation(s)
- Ming Xing
- a Faculty of Pharmaceutical Sciences , UCSI University , No. 1, UCSI Heights, Jalan Menara Gading, Taman Connaught, 56000 Kuala Lumpur , Federal Territory of Kuala Lumpur , Malaysia
| | - Gabriel Akyirem Akowuah
- a Faculty of Pharmaceutical Sciences , UCSI University , No. 1, UCSI Heights, Jalan Menara Gading, Taman Connaught, 56000 Kuala Lumpur , Federal Territory of Kuala Lumpur , Malaysia
| | - Vertika Gautam
- b Department of Chemistry, Faculty of Science , University of Malaya , 50603 Kuala Lumpur , Federal Territory of Kuala Lumpur , Malaysia
| | - Anand Gaurav
- a Faculty of Pharmaceutical Sciences , UCSI University , No. 1, UCSI Heights, Jalan Menara Gading, Taman Connaught, 56000 Kuala Lumpur , Federal Territory of Kuala Lumpur , Malaysia
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Comparative study of the efficacy of pulsed electromagnetic field and low level laser therapy on mitogen-activated protein kinases. Biochem Biophys Rep 2017; 9:316-321. [PMID: 28956019 PMCID: PMC5614620 DOI: 10.1016/j.bbrep.2017.01.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 01/22/2017] [Accepted: 01/24/2017] [Indexed: 12/11/2022] Open
Abstract
Mitogen-Activated Protein Kinases (MAPKs) consist of three major signaling members: extracellular signal-regulated kinase (ERK), p38 and C-JUN N-terminal kinase (JNK). We investigated physiological effects of Pulsed Electromagnetic Field Therapy (PEMFT) and Low Level Laser Therapy (LLLT) on human body, adopting the expression level of mitogen-activated protein kinases as an indicator via assessment of the activation levels of three major families of MAPKS, ERK, p38 and JNK in the peripheral lymphocytes of patients before and after the therapies. Assessment for the expression levels of MAPKs families' were done, in the peripheral lymphocytes of patients recently have appendectomy, using flow cytometric analysis of multiple signaling pathways, pre and post LLLT and PEMFT application (twice daily for 6 successive days) on the appendectomy wound. There were non-significant differences in the expression levels of MAPKs families' pre- therapies application. But there were significant increase in the ERK expression levels post application of LLLT compared to its pre application (p<0.01). Also, there was significant increase in the ERK, p38 and C-Jun N terminal expression level values post application of PEMFT compared to its pre application expression levels (p<0.01 for each). The present study demonstrates that PEMFT has a powerful healing effect more than LLLT as it increase the activation of ERK, P38 and C-Jun-N Terminal while LLLT only increase the activation of ERK. LLLT has more potent pain decreasing effect than PEMFT as it does not activate P38 pathway like PEMFT. PEMFT stimulates all pathways of MAPKs including ERK, P38 and C-Jun-terminal. LLLT stimulates only the ERK pathway in MAPKS activation pathways. PEMFT has a powerful healing effect more than LLLT as it increase the activation of ERK, P38 and C-Jun-N Terminal. LLLT has more potent pain decreasing effect than PEMFT as it does not activate p38 pathway. PEMFT should not be used as pain killer modality in acute pain but it's very useful to be used in chronic pain management with hypothalamic –ve Ingram due to its stimulatory effect on P38.
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78
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Rajendran V, Gopalakrishnan C, Sethumadhavan R. Pathological role of a point mutation (T315I) in BCR‐ABL1 protein—A computational insight. J Cell Biochem 2017; 119:918-925. [DOI: 10.1002/jcb.26257] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 07/05/2017] [Indexed: 11/08/2022]
Affiliation(s)
- Vidya Rajendran
- Computational Biology LabDepartment of BiotechnologyVellore Institute of Technology UniversityVelloreTamil NaduIndia
| | | | - Rao Sethumadhavan
- Computational Biology LabDepartment of BiotechnologyVellore Institute of Technology UniversityVelloreTamil NaduIndia
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79
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Xie ZC, Dang YW, Wei DM, Chen P, Tang RX, Huang Q, Liu JH, Luo DZ. Clinical significance and prospective molecular mechanism of MALAT1 in pancreatic cancer exploration: a comprehensive study based on the GeneChip, GEO, Oncomine, and TCGA databases. Onco Targets Ther 2017; 10:3991-4005. [PMID: 28860807 PMCID: PMC5558580 DOI: 10.2147/ott.s136878] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Purpose Long noncoding RNAs (lncRNAs) are known to function as regulators in the development and occurrence of various tumors. MALAT1 is a highly conserved lncRNA and has vital functions in diverse tumors, including pancreatic cancer (PC). However, the underlying molecular regulatory mechanism involved in the occurrence and development of PC remains largely unknown. Thus, it is important to explore MALAT1 in PC and elucidate its function, which might offer a new perspective for clinical diagnosis and therapy. Methods First, we used the Gene Expression Omnibus, Oncomine, and The Cancer Genome Atlas databases to determine the clinical diagnostic and prognostic values of MALAT1. We next used our own GeneChip and The Cancer Genome Atlas database to collect the possible target genes of MALAT1 and further utilized a bioinformatics analysis to explore the underlying significant pathways that might be crucial in PC. Finally, we identified several key target genes of MALAT1 and hope to offer references for future research. Results We found that the expression of MALAT1 was significantly elevated in patients with PC. A receiver operating characteristics curve analysis showed a moderate diagnostic value (area under the curve =0.75, sensitivity =0.66, specificity =0.72). A total of 224 important overlapping genes were collected, and six hub genes (CCND1, MAPK8, VEGFA, FOS, CDH1, and HSP90AA1) were identified, of which CCND1, MAPK8, and VEGFA, are important genes in PC. Several pathways, including the mTOR signaling pathway, pathways in cancer, and the MAPK signaling pathway, were suggested to be the vital MALAT1 pathways in PC. Conclusion MALAT1 is suggested to be a promising diagnostic biomarker in PC. Six hub genes (CCND1, MAPK8, VEGFA, FOS, CDH1, and HSP90AA1), and specifically CCND1, MAPK8, and VEGFA, might be key MALAT1 target genes in PC. Due to their possible clinical significance in PC, several pathways, such as the mTOR signaling pathway, pathways in cancer, and the MAPK signaling pathway, are worthy of further study.
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Affiliation(s)
| | | | | | | | | | | | - Jiang-Hua Liu
- Department of Pathology.,Department of Emergency Medicine, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, People's Republic of China
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80
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Balmith M, Soliman MES. Non-active site mutations disturb the loop dynamics, dimerization, viral budding and egress of VP40 of the Ebola virus. MOLECULAR BIOSYSTEMS 2017; 13:585-597. [PMID: 28170013 DOI: 10.1039/c6mb00803h] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The first account of the dynamic features of the loop region of VP40 of the Ebola virus (EboV) using accelerated molecular dynamics (aMD) simulations is reported herein. Due to its major role in the Ebola life cycle, VP40 is considered a promising therapeutic target. The available experimental data on the N-terminal domain (NTD) loop indicates that mutations K127A, T129A and N130A demonstrate an unrecognized role for NTD-plasma membrane (PM) interaction for efficient VP40-PM localization, oligomerization, matrix assembly and egress. Despite experimental results, the molecular description of VP40 and the information it can provide still remain vague. Therefore, to gain further molecular insight into the effect of mutations on the loop region of VP40 and its effects on the overall protein conformation and VP40 dimerization, aMD simulations and post-dynamic analyses were employed for wildtype (WT) and mutant systems. The results showed significant variations in the presence of mutations as per RMSF, RMSD, Rg, PCA and distance calculations in comparison to the WT. These results could provide researchers with insight with regards to the conformational aspects concerning VP40 and its close relation to the experimental data. We believe that the results presented in this study will ultimately provide a useful understanding of the structural landscape of the loop region of VP40, which would contribute towards the discovery of novel EboV inhibitors.
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Affiliation(s)
- Marissa Balmith
- Molecular Modeling and Drug Design Research Group, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4001, South Africa.
| | - Mahmoud E S Soliman
- Molecular Modeling and Drug Design Research Group, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4001, South Africa. and Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Zagazig University, Zagazig, Egypt and College of Pharmacy and Pharmaceutical Sciences, Florida Agricultural and Mechanical University, FAMU, Tallahassee, Florida 32307, USA
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81
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Sinha S, Verma S, Singh A, Somvanshi P, Grover A. Simulation Based Investigation of Deleterious nsSNPs in ATXN2 Gene and Its Structural Consequence Toward Spinocerebellar Ataxia. J Cell Biochem 2017; 119:499-510. [PMID: 28612427 DOI: 10.1002/jcb.26209] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 06/12/2017] [Indexed: 12/11/2022]
Abstract
Spinocerebellar degeneration, termed as ataxia is a neurological disorder of central nervous system, characterized by limb in-coordination and a progressive gait. The patient also demonstrates specific symptoms of muscle weakness, slurring of speech, and decreased vibration senses. Expansion of polyglutamine trinucleotide (CAG) within ATXN2 gene with 35 or more repeats, results in spinocerebellar ataxia type-2. Protein ataxin-2 coded by ATXN2 gene has been reported to have a crucial role in translation of the genetic information through sequestering the histone acetyl transferases (HAT) resulting in a state of hypo-acetylation. In the present study, we have evaluated the outcome for 122 non synonymous single nucleotide polymorphisms (nsSNPs) reported within ATXN2 gene through computational tools such as SIFT, PolyPhen 2.0, PANTHER, I-mutant 2.0, Phd-SNP, Pmut, MutPred. The apo and mutant (L305V and Q339L) form of structures for the ataxin-2 protein were modeled for gaining insights toward 3D spatial arrangement. Further, molecular dynamics simulations and structural analysis were performed to observe the brunt of disease associated nsSNPs toward the strength and secondary properties of ataxin-2 protein structure. Our results showed that, L305V is a highly deleterious and disease causing point substitution. Analysis based on RMSD, RMSF, Rg, SASA, number of hydrogen bonds (NH bonds), covariance matrix trace, projection analysis for eigen vector demonstrated a significant instability and conformation along with rise in mutant flexibility values in comparison to the apo form of ataxin-2 protein. The study provides a blue print of computational methodologies to examine the ataxin-blend SNPs. J. Cell. Biochem. 119: 499-510, 2018. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Siddharth Sinha
- Department of Biotechnology, TERI University, New Delhi, 110070, India
| | - Sharad Verma
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Aditi Singh
- Department of Biotechnology, TERI University, New Delhi, 110070, India.,School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Pallavi Somvanshi
- Department of Biotechnology, TERI University, New Delhi, 110070, India
| | - Abhinav Grover
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067, India
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82
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Yan L, Zhang L, Zhang Y, Qiao X, Pan J, Liu H, Lu S, Xiang B, Lu T, Yuan H. Insight into the key features for ligand binding in Y1230 mutated c-Met kinase domain by molecular dynamics simulations. J Biomol Struct Dyn 2017; 36:2015-2031. [DOI: 10.1080/07391102.2017.1340852] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Libo Yan
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Discovery for Metabolic Disease and Laboratory of Molecular Design and Drug Discovery, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, P.R. China
| | - Li Zhang
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Discovery for Metabolic Disease and Laboratory of Molecular Design and Drug Discovery, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, P.R. China
| | - Yanmin Zhang
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Discovery for Metabolic Disease and Laboratory of Molecular Design and Drug Discovery, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, P.R. China
| | - Xin Qiao
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Discovery for Metabolic Disease and Laboratory of Molecular Design and Drug Discovery, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, P.R. China
| | - Jing Pan
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Discovery for Metabolic Disease and Laboratory of Molecular Design and Drug Discovery, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, P.R. China
| | - Haichun Liu
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Discovery for Metabolic Disease and Laboratory of Molecular Design and Drug Discovery, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, P.R. China
| | - Shuai Lu
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Discovery for Metabolic Disease and Laboratory of Molecular Design and Drug Discovery, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, P.R. China
| | - Bingren Xiang
- Center for instrument analysis, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, P.R. China
| | - Tao Lu
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Discovery for Metabolic Disease and Laboratory of Molecular Design and Drug Discovery, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, P.R. China
| | - Haoliang Yuan
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Discovery for Metabolic Disease and Laboratory of Molecular Design and Drug Discovery, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, P.R. China
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Bagherzadeh K, Maleki M, Golestani A, Khajeh K, Amanlou M. Chondrotinase ABC I thermal stability is enhanced by site-directed mutagenesis: a molecular dynamic simulations approach. J Biomol Struct Dyn 2017; 36:679-688. [DOI: 10.1080/07391102.2017.1294110] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Kowsar Bagherzadeh
- Razi Drug Research Center, Iran University of Medical Sciences, Tehran, Iran
- Faculty of Pharmacy and Pharmaceutical Sciences Research Center, Department of Medicinal Chemistry, Tehran University of Medical Sciences, Tehran, Iran
| | - Monireh Maleki
- Department of Clinical Biochemistry, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Abolfazl Golestani
- Department of Clinical Biochemistry, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Khosro Khajeh
- Faculty of Biological Sciences, Department of Biochemistry, Tarbiat Modares University, Tehran, Iran
| | - Massoud Amanlou
- Faculty of Pharmacy and Pharmaceutical Sciences Research Center, Department of Medicinal Chemistry, Tehran University of Medical Sciences, Tehran, Iran
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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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85
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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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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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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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Candidate SNP Markers of Chronopathologies Are Predicted by a Significant Change in the Affinity of TATA-Binding Protein for Human Gene Promoters. BIOMED RESEARCH INTERNATIONAL 2016; 2016:8642703. [PMID: 27635400 PMCID: PMC5011241 DOI: 10.1155/2016/8642703] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Revised: 06/25/2016] [Accepted: 06/28/2016] [Indexed: 01/14/2023]
Abstract
Variations in human genome (e.g., single nucleotide polymorphisms, SNPs) may be associated with hereditary diseases, their complications, comorbidities, and drug responses. Using Web service SNP_TATA_Comparator presented in our previous paper, here we analyzed immediate surroundings of known SNP markers of diseases and identified several candidate SNP markers that can significantly change the affinity of TATA-binding protein for human gene promoters, with circadian consequences. For example, rs572527200 may be related to asthma, where symptoms are circadian (worse at night), and rs367732974 may be associated with heart attacks that are characterized by a circadian preference (early morning). By the same method, we analyzed the 90 bp proximal promoter region of each protein-coding transcript of each human gene of the circadian clock core. This analysis yielded 53 candidate SNP markers, such as rs181985043 (susceptibility to acute Q fever in male patients), rs192518038 (higher risk of a heart attack in patients with diabetes), and rs374778785 (emphysema and lung cancer in smokers). If they are properly validated according to clinical standards, these candidate SNP markers may turn out to be useful for physicians (to select optimal treatment for each patient) and for the general population (to choose a lifestyle preventing possible circadian complications of diseases).
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