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Qureshi R, Zou B, Alam T, Wu J, Lee VHF, Yan H. Computational Methods for the Analysis and Prediction of EGFR-Mutated Lung Cancer Drug Resistance: Recent Advances in Drug Design, Challenges and Future Prospects. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023; 20:238-255. [PMID: 35007197 DOI: 10.1109/tcbb.2022.3141697] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Lung cancer is a major cause of cancer deaths worldwide, and has a very low survival rate. Non-small cell lung cancer (NSCLC) is the largest subset of lung cancers, which accounts for about 85% of all cases. It has been well established that a mutation in the epidermal growth factor receptor (EGFR) can lead to lung cancer. EGFR Tyrosine Kinase Inhibitors (TKIs) are developed to target the kinase domain of EGFR. These TKIs produce promising results at the initial stage of therapy, but the efficacy becomes limited due to the development of drug resistance. In this paper, we provide a comprehensive overview of computational methods, for understanding drug resistance mechanisms. The important EGFR mutants and the different generations of EGFR-TKIs, with the survival and response rates are discussed. Next, we evaluate the role of important EGFR parameters in drug resistance mechanism, including structural dynamics, hydrogen bonds, stability, dimerization, binding free energies, and signaling pathways. Personalized drug resistance prediction models, drug response curve, drug synergy, and other data-driven methods are also discussed. Recent advancements in deep learning; such as AlphaFold2, deep generative models, big data analytics, and the applications of statistics and permutation are also highlighted. We explore limitations in the current methodologies, and discuss strategies to overcome them. We believe this review will serve as a reference for researchers; to apply computational techniques for precision medicine, analyzing structures of protein-drug complexes, drug discovery, and understanding the drug response and resistance mechanisms in lung cancer patients.
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Balkenhol J, Bencurova E, Gupta SK, Schmidt H, Heinekamp T, Brakhage A, Pottikkadavath A, Dandekar T. Prediction and validation of host-pathogen interactions by a versatile inference approach using Aspergillus fumigatus as a case study. Comput Struct Biotechnol J 2022; 20:4225-4237. [PMID: 36051885 PMCID: PMC9399266 DOI: 10.1016/j.csbj.2022.07.050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 07/29/2022] [Accepted: 07/29/2022] [Indexed: 11/03/2022] Open
Abstract
Biological networks are characterized by diverse interactions and dynamics in time and space. Many regulatory modules operate in parallel and are interconnected with each other. Some pathways are functionally known and annotated accordingly, e.g., endocytosis, migration, or cytoskeletal rearrangement. However, many interactions are not so well characterized. For reconstructing the biological complexity in cellular networks, we combine here existing experimentally confirmed and analyzed interactions with a protein-interaction inference framework using as basis experimentally confirmed interactions from other organisms. Prediction scoring includes sequence similarity, evolutionary conservation of interactions, the coexistence of interactions in the same pathway, orthology as well as structure similarity to rank and compare inferred interactions. We exemplify our inference method by studying host-pathogen interactions during infection of Mus musculus (phagolysosomes in alveolar macrophages) with Aspergillus fumigatus (conidia, airborne, asexual spores). Three of nine predicted critical host-pathogen interactions could even be confirmed by direct experiments. Moreover, we suggest drugs that manipulate the host-pathogen interaction.
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Affiliation(s)
| | - Elena Bencurova
- Department of Bioinformatics, University of Würzburg, Würzburg, Germany
| | - Shishir K Gupta
- Evolutionary Genomics Group, Center for Computational and Theoretical Biology, University of Würzburg, 97078 Würzburg, Germany
| | - Hella Schmidt
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (Leibniz-HKI), 07745 Jena, Germany
| | - Thorsten Heinekamp
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (Leibniz-HKI), 07745 Jena, Germany
| | - Axel Brakhage
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (Leibniz-HKI), 07745 Jena, Germany
| | - Aparna Pottikkadavath
- Department of Structural Biology, Rudolf Virchow Center for Integrative and Translational Bioimaging, University of Würzburg, 97074 Würzburg, Germany
| | - Thomas Dandekar
- Department of Bioinformatics, University of Würzburg, Würzburg, Germany
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Trivedi M, Singh S, Pandey T, Gupta SK, Verma RS, Pandey R. Sesquiterpenoids isolated from davana (Artemisia pallens Wall. ex DC) mitigates parkinsonism in Caenorhabditis elegans disease model. Biochem Biophys Res Commun 2022; 609:15-22. [DOI: 10.1016/j.bbrc.2022.04.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 03/30/2022] [Accepted: 04/01/2022] [Indexed: 11/02/2022]
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Pathanraj D, Choowongkomon K, Roytrakul S, Yokthongwattana C. Structural Distinctive 26SK, a Ribosome-Inactivating Protein from Jatropha curcas and Its Biological Activities. Appl Biochem Biotechnol 2021; 193:3877-3897. [PMID: 34669111 DOI: 10.1007/s12010-021-03714-6] [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: 07/12/2021] [Accepted: 10/08/2021] [Indexed: 11/28/2022]
Abstract
Ribosome-inactivating proteins (RIPs) are a group of proteins exhibiting N-glycosidase activity leading to an inactivation of protein synthesis. Thirteen predicted Jatropha curcas RIP sequences could be grouped into RIP types 1 or 2. The expression of the RIP genes was detected in seed kernels, seed coats, and leaves. The full-length cDNA of two RIP genes (26SK and 34.7(A)SK) were cloned and studied. The 34.7(A)SK protein was successfully expressed in the host cells while it was difficult to produce even only a small amount of the 26SK protein. Therefore, the crude proteins were used from E. coli expressing 26SK and 34.7(A)SK constructs and they showed RIP activity. Only the cell lysate from 26SK could inhibit the growth of E. coli. In addition, the crude protein extracted from 26SK expressing cells displayed the effect on the growth of MDA-MB-231, a human breast cancer cell line. Based on in silico analysis, all 13 J. curcas RIPs contained RNA and ribosomal P2 stalk protein binding sites; however, the C-terminal region of the P2 stalk binding site was lacking in the 26SK structure. In addition, an amphipathic distribution between positive and negative potential was observed only in the 26SK protein, similar to that found in the anti-microbial peptide. These findings suggested that this 26SK protein structure might have contributed to its toxicity, suggesting potential uses against pathogenic bacteria in the future.
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Affiliation(s)
- Danulada Pathanraj
- Interdisciplinary Program in Genetic Engineering, Graduate School, Kasetsart University, 50 Ngamwongwan Rd., Bangkok, 10900, Thailand
| | - Kiattawee Choowongkomon
- Department of Biochemistry, Faculty of Science, Kasetsart University, 50 Ngamwongwan Rd., Bangkok, 10900, Thailand
| | - Sittiruk Roytrakul
- Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology, Pathum Thani, 12120, Thailand
| | - Chotika Yokthongwattana
- Department of Biochemistry, Faculty of Science, Kasetsart University, 50 Ngamwongwan Rd., Bangkok, 10900, Thailand.
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Đurić MJ, Subotić AR, Prokić LT, Trifunović-Momčilov MM, Cingel AD, Dragićević MB, Simonović AD, Milošević SM. Molecular Characterization and Expression of Four Aquaporin Genes in Impatiens walleriana During Drought Stress and Recovery. PLANTS (BASEL, SWITZERLAND) 2021; 10:154. [PMID: 33466920 PMCID: PMC7829780 DOI: 10.3390/plants10010154] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 12/23/2020] [Accepted: 01/06/2021] [Indexed: 12/19/2022]
Abstract
Aquaporins comprise a large group of transmembrane proteins responsible for water transport, which is crucial for plant survival under stress conditions. Despite the vital role of aquaporins, nothing is known about this protein family in Impatiens walleriana, a commercially important horticultural plant, which is sensitive to drought stress. In the present study, attention is given to the molecular characterization of aquaporins in I. walleriana and their expression during drought stress and recovery. We identified four I. walleriana aquaporins: IwPIP1;4, IwPIP2;2, IwPIP2;7 and IwTIP4;1. All of them had conserved NPA motifs (Asparagine-Proline-Alanine), transmembrane helices (TMh), pore characteristics, stereochemical properties and tetrameric structure of holoprotein. Drought stress and recovery treatment affected the aquaporins expression in I. walleriana leaves, which was up- or downregulated depending on stress intensity. Expression of IwPIP2;7 was the most affected of all analyzed I. walleriana aquaporins. At 15% and 5% soil moisture and recovery from 15% and 5% soil moisture, IwPIP2;7 expression significantly decreased and increased, respectively. Aquaporins IwPIP1;4 and IwTIP4;1 had lower expression in comparison to IwPIP2;7, with moderate expression changes in response to drought and recovery, while IwPIP2;2 expression was of significance only in recovered plants. Insight into the molecular structure of I. walleriana aquaporins expanded knowledge about plant aquaporins, while its expression during drought and recovery contributed to I. walleriana drought tolerance mechanisms and re-acclimation.
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Affiliation(s)
- Marija J. Đurić
- Institute for Biological Research “Siniša Stanković”, National Institute of Republic of Serbia, Department of Plant Physiology, University of Belgrade, Bulevar Despota Stefana 142, 11060 Belgrade, Serbia; (A.R.S.); (M.M.T.-M.); (A.D.C.); (M.B.D.); (A.D.S.); (S.M.M.)
| | - Angelina R. Subotić
- Institute for Biological Research “Siniša Stanković”, National Institute of Republic of Serbia, Department of Plant Physiology, University of Belgrade, Bulevar Despota Stefana 142, 11060 Belgrade, Serbia; (A.R.S.); (M.M.T.-M.); (A.D.C.); (M.B.D.); (A.D.S.); (S.M.M.)
| | - Ljiljana T. Prokić
- Department for Agrochemistry and Plant Physiology, Faculty of Agriculture, University of Belgrade, Nemanjina 6, 11080 Belgrade, Serbia;
| | - Milana M. Trifunović-Momčilov
- Institute for Biological Research “Siniša Stanković”, National Institute of Republic of Serbia, Department of Plant Physiology, University of Belgrade, Bulevar Despota Stefana 142, 11060 Belgrade, Serbia; (A.R.S.); (M.M.T.-M.); (A.D.C.); (M.B.D.); (A.D.S.); (S.M.M.)
| | - Aleksandar D. Cingel
- Institute for Biological Research “Siniša Stanković”, National Institute of Republic of Serbia, Department of Plant Physiology, University of Belgrade, Bulevar Despota Stefana 142, 11060 Belgrade, Serbia; (A.R.S.); (M.M.T.-M.); (A.D.C.); (M.B.D.); (A.D.S.); (S.M.M.)
| | - Milan B. Dragićević
- Institute for Biological Research “Siniša Stanković”, National Institute of Republic of Serbia, Department of Plant Physiology, University of Belgrade, Bulevar Despota Stefana 142, 11060 Belgrade, Serbia; (A.R.S.); (M.M.T.-M.); (A.D.C.); (M.B.D.); (A.D.S.); (S.M.M.)
| | - Ana D. Simonović
- Institute for Biological Research “Siniša Stanković”, National Institute of Republic of Serbia, Department of Plant Physiology, University of Belgrade, Bulevar Despota Stefana 142, 11060 Belgrade, Serbia; (A.R.S.); (M.M.T.-M.); (A.D.C.); (M.B.D.); (A.D.S.); (S.M.M.)
| | - Snežana M. Milošević
- Institute for Biological Research “Siniša Stanković”, National Institute of Republic of Serbia, Department of Plant Physiology, University of Belgrade, Bulevar Despota Stefana 142, 11060 Belgrade, Serbia; (A.R.S.); (M.M.T.-M.); (A.D.C.); (M.B.D.); (A.D.S.); (S.M.M.)
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Adiba M, Das T, Paul A, Das A, Chakraborty S, Hosen MI, Nabi AN. In silico characterization of coding and non-coding SNPs of the androgen receptor gene. INFORMATICS IN MEDICINE UNLOCKED 2021. [DOI: 10.1016/j.imu.2021.100556] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
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7
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Farhadi Z, Farhadi T, Hashemian SM. Virtual screening for potential inhibitors of β(1,3)-D-glucan synthase as drug candidates against fungal cell wall. J Drug Assess 2020; 9:52-59. [PMID: 32284908 PMCID: PMC7144292 DOI: 10.1080/21556660.2020.1734010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 02/07/2020] [Indexed: 01/17/2023] Open
Abstract
Background To enhance the outcome in patients with invasive candidiasis, initiation of an efficient antifungal treatment in a suitable dosage is necessary. Echinocandins (e.g. caspofungin) inhibit the enzyme β(1,3)-D-glucan synthase of the fungal cell wall. Compared to azoles and other antifungal agents, echinocandins have lower adverse effects and toxicity in humans. Echinocandins are available in injectable (intravenous) form. Methods In this study, to identify the novel oral drug-like compounds that affect the fungal cell wall, downloaded oral drug-like compounds from the ZINC database were processed with a virtual screening procedure. The docking free energies were calculated and compared with the known inhibitor caspofungin. Four molecules were selected as the most potent ligands and subjected to hydrogen bonds analysis. Results Considering the hydrogen bond analysis, two compounds (ZINC71336662 and ZINC40910772) were predicted to better interact with the active site of β(1,3)-D-glucan synthase compared with caspofungin. Conclusion The introduced compound in this study may be valuable to analyze experimentally as a novel oral drug candidate targeting fungal cell walls.
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Affiliation(s)
- Zinat Farhadi
- Chronic Respiratory Diseases Research Center (CRDRC), National Research Institute of Tuberculosis and Lung Diseases (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Behavioral Disease Counseling Center, Marvdasht Health Center, Shiraz University of Medical Sciences, Shiraz, Iran.,Department of Microbiology, Shiraz Branch, Islamic Azad University, Shiraz, Iran
| | - Tayebeh Farhadi
- Chronic Respiratory Diseases Research Center (CRDRC), National Research Institute of Tuberculosis and Lung Diseases (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Seyed MohammadReza Hashemian
- Chronic Respiratory Diseases Research Center (CRDRC), National Research Institute of Tuberculosis and Lung Diseases (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Critical Care Department, Farhikhtegan Hospital, Tehran Medical Branch, Islamic Azad University, Tehran, Iran
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Naseem M, Srivastava M, Osmanoglu O, Iqbal J, Howari FM, AlRemeithi FA, Dandekar T. Molecular Modeling of the Interaction Between Stem Cell Peptide and Immune Receptor in Plants. Methods Mol Biol 2020; 2094:67-77. [PMID: 31797292 DOI: 10.1007/978-1-0716-0183-9_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Molecular docking enables comprehensive exploration of interactions between chemical moieties and proteins. Modeling and docking approaches are useful to determine the three-dimensional (3D) structure of experimentally uncrystallized proteins and subsequently their interactions with various inhibitors and activators or peptides. Here, we describe a protocol for carrying out molecular modeling and docking of stem cell peptide CLV3p on plant innate immune receptor FLS2.
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Affiliation(s)
- Muhammad Naseem
- Department of Life and Environmental Sciences, College of Natural and Health Sciences, Zayed University, Abu Dhabi, UAE
- Department of Bioinformatics, Biocenter, University of Wuerzburg, Wuerzburg, Germany
| | - Mugdha Srivastava
- Department of Bioinformatics, Biocenter, University of Wuerzburg, Wuerzburg, Germany
| | - Ozge Osmanoglu
- Department of Bioinformatics, Biocenter, University of Wuerzburg, Wuerzburg, Germany
| | - Jibran Iqbal
- Department of Life and Environmental Sciences, College of Natural and Health Sciences, Zayed University, Abu Dhabi, UAE
| | - Fares M Howari
- Department of Life and Environmental Sciences, College of Natural and Health Sciences, Zayed University, Abu Dhabi, UAE
| | - Fatima A AlRemeithi
- Department of Life and Environmental Sciences, College of Natural and Health Sciences, Zayed University, Abu Dhabi, UAE
| | - Thomas Dandekar
- Department of Bioinformatics, Biocenter, University of Wuerzburg, Wuerzburg, Germany.
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The functional impact of the C/N-terminal extensions of the mouse retinal IMPDH1 isoforms: a kinetic evaluation. Mol Cell Biochem 2019; 465:155-164. [PMID: 31838626 DOI: 10.1007/s11010-019-03675-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 12/07/2019] [Indexed: 10/25/2022]
Abstract
Mutations in the retinal inosine monophosphate dehydrogenase1 (IMPDH1) gene is believed to be one cause of retinitis pigmentosa (RP). The main structural difference between the mutation-susceptible retinal isoforms with canonical one resides in the C- and N-terminal extensions. There are limited studies on the structure and function of terminal peptide extensions of the IMPDH1 retinal isoforms. Using recombinant murine IMPDH1 (mH1), we evaluated the kinetics of the retinal isoforms along with inhibition by some of the purine nucleotides. Molecular modeling tools were also applied to study the probable effect(s) of the terminal peptide tails on the function of the retinal isoforms. Molecular dynamic simulations indicated the possible impact of the end-terminal segments on the enzyme function through interactions with the enzyme's finger domain, affecting its critical pseudo barrel structure. The higher experimentally-determined Km and Ki values of the retinal mIMPDH1 (546) and mIMPDH1 (603) relative to that of the canonical isoform, mIMPDH1 (514), might clearly be due to these interactions. Furthermore and despite of the canonical isoform, the retinal isoforms of mH1 exhibited no NAD+ substrate inhibition. The resent data would certainly provide the ground for future evaluation of the physiological significance of these variations.
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Palanivel H, Easwaran M, Meena A, Chandrasekaran S, Abdul Kader M, Murali A. Structural dynamics and modeling of curcin protein: docking against pterin derivatives. SN APPLIED SCIENCES 2019. [DOI: 10.1007/s42452-019-0752-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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11
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Liu J, Wei B, Che C, Gong Z, Jiang Y, Si M, Zhang J, Yang G. Enhanced stability of manganese superoxide dismutase by amino acid replacement designed via molecular dynamics simulation. Int J Biol Macromol 2019; 128:297-303. [PMID: 30685308 DOI: 10.1016/j.ijbiomac.2019.01.126] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Revised: 01/23/2019] [Accepted: 01/23/2019] [Indexed: 12/27/2022]
Abstract
In order to improve manganese-SOD stability, three mutations were constructed via site-directed mutagenesis, and the root mean square fluctuation (RMSF) and root mean square deviation (RMSD) were used as stability assessment indexes. The amino acids of V140, E155 and E215 from wild-type mouse Mn-SOD was replaced to L140, W155 and W215, and a recombinant plasmid containing DNA segment coding wild-type and mutant Mn-SOD protein was transformed into Escherichia coli BL21 for expression. The highest enzyme activity of the mutations-MnSOD was 2050 U/mg. In addition, the recombinant protein, TM-MnSODV140L, E155W, E215W exhibited higher working temperature and improved stability compared with the wild-type Mn-SOD. Furthermore, CD spectrum analysis of the improved mutants and wild-type enzyme showed that there was no significant change in their secondary structures. This study not only expands the scope of the application of enzymes, but also helps us understand the relationship between protein structure and function.
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Affiliation(s)
- Jinfeng Liu
- College of Life Sciences, Qufu Normal University, Qufu 273165, Shandong, China.
| | - Beibei Wei
- College of Life Sciences, Qufu Normal University, Qufu 273165, Shandong, China
| | - Chengchuan Che
- College of Life Sciences, Qufu Normal University, Qufu 273165, Shandong, China
| | - Zhijin Gong
- College of Life Sciences, Qufu Normal University, Qufu 273165, Shandong, China
| | - Yueshui Jiang
- College of Life Sciences, Qufu Normal University, Qufu 273165, Shandong, China
| | - Meiru Si
- College of Life Sciences, Qufu Normal University, Qufu 273165, Shandong, China
| | - Junming Zhang
- College of Life Sciences, Qufu Normal University, Qufu 273165, Shandong, China
| | - Ge Yang
- College of Life Sciences, Qufu Normal University, Qufu 273165, Shandong, China.
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Exploring Highly Antigenic Protein of Campylobacter jejuni for Designing Epitope Based Vaccine: Immunoinformatics Approach. Int J Pept Res Ther 2018. [DOI: 10.1007/s10989-018-9764-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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13
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Nailwal M, Chauhan JB. Computational Analysis of High-Risk SNPs in Human DBY Gene Responsible for Male Infertility: A Functional and Structural Impact. Interdiscip Sci 2018. [PMID: 29520635 DOI: 10.1007/s12539-018-0290-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
BACKGROUND DEAD-box helicase 3, Y-linked (DBY) is a candidate gene of the AZF region which is involved in spermatogenesis process. Mutations in the DBY gene may disrupt the spermatogenesis and lead to infertility in men. Identification of functionally neutral mutation from the disease-causing mutation is the biggest challenge in human genetic variation analysis. Owing to the importance of DBY in male infertility, functional analysis was carried out to reveal the association between genetic mutation and phenotypic variation through various in silico approaches. METHODS The present study analyzed the functional consequences of the nsSNPs in human DBY gene using SIFT, PolyPhen 2, PROVEAN, SNAP2, PMut, nsSNPAnalyzer, PhD-SNP and SNPs&GO along with stability analysis through I-Mutant2.0, MuPro and iPTREE-STAB. The conservational analysis of amino acid residues, biophysical properties and conserved domains of the DBY protein was analyzed using various computational tools. The 3D structure of the protein was generated using SPARKS-X and validated using RAMPAGE. RESULTS Out of 1130 SNPs reported in dbSNP, only one nsSNP (G300D) was found to have a functional effect on stability as well as the function of the DBY protein. The results showed the presence of G300 in the putative structure of DBY domain. CONCLUSION To the best of our knowledge, this is the first study to detect pathologically significant nsSNPs (G300D) through a computational approach in the DBY which can be useful for development in potent drug discovery studies.
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Affiliation(s)
- Mili Nailwal
- P.G. Department of Genetics, Ashok and Rita Patel Institute of Integrated Study and Research in Biotechnology and Allied Sciences (ARIBAS), New Vallabh Vidyanagar, Dist-Anand, Gujarat, 388121, India
| | - Jenabhai B Chauhan
- P.G. Department of Genetics, Ashok and Rita Patel Institute of Integrated Study and Research in Biotechnology and Allied Sciences (ARIBAS), New Vallabh Vidyanagar, Dist-Anand, Gujarat, 388121, India.
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Constructing novel chimeric DNA vaccine against Salmonella enterica based on SopB and GroEL proteins: an in silico approach. JOURNAL OF PHARMACEUTICAL INVESTIGATION 2017. [DOI: 10.1007/s40005-017-0360-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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15
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Singh HB, Deka D, Das D, Borbora D. Computational prediction of the effects of non-synonymous single nucleotide polymorphisms in the human Quinone Oxidoreductase 1 (NQO1). Meta Gene 2017. [DOI: 10.1016/j.mgene.2016.12.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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16
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Farhadi T, Ranjbar MM. Designing and modeling of complex DNA vaccine based on MOMP of Chlamydia trachomatis: an in silico approach. ACTA ACUST UNITED AC 2016. [DOI: 10.1007/s13721-016-0142-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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17
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Goswami AM. Computational analysis, structural modeling and ligand binding site prediction of Plasmodium falciparum 1-deoxy-d-xylulose-5-phosphate synthase. Comput Biol Chem 2016; 66:1-10. [PMID: 27842226 DOI: 10.1016/j.compbiolchem.2016.10.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Revised: 10/21/2016] [Accepted: 10/24/2016] [Indexed: 11/27/2022]
Abstract
Malaria remains one of the most serious infectious diseases in the world. There are five human species of the Plasmodium genus, of which Plasmodium falciparum is the most virulent and responsible for the vast majority of malaria related deaths. The unique biochemical processes that exist in Plasmodium falciparum provide a useful way to develop novel inhibitors. One such biochemical pathway is the methyl erythritol phosphate pathway (MEP), required to synthesize isoprenoid precursors. In the present study, a detailed computational analysis has been performed for 1-deoxy-d-xylulose-5-phosphate synthase, a key enzyme in MEP. The protein is found to be stable and residues from 825 to 971 are highly conserved across species. The homology model of the enzyme is developed using three web-based servers and Modeller software. It has twelve disordered regions indicating its druggability. Virtual screening of ZINC database identifies ten potential compounds in thiamine diphosphate binding region of the enzyme.
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Affiliation(s)
- Achintya Mohan Goswami
- Department of Physiology, Krishnagar Govt. College, Krishnagar, Nadia, West Bengal, India.
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Farhadi T, Ovchinnikov RS, Ranjbar MM. In silico designing of some agonists of toll-like receptor 5 as a novel vaccine adjuvant candidates. ACTA ACUST UNITED AC 2016. [DOI: 10.1007/s13721-016-0138-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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19
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Zhang S, Cui FC, Cao Y, Li YQ. Sequence identification, structure prediction and validation of tannase from Aspergillusniger N5-5. CHINESE CHEM LETT 2016. [DOI: 10.1016/j.cclet.2016.04.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Goswami AM. Structural modeling and in silico analysis of non-synonymous single nucleotide polymorphisms of human 3β-hydroxysteroid dehydrogenase type 2. Meta Gene 2015; 5:162-72. [PMID: 26288759 PMCID: PMC4539073 DOI: 10.1016/j.mgene.2015.07.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2015] [Accepted: 07/23/2015] [Indexed: 02/01/2023] Open
Abstract
Single-nucleotide polymorphisms (SNPs), a most common type of genetic mutations, result from single base pair alterations. Non-synonymous SNPs (nsSNP) occur in the coding regions of a gene and result in single amino acid substitution which might have the potential to affect the function as well as structure of the corresponding protein. In human the 3β-hydroxysteroid dehydrogenases/Δ4,5-isomerase type 2 (HSD3B2) is an important membrane-bound enzyme involved in the dehydrogenation and Δ4,5-isomerization of the Δ5-steroid precursors into their respective Δ4-ketosteroids in the biosynthesis of steroid hormones such as glucocorticoids, mineralocorticoids, progesterone, androgens, and estrogens in tissues such as adrenal gland, ovary, and testis. Most of the nsSNPs of HSD3B2 are still uncharacterized in terms of their disease causing potential. So, this study has been undertaken to explore and extend the knowledge related to the effect of nsSNPs on the stability and function of the HSD3B2. In this study sixteen nsSNP of HSD3B2 were subjected to in silico analysis using nine different algorithms: SIFT, PROVEAN, PolyPhen, MutPred, SNPeffect, nsSNP Analyzer, PhD SNP, stSNP, and I Mutant 2.0. The results obtained from the analysis revealed that the prioritization of diseases associated amino acid substitution as evident from possible alteration in structure–function relationship. Structural phylogenetic analysis using ConSurf revealed that the functional residues are highly conserved in human HSD3B2; and most of the disease associated nsSNPs are within these conserved residues. Structural theoritical models of HSD3B2 were created using HHPred, Phyre2 and RaptorX server. The predicted models were evaluated to get the best one for structural understanding of amino acid substitutions in three dimensional spaces.
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Affiliation(s)
- Achintya Mohan Goswami
- Department of Physiology, Krishnagar Govt. College, Krishnagar, Nadia, West Bengal, India
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Wu Y, Mao Y, Jin S, Hou J, Du H, Yang M, Wu L. Identification, characterization and structure analysis of a type I ribosome-inactivating protein from Sapium sebiferum (Euphorbiaceae). Biochem Biophys Res Commun 2015; 463:557-62. [DOI: 10.1016/j.bbrc.2015.05.089] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 05/28/2015] [Indexed: 11/26/2022]
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Designing of Complex Multi-epitope Peptide Vaccine Based on Omps of Klebsiella pneumoniae: An In Silico Approach. Int J Pept Res Ther 2015. [DOI: 10.1007/s10989-015-9461-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Akhoon BA, Singh KP, Varshney M, Gupta SK, Shukla Y, Gupta SK. Understanding the mechanism of atovaquone drug resistance in Plasmodium falciparum cytochrome b mutation Y268S using computational methods. PLoS One 2014; 9:e110041. [PMID: 25334024 PMCID: PMC4198183 DOI: 10.1371/journal.pone.0110041] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Accepted: 09/15/2014] [Indexed: 11/25/2022] Open
Abstract
The rapid appearance of resistant malarial parasites after introduction of atovaquone (ATQ) drug has prompted the search for new drugs as even single point mutations in the active site of Cytochrome b protein can rapidly render ATQ ineffective. The presence of Y268 mutations in the Cytochrome b (Cyt b) protein is previously suggested to be responsible for the ATQ resistance in Plasmodium falciparum (P. falciparum). In this study, we examined the resistance mechanism against ATQ in P. falciparum through computational methods. Here, we reported a reliable protein model of Cyt bc1 complex containing Cyt b and the Iron-Sulphur Protein (ISP) of P. falciparum using composite modeling method by combining threading, ab initio modeling and atomic-level structure refinement approaches. The molecular dynamics simulations suggest that Y268S mutation causes ATQ resistance by reducing hydrophobic interactions between Cyt bc1 protein complex and ATQ. Moreover, the important histidine contact of ATQ with the ISP chain is also lost due to Y268S mutation. We noticed the induced mutation alters the arrangement of active site residues in a fashion that enforces ATQ to find its new stable binding site far away from the wild-type binding pocket. The MM-PBSA calculations also shows that the binding affinity of ATQ with Cyt bc1 complex is enough to hold it at this new site that ultimately leads to the ATQ resistance.
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Affiliation(s)
- Bashir A. Akhoon
- Department of Bioinformatics, Systems Toxicology Group, CSIR-Indian Institute of Toxicology Research, Lucknow, India
| | - Krishna P. Singh
- Department of Bioinformatics, Systems Toxicology Group, CSIR-Indian Institute of Toxicology Research, Lucknow, India
| | - Megha Varshney
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India
| | - Shishir K. Gupta
- Department of Bioinformatics, Biocenter, Am Hubland, University of Würzburg, Würzburg, Germany
| | - Yogeshwar Shukla
- Department of Proteomics, CSIR-Indian Institute of Toxicology Research, Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), New Delhi, India
| | - Shailendra K. Gupta
- Department of Bioinformatics, Systems Toxicology Group, CSIR-Indian Institute of Toxicology Research, Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), New Delhi, India
- * E-mail:
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Zhou C, Hou C, Zhang Q, Wei X. Enhanced hybrid search algorithm for protein structure prediction using the 3D-HP lattice model. J Mol Model 2013; 19:3883-91. [DOI: 10.1007/s00894-013-1907-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Accepted: 05/30/2013] [Indexed: 10/26/2022]
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Lesitha Jeeva Kumari J, Sudandiradoss C. Computational investigation of theoretical models of cleavable and uncleavable mucin 1 isoforms. MOLECULAR BIOSYSTEMS 2013; 9:2473-88. [DOI: 10.1039/c3mb70200f] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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