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Rakib TM, Islam MS, Tanaka S, Yabuki A, Pervin S, Maki S, Faruq AA, Tacharina MR, Yamato O. Novel Mutation in the Feline GAA Gene in a Cat with Glycogen Storage Disease Type II (Pompe Disease). Animals (Basel) 2023; 13:ani13081336. [PMID: 37106898 PMCID: PMC10135178 DOI: 10.3390/ani13081336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 04/06/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023] Open
Abstract
Glycogen storage disease type II (Pompe disease: PD) is an autosomal recessively inherited fatal genetic disorder that results from the deficiency of a glycogen hydrolyzing enzyme, acid α-glucosidase encoded by the GAA gene. Here, we describe the molecular basis of genetic defects in an 8-month-old domestic short-haired cat with PD. The cat was previously diagnosed with PD based on the clinical and pathological findings of hypertrophic cardiomyopathy and excessive accumulation of glycogen in the cardiac muscles. Sanger sequencing was performed on 20 exons of the feline GAA gene using genomic DNA extracted from paraffin-embedded liver tissues. The affected cat was found to be homozygous for the GAA:c.1799G>A mutation resulting in an amino acid substitution (p.R600H) of acid α-glucosidase, a codon position of which is identical with three missense mutations (p.R600C, p.R600L, and p.R600H) causing human infantile-onset PD (IOPD). Several stability and pathogenicity predictors have also shown that the feline mutation is deleterious and severely decreases the stability of the GAA protein. The clinical, pathological, and molecular findings in the cat were similar to those of IOPD in humans. To our knowledge, this is the first report of a pathogenic mutation in a cat. Feline PD is an excellent model for human PD, especially IOPD.
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Affiliation(s)
- Tofazzal Md Rakib
- Laboratory of Clinical Pathology, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima 890-0065, Japan
- Faculty of Veterinary Medicine, Chattogram Veterinary and Animal Sciences University, Khulshi, Chattogram 4225, Bangladesh
| | - Md Shafiqul Islam
- Laboratory of Clinical Pathology, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima 890-0065, Japan
- Faculty of Veterinary Medicine, Chattogram Veterinary and Animal Sciences University, Khulshi, Chattogram 4225, Bangladesh
| | - Shigeki Tanaka
- Alpha Animal Hospital, Kawanakajima, Nagano 381-2226, Japan
| | - Akira Yabuki
- Laboratory of Clinical Pathology, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima 890-0065, Japan
| | - Shahnaj Pervin
- Laboratory of Clinical Pathology, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima 890-0065, Japan
| | - Shinichiro Maki
- Laboratory of Clinical Pathology, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima 890-0065, Japan
| | - Abdullah Al Faruq
- Laboratory of Clinical Pathology, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima 890-0065, Japan
- Faculty of Veterinary Medicine, Chattogram Veterinary and Animal Sciences University, Khulshi, Chattogram 4225, Bangladesh
| | - Martia Rani Tacharina
- Laboratory of Clinical Pathology, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima 890-0065, Japan
- Faculty of Veterinary Medicine, Airlangga University, Mulyorejo, Surabaya 60115, Indonesia
| | - Osamu Yamato
- Laboratory of Clinical Pathology, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima 890-0065, Japan
- Faculty of Veterinary Medicine, Airlangga University, Mulyorejo, Surabaya 60115, Indonesia
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Huang W, Zhang Y, Zhou R. Induced pluripotent stem cell for modeling Pompe disease. Front Cardiovasc Med 2022; 9:1061384. [PMID: 36620633 PMCID: PMC9815144 DOI: 10.3389/fcvm.2022.1061384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 11/25/2022] [Indexed: 12/24/2022] Open
Abstract
Pompe disease (PD) is a rare, autosomal recessive, inherited, and progressive metabolic disorder caused by α-glucosidase defect in lysosomes, resulting in abnormal glycogen accumulation. Patients with PD characteristically have multisystem pathological disorders, particularly hypertrophic cardiomyopathy, muscle weakness, and hepatomegaly. Although the pathogenesis and clinical outcomes of PD are well-established, disease-modeling ability, mechanism elucidation, and drug development targeting PD have been substantially limited by the unavailable PD-relevant cell models. This obstacle has been overcome with the help of induced pluripotent stem cell (iPSC) reprogramming technology, thus providing a powerful tool for cell replacement therapy, disease modeling, drug screening, and drug toxicity assessment. This review focused on the exciting achievement of PD disease modeling and mechanism exploration using iPSC.
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Affiliation(s)
- Wenjun Huang
- National Regional Children's Medical Center (Northwest), Key Laboratory of Precision Medicine to Pediatric Diseases of Shaanxi Province, Xi'an Key Laboratory of Children's Health and Diseases, Shaanxi Institute for Pediatric Diseases, Xi'an Children's Hospital, Affiliated Children's Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Yanmin Zhang
- National Regional Children's Medical Center (Northwest), Key Laboratory of Precision Medicine to Pediatric Diseases of Shaanxi Province, Xi'an Key Laboratory of Children's Health and Diseases, Shaanxi Institute for Pediatric Diseases, Xi'an Children's Hospital, Affiliated Children's Hospital of Xi'an Jiaotong University, Xi'an, China,Department of Cardiology, Xi'an Children's Hospital, Affiliated Children's Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Rui Zhou
- National Regional Children's Medical Center (Northwest), Key Laboratory of Precision Medicine to Pediatric Diseases of Shaanxi Province, Xi'an Key Laboratory of Children's Health and Diseases, Shaanxi Institute for Pediatric Diseases, Xi'an Children's Hospital, Affiliated Children's Hospital of Xi'an Jiaotong University, Xi'an, China,*Correspondence: Rui Zhou ✉
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Mondal A, Goswami AM, Saha T. In silico prediction of the functional consequences of nsSNPs in human beta-catenin gene. GENE REPORTS 2021. [DOI: 10.1016/j.genrep.2021.101066] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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Thirumal Kumar D, Udhaya Kumar S, Magesh R, George Priya Doss C. Investigating mutations at the hotspot position of the ERBB2 and screening for the novel lead compound to treat breast cancer - a computational approach. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2020; 123:49-71. [PMID: 33485488 DOI: 10.1016/bs.apcsb.2020.10.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Membrane proteins are the most common types of cancer that are active in the prognosis. Membrane proteins are a distinguishing characteristic of a cancer cell. In tumor cell therapy, the overexpressed membrane proteins are becoming ever more relevant. The 3-kinase (PI3K)/AKT phosphatidylinositol pathway is downstream triggered by different extracellular signals, and this signaling pathway activation impacts a variety of proliferation of the cellular processes like cell growth and surviving. Frequent PI3K/AKT dysregulation in human cancer has rendered proteins of this pathway desirable for diagnostic markers. Members of the ERBB family-like ERBB2 and ERBB3 activate intracellular signaling pathways such as PI3K/AKT. The mutations in these proteins dysfunctions the proteins in the downstream. Considering this importance, we have developed a computational pipeline to identify the mutation position with a highest number of mutations and to screen them for pathogenicity, stability, conservation, and structural changes using PredictSNP, iStable, ConSurf, and GROMACS simulation software respectively. Further, a virtual screening approach was initiated to find the most similar non-toxic lead compound, which could be an alternative to the currently used lapatinib. To conclude, protein-ligand dynamics were undertaken to study the actions of native and mutants with the lapatinib and the lead compound. From the overall analysis, we identified position 755 with leucine in the native condition is prone to frequent mutations. The leucine at 755th position is more prone to mutate as serine and tryptophan. Further from the computational analysis, we identified that the mutation L755S is more significant than the L755W mutation. We have witnessed CID140590176 be a potential lead compound with no toxicity. The behavior of the lead compound has shown more compactness with an increased number of intermolecular hydrogen bonds in the ERBB2 with L755S. This lead compound can be further taken for experimental validations, and we believe that this lead compound could be a potent ERBB2 inhibitor.
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Affiliation(s)
- D Thirumal Kumar
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - S Udhaya Kumar
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India.
| | - R Magesh
- Faculty of Biomedical Sciences, Technology & Research, Department of Biotechnology, Sri Ramachandra University, Chennai, Tamil Nadu, India
| | - C George Priya Doss
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India.
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Zhang X, Qiu W, Liu H, Ye X, Sun Y, Fan Y, Yu Y. RT-PCR analysis of mRNA revealed the splice-altering effect of rare intronic variants in monogenic disorders. Ann Hum Genet 2020; 84:456-462. [PMID: 32776513 DOI: 10.1111/ahg.12400] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 06/24/2020] [Accepted: 07/06/2020] [Indexed: 11/28/2022]
Abstract
BACKGROUND Variants perturbing the normal splicing of pre-mRNA can lead to human diseases. The splice-altering effect and eventual consequence on gene function was sometimes uncertain and hinders a definitive molecular diagnosis. METHODS The impact of four rare intronic variants on splicing was analyzed through reverse transcription - polymerase chain reaction (RT-PCR) analysis of mRNA derived from the peripheral blood of patients. The results were compared with in-silico prediction. Potential implication on molecular diagnosis was discussed. RESULTS Four rare intronic variants of SLC9A6, DLG3, GAA, and OCRL were identified in patients with suspected disorders, respectively. Although these four variants were all predicted to alter splicing by in-silico tools, RT-PCR analysis of mRNA derived from peripheral blood showed these variants affected splicing in different ways: c.899+3_899+6del of SLC9A6 resulted in one-exon skipping and an out-of-frame transcript; c.905-2A > G of DLG3 resulted in a mix of in-frame transcripts; c.1195-11T > A of GAA resulted in the in-frame insertion of nine nucleotides; c.723-2A > C of OCRL resulted in one-exon skipping and in-frame deletion of 102 nucleotides. The consequence revealed by mRNA analysis is essential for accurate interpretation of pathogenicity. CONCLUSION Four intronic variants all caused aberrant mRNA splicing. For intronic variants with uncertain impact on splicing, mRNA analysis is helpful for ascertainment of alternative splicing and accurate interpretation of pathogenicity.
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Affiliation(s)
- Xia Zhang
- Department of Pediatric Endocrinology/Genetics, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Institute for Pediatric Research, Shanghai, China
| | - Wenjuan Qiu
- Department of Pediatric Endocrinology/Genetics, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Institute for Pediatric Research, Shanghai, China
| | - Huili Liu
- Department of Pediatric Endocrinology/Genetics, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Institute for Pediatric Research, Shanghai, China
| | - Xiantao Ye
- Department of Pediatric Endocrinology/Genetics, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Institute for Pediatric Research, Shanghai, China
| | - Yu Sun
- Department of Pediatric Endocrinology/Genetics, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Institute for Pediatric Research, Shanghai, China
| | - Yanjie Fan
- Department of Pediatric Endocrinology/Genetics, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Institute for Pediatric Research, Shanghai, China
| | - Yongguo Yu
- Department of Pediatric Endocrinology/Genetics, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Institute for Pediatric Research, Shanghai, China
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Taverna S, Cammarata G, Colomba P, Sciarrino S, Zizzo C, Francofonte D, Zora M, Scalia S, Brando C, Curto AL, Marsana EM, Olivieri R, Vitale S, Duro G. Pompe disease: pathogenesis, molecular genetics and diagnosis. Aging (Albany NY) 2020; 12:15856-15874. [PMID: 32745073 PMCID: PMC7467391 DOI: 10.18632/aging.103794] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Accepted: 07/14/2020] [Indexed: 12/14/2022]
Abstract
Pompe disease (PD) is a rare autosomal recessive disorder caused by mutations in the GAA gene, localized on chromosome 17 and encoding for acid alpha-1,4-glucosidase (GAA). Currently, more than 560 mutations spread throughout GAA gene have been reported. GAA catalyzes the hydrolysis of α-1,4 and α-1,6-glucosidic bonds of glycogen and its deficiency leads to lysosomal storage of glycogen in several tissues, particularly in muscle. PD is a chronic and progressive pathology usually characterized by limb-girdle muscle weakness and respiratory failure. PD is classified as infantile and childhood/adult forms. PD patients exhibit a multisystemic manifestation that depends on age of onset. Early diagnosis is essential to prevent or reduce the irreversible organ damage associated with PD progression. Here, we make an overview of PD focusing on pathogenesis, clinical phenotypes, molecular genetics, diagnosis, therapies, autophagy and the role of miRNAs as potential biomarkers for PD.
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Affiliation(s)
- Simona Taverna
- Institute for Biomedical Research and Innovation (IRIB-CNR), National Research Council of Italy, Palermo, Italy
| | - Giuseppe Cammarata
- Institute for Biomedical Research and Innovation (IRIB-CNR), National Research Council of Italy, Palermo, Italy
| | - Paolo Colomba
- Institute for Biomedical Research and Innovation (IRIB-CNR), National Research Council of Italy, Palermo, Italy
| | - Serafina Sciarrino
- Institute for Biomedical Research and Innovation (IRIB-CNR), National Research Council of Italy, Palermo, Italy
| | - Carmela Zizzo
- Institute for Biomedical Research and Innovation (IRIB-CNR), National Research Council of Italy, Palermo, Italy
| | - Daniele Francofonte
- Institute for Biomedical Research and Innovation (IRIB-CNR), National Research Council of Italy, Palermo, Italy
| | - Marco Zora
- Institute for Biomedical Research and Innovation (IRIB-CNR), National Research Council of Italy, Palermo, Italy
| | - Simone Scalia
- Institute for Biomedical Research and Innovation (IRIB-CNR), National Research Council of Italy, Palermo, Italy
| | - Chiara Brando
- Institute for Biomedical Research and Innovation (IRIB-CNR), National Research Council of Italy, Palermo, Italy
| | - Alessia Lo Curto
- Institute for Biomedical Research and Innovation (IRIB-CNR), National Research Council of Italy, Palermo, Italy
| | - Emanuela Maria Marsana
- Institute for Biomedical Research and Innovation (IRIB-CNR), National Research Council of Italy, Palermo, Italy
| | - Roberta Olivieri
- Institute for Biomedical Research and Innovation (IRIB-CNR), National Research Council of Italy, Palermo, Italy
| | - Silvia Vitale
- Institute for Biomedical Research and Innovation (IRIB-CNR), National Research Council of Italy, Palermo, Italy
| | - Giovanni Duro
- Institute for Biomedical Research and Innovation (IRIB-CNR), National Research Council of Italy, Palermo, Italy
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Datta S, Rajnish KN, George Priya Doss C, Melvin Samuel S, Selvarajan E, Zayed H. Enzyme therapy: a forerunner in catalyzing a healthy society? Expert Opin Biol Ther 2020; 20:1151-1174. [PMID: 32597245 DOI: 10.1080/14712598.2020.1787980] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
INTRODUCTION The use of enzymes in various industries has been prevalent for centuries. However, their potency as therapeutics remained latent until the late 1950 s, when scientists finally realized the gold mine they were sitting on. Enzyme therapy has seen rapid development over the past few decades and has been widely used for the therapy of myriad diseases, including lysosomal storage disorders, cancer, Alzheimer's disease, irritable bowel syndrome, exocrine pancreatic insufficiency, and hyperuricemia. Enzymes are also used for wound healing, the treatment of microbial infections, and gene therapy. AREAS COVERED This is a comprehensive review of the therapeutic use of enzymes that can act as a guidepost for researchers and academicians and presents a general overview of the developments in enzyme therapy over the years, along with updates on recent advancements in enzyme therapy research. EXPERT OPINION Although enzyme therapy is immensely beneficial and induces little auxiliary damage, it has several drawbacks, ranging from high cost, low stability, low production, and hyperimmune responses to the failure to cure a variety of the problems associated with a disease. Further fine-tuning and additional clinical efficacy studies are required to establish enzyme therapy as a forerunner to catalyzing a healthy society.
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Affiliation(s)
- Saptashwa Datta
- Department of Genetic Engineering, School of Bioengineering, SRM Institute of Science and Technology , Kattankulathur, TN, India
| | - K Narayanan Rajnish
- Department of Genetic Engineering, School of Bioengineering, SRM Institute of Science and Technology , Kattankulathur, TN, India
| | - C George Priya Doss
- Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology , Vellore, TN, India
| | - S Melvin Samuel
- Materials Science and Engineering, University of Wisconsin-Milwaukee , Milwaukee, WI, United States
| | - E Selvarajan
- Department of Genetic Engineering, School of Bioengineering, SRM Institute of Science and Technology , Kattankulathur, TN, India
| | - Hatem Zayed
- Department of Biomedical Sciences, College of Health and Sciences, QU Health, Qatar University , Doha, Qatar
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Shaik NA, Al‐Qahtani F, Nasser K, Jamil K, Alrayes NM, Elango R, Awan ZA, Banaganapalli B. Molecular insights into the coding region mutations of low‐density lipoprotein receptor adaptor protein 1 (LDLRAP1) linked to familial hypercholesterolemia. J Gene Med 2020; 22:e3176. [DOI: 10.1002/jgm.3176] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 02/03/2020] [Accepted: 02/06/2020] [Indexed: 12/20/2022] Open
Affiliation(s)
- Noor A. Shaik
- Department of Genetic Medicine, Faculty of MedicineKing Abdulaziz University Jeddah Saudi Arabia
- Princess Al‐Jawhara Al‐Brahim Center of Excellence in Research of Hereditary DisordersKing Abdulaziz University Jeddah Saudi Arabia
| | - Faten Al‐Qahtani
- Department of Genetic Medicine, Faculty of MedicineKing Abdulaziz University Jeddah Saudi Arabia
| | - Khalidah Nasser
- Princess Al‐Jawhara Al‐Brahim Center of Excellence in Research of Hereditary DisordersKing Abdulaziz University Jeddah Saudi Arabia
- Department of Medical Laboratory Technology, Faculty of Applied Medical SciencesKing Abdulaziz University Jeddah Saudi Arabia
| | - Kaiser Jamil
- Deptartment of GeneticsBhagwan Mahavir Medical Research Centre Hyderabad India
| | - Nuha Mohammad Alrayes
- Princess Al‐Jawhara Al‐Brahim Center of Excellence in Research of Hereditary DisordersKing Abdulaziz University Jeddah Saudi Arabia
- Department of Medical Laboratory Technology, Faculty of Applied Medical SciencesKing Abdulaziz University Jeddah Saudi Arabia
| | - Ramu Elango
- Department of Genetic Medicine, Faculty of MedicineKing Abdulaziz University Jeddah Saudi Arabia
- Princess Al‐Jawhara Al‐Brahim Center of Excellence in Research of Hereditary DisordersKing Abdulaziz University Jeddah Saudi Arabia
| | - Zuhier Ahmed Awan
- Department of Clinical Biochemistry, Faculty of MedicineKing Abdulaziz University Jeddah Saudi Arabia
| | - Babajan Banaganapalli
- Department of Genetic Medicine, Faculty of MedicineKing Abdulaziz University Jeddah Saudi Arabia
- Princess Al‐Jawhara Al‐Brahim Center of Excellence in Research of Hereditary DisordersKing Abdulaziz University Jeddah Saudi Arabia
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Thirumal Kumar D, Jain N, Udhaya Kumar S, George Priya Doss C, Zayed H. Identification of potential inhibitors against pathogenic missense mutations of PMM2 using a structure-based virtual screening approach. J Biomol Struct Dyn 2020; 39:171-187. [PMID: 31870226 DOI: 10.1080/07391102.2019.1708797] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The autosomal recessive phosphomannomutase 2-congenital disorder of glycosylation (PMM2-CDG) is characterized by defective functioning of the PMM2 enzyme, which is necessary for the conversion of mannose-6-phosphate into mannose-1-phosphate. Here, a computational pipeline was drawn to identify the most significant mutations, and further, we used a virtual screening approach to identify a new lead compound to treat the identified significant mutations. We searched for missense mutation data related to PMM2-CDG in HGMD®, UniProt, and ClinVar. Our search yielded a total of 103 mutations, of which 91 are missense mutations. The D65Y, I132N, I132T, and F183S mutations were classified as deleterious, destabilizing, and altering the biophysical properties using the PredictSNP, iStable, and Align GVGD in silico prediction tools. Additionally, we applied a multistep protocol to screen for an alternative lead compound to the existing CID2876053 (1-(3-chlorophenyl)-3,3-bis(pyridine-2-yl)urea) with affinity to these identified significant mutants. Two compounds, CHEMBL1491007 (6-chloro-4-phenyl-3-(4-pyridin-2-ylpiperazin-1-yl)-1H-quinolin-2-one) and CHEMBL3653029 (5-chloro-4-[6-[(3-fluorophenyl)methylamino]pyridin-2-yl]-N-(piperidin-4-ylmethyl)pyridin-2-amine), exhibited the highest binding affinity with the selected mutants and were chosen for further analysis. Through molecular docking, molecular dynamics simulation, and MMPBSA analysis, we found that the known compound, i.e. CID2876053, has stronger interaction with the D65Y mutant. The newly identified lead compound CHEMBL1491007 showed stronger interaction with the I132N and I132T mutants, whereas the most deleterious mutant, F183S, showed stronger interaction with CHEMBL3653029. This study is expected to aid in the field of precision medicine, and further to in vivo and in vitro analysis of these lead compounds might shed light on the treatment of PMM2-CDG. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- D Thirumal Kumar
- School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, India
| | - Nikita Jain
- School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, India
| | - S Udhaya Kumar
- School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, India
| | - C George Priya Doss
- School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, India
| | - Hatem Zayed
- Department of Biomedical Sciences, College of Health and Sciences, Qatar University, Doha, Qatar
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Tanwar H, Kumar DT, Doss CGP, Zayed H. Bioinformatics classification of mutations in patients with Mucopolysaccharidosis IIIA. Metab Brain Dis 2019; 34:1577-1594. [PMID: 31385193 PMCID: PMC6858298 DOI: 10.1007/s11011-019-00465-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 07/08/2019] [Indexed: 02/06/2023]
Abstract
Mucopolysaccharidosis (MPS) IIIA, also known as Sanfilippo syndrome type A, is a severe, progressive disease that affects the central nervous system (CNS). MPS IIIA is inherited in an autosomal recessive manner and is caused by a deficiency in the lysosomal enzyme sulfamidase, which is required for the degradation of heparan sulfate. The sulfamidase is produced by the N-sulphoglucosamine sulphohydrolase (SGSH) gene. In MPS IIIA patients, the excess of lysosomal storage of heparan sulfate often leads to mental retardation, hyperactive behavior, and connective tissue impairments, which occur due to various known missense mutations in the SGSH, leading to protein dysfunction. In this study, we focused on three mutations (R74C, S66W, and R245H) based on in silico pathogenic, conservation, and stability prediction tool studies. The three mutations were further subjected to molecular dynamic simulation (MDS) analysis using GROMACS simulation software to observe the structural changes they induced, and all the mutants exhibited maximum deviation patterns compared with the native protein. Conformational changes were observed in the mutants based on various geometrical parameters, such as conformational stability, fluctuation, and compactness, followed by hydrogen bonding, physicochemical properties, principal component analysis (PCA), and salt bridge analyses, which further validated the underlying cause of the protein instability. Additionally, secondary structure and surrounding amino acid analyses further confirmed the above results indicating the loss of protein function in the mutants compared with the native protein. The present results reveal the effects of three mutations on the enzymatic activity of sulfamidase, providing a molecular explanation for the cause of the disease. Thus, this study allows for a better understanding of the effect of SGSH mutations through the use of various computational approaches in terms of both structure and functions and provides a platform for the development of therapeutic drugs and potential disease treatments.
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Affiliation(s)
- Himani Tanwar
- Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India
| | - D Thirumal Kumar
- Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India
| | - C George Priya Doss
- Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India.
| | - Hatem Zayed
- Department of Biomedical Sciences, College of Health and Sciences, Qatar University, Doha, Qatar.
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Agrahari AK, Pieroni E, Gatto G, Kumar A. The impact of missense mutation in PIGA associated to paroxysmal nocturnal hemoglobinuria and multiple congenital anomalies-hypotonia-seizures syndrome 2: A computational study. Heliyon 2019; 5:e02709. [PMID: 31687525 PMCID: PMC6820265 DOI: 10.1016/j.heliyon.2019.e02709] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Revised: 08/12/2019] [Accepted: 10/17/2019] [Indexed: 12/17/2022] Open
Abstract
Paroxysmal nocturnal hemoglobinuria (PNH) is an acquired clonal blood disorder that manifests with hemolytic anemia, thrombosis, and peripheral blood cytopenias. The disease is caused by the deficiency of two glycosylphosphatidylinositols (GPI)-anchored proteins (CD55 and CD59) in the hemopoietic stem cells. The deficiency of GPI-anchored proteins has been associated with the somatic mutations in phosphatidylinositol glycan class A (PIGA). However, the mutations that do not cause PNH is associated with the multiple congenital anomalies-hypotonia-seizures syndrome 2 (MCAHS2). To best of our knowledge, no computational study has been performed to explore at an atomistic level the impact of PIGA missense mutations on the structure and dynamics of the protein. Therefore, we focused our study to provide molecular insights into the changes in protein structural dynamics upon mutation. In the initial step, screening for the most pathogenic mutations from the pool of publicly available mutations was performed. Further, to get a better understanding, pathogenic mutations were mapped to the modeled structure and the resulting protein was subjected to 100 ns molecular dynamics simulation. The residues close to C- and N-terminal regions of the protein were found to exhibit greater flexibility upon mutation. Our study suggests that four mutations are highly effective in altering the structural conformation and stability of the PIGA protein. Among them, mutant G48D was found to alter protein's structural dynamics to the greatest extent, both on a local and a global scale.
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Affiliation(s)
- Ashish Kumar Agrahari
- Department of Integrative Biology, School of Biosciences and Technology, VIT, Vellore, Tamil Nadu 632014, India
- Research Center for Computer-Aided Drug Discovery, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Enrico Pieroni
- CRS4 – Modeling & Simulation Group, Biosciences Department, 09010, Pula, Italy
| | - Gianluca Gatto
- Department of Electrical and Electronic Engineering, University of Cagliari, via Marengo 2, 09123 Cagliari, Italy
| | - Amit Kumar
- Department of Electrical and Electronic Engineering, University of Cagliari, via Marengo 2, 09123 Cagliari, Italy
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Agrahari AK, Doss GPC, Siva R, Magesh R, Zayed H. Molecular insights of the G2019S substitution in LRRK2 kinase domain associated with Parkinson's disease: A molecular dynamics simulation approach. J Theor Biol 2019; 469:163-171. [PMID: 30844370 DOI: 10.1016/j.jtbi.2019.03.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 02/15/2019] [Accepted: 03/01/2019] [Indexed: 12/19/2022]
Abstract
The G2019S substitution in the Leucine-rich repeat kinase 2 (LRRK2) is significantly associated with Parkinson's disease (PD). This substitution was identified in both familial and sporadic forms of PD with a higher frequency. Few computational studies have reported the impact of G2019S substitution on inhibitors of the kinase domain of LRRK2. However, no computational study deeply investigated the possible impact of the G2019S substitution on the kinase domain in its Apo conformation. Therefore, in this study, we used 200 ns molecular dynamic simulation using the GROMACS 5.1.4 package software to investigate the impact of the G2019S substitution on the structure of the kinase domain of LRRK2. Our results indicate that the G2019S substitution affects the dynamics and stability of LRRK2 by decreasing the flexibility and increasing the compactness of the kinase domain and showing its tendency to be in an active conformation for long time interval because of the high energy barrier between active and inactive conformation. This study predicts the molecular pathogenicity mechanism of the G2019S on patients with PD and provides a potential platform for developing therapeutics for patients with PD that harbor this amino acid substitution.
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Affiliation(s)
- Ashish Kumar Agrahari
- Department of Integrative Biology, School of Biosciences and Technology, VIT, Vellore, Tamil Nadu 632014, India
| | - George Priya C Doss
- Department of Integrative Biology, School of Biosciences and Technology, VIT, Vellore, Tamil Nadu 632014, India.
| | - R Siva
- Department of Integrative Biology, School of Biosciences and Technology, VIT, Vellore, Tamil Nadu 632014, India
| | - R Magesh
- Department of Biotechnology, Sri Ramachandra Institute of Higher Education and Research (SRIHER), Deemed to be University (DU), Porur, Chennai, 600116, India
| | - Hatem Zayed
- Department of Biomedical Sciences, College of Health and Sciences, Qatar University, Doha, Qatar.
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