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Usama, Khan Z, Ali A, Shah M, Imran M. Differential glycosylation in mutant vitamin D-binding protein decimates the binding stability of vitamin D. J Biomol Struct Dyn 2024; 42:5365-5375. [PMID: 37357441 DOI: 10.1080/07391102.2023.2226742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 06/10/2023] [Indexed: 06/27/2023]
Abstract
Vitamin D (VD) is produced by the skin upon exposure to sunlight or is obtained from dietary sources. Several risk factors are associated with VD deficiency including mutations and post-translational modifications in its transport protein known as vitamin D binding protein (VDBP) or GC-globulin. The two common single nucleotide polymorphisms rs7041 and rs4588 create three major isoforms of VDBP, including GC-1F also called wild type, GC1S, and GC-2. The 3D models for both GC-1F and GC-2 were constructed in their glycosylated states to decipher the effect of these mutations on the overall conformational changes and VD-binding affinity. The binding affinities were estimated using the Molecular Mechanics Poison-Boltzmann surface area (MM-PBSA) method and conformational changes were investigated after free energy landscapes estimations. Total free energies suggest that GC-1F exhibits stronger affinity (ΔE = -116.09 kJ/mol) than GC-2 (ΔE = -95 kJ/mol) variant with VD. The GC-1F isoforms had more streamlined motion compared to GC-2 isoforms, predicting a trade-off between cross-talk residues that significantly impacts protein structural stability. The data suggest that glycation at Thr418 plays a vital role in the overall VDBP-VD affinity by stabilizing the N-T loop that holds the domain I (VD-pocket) and domain III intact. The loss of glycation in GC-2 has a pivotal role in the inter-domain conformational stability of VDBP, which may ultimately affect VD transportation and maturation. These findings describe a novel mechanism in how mutations distant from the VD-active site change the overall conformational of the VDBP and abrogate the VDBP-VD interaction.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Usama
- Biochemistry Section, Institute of Chemical Sciences, University of Peshawar, Peshawar, Khyber Pakhtunkhwa, Pakistan
| | - Zahid Khan
- Biochemistry Section, Institute of Chemical Sciences, University of Peshawar, Peshawar, Khyber Pakhtunkhwa, Pakistan
| | - Aktar Ali
- Biological Screening Core, Warren Family Center for Drug Discovery, University of Notre Dame, Notre Dame, Indiana, USA
| | - Masaud Shah
- Department of Physiology, School of Medicine, Ajou University, Suwon, South Korea
| | - Muhammad Imran
- Biochemistry Section, Institute of Chemical Sciences, University of Peshawar, Peshawar, Khyber Pakhtunkhwa, Pakistan
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Luo H, Ma Y, Bi J, Li Z, Wang Y, Su Z, Gerstweiler L, Ren Y, Zhang S. Experimental and molecular dynamics simulation studies on the physical properties of three HBc-VLP derivatives as nanoparticle protein vaccine candidates. Vaccine 2024:S0264-410X(24)00599-1. [PMID: 38811268 DOI: 10.1016/j.vaccine.2024.05.040] [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: 02/01/2024] [Revised: 05/19/2024] [Accepted: 05/20/2024] [Indexed: 05/31/2024]
Abstract
Self-assembling virus-like particles (VLPs) are promising platforms for vaccine development. However, the unpredictability of the physical properties, such as self-assembly capability, hydrophobicity, and overall stability in engineered protein particles fused with antigens, presents substantial challenges in their downstream processing. We envision that these challenges can be addressed by combining more precise computer-aided molecular dynamics (MD) simulations with experimental studies on the modified products, with more to-date forcefield descriptions and larger models closely resembling real assemblies, realized by rapid advancement in computing technology. In this study, three chimeric designs based on the hepatitis B core (HBc) protein as model vaccine candidates were constructed to study and compare the influence of inserted epitopes as well as insertion strategy on HBc modifications. Large partial VLP models containing 17 chains for the HBc chimeric model vaccines were constructed based on the wild-type (wt) HBc assembly template. The findings from our simulation analysis have demonstrated good consistency with experimental results, pertaining to the surface hydrophobicity and overall stability of the chimeric vaccine candidates. Furthermore, the different impact of foreign antigen insertions on the HBc scaffold was investigated through simulations. It was found that separately inserting two epitopes into the HBc platform at the N-terminal and the major immunogenic regions (MIR) yields better results compared to a serial insertion at MIR in terms of protein structural stability. This study substantiates that an MD-guided design approach can facilitate vaccine development and improve its manufacturing efficiency by predicting products with extreme surface hydrophobicity or structural instability.
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Affiliation(s)
- Hong Luo
- School of Chemical Engineering, Faculty of Science, Engineering and Technology, University of Adelaide, Adelaide 5005, Australia; State Key Laboratory of Biochemical Engineering, Key Laboratory of Biopharmaceutical Preparation and Delivery (CAS), Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, PR China; Institute of Pharmaceutical and Food Engineering, Shanxi University of Chinese Medicine, Jinzhong 030619, PR China
| | - Yanyan Ma
- State Key Laboratory of Biochemical Engineering, Key Laboratory of Biopharmaceutical Preparation and Delivery (CAS), Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, PR China
| | - Jingxiu Bi
- School of Chemical Engineering, Faculty of Science, Engineering and Technology, University of Adelaide, Adelaide 5005, Australia
| | - Zhengjun Li
- State Key Laboratory of Biochemical Engineering, Key Laboratory of Biopharmaceutical Preparation and Delivery (CAS), Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, PR China
| | - Yingli Wang
- Institute of Pharmaceutical and Food Engineering, Shanxi University of Chinese Medicine, Jinzhong 030619, PR China
| | - Zhiguo Su
- State Key Laboratory of Biochemical Engineering, Key Laboratory of Biopharmaceutical Preparation and Delivery (CAS), Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, PR China
| | - Lukas Gerstweiler
- School of Chemical Engineering, Faculty of Science, Engineering and Technology, University of Adelaide, Adelaide 5005, Australia.
| | - Ying Ren
- State Key Laboratory of Mesoscience and Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, PR China; School of Chemical Engineering, University of Chinese Academy of Sciences, Beijing 100049, PR China.
| | - Songping Zhang
- State Key Laboratory of Biochemical Engineering, Key Laboratory of Biopharmaceutical Preparation and Delivery (CAS), Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, PR China.
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Panchal NK, Samdani P, Sengupta T, Prince SE. Computational Analysis of Non-synonymous SNPs in ATM Kinase: Structural Insights, Functional Implications, and Inhibitor Discovery. Mol Biotechnol 2024:10.1007/s12033-024-01120-x. [PMID: 38489015 DOI: 10.1007/s12033-024-01120-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 02/13/2024] [Indexed: 03/17/2024]
Abstract
Ataxia telangiectasia-mutated (ATM) protein kinase, a key player in cellular integrity regulation, is known for its role in DNA damage response. This study investigates the broader impact of ATM on cellular processes and potential clinical manifestations arising from mutations, aiming to expand our understanding of ATM's diverse functions beyond conventional roles. The research employs a comprehensive set of computational techniques for a thorough analysis of ATM mutations. The mutation data are curated from dbSNP and HuVarBase databases. A meticulous assessment is conducted, considering factors such as deleterious effects, protein stability, oncogenic potential, and biophysical characteristics of the identified mutations. Conservation analysis, utilizing diverse computational tools, provides insights into the evolutionary significance of these mutations. Molecular docking and dynamic simulation analyses are carried out for selected mutations, investigating their interactions with Y2080D, AZD0156, and quercetin inhibitors to gauge potential therapeutic implications. Among the 419 mutations scrutinized, five (V1913C, Y2080D, L2656P, C2770G, and C2930G) are identified as both disease causing and protein destabilizing. The study reveals the oncogenic potential of these mutations, supported by findings from the COSMIC database. Notably, Y2080D is associated with haematopoietic and lymphoid cancers, while C2770G shows a correlation with squamous cell carcinomas. Molecular docking and dynamic simulation analyses highlight strong binding affinities of quercetin for Y2080D and AZD0156 for C2770G, suggesting potential therapeutic options. In summary, this computational analysis provides a comprehensive understanding of ATM mutations, revealing their potential implications in cellular integrity and cancer development. The study underscores the significance of Y2080D and C2770G mutations, offering valuable insights for future precision medicine targeting-specific ATM. Despite informative computational analyses, a significant research gap exists, necessitating essential in vitro and in vivo studies to validate the predicted effects of ATM mutations on protein structure and function.
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Affiliation(s)
- Nagesh Kishan Panchal
- Department of Biotechnology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, 632 014, India
| | - Poorva Samdani
- Department of Biomedical Sciences, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, India
| | - Tiasa Sengupta
- Department of Biomedical Sciences, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, India
| | - Sabina Evan Prince
- Department of Biotechnology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, 632 014, India.
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Panchal NK, Mohanty S, Prince SE. Computational insights into NIMA-related kinase 6: unraveling mutational effects on structure and function. Mol Cell Biochem 2023:10.1007/s11010-023-04910-0. [PMID: 38117419 DOI: 10.1007/s11010-023-04910-0] [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: 09/09/2023] [Accepted: 11/25/2023] [Indexed: 12/21/2023]
Abstract
The NEK6 (NIMA-related kinase 6) serine/threonine kinase is a pivotal player in a multitude of cellular processes, including the regulation of the cell cycle and the response to DNA damage. Its significance extends to disease pathogenesis, as changes in NEK6 activity have been linked to the development of cancer. Non-synonymous single nucleotide polymorphisms (nsSNPs) in NEK6 have been linked to cancer as they alter the protein's native structure and function. The association between NEK6 activity and cancer development has prompted researchers to explore the effects of genetic variations within the NEK6 gene. Therefore, we utilized advanced computational tools to analyze 155 high-confidence nsSNPs in the NEK6 gene. From this analysis, 21 nsSNPs were identified as potentially harmful, raising concerns about their impact on NEK6 activity and cancer risk. These 21 mutations were then examined for structural alterations, and eight of nsSNPs (I51M, V76A, I134N, Y152D, R171Q, V186G, L237R, and C285S) were found to destabilize the protein. Among the destabilizing mutations screened, a specific mutation, R171Q, stood out due to its conserved nature. To understand its impact on the protein and conformation, all-atom molecular dynamics simulations (MDS) for 100 ns were performed for both Wildtype NEK6 (WT-NEK6) and R171Q. The simulations revealed that the R171Q variant was unstable and led to significant conformational changes in NEK6. This study provides valuable insights into NEK6 dysfunction caused by single amino acid alterations, offering a novel understanding of the molecular mechanisms underlying NEK6-related cancer progression.
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Affiliation(s)
- Nagesh Kishan Panchal
- Department of Biotechnology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, 632 014, India
| | - Shruti Mohanty
- Department of Biomedical Sciences, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, 632014, India
| | - Sabina Evan Prince
- Department of Biotechnology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, 632 014, India.
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Dristy TT, Noor AR, Dey P, Saha A. Structural analysis and conformational dynamics of SOCS1 gene mutations involved in diffuse large B-cell lymphoma. Gene 2023; 864:147293. [PMID: 36813059 DOI: 10.1016/j.gene.2023.147293] [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: 09/27/2022] [Revised: 01/28/2023] [Accepted: 02/15/2023] [Indexed: 02/22/2023]
Abstract
OBJECTIVES The SOCS1 gene is frequently mutated in primary Diffuse Large B-Cell Lymphoma (DLBCL) patients and is associated with a reduced survival rate. Using various computational techniques, the current study aims to identify Single Nucleotide Polymorphisms (SNPs) in the SOCS1 gene that are associated with the mortality rate of DLBCL patients. This study also evaluates the effects of SNPs on the structural instability of the SOCS1 protein in DLBCL patient. METHODS The cBioPortal webserver was used for mutations and determining how the SNP mutations affect the SOCS1 protein with various algorithms (PolyPhen-2.0, Provean, PhD-SNPg, SNPs&GO, SIFT, FATHMM, Predict SNP and SNAP). Five webservers (I-Mutant 2.0, MUpro, mCSM, DUET and SDM) were used for protein instability and the conserved status and were also predicted through different tools (ConSurf, Expasy, SOMPA). Lastly, MD simulations were run on the two chosen mutations (S116N and V128G) using GROMACS 5.0.1 to study how the mutations change the structure of SOCS1. RESULTS Among the 93 SOCS1 mutations detected in DLBCL patients, nine mutations were found to have a detrimental effect (damaging/deleterious/pathogenic/altered) on the SOCS1 protein. All the nine selected mutations are in the conserved region and four are on the extended strand site, four on the random coil site and one on the alpha helix position of the secondary protein structure. After anticipating the structural effects of these nine mutations, two were chosen (S116N and V128G) based on mutational frequency, location within the protein, structural effect (primary, secondary and tertiary) on stability and conservation status within the SOCS1 protein. The simulation of a 50 ns time interval revealed that the Rg value of S116N (2.17 nm) is higher than that of WT (1.98 nm), indicating a loss of structural compactness. In the case of the RMSD value, this mutated type (V128G) shows more deviation (1.54 nm) in comparison to the wild-type (2.14 nm) and another mutant type (S116N) (2.12 nm). The average RMSF values of wild-type and mutant types (V128G and S116N) were 0.88 nm, 0.49 nm, and 0.93 nm, respectively. The RMSF result shows that the mutant V128G structure is more stable than the wild-type and mutant S116N structures. CONCLUSION Based on all these computational predictions, this study finds that certain mutations, particularly S116N, have a destabilising and robust effect on the SOCS1 protein. These results can be used to learn more about the importance of SOCS1 mutations in DLBCL patients and to develop new ways to treat DLBCL.
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Affiliation(s)
- Tamanna Tasnim Dristy
- Department of Genetic Engineering and Biotechnology, East West University (EWU), Bangladesh
| | - Al-Rownoka Noor
- Department of Genetic Engineering and Biotechnology, East West University (EWU), Bangladesh
| | - Puja Dey
- Faculty of Medicine, Shimane University, Japan
| | - Ayan Saha
- Department of Bioinformatics and Biotechnology, Asian University for Women, Bangladesh.
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Pinto ÉSM, Krause MJ, Dorn M, Feltes BC. The nucleotide excision repair proteins through the lens of molecular dynamics simulations. DNA Repair (Amst) 2023; 127:103510. [PMID: 37148846 DOI: 10.1016/j.dnarep.2023.103510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 04/07/2023] [Accepted: 04/23/2023] [Indexed: 05/08/2023]
Abstract
Mutations that affect the proteins responsible for the nucleotide excision repair (NER) pathway can lead to diseases such as xeroderma pigmentosum, trichothiodystrophy, Cockayne syndrome, and Cerebro-oculo-facio-skeletal syndrome. Hence, understanding their molecular behavior is needed to elucidate these diseases' phenotypes and how the NER pathway is organized and coordinated. Molecular dynamics techniques enable the study of different protein conformations, adaptable to any research question, shedding light on the dynamics of biomolecules. However, as important as they are, molecular dynamics studies focused on DNA repair pathways are still becoming more widespread. Currently, there are no review articles compiling the advancements made in molecular dynamics approaches applied to NER and discussing: (i) how this technique is currently employed in the field of DNA repair, focusing on NER proteins; (ii) which technical setups are being employed, their strengths and limitations; (iii) which insights or information are they providing to understand the NER pathway or NER-associated proteins; (iv) which open questions would be suited for this technique to answer; and (v) where can we go from here. These questions become even more crucial considering the numerous 3D structures published regarding the NER pathway's proteins in recent years. In this work, we tackle each one of these questions, revising and critically discussing the results published in the context of the NER pathway.
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Affiliation(s)
| | - Mathias J Krause
- Institute for Applied and Numerical Mathematics, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Márcio Dorn
- Center for Biotechnology, Federal University of Rio Grande do Sul, RS, Brazil; Institute of Informatics, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil; National Institute of Science and Technology - Forensic Science, Porto Alegre, RS, Brazil
| | - Bruno César Feltes
- Institute of Informatics, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
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Souissi A, Abdelmalek Driss D, Chakchouk I, Ben Said M, Ben Ayed I, Mosrati MA, Elloumi I, Tlili A, Aifa S, Masmoudi S. Molecular insights into MYO3A kinase domain variants explain variability in both severity and progression of DFNB30 hearing impairment. J Biomol Struct Dyn 2022; 40:10940-10951. [PMID: 34423747 DOI: 10.1080/07391102.2021.1953600] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Hereditary hearing impairment (HI) is a common disease with the highest incidence among sensory defects. Several genes have been identified to affect stereocilia structure causing HI, including the unconventional myosin3A. Interestingly, we noticed that variants in MYO3A gene have been previously found to cause variable HI onset and severity. Using clinical exome sequencing, we identified a novel pathogenic variant p.(Lys50Arg) in the MYO3A kinase domain (MYO3A-KD). Previous in vitro studies supported its damaging effect as a 'kinase-dead' mutant. We further analyzed this variation through molecular dynamics which predicts that changes in flexibility of MYO3A structure would influence the protein-ATP binding properties. This Lys50Arg mutation segregated with congenital profound non-syndromic HI. To better investigate this variability, we collected previously identified MYO3A-KDs variants, p.(Tyr129Cys), p.(His142Gln) and p.(Pro189Thr), and built both wild type and mutant 3 D MYO3A-KD models to assess their impact on the protein structure and function. Our results suggest that KD mutations could either cause a congenital profound form of HI, when particularly affecting the kinase activity and preventing the auto-phosphorylation of the motor, or a late onset and progressive form, when partially or completely inactivating the MYO3A protein. In conclusion, we report a novel pathogenic variant affecting the ATP-binding site within the MYO3A-KD causing congenital profound HI. Through computational approaches we provide a deeper understanding on the correlation between the effects of MYO3A-KD mutations and the variable hearing phenotypes. To the best of our knowledge this is the first study to correlate mutations' genotypes with the variable phenotypes of DFNB30.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Amal Souissi
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Dorra Abdelmalek Driss
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Imen Chakchouk
- Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX, USA
| | - Mariem Ben Said
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Ikhlas Ben Ayed
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia.,Medical Genetic Department, University Hedi Chaker Hospital of Sfax, Sfax, Tunisia
| | - Mohamed Ali Mosrati
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Ines Elloumi
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Abdelaziz Tlili
- Department of Applied Biology, College of Sciences, University of Sharjah, Sharjah, United Arab Emirates.,Human Genetics and Stem Cell Laboratory, Research Institute of Sciences and Engineering, University of Sharjah, Sharjah, United Arab Emirates
| | - Sami Aifa
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Saber Masmoudi
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
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Chear CT, Mat Ripen A, Mohamad SB. Deciphering the structural and functional impact of Q657L mutation in NLRC4 using computational methods. MOLECULAR SIMULATION 2022. [DOI: 10.1080/08927022.2022.2080822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Chai Teng Chear
- Primary Immunodeficiency Unit, Allergy and Immunology Research Centre, Institute for Medical Research, National Institutes of Health, Ministry of Health Malaysia, Selangor, Malaysia
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Adiratna Mat Ripen
- Primary Immunodeficiency Unit, Allergy and Immunology Research Centre, Institute for Medical Research, National Institutes of Health, Ministry of Health Malaysia, Selangor, Malaysia
| | - Saharuddin Bin Mohamad
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, Kuala Lumpur, Malaysia
- Centre of Research in Systems Biology, Structural Bioinformatics and Human Digital Imaging (CRYSTAL), Universiti Malaya, Kuala Lumpur, Malaysia
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