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Nagasubramanian K, Jha S, Rathore AS, Gupta K. Identification of small molecule modulators of class II transactivator-I using computational approaches. J Biomol Struct Dyn 2023; 41:8349-8361. [PMID: 36224172 DOI: 10.1080/07391102.2022.2133011] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 09/30/2022] [Indexed: 10/17/2022]
Abstract
Major histocompatibility complex II (MHCII), a mediator of the innate and adaptive immune system, plays a central role in regulating inflammation and its progression. Class II transactivator (CIITA) is a master regulator of MHCII expression and controls antigen presentation followed by T-cell activation. Regulation of inflammation by modulation of CIITA has been suggested as a promising intervention for several disorders, including neuroinflammation, rheumatoid arthritis and other autoimmune diseases. This study aimed to (i) identify possible pharmacological agents which could bind to and inhibit isoform I of CIITA (CIITA-I) and (ii) determine their strength of interactions. The structure of CIITA-I isoform was predicted using phyre2 and refined via 3D refine. Loops were refined using ModBase, followed by quality assessment based on ERRAT value. The refined 3D structure was subjected to docking via Maestro (from Schrodinger) using glide module against small molecule databases. Molecules having the least glide score and favorable ADME properties were subjected to molecular simulation by GROMACS. We used the 3D refined structure of CIITA-I, with a score of 83.4% in ERRAT for docking studies. The ligand 4-(2-((6-oxo-4-phenyl-1,6-dihydropyrimidin-2-yl) thio) acetamido) benzamide (ZINC5154833), showed maximum glide score (-6.591) followed by N-[4-(3-oxo-3-{4-[3-(trifluoromethyl) phenyl] piperazin-1-yl} propyl)-1,3-thiazol-2-yl] benzamide (F5254-0161, glide score -6.41). Simulation studies using GROMACS showed F5254-0161 to have a more stable interaction with CIITA-I. Based on our analysis, we propose ZINC5154833 and F5254-0161 as potential modulators for CIITA-I.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Kishore Nagasubramanian
- School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, Tamil Nadu, India
| | - Shanker Jha
- School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, Tamil Nadu, India
| | - Anuranjan Singh Rathore
- School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, Tamil Nadu, India
| | - Krishnakant Gupta
- School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, Tamil Nadu, India
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Adetunji JA, Ogunyemi OM, Gyebi GA, Adewumi AE, Olaiya CO. Atomistic simulations suggest dietary flavonoids from Beta vulgaris (beet) as promising inhibitors of human angiotensin-converting enzyme and 2-alpha-adrenergic receptors in hypertension. BIOINFORMATICS ADVANCES 2023; 3:vbad133. [PMID: 37822725 PMCID: PMC10562952 DOI: 10.1093/bioadv/vbad133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 09/08/2023] [Indexed: 10/13/2023]
Abstract
Motivation Beta vulgaris (beet) is extensively reported for its antihypertensive activity. However, the mechanismunderpinning its antihypertensive activity is not well understood. In this study, we evaluated the in silico interactionsof 70 compounds derived from beta vulgaris against the active sites of angiotensin-converting enzyme (ACE) and alpha-adrenergic receptor (AR). Results Structure-based virtual screening against angiotensin-converting enzyme revealed that, Cochliophilin A (-9.0 Kcal/mol), Miraxanthin (-8.3 Kcal/mol), and quercimeritrin (-9.7 Kcal/mol) had lower docking scores than the reference lisinopril (-7.9 Kcal/mol). These compounds exhibited dual binding tendency as they also ranked top compounds upon screening against adrenergic receptor. The thermodynamic parameters computed from the resulting trajectories obtained from the 100 ns full atomistic molecular dynamics simulation revealed structural stability and conformational flexibility of the ligand-receptor complexes as indicated by the RMSD, RMSF, RoG, SASA, and H-bond calculations. The molecular mechanics with generalized Born and surface area solvation binding energy calculations revealed that the proteins exhibit considerable binding energy with the phytochemicals in a dynamic environment. Furthermore, the hit compounds possess good physicochemical properties and drug-likeness. Overall, cochliophilin and quercimeritrin are promising dual-target directed flavonoids from Beta vulgaris; and are suggested for further experimental and preclinical evaluation. Availability and implementation All data was provided in the manuscript.
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Affiliation(s)
- Joy A Adetunji
- Nutritional and Industrial Biochemistry Laboratory, Department of Biochemistry, Faculty of Basic Medical Sciences, College of Medicine, University of Ibadan, Ibadan 200005, Nigeria
| | - Oludare M Ogunyemi
- Nutritional and Industrial Biochemistry Laboratory, Department of Biochemistry, Faculty of Basic Medical Sciences, College of Medicine, University of Ibadan, Ibadan 200005, Nigeria
| | - Gideon A Gyebi
- Department of Biochemistry, Faculty of Science and Technology, Bingham University, Karu, Nigeria
- Natural Products and Structural (Bio-Chem)-informatics Research Laboratory (NpsBC-Rl), Bingham University, Nasarawa, Nigeria
| | - Anuoluwapo E Adewumi
- Nutritional and Industrial Biochemistry Laboratory, Department of Biochemistry, Faculty of Basic Medical Sciences, College of Medicine, University of Ibadan, Ibadan 200005, Nigeria
| | - Charles O Olaiya
- Nutritional and Industrial Biochemistry Laboratory, Department of Biochemistry, Faculty of Basic Medical Sciences, College of Medicine, University of Ibadan, Ibadan 200005, Nigeria
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Khan N, Khan K, Badshah Y, Trembley JH, Ashraf NM, Shabbir M, Danish L, Afsar T, Almajwal A, Justin S, Hasan Z, Razak S. Investigating pathogenic SNP of PKCι in HCV-induced hepatocellular carcinoma. Sci Rep 2023; 13:12504. [PMID: 37532886 PMCID: PMC10397245 DOI: 10.1038/s41598-023-39804-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 07/31/2023] [Indexed: 08/04/2023] Open
Abstract
Hepatocellular carcinoma is a leading cause of cancer-related deaths due to its complexity in diagnosis, chemo-resistance, and aggressive nature. Identifying pathogenic single nucleotide polymorphism (SNP) in protein kinase C iota (PKCι) can be a potential biomarker in the prognosis and treatment of HCC. This study investigated the association between a SNP in PRKCI and the Pakistani population's hepatocellular carcinoma (HCC) risk. Obtained samples were first evaluated for ALT measurements and viral load quantification through reverse transcriptase-PCR. The PKCι nsSNP rs1199520604 was evaluated computationally by multiple consensus bioinformatics tools for predicting its potential deleterious effects. Its association with hepatitis C virus- (HCV) mediated HCC was then investigated through ARMS-PCR (Amplification Refractory Mutation System Polymerase Chain Reaction). SNP analysis of rs1199520604 was performed in 100 cases and 100 controls. Variant rs1199520604's homozygous T genotype is a risk factor allele for the HCV-induced HCC (odds ratio: 4.13, relative risk: 2.01, P-value < 0.0001). The heterozygous genotype is determined to protect HCV patients from HCC development (P < 0.001). The study highlighted the disease association of variant rs1199520604 with HCV-induced HCC in the Pakistani populations. This variant, after further validation through high-throughput investigation on a larger cohort, has the potential to be translated at the clinical level.
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Affiliation(s)
- Naila Khan
- Department of Healthcare Biotechnology, Atta-Ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Khushbukhat Khan
- Department of Healthcare Biotechnology, Atta-Ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Yasmin Badshah
- Department of Healthcare Biotechnology, Atta-Ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Janeen H Trembley
- Research Service, Minneapolis VA Health Care System, Minneapolis, MN, USA
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Naeem Mahmood Ashraf
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore, Pakistan
| | - Maria Shabbir
- Department of Healthcare Biotechnology, Atta-Ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan.
| | - Lubna Danish
- Agricultural Research Institute, Tarnab, Peshawar, Pakistan
| | - Tayyaba Afsar
- Department of Community Health Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Ali Almajwal
- Department of Community Health Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Saira Justin
- Department of Healthcare Biotechnology, Atta-Ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Zafarul Hasan
- College of Nursing, Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Suhail Razak
- Department of Community Health Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia.
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Hidayatullah A, Putra WE, Sustiprijatno S, Rifa'i M, Widiastuti D, Heikal MF, Permatasari GW. Concatenation of molecular docking and dynamics simulation of human papillomavirus type 16 E7 oncoprotein targeted ligands: In quest of cervical cancer's treatment. AN ACAD BRAS CIENC 2023; 95:e20220633. [PMID: 37466536 DOI: 10.1590/0001-3765202320220633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 10/23/2022] [Indexed: 07/20/2023] Open
Abstract
The Human papillomaviruses type 16 E7 oncoprotein is a 98-amino-acid, 11-kilodalton acidic oncoprotein with three conserved portions. Due to its interaction with the pRb-E2F complex, CKII, CKI (mostly p21), and even HDAC1, it possesses strong transformative and carcinogenic qualities that inhibit normal differentiation and cell cycle regulation. Here, we target the E7 oncoprotein using two prior research active compounds: asarinin and thiazolo[3,2-a]benzimidazole-3(2H)-one,2-(2-fluorobenzylideno)-7,8-dimethyl (thiazolo), and valproic acid as a control. We are performing molecular docking followed by molecular dynamic analysis. By acting as competitive inhibitors in the binding site, it was hypothesized that both drugs would inhibit E7-mediated pRb degradation and E7-mediated p21 degradation, resulting in decreased cell cycle progression, immortalization, and proliferation. In addition, we expect that the direct inhibitory action of valproic acid in E7 will target the CKII-mediated phosphorylation pathway necessary for destabilizing p130 and pRb. According to the results of the dynamic simulation, stable interactions exist between every compound. Despite the instability of E7 protein, stability results indicate that both natural chemicals are preferable, with thiazolo outperforming valproic acid.
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Affiliation(s)
- Arief Hidayatullah
- United Nations Development Programme Indonesia, Health Governance Initiative, Eijkman-RSCM Building, Jakarta, 10430, Indonesia
| | - Wira E Putra
- Universitas Negeri Malang, Biotechnology Study Program, Department of Applied Sciences, Faculty of Mathematics and Natural Sciences, East Java 65145, Indonesia
| | - Sustiprijatno Sustiprijatno
- National Research and Innovation Agency, Research Center for Plant Conservation, Botanic Gardens and Forestry, Cibinong-Bogor, West Java 45262, Indonesia
| | - Muhaimin Rifa'i
- Brawijaya University, Department of Biology, Faculty of Mathematics and Natural Sciences, East Java, 65145, Indonesia
| | - Diana Widiastuti
- Universitas Pakuan, Department of Chemistry, Faculty of Mathematics and Natural Science, West Java, 45262, Indonesia
| | - Muhammad F Heikal
- Khon Kaen University, Tropical Medicine International Program, Faculty of Medicine, Khon Kaen 40000, Thailand
| | - Galuh W Permatasari
- Indonesian Research Institute for Biotechnology and Bioindustry, Bogor, West Java, 45262, Indonesia
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Heikal MF, Putra WE, Sustiprijatno, Rifa’i M, Hidayatullah A, Ningsih FN, Widiastuti D, Shuib AS, Zulfiani BF, Hanasepti AF. In Silico Screening and Molecular Dynamics Simulation of Potential Anti-Malarial Agents from Zingiberaceae as Potential Plasmodium falciparum Lactate Dehydrogenase (PfLDH) Enzyme Inhibitors. Trop Life Sci Res 2023; 34:1-20. [PMID: 38144376 PMCID: PMC10735256 DOI: 10.21315/tlsr2023.34.2.1] [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: 02/10/2022] [Accepted: 09/06/2022] [Indexed: 12/26/2023] Open
Abstract
Malaria continues to be a major public health issue in a number of countries, particularly in tropical regions-the emergence of drug-resistant Plasmodium falciparum encourages new drug discovery research. The key to Plasmodium falciparum survival is energy production up to 100 times greater than other parasites, primarily via the PfLDH. This study targets PfLDH with natural bioactive compounds from the Zingiberaceae family through molecular docking and molecular dynamic studies. Sulcanal, quercetin, shogosulfonic acid C, galanal A and naringenin are the Top 5 compounds with a lower binding energy value than chloroquine, which was used as a control in this study. By binding to NADH and substrate binding site residues, the majority of them are expected to inhibit pyruvate conversion to lactate and NAD+ regeneration. When compared to sulcanal and control drugs, the molecular dynamics (MD) simulation study indicated that quercetin may be the most stable molecule when interacting with PfLDH.
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Affiliation(s)
- Muhammad Fikri Heikal
- Tropical Medicine International Program, Faculty of Medicine, Khon Kaen University, 123, Mittraparp Highway, Muang District Khon Kaen 40002 Thailand
| | - Wira Eka Putra
- Biotechnology Study Program, Department of Applied Sciences, Faculty of Mathematics and Natural Sciences, Universitas Negeri Malang, Jl. Cakrawala No.5, Sumbersari, Kec. Lowokwaru, Kota Malang, 65145 East Java. Indonesia
| | - Sustiprijatno
- Research Center for Plant Conservation, Botanic Gardens and Forestry, National Research and Innovation Agency, Cibinong-Bogor, West Java, Indonesia
| | - Muhaimin Rifa’i
- Department of Biology, Faculty of Mathematics and Natural Sciences, Brawijaya University, Jl. Veteran, Ketawanggede, Kec. Lowokwaru, Kota Malang, 65145 East Java, Indonesia
| | - Arief Hidayatullah
- Health Governance Initiative, United Nations Development Programme Indonesia, Eijkman-RSCM Building, Jakarta, Indonesia
| | - Febby Nurdiya Ningsih
- Research Center for Vaccine and Drug, National Research and Innovation Agency, South Tangerang, Indonesia
| | - Diana Widiastuti
- Department of Chemistry, Faculty of Mathematics and Natural Science, Universitas Pakuan, Jl. Pakuan, Tegallega. Kecamatan Bogor Tengah, Kota Bogor, 16143 West Java, Indonesia
| | - Adawiyah Suriza Shuib
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, 50603 Kuala Lumpur, Malaysia
| | - Baiq Feby Zulfiani
- Biotechnology Study Program, Department of Applied Sciences, Faculty of Mathematics and Natural Sciences, Universitas Negeri Malang, Jl. Cakrawala No.5, Sumbersari, Kec. Lowokwaru, Kota Malang, 65145 East Java. Indonesia
| | - Afrabias Firyal Hanasepti
- Biotechnology Study Program, Department of Applied Sciences, Faculty of Mathematics and Natural Sciences, Universitas Negeri Malang, Jl. Cakrawala No.5, Sumbersari, Kec. Lowokwaru, Kota Malang, 65145 East Java. Indonesia
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Dolinska MB, Anderson DE, Sergeev YV. In vitro characterization of the intramelanosomal domain of human recombinant TYRP1 and its oculocutaneous albinism type 3-related mutant variants. Protein Sci 2023; 32:e4518. [PMID: 36412553 PMCID: PMC9793978 DOI: 10.1002/pro.4518] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 11/16/2022] [Accepted: 11/18/2022] [Indexed: 11/23/2022]
Abstract
Tyrosinase related protein 1 (TYRP1) is the most abundant melanosomal protein of the melanocyte, where plays an important role in the synthesis of eumelanin, possibly catalyzing the oxidation of 5,6-dihydroxyindole-2-carboxylic acid to 5,6-quinone-2-carboxylic acid. Mutations to the TYRP1 gene can result in oculocutaneous albinism type 3 (OCA3), a rare disease characterized by reduced synthesis of melanin in skin, hair, and eyes. To investigate the effect of genetic mutations on the TYRP1 structure, function, and stability, we engineered the intramelanosomal domain of TYRP1 and its mutant variants mimicking either OCA3-related changes, C30R, H215Y, D308N, and R326H or R87G mutant variant, analogous to OCA1-related pathogenic effect in tyrosinase. Proteins were produced in Trichoplusia Ni larvae, then purified, and analyzed by biochemical methods. Data shows that D308N and R326H mutants keep the native conformations and demonstrate no change in their stability and enzymatic activity. In contrast, mutations C30R and R87G localized in the Cys-rich domain show the variants misfolding during the purification process. The H215Y variant disrupts the binding of Zn2+ in the active site and thus reduces the strength of the enzyme/substrate interactions. Our results, consistent with the clinical and in silico studies, show that mutations at the protein surface are expected to have a negligible phenotype change compared to that of TYRP1. For the mutations with severe phenotype changes, which were localized in the Cys-rich domain or the active site, we confirmed a complete or partial protein misfolding as the possible mechanism of protein malfunction caused by OCA3 inherited mutations.
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Affiliation(s)
| | - David E. Anderson
- National Institute of Diabetes and Digestive and Kidney DiseasesNational Institutes of HealthBethesdaMarylandUSA
| | - Yuri V. Sergeev
- National Eye InstituteNational Institutes of HealthBethesdaMarylandUSA
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Mahmood TB, Hossan MI, Mahmud S, Shimu MSS, Alam MJ, Bhuyan MMR, Emran TB. Missense mutations in spike protein of SARS‐CoV‐2 delta variant contribute to the alteration in viral structure and interaction with hACE2 receptor. Immun Inflamm Dis 2022; 10:e683. [PMID: 36039645 PMCID: PMC9382871 DOI: 10.1002/iid3.683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 07/17/2022] [Accepted: 07/22/2022] [Indexed: 11/11/2022] Open
Abstract
Introduction Many of the global pandemics threaten human existence over the decades among which coronavirus disease (COVID‐19) is the newest exposure circulating worldwide. The RNA encoded severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) virus is referred as the pivotal agent of this deadly disease that induces respiratory tract infection by interacting host ACE2 receptor with its spike glycoprotein. Rapidly evolving nature of this virus modified into new variants helps in perpetrating immune escape and protection against host defense mechanism. Consequently, a new isolate, delta variant originated from India is spreading perilously at a higher infection rate. Methods In this study, we focused to understand the conformational and functional significance of the missense mutations found in the spike glycoprotein of SARS‐CoV‐2 delta variant performing different computational analysis. Results From physiochemical analysis, we found that the acidic isoelectric point of the virus elevated to basic pH level due to the mutations. The targeted mutations were also found to change the interactive bonding pattern and conformational stability analyzed by the molecular dynamic's simulation. The molecular docking study also revealed that L452R and T478K mutations found in the RBD domain of delta variant spike protein contributed to alter interaction with the host ACE2 receptor. Conclusions Overall, this study provided insightful evidence to understand the morphological and attributive impact of the mutations on SARS‐CoV‐2 delta variant.
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Affiliation(s)
- Tousif Bin Mahmood
- Department of Biotechnology and Genetic Engineering Noakhali Science and Technology University Noakhali Bangladesh
| | - Mohammad Imran Hossan
- Department of Biotechnology and Genetic Engineering Noakhali Science and Technology University Noakhali Bangladesh
| | - Shafi Mahmud
- Department of Genetic Engineering and Biotechnology University of Rajshahi Rajshahi Bangladesh
| | | | - Md. Jahidul Alam
- Department of Applied Chemistry and Chemical Engineering Noakhali Science and Technology University Noakhali Bangladesh
| | - Md. Mahfuzur Rahman Bhuyan
- Department of Biochemistry and Molecular Biology Noakhali Science and Technology University Noakhali Bangladesh
| | - Talha Bin Emran
- Department of Pharmacy BGC Trust University Bangladesh Chittagong Bangladesh
- Department of Pharmacy Faculty of Allied Health Sciences, Daffodil International University Dhaka Bangladesh
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Mahtarin R, Islam S, Islam MJ, Ullah MO, Ali MA, Halim MA. Structure and dynamics of membrane protein in SARS-CoV-2. J Biomol Struct Dyn 2022; 40:4725-4738. [PMID: 33353499 PMCID: PMC7784837 DOI: 10.1080/07391102.2020.1861983] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 12/05/2020] [Indexed: 12/15/2022]
Abstract
SARS-CoV-2 membrane (M) protein performs a variety of critical functions in virus infection cycle. However, the expression and purification of membrane protein structure is difficult despite tremendous progress. In this study, the 3 D structure is modeled followed by intensive validation and molecular dynamics simulation. The lack of suitable homologous templates (>30% sequence identities) leads us to construct the membrane protein models using template-free modeling (de novo or ab initio) approach with Robetta and trRosetta servers. Comparing with other model structures, it is evident that trRosetta (TM-score: 0.64; TM region RMSD: 2 Å) can provide the best model than Robetta (TM-score: 0.61; TM region RMSD: 3.3 Å) and I-TASSER (TM-score: 0.45; TM region RMSD: 6.5 Å). 100 ns molecular dynamics simulations are performed on the model structures by incorporating membrane environment. Moreover, secondary structure elements and principal component analysis (PCA) have also been performed on MD simulation data. Finally, trRosetta model is utilized for interpretation and visualization of interacting residues during protein-protein interactions. The common interacting residues including Phe103, Arg107, Met109, Trp110, Arg131, and Glu135 in the C-terminal domain of M protein are identified in membrane-spike and membrane-nucleocapsid protein complexes. The active site residues are also predicted for potential drug and peptide binding. Overall, this study might be helpful to design drugs and peptides against the modeled membrane protein of SARS-CoV-2 to accelerate further investigation. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Rumana Mahtarin
- Division of Infectious Diseases and Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - Shafiqul Islam
- Division of Infectious Diseases and Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - Md. Jahirul Islam
- Division of Infectious Diseases and Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - M Obayed Ullah
- Division of Infectious Diseases and Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - Md Ackas Ali
- Division of Infectious Diseases and Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - Mohammad A. Halim
- Division of Infectious Diseases and Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
- Department of Physical Sciences, University of Arkansas - Fort Smith, Fort Smith, AR, USA
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Molecular Dynamics Simulation and Essential Dynamics of Deleterious Proline 12 Alanine Single-Nucleotide Polymorphism in PPARγ2 Associated with Type 2 Diabetes, Cardiovascular Disease, and Nonalcoholic Fatty Liver Disease. PPAR Res 2022; 2022:3833668. [PMID: 35547362 PMCID: PMC9085344 DOI: 10.1155/2022/3833668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 01/26/2022] [Accepted: 01/29/2022] [Indexed: 11/25/2022] Open
Abstract
Background. Peroxisome proliferator-activated receptor-γ (PPARγ) gene is located at 3p25 position. PPARγ functions as the master regulator of glucose homeostasis and lipoprotein metabolism, and recent studies have reported that it is involved in various metabolic diseases such as diabetes mellitus, hyperlipidemia, coronary artery disease (CAD), and nonalcoholic fatty liver disease (NAFLD). PPARγ1 and PPARγ2 are necessary for the development of adipose tissue and insulin sensitivity regulation. But PPARγ2 is the isoform that was controlled in response to nutrient intake and obesity. Methodology. In this study, we used computational techniques to show the impact of Pro12Ala polymorphism on PPARγ2. The 3-D structure of PPARγ2 was modeled using I-TASSER server. The modeled structure was validated with the ZLab server, and the mutation was created with SPDB viewer. Stability prediction tools were used. Molecular dynamics simulation (MDS) was used to understand the structural and functional behavior of the wild type and mutant. Essential dynamics was also applied. Results and Conclusions. Stability prediction tools were showed that this mutation has a destabilizing effect on the PPARγ2 structure. The RMSD, RMSF, Rg, SASA, and DSSP were in line with H-bond results that showed less flexibility in the mutant structure. Essential dynamics was used to verify MDS results. Pro12Ala polymorphism leads to rigidity of the PPARγ2 protein and might disturb the conformational changes and interactions of PPARγ2 and results in type 2 diabetes mellitus (T2DM), CAD, and NAFLD. This study can help scientists to develop a drug therapy against these diseases.
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Alam MS, Uddin MS, Shamsuddin T, Rubayed M, Sharmin T, Akter R, Hosen SMZ. Repurposing of existing antibiotics for the treatment of diabetes mellitus. In Silico Pharmacol 2022; 10:4. [PMID: 35273901 PMCID: PMC8898203 DOI: 10.1007/s40203-021-00118-6] [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: 06/20/2021] [Accepted: 11/22/2021] [Indexed: 02/02/2023] Open
Abstract
Proline specific serine protease enzyme, dipeptidyl peptidase IV (DPP-4) has become a promising target for diabetes, as it stops glucagon-like peptide 1 (GLP-1) from becoming inactive, resulting in higher levels of active GLP-1. This lowers glucose levels by increasing insulin secretion and decreasing glucagon secretion. DPP-4 is also linked to a higher BMI and a 0.7 to 1% reduction in HbA1c. Currently available DPP-4 inhibitor drugs showed less promising anti-diabetic activity as this class associated with many side effects due to non-selectivity and therefore searching on more potent DPP-4 inhibitors are still ongoing. In our present study, we investigate the inhibition of DPP-4 through a series of antibiotic compounds which were previously reported to be used in diabetic foot infections and compared with existing DPP-4 inhibitors. To obtain this objective, three-dimensional crystal structure of DPP-4 was retrieved from the protein data bank (PDB id: 1 × 70). A systematic computational method combining molecular docking, MM-GBSA binding energy calculation, MD simulations, MM-PBSA binding free energy calculations and ADME were used to find best DPP-4 inhibitor. Molecular docking results revealed that clindamycin has a higher affinity towards the catalytic sides of DPP-4 and built solid hydrophobic and polar interactions with the amino acids involved in the binding region of DPP-4, such as S1 subsite, S2 subsite and S2 extensive subsite. MD simulations results showed clindamycin as potent virtual hit and suggested that it binds with DPP-4 in competitive manner, which virtually indicate that besides antibiotic activity clindamycin has anti-diabetic activity. Supplementary Information The online version contains supplementary material available at 10.1007/s40203-021-00118-6.
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Affiliation(s)
- Muhammad Shaiful Alam
- Molecular Modeling Drug-Design and Discovery Laboratory, Pharmacology Research Division, BCSIR Laboratories, Chattogram, 4220 Bangladesh
- Department of Pharmacy, University of Science and Technology Chittagong, Chattogram, 4202 Bangladesh
| | - Md. Sohorab Uddin
- Department of Pharmacy, University of Chittagong, Chattogram, 4331 Bangladesh
| | - Tahmida Shamsuddin
- Department of Applied Chemistry, University of Chittagong, Chattogram, 4331 Bangladesh
| | - Maruf Rubayed
- Department of Pharmacy, University of Science and Technology Chittagong, Chattogram, 4202 Bangladesh
| | - Tania Sharmin
- Molecular Modeling Drug-Design and Discovery Laboratory, Pharmacology Research Division, BCSIR Laboratories, Chattogram, 4220 Bangladesh
| | - Rasheda Akter
- Molecular Modeling Drug-Design and Discovery Laboratory, Pharmacology Research Division, BCSIR Laboratories, Chattogram, 4220 Bangladesh
| | - S. M. Zahid Hosen
- Molecular Modeling Drug-Design and Discovery Laboratory, Pharmacology Research Division, BCSIR Laboratories, Chattogram, 4220 Bangladesh
- Pancreatic Research Group, Ingham Institute for Applied Medical Research, Faculty of Medicine, South Western Sydney Clinical School, The University of New South Wales 2170, Sydney, Australia
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11
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Efaz FM, Islam S, Talukder SA, Akter S, Tashrif MZ, Ali MA, Sufian MA, Parves MR, Islam MJ, Halim MA. Repurposing fusion inhibitor peptide against SARS-CoV-2. J Comput Chem 2021; 42:2283-2293. [PMID: 34591335 DOI: 10.1002/jcc.26758] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 08/03/2021] [Accepted: 09/19/2021] [Indexed: 11/08/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is continuously evolving. Although several vaccines were approved, this pandemic is still a major threat to public life. Till date, no established therapies are available against SARS-CoV-2. Peptide inhibitors hold great promise for this viral pathogen due to their efficacy, safety, and specificity. In this study, seventeen antiviral peptides which were known to inhibit SARS-CoV-1 are collected and computationally screened against heptad repeat 1 (HR1) of the SARS-CoV-2 spike protein (S2). Out of 17 peptides, Fp13 and Fp14 showed better binding affinity toward HR1 compared to a control peptide EK1 (a modified pan-coronavirus fusion inhibitor) in molecular docking. To explore the time-dependent interactions of the fusion peptide with HR1, molecular dynamics simulation was performed incorporating lipid membrane. During 100 ns MD simulation, structural and energy parameters of Fp13-HR1 and Fp14-HR1 complexes demonstrated lower fluctuations compared to the control EK1-HR1 complex. Furthermore, principal component analysis and free energy landscape study revealed that these two peptides (Fp13 and Fp14) strongly bind to the HR1 with higher affinity than that of control EK1. Tyr917, Asn919, Gln926, lys933, and Gln949 residues in HR1 protein were found to be crucial residues for peptide interaction. Notably, Fp13, Fp14 showed reasonably better binding free energy and hydrogen bond contribution than that of EK1. Taken together, Fp13 and Fp14 peptides may be highly specific for HR1 which can potentially prevent the formation of the fusion core and could be further developed as therapeutics for treatment or prophylaxis of SARS-CoV-2 infection.
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Affiliation(s)
- Faiyaz Md Efaz
- Division of Infectious disease and Division of Computer Aided Drug Design, The Red-Green Research Centre, Dhaka, Bangladesh
| | - Shafiqul Islam
- Division of Infectious disease and Division of Computer Aided Drug Design, The Red-Green Research Centre, Dhaka, Bangladesh
| | - Shafi Ahmad Talukder
- Division of Infectious disease and Division of Computer Aided Drug Design, The Red-Green Research Centre, Dhaka, Bangladesh
| | - Shaila Akter
- Division of Infectious disease and Division of Computer Aided Drug Design, The Red-Green Research Centre, Dhaka, Bangladesh
| | - Md Zakaria Tashrif
- Division of Infectious disease and Division of Computer Aided Drug Design, The Red-Green Research Centre, Dhaka, Bangladesh
| | - Md Ackas Ali
- Division of Infectious disease and Division of Computer Aided Drug Design, The Red-Green Research Centre, Dhaka, Bangladesh
| | - Md Abu Sufian
- School of Pharmacy, Temple University, Philadelphia, Pennsylvania, USA
| | - Md Rimon Parves
- Division of Infectious disease and Division of Computer Aided Drug Design, The Red-Green Research Centre, Dhaka, Bangladesh
| | - Md Jahirul Islam
- Division of Infectious disease and Division of Computer Aided Drug Design, The Red-Green Research Centre, Dhaka, Bangladesh
| | - Mohammad A Halim
- Department of Physical Sciences, University of Arkansas-Fort Smith, Fort Smith, Arkansas, USA.,Department of Chemistry and Biochemistry, Kennesaw State University, Kennesaw, Georgia, USA
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12
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Integrative Bioinformatics approaches to therapeutic gene target selection in various cancers for Nitroglycerin. Sci Rep 2021; 11:22036. [PMID: 34764329 PMCID: PMC8586365 DOI: 10.1038/s41598-021-01508-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 07/27/2021] [Indexed: 12/30/2022] Open
Abstract
Integrative Bioinformatics analysis helps to explore various mechanisms of Nitroglycerin activity in different types of cancers and help predict target genes through which Nitroglycerin affect cancers. Many publicly available databases and tools were used for our study. First step in this study is identification of Interconnected Genes. Using Pubchem and SwissTargetPrediction Direct Target Genes (activator, inhibitor, agonist and suppressor) of Nitroglycerin were identified. PPI network was constructed to identify different types of cancers that the 12 direct target genes affected and the Closeness Coefficient of the direct target genes so identified. Pathway analysis was performed to ascertain biomolecules functions for the direct target genes using CluePedia App. Mutation Analysis revealed Mutated Genes and types of cancers that are affected by the mutated genes. While the PPI network construction revealed the types of cancer that are affected by 12 target genes this step reveals the types of cancers affected by mutated cancers only. Only mutated genes were chosen for further study. These mutated genes were input into STRING to perform NW Analysis. NW Analysis revealed Interconnected Genes within the mutated genes as identified above. Second Step in this study is to predict and identify Upregulated and Downregulated genes. Data Sets for the identified cancers from the above procedure were obtained from GEO Database. DEG Analysis on the above Data sets was performed to predict Upregulated and Downregulated genes. A comparison of interconnected genes identified in step 1 with Upregulated and Downregulated genes obtained in step 2 revealed Co-Expressed Genes among Interconnected Genes. NW Analysis using STRING was performed on Co-Expressed Genes to ascertain Closeness Coefficient of Co-Expressed genes. Gene Ontology was performed on Co-Expressed Genes to ascertain their Functions. Pathway Analysis was performed on Co-Expressed Genes to identify the Types of Cancers that are influenced by co-expressed genes. The four types of cancers identified in Mutation analysis in step 1 were the same as the ones that were identified in this pathway analysis. This further corroborates the 4 types of cancers identified in Mutation analysis. Survival Analysis was done on the co-expressed genes as identified above using Survexpress. BIOMARKERS for Nitroglycerin were identified for four types of cancers through Survival Analysis. The four types of cancers are Bladder cancer, Endometrial cancer, Melanoma and Non-small cell lung cancer.
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Engineering of Cytolethal Distending Toxin B by Its Reducing Immunogenicity and Maintaining Stability as a New Drug Candidate for Tumor Therapy; an In Silico Study. Toxins (Basel) 2021; 13:toxins13110785. [PMID: 34822569 PMCID: PMC8624547 DOI: 10.3390/toxins13110785] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 10/30/2021] [Accepted: 11/01/2021] [Indexed: 12/25/2022] Open
Abstract
The cytolethal distending toxin (CDT), Haemophilus ducreyi, is one of the bacterial toxins that have recently been considered for targeted therapies, especially in cancer therapies. CDT is an A-B2 exotoxin. Its catalytic subunit (CdtB) is capable of inducing DNA double strand breaks, cell cycle arrest and apoptosis in host eukaryotic cells. The sequence alignment indicates that the CdtB is structurally homologyr to phosphatases and deoxyribonucleases I (DNase I). Recently, it has been found that CdtB toxicity is mainly related to its nuclease activity. The immunogenicity of CDT can reduce its effectiveness in targeted therapies. However, the toxin can be very useful if its immunogenicity is significantly reduced. Detecting hotspot ectopic residues by computational servers and then mutating them to eliminate B-cell epitopes is a promising approach to reduce the immunogenicity of foreign protein-based therapeutics. By the mentioned method, in this study, we try to reduce the immunogenicity of the CdtB- protein sequence. This study initially screened residue of the CdtB is B-cell epitopes both linearly and conformationally. By overlapping the B-cell epitopes with the excluded conserve residues, and active and enzymatic sites, four residues were allowed to be mutated. There were two mutein options that show reduced antigenicity probability. Option one was N19F, G74I, and S161F with a VaxiJen score of 0.45 and the immune epitope database (IEDB) score of 1.80, and option two was N19F, G74I, and S161W with a VaxiJen score of 0.45 and IEDB score of 1.88. The 3D structure of the proposed sequences was evaluated and refined. The structural stability of native and mutant proteins was accessed through molecular dynamic simulation. The results showed that the mutations in the mutants caused no considerable changes in their structural stability. However, mutant 1 reveals more thermodynamic stability during the simulation. The applied approaches in this study can be used as rough guidelines for finding hot spot immunogen regions in the therapeutic proteins. Our results provide a new version of CdtB that, due to reduced immunogenicity and increased stability, can be used in toxin-based drugs such as immunotoxins.
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Kothandan R, Uthayasooriyan P, Vairamani S. Search for RNA aptamers against non-structural protein of SARS-CoV-2: Design using molecular dynamics approach. BENI-SUEF UNIVERSITY JOURNAL OF BASIC AND APPLIED SCIENCES 2021; 10:64. [PMID: 34660818 PMCID: PMC8506486 DOI: 10.1186/s43088-021-00152-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Accepted: 09/28/2021] [Indexed: 02/07/2023] Open
Abstract
Background Recent outbreak of deadly Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) urges the scientist to identify the potential vaccine or drug to control the disease. SARS-CoV-2 with its single stranded RNA genome (length ~ 30 kb) is enveloped with active spike proteins. The genome is non-segmental with 5'-cap and 3'-poly tail and acts as a mRNA for the synthesis of replicase polyproteins. The replicase gene lying downstream to 5'-end encodes for non-structural protein, which in turn pose multiple functions ranging from envelope to nucleocapsid development. This study aims to identify the highly stable, effective and less toxic single strand RNA-based aptamers against non-structural protein 10 (NSP10). NSP10 is the significant activator of methyltransferase enzymes (NSP14 and NSP16) in SARS-CoV-2. Inhibiting the activation of methyltransferase leads to partial viral RNA capping or lack of capping, which makes the virus particles susceptible to host defence system. Results In this study, we focused on designing RNA aptamers through computational approach, docking of protein-aptamer followed by molecular dynamics simulation to perceive the binding stability of complex. Docking study reveals the high binding affinity of three aptamers namely RNA-053, 001, 010 to NSP10 with the HADDOCK score of - 88.5 ± 7.0, - 87.7 ± 11.5, - 86.1 ± 12 respectively. Molecular Dynamics suggests high conformational stability between the aptamer and the protein. Among the screened aptamers two aptamers maintained at least 3-4 intermolecular H-bonds throughout the simulation period. Conclusions The study identifies the potential aptamer candidate against less investigated but significant antiviral target i.e., NSP10/NSP16 interface complex. Supplementary Information The online version contains supplementary material available at 10.1186/s43088-021-00152-5.
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Affiliation(s)
- Ram Kothandan
- Bioinformatics Laboratory, Department of Biotechnology, Kumaraguru College of Technology, Coimbatore, India
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15
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Khoruddin NA, Noorizhab MN, Teh LK, Mohd Yusof FZ, Salleh MZ. Pathogenic nsSNPs that increase the risks of cancers among the Orang Asli and Malays. Sci Rep 2021; 11:16158. [PMID: 34373545 PMCID: PMC8352870 DOI: 10.1038/s41598-021-95618-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Accepted: 07/26/2021] [Indexed: 02/07/2023] Open
Abstract
Single-nucleotide polymorphisms (SNPs) are the most common genetic variations for various complex human diseases, including cancers. Genome-wide association studies (GWAS) have identified numerous SNPs that increase cancer risks, such as breast cancer, colorectal cancer, and leukemia. These SNPs were cataloged for scientific use. However, GWAS are often conducted on certain populations in which the Orang Asli and Malays were not included. Therefore, we have developed a bioinformatic pipeline to mine the whole-genome sequence databases of the Orang Asli and Malays to determine the presence of pathogenic SNPs that might increase the risks of cancers among them. Five different in silico tools, SIFT, PROVEAN, Poly-Phen-2, Condel, and PANTHER, were used to predict and assess the functional impacts of the SNPs. Out of the 80 cancer-related nsSNPs from the GWAS dataset, 52 nsSNPs were found among the Orang Asli and Malays. They were further analyzed using the bioinformatic pipeline to identify the pathogenic variants. Three nsSNPs; rs1126809 (TYR), rs10936600 (LRRC34), and rs757978 (FARP2), were found as the most damaging cancer pathogenic variants. These mutations alter the protein interface and change the allosteric sites of the respective proteins. As TYR, LRRC34, and FARP2 genes play important roles in numerous cellular processes such as cell proliferation, differentiation, growth, and cell survival; therefore, any impairment on the protein function could be involved in the development of cancer. rs1126809, rs10936600, and rs757978 are the important pathogenic variants that increase the risks of cancers among the Orang Asli and Malays. The roles and impacts of these variants in cancers will require further investigations using in vitro cancer models.
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Affiliation(s)
- Nurul Ain Khoruddin
- Integrative Pharmacogenomics Institute (iPROMISE), Universiti Teknologi MARA (UiTM), Selangor Branch, Puncak Alam Campus, 42300, Puncak Alam, Selangor, Malaysia
- Faculty of Applied Sciences, Universiti Teknologi MARA (UiTM), Shah Alam Campus, Selangor, Malaysia
| | - Mohd NurFakhruzzaman Noorizhab
- Integrative Pharmacogenomics Institute (iPROMISE), Universiti Teknologi MARA (UiTM), Selangor Branch, Puncak Alam Campus, 42300, Puncak Alam, Selangor, Malaysia
- Faculty of Pharmacy, Universiti Teknologi MARA (UiTM), Selangor Branch, Puncak Alam Campus, 42300, Puncak Alam, Selangor, Malaysia
| | - Lay Kek Teh
- Integrative Pharmacogenomics Institute (iPROMISE), Universiti Teknologi MARA (UiTM), Selangor Branch, Puncak Alam Campus, 42300, Puncak Alam, Selangor, Malaysia
- Faculty of Pharmacy, Universiti Teknologi MARA (UiTM), Selangor Branch, Puncak Alam Campus, 42300, Puncak Alam, Selangor, Malaysia
| | - Farida Zuraina Mohd Yusof
- Integrative Pharmacogenomics Institute (iPROMISE), Universiti Teknologi MARA (UiTM), Selangor Branch, Puncak Alam Campus, 42300, Puncak Alam, Selangor, Malaysia
- Faculty of Applied Sciences, Universiti Teknologi MARA (UiTM), Shah Alam Campus, Selangor, Malaysia
| | - Mohd Zaki Salleh
- Integrative Pharmacogenomics Institute (iPROMISE), Universiti Teknologi MARA (UiTM), Selangor Branch, Puncak Alam Campus, 42300, Puncak Alam, Selangor, Malaysia.
- Faculty of Pharmacy, Universiti Teknologi MARA (UiTM), Selangor Branch, Puncak Alam Campus, 42300, Puncak Alam, Selangor, Malaysia.
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16
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Computational Analysis of Gly482Ser Single-Nucleotide Polymorphism in PPARGC1A Gene Associated with CAD, NAFLD, T2DM, Obesity, Hypertension, and Metabolic Diseases. PPAR Res 2021; 2021:5544233. [PMID: 34394332 PMCID: PMC8360745 DOI: 10.1155/2021/5544233] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 06/28/2021] [Accepted: 07/07/2021] [Indexed: 12/25/2022] Open
Abstract
Peroxisome proliferator-activated receptor-gamma coactivator 1-alpha (PPARGC1A) regulates the expression of energy metabolism's genes and mitochondrial biogenesis. The essential roles of PPARGC1A encouraged the researchers to assess the relation between metabolism-related diseases and its variants. To study Gly482Ser (+1564G/A) single-nucleotide polymorphism (SNP) after PPARGC1A modeling, we substitute Gly482 for Ser482. Stability prediction tools showed that this substitution decreases the stability of PPARGC1A or has a destabilizing effect on this protein. We then utilized molecular dynamics simulation of both the Gly482Ser variant and wild type of the PPARGC1A protein to analyze the structural changes and to reveal the conformational flexibility of the PPARGC1A protein. We observed loss flexibility in the RMSD plot of the Gly482Ser variant, which was further supported by a decrease in the SASA value in the Gly482Ser variant structure of PPARGC1A and an increase of H-bond with the increase of β-sheet and coil and decrease of turn in the DSSP plot of the Gly482Ser variant. Such alterations may significantly impact the structural conformation of the PPARGC1A protein, and it might also affect its function. It showed that the Gly482Ser variant affects the PPARGC1A structure and makes the backbone less flexible to move. In general, molecular dynamics simulation (MDS) showed more flexibility in the native PPARGC1A structure. Essential dynamics (ED) also revealed that the range of eigenvectors in the conformational space has lower extension of motion in the Gly482Ser variant compared with WT. The Gly482Ser variant also disrupts PPARGC1A interaction. Due to this single-nucleotide polymorphism in PPARGC1A, it became more rigid and might disarray the structural conformation and catalytic function of the protein and might also induce type 2 diabetes mellitus (T2DM), coronary artery disease (CAD), and nonalcoholic fatty liver disease (NAFLD). The results obtained from this study will assist wet lab research in expanding potent treatment on T2DM.
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17
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Hydrophobic Residues Confer the Helicity and Membrane Permeability of Ocellatin-1 Antimicrobial Peptide Scaffold Towards Therapeutics. Int J Pept Res Ther 2021. [DOI: 10.1007/s10989-021-10265-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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18
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Al-Subaie AM, Kamaraj B. The Structural Effect of FLT3 Mutations at 835th Position and Their Interaction with Acute Myeloid Leukemia Inhibitors: In Silico Approach. Int J Mol Sci 2021; 22:7602. [PMID: 34299222 PMCID: PMC8303888 DOI: 10.3390/ijms22147602] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 06/30/2021] [Accepted: 07/09/2021] [Indexed: 12/25/2022] Open
Abstract
FMS-like tyrosine kinase 3 (FLT3) gene mutations have been found in more than one-third of Acute Myeloid Leukemia (AML) cases. The most common point mutation in FLT3 occurs at the 835th residue (D835A/E/F/G/H/I/N/V/Y), in the activation loop region. The D835 residue is critical in maintaining FLT3 inactive conformation; these mutations might influence the interaction with clinically approved AML inhibitors used to treat the AML. The molecular mechanism of each of these mutations and their interactions with AML inhibitors at the atomic level is still unknown. In this manuscript, we have investigated the structural consequence of native and mutant FLT-3 proteins and their molecular mechanisms at the atomic level, using molecular dynamics simulations (MDS). In addition, we use the molecular docking method to investigate the binding pattern between the FLT-3 protein and AML inhibitors upon mutations. This study apparently elucidates that, due to mutations in the D835, the FLT-3 structure loses its conformation and becomes more flexible compared to the native FLT3 protein. These structural changes are suggested to contribute to the relapse and resistance responses to AML inhibitors. Identifying the effects of FLT3 at the molecular level will aid in developing a personalized therapeutic strategy for treating patients with FLT-3-associated AML.
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Affiliation(s)
- Abeer M. Al-Subaie
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia;
| | - Balu Kamaraj
- Department of Neuroscience Technology, College of Applied Medical Sciences in Jubail, Imam Abdulrahman Bin Faisal University, Jubail 35816, Saudi Arabia
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19
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Aljindan RY, Al-Subaie AM, Al-Ohali AI, Kumar D T, Doss C GP, Kamaraj B. Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. Comput Biol Med 2021; 135:104654. [PMID: 34346317 PMCID: PMC8282961 DOI: 10.1016/j.compbiomed.2021.104654] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 07/12/2021] [Accepted: 07/13/2021] [Indexed: 12/22/2022]
Abstract
COVID-19 is an infectious and pathogenic viral disease caused by SARS-CoV-2 that leads to septic shock, coagulation dysfunction, and acute respiratory distress syndrome. The spreading rate of SARS-CoV-2 is higher than MERS-CoV and SARS-CoV. The receptor-binding domain (RBD) of the Spike-protein (S-protein) interacts with the human cells through the host angiotensin-converting enzyme 2 (ACE2) receptor. However, the molecular mechanism of pathological mutations of S-protein is still unclear. In this perspective, we investigated the impact of mutations in the S-protein and their interaction with the ACE2 receptor for SAR-CoV-2 viral infection. We examined the stability of pathological nonsynonymous mutations in the S-protein, and the binding behavior of the ACE2 receptor with the S-protein upon nonsynonymous mutations using the molecular docking and MM_GBSA approaches. Using the extensive bioinformatics pipeline, we screened the destabilizing (L8V, L8W, L18F, Y145H, M153T, F157S, G476S, L611F, A879S, C1247F, and C1254F) and stabilizing (H49Y, S50L, N501Y, D614G, A845V, and P1143L) nonsynonymous mutations in the S-protein. The docking and binding free energy (ddG) scores revealed that the stabilizing nonsynonymous mutations show increased interaction between the S-protein and the ACE2 receptor compared to native and destabilizing S-proteins and that they may have been responsible for the virulent high level. Further, the molecular dynamics simulation (MDS) approach reveals the structural transition of mutants (N501Y and D614G) S-protein. These insights might help researchers to understand the pathological mechanisms of the S-protein and provide clues regarding mutations in viral infection and disease propagation. Further, it helps researchers to develop an efficient treatment approach against this SARS-CoV-2 pandemic.
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Affiliation(s)
- Reem Y Aljindan
- Department of Microbiology, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia.
| | - Abeer M Al-Subaie
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia.
| | - Ahoud I Al-Ohali
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia.
| | - Thirumal Kumar D
- Meenakshi Academy of Higher Education and Research, Chennai, Tamil Nadu, 600078, India.
| | - George Priya Doss C
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India.
| | - Balu Kamaraj
- Department of Neuroscience Technology, College of Applied Medical Sciences in Jubail, Imam Abdulrahman Bin Faisal University, Jubail, Saudi Arabia.
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20
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Zalloum WA, Zalloum N. Comparative QM/MM Molecular Dynamics and Umbrella Sampling Simulations: Interaction of the Zinc-Bound Intermediate Gem-Diolate Trapoxin A Inhibitor and Acetyl-l-lysine Substrate with Histone Deacetylase 8. J Phys Chem B 2021; 125:5321-5337. [PMID: 33998791 DOI: 10.1021/acs.jpcb.1c01696] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Targeting the genetic material without destruction is a priority to develop safe anticancer drugs. Histone deacetylase 8 (HDAC8), which is proved to be involved in carcinogenesis, is an enzyme associated with the chromatin for post-translational deacetylation of acetylated lysine. In this study, HDAC8 co-crystallized with the intermediate state tetrapeptide Trapoxin A (TA) inhibitor and the holoenzyme are utilized to find their conformational ensembles. Furthermore, the co-crystallized intermediate gem-diolate TA was used to find optimum interactions with the active site residues by conventional molecular dynamics (MD) simulation and QM/MM umbrella sampling. Finally, the intermediate state of the acetyl-l-lysine substrate was explored by QM/MM steered MD and compared to the binding of the intermediate state of the inhibitor. This research showed that HDAC8 is flexible and exists in conformational ensembles in its holoenzyme state. Binding of the intermediate state TA stabilizes its conformation. The optimum binding to the active site of HDAC8 for structures of gem-diolate TA (intermediate state) and acetyl-l-lysine (intermediate state) was determined according to the corresponding energy profiles. The use of these models will aid in the design of potentially reversible, potent, and selective inhibitors of HDAC8 for cancer treatment.
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Affiliation(s)
- Waleed A Zalloum
- Department of Pharmacy, Faculty of Health Science, American University of Madaba, P.O. Box 2882, Amman 11821, Jordan
| | - Needa Zalloum
- Department of Biopharmaceutics and Clinical Pharmacy, Faculty of Pharmacy, University of Jordan, Amman 11942, Jordan
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21
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Qu Y, Wang L, Yin S, Zhang B, Jiao Y, Sun Y, Middelberg A, Bi J. Stability of Engineered Ferritin Nanovaccines Investigated by Combined Molecular Simulation and Experiments. J Phys Chem B 2021; 125:3830-3842. [PMID: 33825471 DOI: 10.1021/acs.jpcb.1c00276] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Human ferritin is regarded as an attractive and promising vaccine platform because of its uniform structure, good plasticity, and desirable thermal and chemical stabilities. Besides, it is biocompatible and presumed safe when used as a vaccine carrier. However, there is a lack of knowledge of how different antigen insertion sites on the ferritin nanocage impact the resulting protein stability and performance. To address this question, we selected Epstein-Barr nuclear antigen 1 as a model epitope and fused it at the DNA level with different insertion sites, namely, the N- and C-termini of ferritin, to engineer proteins E1F1 and F1E1, respectively. Protein properties including hydrophobicity and thermal, pH, and chemical stability were investigated both by molecular dynamics (MD) simulation and by experiments. Both methods demonstrate that the insertion site plays an important role in protein properties. The C-terminus insertion (F1E1) leads to a less hydrophobic surface and more tolerance to the external influence of high temperature, pH, and high concentration of chemical denaturants compared to N-terminus insertion (E1F1). Simulated protein hydrophobicity and thermal stability by MD were in high accordance with experimental results. Thus, MD simulation can be used as a valuable tool to engineer nanovaccine candidates, cutting down costs by reducing the experimental effort and accelerating vaccine design.
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Affiliation(s)
- Yiran Qu
- School of Chemical Engineering and Advanced Materials, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Lijie Wang
- Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of the Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Shuang Yin
- School of Chemical Engineering and Advanced Materials, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Bingyang Zhang
- School of Chemical Engineering and Advanced Materials, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Yan Jiao
- School of Chemical Engineering and Advanced Materials, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Yan Sun
- Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of the Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Anton Middelberg
- School of Chemical Engineering and Advanced Materials, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Jingxiu Bi
- School of Chemical Engineering and Advanced Materials, The University of Adelaide, Adelaide, South Australia 5005, Australia
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22
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Galeb HA, Wilkinson EL, Stowell AF, Lin H, Murphy ST, Martin‐Hirsch PL, Mort RL, Taylor AM, Hardy JG. Melanins as Sustainable Resources for Advanced Biotechnological Applications. GLOBAL CHALLENGES (HOBOKEN, NJ) 2021; 5:2000102. [PMID: 33552556 PMCID: PMC7857133 DOI: 10.1002/gch2.202000102] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 11/04/2020] [Indexed: 05/17/2023]
Abstract
Melanins are a class of biopolymers that are widespread in nature and have diverse origins, chemical compositions, and functions. Their chemical, electrical, optical, and paramagnetic properties offer opportunities for applications in materials science, particularly for medical and technical uses. This review focuses on the application of analytical techniques to study melanins in multidisciplinary contexts with a view to their use as sustainable resources for advanced biotechnological applications, and how these may facilitate the achievement of the United Nations Sustainable Development Goals.
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Affiliation(s)
- Hanaa A. Galeb
- Department of ChemistryLancaster UniversityLancasterLA1 4YBUK
- Department of ChemistryScience and Arts CollegeRabigh CampusKing Abdulaziz UniversityJeddah21577Saudi Arabia
| | - Emma L. Wilkinson
- Department of Biomedical and Life SciencesLancaster UniversityLancasterLA1 4YGUK
| | - Alison F. Stowell
- Department of Organisation, Work and TechnologyLancaster University Management SchoolLancaster UniversityLancasterLA1 4YXUK
| | - Hungyen Lin
- Department of EngineeringLancaster UniversityLancasterLA1 4YWUK
| | - Samuel T. Murphy
- Department of EngineeringLancaster UniversityLancasterLA1 4YWUK
- Materials Science InstituteLancaster UniversityLancasterLA1 4YBUK
| | - Pierre L. Martin‐Hirsch
- Lancashire Teaching Hospitals NHS TrustRoyal Preston HospitalSharoe Green LanePrestonPR2 9HTUK
| | - Richard L. Mort
- Department of Biomedical and Life SciencesLancaster UniversityLancasterLA1 4YGUK
| | - Adam M. Taylor
- Lancaster Medical SchoolLancaster UniversityLancasterLA1 4YWUK
| | - John G. Hardy
- Department of ChemistryLancaster UniversityLancasterLA1 4YBUK
- Materials Science InstituteLancaster UniversityLancasterLA1 4YBUK
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Singh A, Thakur M, Singh SK, Sharma LK, Chandra K. Exploring the effect of nsSNPs in human YPEL3 gene in cellular senescence. Sci Rep 2020; 10:15301. [PMID: 32943700 PMCID: PMC7498449 DOI: 10.1038/s41598-020-72333-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Accepted: 08/28/2020] [Indexed: 12/19/2022] Open
Abstract
YPEL3 that induces cellular senescence in both normal and tumour cells of humans may show altered expression under the influence of incidental mutations. In this study, we proposed the first structure of Native YPEL3 protein and its five possible deleterious mutants—V40M, C61Y, G98R, G108S, and A131T and predicted their deleterious effects to alter stability, flexibility and conformational changes in the protein. The MD simulation (RMSD, RMSF, Rg, h-bond and SASA) analysis revealed that the variants V40M, G98R and G108S increased the flexibility in protein, and variant V40M imparted more compactness to the protein.. In general, variants attributed changes in the native conformation and structure of the YPEL3 protein which might affect the native function of cellular senescence. The study provides opportunities for health professionals and practitioners in formulating précised medicines to effectively cure various cancers. We propose in-vitro or in-vivo studies should consider these reported nsSNPs while examining any malfunction in the YPEL3 protein.
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Affiliation(s)
- Abhishek Singh
- Zoological Survey of India, New Alipore, Kolkata, 700053, India.
| | - Mukesh Thakur
- Zoological Survey of India, New Alipore, Kolkata, 700053, India.
| | | | | | - Kailash Chandra
- Zoological Survey of India, New Alipore, Kolkata, 700053, India
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Emadi E, Akhoundi F, Kalantar SM, Emadi-Baygi M. Predicting the most deleterious missense nsSNPs of the protein isoforms of the human HLA-G gene and in silico evaluation of their structural and functional consequences. BMC Genet 2020; 21:94. [PMID: 32867672 PMCID: PMC7457528 DOI: 10.1186/s12863-020-00890-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 07/19/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The Human Leukocyte Antigen G (HLA-G) protein is an immune tolerogenic molecule with 7 isoforms. The change of expression level and some polymorphisms of the HLA-G gene are involved in various pathologies. Therefore, this study aimed to predict the most deleterious missense non-synonymous single nucleotide polymorphisms (nsSNPs) in HLA-G isoforms via in silico analyses and to examine structural and functional effects of the predicted nsSNPs on HLA-G isoforms. RESULTS Out of 301 reported SNPs in dbSNP, 35 missense SNPs in isoform 1, 35 missense SNPs in isoform 5, 8 missense SNPs in all membrane-bound HLA-G isoforms and 8 missense SNPs in all soluble HLA-G isoforms were predicted as deleterious by all eight servers (SIFT, PROVEAN, PolyPhen-2, I-Mutant 3.0, SNPs&GO, PhD-SNP, SNAP2, and MUpro). The Structural and functional effects of the predicted nsSNPs on HLA-G isoforms were determined by MutPred2 and HOPE servers, respectively. Consurf analyses showed that the majority of the predicted nsSNPs occur in conserved sites. I-TASSER and Chimera were used for modeling of the predicted nsSNPs. rs182801644 and rs771111444 were related to creating functional patterns in 5'UTR. 5 SNPs in 3'UTR of the HLA-G gene were predicted to affect the miRNA target sites. Kaplan-Meier analysis showed the HLA-G deregulation can serve as a prognostic marker for some cancers. CONCLUSIONS The implementation of in silico SNP prioritization methods provides a great framework for the recognition of functional SNPs. The results obtained from the current study would be called laboratory investigations.
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Affiliation(s)
- Elaheh Emadi
- Department of Genetics, Faculty of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Fatemeh Akhoundi
- Department of Genetics, Faculty of Basic Sciences, Shahrekord University, Shahrekord, Iran
| | - Seyed Mehdi Kalantar
- Department of Genetics, Faculty of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Modjtaba Emadi-Baygi
- Department of Genetics, Faculty of Basic Sciences, Shahrekord University, Shahrekord, Iran.
- Research Institute of Biotechnology, Shahrekord University, Shahrekord, Iran.
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25
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Alzahrani FA, Ahmed F, Sharma M, Rehan M, Mahfuz M, Baeshen MN, Hawsawi Y, Almatrafi A, Alsagaby SA, Kamal MA, Warsi MK, Choudhry H, Jamal MS. Investigating the pathogenic SNPs in BLM helicase and their biological consequences by computational approach. Sci Rep 2020; 10:12377. [PMID: 32704157 PMCID: PMC7378827 DOI: 10.1038/s41598-020-69033-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 07/06/2020] [Indexed: 12/15/2022] Open
Abstract
The BLM helicase protein plays a vital role in DNA replication and the maintenance of genomic integrity. Variation in the BLM helicase gene resulted in defects in the DNA repair mechanism and was reported to be associated with Bloom syndrome (BS) and cancer. Despite extensive investigation of helicase proteins in humans, no attempt has previously been made to comprehensively analyse the single nucleotide polymorphism (SNPs) of the BLM gene. In this study, a comprehensive analysis of SNPs on the BLM gene was performed to identify, characterize and validate the pathogenic SNPs using computational approaches. We obtained SNP data from the dbSNP database version 150 and mapped these data to the genomic coordinates of the "NM_000057.3" transcript expressing BLM helicase (P54132). There were 607 SNPs mapped to missense, 29 SNPs mapped to nonsense, and 19 SNPs mapped to 3'-UTR regions. Initially, we used many consensus tools of SIFT, PROVEAN, Condel, and PolyPhen-2, which together increased the accuracy of prediction and identified 18 highly pathogenic non-synonymous SNPs (nsSNPs) out of 607 SNPs. Subsequently, these 18 high-confidence pathogenic nsSNPs were analysed for BLM protein stability, structure-function relationships and disease associations using various bioinformatics tools. These 18 mutants of the BLM protein along with the native protein were further investigated using molecular dynamics simulations to examine the structural consequences of the mutations, which might reveal their malfunction and contribution to disease. In addition, 28 SNPs were predicted as "stop gained" nonsense SNPs and one SNP was predicted as "start lost". Two SNPs in the 3'UTR were found to abolish miRNA binding and thus may enhance the expression of BLM. Interestingly, we found that BLM mRNA overexpression is associated with different types of cancers. Further investigation showed that the dysregulation of BLM is associated with poor overall survival (OS) for lung and gastric cancer patients and hence led to the conclusion that BLM has the potential to be used as an important prognostic marker for the detection of lung and gastric cancer.
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Affiliation(s)
- Faisal A Alzahrani
- Department of Biochemistry, Faculty of Science, Stem Cells Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
- Aston Medical Research Institute, Aston Medical School, Aston University, Birmingham, B4 7ET, UK
| | - Firoz Ahmed
- Department of Biochemistry, College of Science, University of Jeddah, Jeddah, 21589, Saudi Arabia.
- University of Jeddah Centre for Scientific and Medical Research (UJ-CSMR), University of Jeddah, Jeddah, 21589, Saudi Arabia.
| | - Monika Sharma
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER), Mohali, India
| | - Mohd Rehan
- King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Maryam Mahfuz
- Department of Computer Science, Jamia Millia Islamia, New Delhi, Delhi, India
| | - Mohammed N Baeshen
- Department of Biology, College of Science, University of Jeddah, Jeddah, 21589, Saudi Arabia
| | - Yousef Hawsawi
- Department of Genetics, Research Center, King Faisal Specialist Hospital, and Research Center, MBC-03, PO Box 3354, Riyadh, 11211, Saudi Arabia
| | - Ahmed Almatrafi
- Department of Biology, Faculty of Science, University of Taibah, Medinah, Saudi Arabia
| | - Suliman Abdallah Alsagaby
- Department of Medical Laboratories, Central Biosciences Research Laboratories, College of Science in Al Zulfi, Majmaah University, Al Majma'ah, Saudi Arabia
| | - Mohammad Azhar Kamal
- Department of Biochemistry, College of Science, University of Jeddah, Jeddah, 21589, Saudi Arabia
- University of Jeddah Centre for Scientific and Medical Research (UJ-CSMR), University of Jeddah, Jeddah, 21589, Saudi Arabia
| | - Mohiuddin Khan Warsi
- Department of Biochemistry, College of Science, University of Jeddah, Jeddah, 21589, Saudi Arabia
- University of Jeddah Centre for Scientific and Medical Research (UJ-CSMR), University of Jeddah, Jeddah, 21589, Saudi Arabia
| | - Hani Choudhry
- Department of Biochemistry, Cancer Metabolism and Epigenetic Unit, Faculty of Science, Cancer and Mutagenesis Unit, King Fahd Center for Medical Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mohammad Sarwar Jamal
- King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia.
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.
- Integrative Biosciences Center, Wayne State University, Detroit, MI, 48202, USA.
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Akın-Balı DF, Al-Khafaji K, Aktas SH, Taskin-Tok T. Bioinformatic and computational analysis for predominant mutations of the Nrf2/Keap1 complex in pediatric leukemia. J Biomol Struct Dyn 2020; 39:4290-4303. [PMID: 32469262 DOI: 10.1080/07391102.2020.1775702] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The levels of reactive oxygen species (ROS) are tightly controlled and regulated by Nuclear Factor Erythroid-2-Like 2 (Nrf2) transcription factor, which is the main regulator of antioxidant responses and its suppressor protein Kelch-like ECH-associated protein 1 (Keap1). Our previous study has identified six novel changes in Nrf2/Keap1 pathway in pediatric ALL, which were described for the first time. These changes in the pathway are likely to alter the evolutionary process of amino acids and cause structural changes in the final products of genes. In this study, we aimed to compare the pathogenicity of eight determined mutations reported in our previous study by utilizing different programs with different algorithms and molecular dynamics simulation. Since it is too difficult to handle each existing mutation in a wet laboratory, in silico methods may give suggestion to choose the important mutations for further analysis and to establish the appropriate patient population and conduct wet laboratory studies. For this purpose, four different algorithms were used to evaluate the effects of single amino acid mutation. In addition, root-mean-square deviation, root-mean-square fluctuation and free-energy landscape analyses were performed to observe stability, flexibility and energetically favorable conformations, respectively, for each amino acid mutation. As a result, our study emphasizes the importance of Keap1 mutations in pediatric ALL Nrf2/Keap1 pathway, a total of eight mutations, two of which were shown for the first time in our study. Especially the mutations in the Keap1 Broad-Complex, Tramtrack and Bric-à-brac domain are worthy of attention.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Dilara Fatma Akın-Balı
- Faculty of Medicine, Department of Medical Biology, Nigde Omer Halisdemir University, Nigde, Turkey
| | - Khattab Al-Khafaji
- Faculty of Arts and Sciences, Department of Chemistry, Gaziantep University, Gaziantep, Turkey
| | - Sedef Hande Aktas
- Vocational School of Health Services, Eskisehir Osmangazi University, Eskisehir, Turkey
| | - Tugba Taskin-Tok
- Faculty of Arts and Sciences, Department of Chemistry, Gaziantep University, Gaziantep, Turkey.,Department of Bioinformatics and Computational Biology, Institute of Health Sciences, Gaziantep University, Gaziantep, Turkey
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27
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Protein Stability and Functional Characterization of Intra-Melanosomal Domain of Human Recombinant Tyrosinase-Related Protein 1. Int J Mol Sci 2020; 21:ijms21010331. [PMID: 31947795 PMCID: PMC6981619 DOI: 10.3390/ijms21010331] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 12/28/2019] [Accepted: 12/31/2019] [Indexed: 12/19/2022] Open
Abstract
Pigmentation is the result of a complex process by which the biopolymer melanin is synthesized and packed into melanosomes of melanocytes. Various types of oculocutaneous albinism (OCA), a series of autosomal recessive disorders, are associated with reduced pigmentation in the skin, eyes, and hair due to genetic mutations of proteins involved in melanogenesis. Human tyrosinase (Tyr) and tyrosinase-related protein 1 (Tyrp1) drives the enzymatic process of pigment bio-polymerization. However, within the melanogenic pathway, Tyrp1 has catalytic functions not clearly defined and distinct from Tyr. Here, we characterize the biochemical and biophysical properties of recombinant human Tyrp1. For this purpose, we purified and analyzed the intra-melanosomal domain (Tyrp1tr) for protein stability and enzymatic function in conditions mimicking the environment within melanosomes and the endoplasmic reticulum. The study suggests that Tyrp1tr is a monomeric molecule at ambient temperatures and below (<25 °C). At higher temperatures, >31 °C, higher protein aggregates form with a concurrent decrease of monomers in solution. Also, Tyrp1tr diphenol oxidase activity at pH 5.5 rises as both the pre-incubation temperature and the higher molecular weight protein aggregates formation increases. The enhanced protein activity is consistent with the volume exclusion change caused by protein aggregates.
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28
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Dash R, Ali MC, Dash N, Azad MAK, Hosen SMZ, Hannan MA, Moon IS. Structural and Dynamic Characterizations Highlight the Deleterious Role of SULT1A1 R213H Polymorphism in Substrate Binding. Int J Mol Sci 2019; 20:ijms20246256. [PMID: 31835852 PMCID: PMC6969939 DOI: 10.3390/ijms20246256] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 12/04/2019] [Accepted: 12/09/2019] [Indexed: 12/16/2022] Open
Abstract
Sulfotransferase 1A1 (SULT1A1) is responsible for catalyzing various types of endogenous and exogenous compounds. Accumulating data indicates that the polymorphism rs9282861 (R213H) is responsible for inefficient enzymatic activity and associated with cancer progression. To characterize the detailed functional consequences of this mutation behind the loss-of-function of SULT1A1, the present study deployed molecular dynamics simulation to get insights into changes in the conformation and binding energy. The dynamics scenario of SULT1A1 in both wild and mutated types as well as with and without ligand showed that R213H induced local conformational changes, especially in the substrate-binding loop rather than impairing overall stability of the protein structure. The higher conformational changes were observed in the loop3 (residues, 235-263), turning loop conformation to A-helix and B-bridge, which ultimately disrupted the plasticity of the active site. This alteration reduced the binding site volume and hydrophobicity to decrease the binding affinity of the enzyme to substrates, which was highlighted by the MM-PBSA binding energy analysis. These findings highlight the key insights of structural consequences caused by R213H mutation, which would enrich the understanding regarding the role of SULT1A1 mutation in cancer development and also xenobiotics management to individuals in the different treatment stages.
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Affiliation(s)
- Raju Dash
- Department of Anatomy, Dongguk University College of Medicine, Gyeongju 38066, Korea
| | - Md Chayan Ali
- Department of Biotechnology and Genetic Engineering, Islamic University, Kushtia 7003, Bangladesh
| | - Nayan Dash
- Department of Computer Science and Engineering, BGC Trust University, Bangladesh, Chittagong 4381, Bangladesh
| | - Md Abul Kalam Azad
- Department of Biotechnology and Genetic Engineering, Islamic University, Kushtia 7003, Bangladesh
| | - S M Zahid Hosen
- Pancreatic Research Group, South Western Sydney Clinical School, University of New South Wales, and Ingham Institute for Applied Medical Research, Liverpool, NSW 2170, Australia
| | - Md Abdul Hannan
- Department of Anatomy, Dongguk University College of Medicine, Gyeongju 38066, Korea
- Department of Biochemistry and Molecular Biology, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Il Soo Moon
- Department of Anatomy, Dongguk University College of Medicine, Gyeongju 38066, Korea
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29
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Vianney YM, Tjoa SEE, Aditama R, Dwi Putra SE. Designing a less immunogenic nattokinase from Bacillus subtilis subsp. natto: a computational mutagenesis. J Mol Model 2019; 25:337. [DOI: 10.1007/s00894-019-4225-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 10/09/2019] [Indexed: 12/22/2022]
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30
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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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31
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In silico analysis of non-synonymous single nucleotide polymorphism in a human KLK-2 gene associated with prostate cancer. Meta Gene 2019. [DOI: 10.1016/j.mgene.2019.100578] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
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32
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Changes of Thermostability, Organic Solvent, and pH Stability in Geobacillus zalihae HT1 and Its Mutant by Calcium Ion. Int J Mol Sci 2019; 20:ijms20102561. [PMID: 31137725 PMCID: PMC6566366 DOI: 10.3390/ijms20102561] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 04/23/2019] [Accepted: 04/30/2019] [Indexed: 12/11/2022] Open
Abstract
Thermostable T1 lipase from Geobacillus zalihae has been crystallized using counter-diffusion method under space and Earth conditions. The comparison of the three-dimensional structures from both crystallized proteins show differences in the formation of hydrogen bond and ion interactions. Hydrogen bond and ion interaction are important in the stabilization of protein structure towards extreme temperature and organic solvents. In this study, the differences of hydrogen bond interactions at position Asp43, Thr118, Glu250, and Asn304 and ion interaction at position Glu226 was chosen to imitate space-grown crystal structure, and the impact of these combined interactions in T1 lipase-mutated structure was studied. Using space-grown T1 lipase structure as a reference, subsequent simultaneous mutation D43E, T118N, E226D, E250L, and N304E was performed on recombinant wild-type T1 lipase (wt-HT1) to generate a quintuple mutant term as 5M mutant lipase. This mutant lipase shared similar characteristics to its wild-type in terms of optimal pH and temperature. The stability of mutant 5M lipase improved significantly in acidic and alkaline pH as compared to wt-HT1. 5M lipase was highly stable in organic solvents such as dimethyl sulfoxide (DMSO), methanol, and n-hexane compared to wt-HT1. Both wild-type and mutant lipases were found highly activated in calcium as compared to other metal ions due to the presence of calcium-binding site for thermostability. The presence of calcium prolonged the half-life of mutant 5M and wt-HT1, and at the same time increased their melting temperature (Tm). The melting temperature of 5M and wt-HT1 lipases increased at 8.4 and 12.1 °C, respectively, in the presence of calcium as compared to those without. Calcium enhanced the stability of mutant 5M in 25% (v/v) DMSO, n-hexane, and n-heptane. The lipase activity of wt-HT1 also increased in 25% (v/v) ethanol, methanol, acetonitrile, n-hexane, and n-heptane in the presence of calcium. The current study showed that the accumulation of amino acid substitutions D43E, T118N, E226D, E250L, and N304E produced highly stable T1 mutant when hydrolyzing oil in selected organic solvents such as DMSO, n-hexane, and n-heptane. It is also believed that calcium ion plays important role in regulating lipase thermostability.
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Structure-based identification of potent VEGFR-2 inhibitors from in vivo metabolites of a herbal ingredient. J Mol Model 2019; 25:98. [PMID: 30904971 DOI: 10.1007/s00894-019-3979-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 03/05/2019] [Indexed: 12/22/2022]
Abstract
Vascular endothelial growth factor receptor-2 (VEGFR-2) is one of the regulatory elements of angiogenesis that is expressed highly in various diseases and is also essential for solid tumor growth. The present study was aimed at identifying potent inhibitors of VEGFR-2 by considering herbal secondary metabolites; as natural molecules are less toxic than synthetic derivatives. A structure-based virtual screening protocol consisting of molecular docking, MM-GBSA and ADME/T analysis was initially used to screen a library of in vivo metabolites of the herbal ingredient. Using a fixed cutoff value, four potent virtual hits were identified from molecular docking, ADME/T and binding affinity calculations, which were considered further for molecular dynamics (MD) simulation to broadly describe the binding mechanisms to VEGFR-2. The results suggested that these molecules have high affinity for the catalytic region of VEGFR-2, and form strong hydrophobic and polar interactions with the amino acids involved in the binding site of ATP and linker regions of the catalytic site. Subsequently, the stability of the docked complexes and binding mechanisms were evaluated by MD simulations, and the energy of binding was calculated through MM-PBSA analysis. The results uncovered two virtual hits, designated ZINC14762520 and ZINC36470466, as VEGFR-2 inhibitors, and suggested that they bind to kinase domain in an ATP-competitive manner. These virtual hits will offer a suitable starting point for the further design of their various analogs, allowing a rational search for more effective inhibitors in the future. Graphical abstract.
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34
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Evander Emeltan Tjoa S, Maria Vianney Y, Emantoko Dwi Putra S. In silico mutagenesis: decreasing the immunogenicity of botulinum toxin type A. J Biomol Struct Dyn 2018; 37:4767-4778. [PMID: 30558486 DOI: 10.1080/07391102.2018.1559100] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Botulinum toxin serotype A is a prominent therapeutic enzyme, for both clinical and cosmetic uses. Since this protein is produced by bacteria, it exhibits an allergenic effect when subjected to human therapy. Protein mutagenesis is one method to improve the characteristics of protein. However, in silico study is needed to give suggestion of which amino acid should be mutated. Hence, a lot of money and time can be saved. This study initially screened which residue of the Botulinum toxin serotype A is B-cell epitopes both linearly and conformationally. By overlapping the B-cell epitopes with the excluded conserve sequence, seven residues were allowed to be mutated. There were two proposed muteins showing a reduction in the antigenicity probability: ΔE147, E510F, T1062F, ΔE1080, N1089M and ΔQ1090; and ΔE147, E510F, T1062F, E1080W, N1089M and ΔQ1090. Molecular dynamics simulation of the 3D proposed muteins indicated an increase of flexibility in both muteins compared to that in the native protein. Both muteins have lower antigenicity. In addition, they are similar in structure, stability and functionality compared to the native protein.
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Affiliation(s)
| | - Yoanes Maria Vianney
- Faculty of Biotechnology, University of Surabaya , Surabaya , East Java , Indonesia
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35
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Kumar R, Bansal A, Shukla R, Raj Singh T, Wasudeo Ramteke P, Singh S, Gautam B. In silico screening of deleterious single nucleotide polymorphisms (SNPs) and molecular dynamics simulation of disease associated mutations in gene responsible for oculocutaneous albinism type 6 (OCA 6) disorder. J Biomol Struct Dyn 2018; 37:3513-3523. [PMID: 30204049 DOI: 10.1080/07391102.2018.1520649] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Solute carrier family 24 member 5 (SLC24A5) is a gene that is associated with oculocutaneous albinism type 6 (OCA6) disorder and is involved in skin and hair pigmentation. It is involved in the maturation of melanosomes and melanin synthesis. SLC24A5 gene is located in the chromosomal position of 15q21.1. The present study involves the use of computational techniques in order to obtain a detailed picture of the most probable mutations that are associated with SLC24A5. From the observed result it was found that the mutation S145F is most deleterious and disease associated is predicted using several bioinformatics tools. The 3-D structures of native and mutant (S145F) were modeled in order to understand protein functionality using ab initio Robetta server. The modeled structure validation was done with ERRAT, Verify-3D, Procheck and RAMPAGE Ramachandran plot analysis. The most validated structure undergoes molecular dynamics simulations (MDS) study to understand the structural and functional behaviour of the native and mutant proteins. The MDS result showed the more flexibility in the native SLC24A5 structure. Due to mutation in the SLC24A5 protein structure it became more rigid and might disturb the conformational changes and glycosylation function of protein structure and might play role in inducing the OCA6. This study provides a significant insight into the underlying molecular mechanism involved in albinism associated with OCA6. It further helps scientists to develop a drug therapy against OCA 6 disease. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Rutash Kumar
- a Department of Computational Biology & Bioinformatics , Jacob Institute of Biotechnology & Bio-Engineering, Sam Higginbottom University of Agriculture, Technology and Sciences (SHUATS) , Allahabad , India
| | - Ankush Bansal
- b Department of Biotechnology and Bioinformatics , Jaypee University of Information Technology , Solan , India
| | - Rohit Shukla
- b Department of Biotechnology and Bioinformatics , Jaypee University of Information Technology , Solan , India
| | - Tiratha Raj Singh
- b Department of Biotechnology and Bioinformatics , Jaypee University of Information Technology , Solan , India
| | - Pramod Wasudeo Ramteke
- a Department of Computational Biology & Bioinformatics , Jacob Institute of Biotechnology & Bio-Engineering, Sam Higginbottom University of Agriculture, Technology and Sciences (SHUATS) , Allahabad , India
| | - Satendra Singh
- a Department of Computational Biology & Bioinformatics , Jacob Institute of Biotechnology & Bio-Engineering, Sam Higginbottom University of Agriculture, Technology and Sciences (SHUATS) , Allahabad , India
| | - Budhayash Gautam
- a Department of Computational Biology & Bioinformatics , Jacob Institute of Biotechnology & Bio-Engineering, Sam Higginbottom University of Agriculture, Technology and Sciences (SHUATS) , Allahabad , India
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Wang X, Zhu Y, Shen N, Peng J, Wang C, Liu H, Lu Y. Mutation analysis of a Chinese family with oculocutaneous albinism. Oncotarget 2018; 7:84981-84988. [PMID: 27829221 PMCID: PMC5356713 DOI: 10.18632/oncotarget.13109] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 10/22/2016] [Indexed: 11/25/2022] Open
Abstract
Oculocutaneous albinism (OCA) is an autosomal recessive disorder characterized by either complete lack of or a reduction in melanin biosynthesis in the skin, hair, and eyes. OCA1, the most common and severe type, is caused by mutations in the tyrosinase (TYR) gene. In this study, we report a Chinese family with two members affected by OCA. Blood samples were collected from all family members. Genomic DNA was isolated from blood leukocytes, and all coding exons and adjacent intronic sequences of the TYR gene were examined for mutation analysis using polymerase chain reaction (PCR)-based sequencing. A pedigree chart was drawn, and clinical examinations and paraclinical tests were performed. Compound heterozygous mutations in TYR (c.832C>T and c.929_930insC, which resulted in p.Arg278* and p.Arg311Lysfs*7, respectively) were identified in the two patients with milky skin, white hair, photophobia, and reduced visual acuity, while other family members only carried one of two heterozygous mutations. In addition, a homozygous missense mutation c.814G>A (p.Glu272Lys) in the solute carrier family 45 member 2 (SLC45A2) gene was found in both patients and unaffected family members, suggesting that this may not be a causative mutation. The findings of this study expand the mutational spectrum of OCA. Compound heterozygous mutations (c.832C>T and c.929_930insC) in the TYR gene may be responsible for partial clinical manifestations of OCA, while the homozygous missense mutation c.814G>A (p.Glu272Lys) in the SLC45A2 gene may not be associated with OCA.
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Affiliation(s)
- Xiong Wang
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yaowu Zhu
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Na Shen
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Jing Peng
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Chunyu Wang
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Haiyi Liu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yanjun Lu
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
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Mirza SB, Lee RCH, Chu JJH, Salmas RE, Mavromoustakos T, Durdagi S. Discovery of selective dengue virus inhibitors using combination of molecular fingerprint-based virtual screening protocols, structure-based pharmacophore model development, molecular dynamics simulations and in vitro studies. J Mol Graph Model 2017; 79:88-102. [PMID: 29156382 DOI: 10.1016/j.jmgm.2017.10.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Dengue virus is a major issue of tropical and sub-tropical regions. The proliferation of virus results in immense number of deaths each year because of unavailability of on-shelf drugs. This issue necessitates the design of novel anti-Dengue drugs. The protease enzyme pathway is the critical target for drug design due to its significance in the replication, survival and other cellular activities of Dengue virus. Keeping in mind the worsening situation regarding Dengue virus, approximately eighteen million drug-like compounds from the ZINC small molecule database have been screened against Nonstructural Protein 3 (NS3) previously by our group. In this study, in order to investigate the effect of extended time of molecular dynamics (MD) simulations on structural and dynamical profiles of used complexes, simulation run time is increased from 50-ns to 100-ns for the each system. In addition, a well-known Dengue virus inhibitor (MB21) from literature is used as reference structure (positive control) to compare the proposed molecules. Post-processing MD analyses including Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) calculations were conducted to predict binding free energies of inhibitors from derived trajectory frames of MD simulations. Identified compounds are further directed to Quantum-Polarized Ligand Docking (QPLD), molecular fingerprint-based virtual screening of another small molecule database (Otava Drug Like small molecule database), and Structure-based Pharmacophore Modeling (E-Pharmacophore). Finally, cell proliferation and cytotoxicity tests as well as pre- and post-treatment on HUH7 cells infected with DENV2 NGC strain are applied for four identified hit molecules (ZINC36681949, ZINC44921800, ZINC95518765 and ZINC39500661) to check whether these drugs inhibit DENV2 from entry and/or exit pathways. Based on cell-based Dengue quantification assays, there is no effect seen on pre-treatment of cells with these compounds indicating that the early infection processes of virus is not affected. In contrast, the post-treatment of cells with these compounds after Dengue virus infection has resulted in a significant 1 log PFU/ml reduction of the virus infectious titre.
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Affiliation(s)
- Shaher Bano Mirza
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey; Research Laboratory of Electronics, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; Department of Biosciences, COMSATS Institute of Information Technology (CIIT), Park Road, Chak Shahzad, Islamabad, Pakistan
| | - Regina Ching Hua Lee
- Laboratory of Molecular RNA Virology and Antiviral Strategies, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, Singapore
| | - Justin Jang Hann Chu
- Laboratory of Molecular RNA Virology and Antiviral Strategies, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, Singapore
| | - Ramin Ekhteiari Salmas
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey
| | | | - Serdar Durdagi
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey
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Mirza SB, Lee RCH, Chu JJH, Salmas RE, Mavromoustakos T, Durdagi S. Discovery of selective dengue virus inhibitors using combination of molecular fingerprint-based virtual screening protocols, structure-based pharmacophore model development, molecular dynamics simulations and in vitro studies. J Mol Graph Model 2017; 77:338. [PMID: 28957754 DOI: 10.1016/j.jmgm.2017.08.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 07/20/2017] [Accepted: 08/07/2017] [Indexed: 12/29/2022]
Abstract
Dengue virus is a major issue of tropical and sub-tropical regions. The proliferation of virus results in immense number of deaths each year because of unavailability of on-shelf drugs. This issue necessitates the design of novel anti-Dengue drugs. The protease enzyme pathway is the critical target for drug design due to its significance in the replication, survival and other cellular activities of Dengue virus. Keeping in mind the worsening situation regarding Dengue virus, approximately eighteen million drug-like compounds from the ZINC small molecule database have been screened against Nonstructural Protein 3 (NS3) previously by our group. In this study, in order to investigate the effect of extended time of molecular dynamics (MD) simulations on structural and dynamical profiles of used complexes, simulation run time is increased from 50-ns to 100-ns for the each system. In addition, a well-known Dengue virus inhibitor (MB21) from literature is used as reference structure (positive control) to compare the proposed molecules. Post-processing MD analyses including Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) calculations were conducted to predict binding free energies of inhibitors from derived trajectory frames of MD simulations. Identified compounds are further directed to Quantum-Polarized Ligand Docking (QPLD), molecular fingerprint-based virtual screening of another small molecule database (Otava Drug Like small molecule database), and Structure-based Pharmacophore Modeling (E-Pharmacophore). Finally, cell proliferation and cytotoxicity tests as well as pre- and post-treatment on HUH7 cells infected with DENV2 NGC strain are applied for four identified hit molecules (ZINC36681949, ZINC44921800, ZINC95518765 and ZINC39500661) to check whether these drugs inhibit DENV2 from entry and/or exit pathways. Based on cell-based Dengue quantification assays, there is no effect seen on pre-treatment of cells with these compounds indicating that the early infection processes of virus is not affected. In contrast, the post-treatment of cells with these compounds after Dengue virus infection has resulted in a significant 1logPFU/ml reduction of the virus infectious titre.
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Affiliation(s)
- Shaher Bano Mirza
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey; Research Laboratory of Electronics, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; Department of Biosciences, COMSATS Institute of Information Technology (CIIT), Park Road, Chak Shahzad, Islamabad, Pakistan
| | - Regina Ching Hua Lee
- Laboratory of Molecular RNA Virology and Antiviral Strategies, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, Singapore
| | - Justin Jang Hann Chu
- Laboratory of Molecular RNA Virology and Antiviral Strategies, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, Singapore
| | - Ramin Ekhteiari Salmas
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey
| | | | - Serdar Durdagi
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey.
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Status and future perspectives of single nucleotide polymorphisms (SNPs) markers in farmed fishes: Way ahead using next generation sequencing. GENE REPORTS 2017. [DOI: 10.1016/j.genrep.2016.12.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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40
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Dammalli M, Murthy KR, Pinto SM, Murthy KB, Nirujogi RS, Madugundu AK, Dey G, Nair B, Gowda H, Keshava Prasad TS. Toward Postgenomics Ophthalmology: A Proteomic Map of the Human Choroid–Retinal Pigment Epithelium Tissue. ACTA ACUST UNITED AC 2017; 21:114-122. [DOI: 10.1089/omi.2016.0170] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Manjunath Dammalli
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- Department of Biotechnology, Siddaganga Institute of Technology, Tumkur, India
| | - Krishna R. Murthy
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- Amrita School of Biotechnology, Amrita VishwaVidyapeetham, Kollam, India
- Vittala International Institute of Ophthalmology, Bangalore, India
| | - Sneha M. Pinto
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University, Mangalore, India
| | | | - Raja Sekhar Nirujogi
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Anil K. Madugundu
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Gourav Dey
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- Department of Biotechnology, Manipal University, Manipal, India
| | - Bipin Nair
- Amrita School of Biotechnology, Amrita VishwaVidyapeetham, Kollam, India
| | - Harsha Gowda
- Institute of Bioinformatics, International Technology Park, Bangalore, India
| | - Thottethodi Subrahmanya Keshava Prasad
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University, Mangalore, India
- NIMHANS-IOB Bioinformatics and Proteomics Laboratory, Neurobiology Research Centre, National Institute of Mental Health and Neurosciences, Bangalore, India
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41
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Bhardwaj A, Dhar YV, Asif MH, Bag SK. In Silico identification of SNP diversity in cultivated and wild tomato species: insight from molecular simulations. Sci Rep 2016; 6:38715. [PMID: 27929054 PMCID: PMC5144076 DOI: 10.1038/srep38715] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 11/15/2016] [Indexed: 12/12/2022] Open
Abstract
Single Nucleotide Polymorphisms (SNPs), an important source of genetic variations, are often used in crop improvement programme. The present study represented comprehensive In silico analysis of nucleotide polymorphisms in wild (Solanum habrochaites) and cultivated (Solanum lycopersicum) species of tomato to explore the consequence of substitutions both at sequence and structure level. A total of 8978 SNPs having Ts/Tv (Transition/Transversion) ratio 1.75 were identified from the Expressed Sequence Tag (EST) and Next Generation Sequence (NGS) data of both the species available in public databases. Out of these, 1838 SNPs were non-synonymous and distributed in 988 protein coding genes. Among these, 23 genes containing 96 SNPs were involved in traits markedly different between the two species. Furthermore, there were 28 deleterious SNPs distributed in 27 genes and a few of these genes were involved in plant pathogen interaction and plant hormone pathways. Molecular docking and simulations of several selected proteins showed the effect of SNPs in terms of compactness, conformation and interaction ability. Observed SNPs exhibited various types of motif binding effects due to nucleotide changes. SNPs that provide the evidence of differential motif binding and interaction behaviour could be effectively used for the crop improvement program.
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Affiliation(s)
- Archana Bhardwaj
- Academy of Scientific and Innovative Research (AcSIR), CSIR-NBRI Campus, Lucknow, India
- Council of Scientific and Industrial Research - National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001, India
| | - Yogeshwar Vikram Dhar
- Academy of Scientific and Innovative Research (AcSIR), CSIR-NBRI Campus, Lucknow, India
- Council of Scientific and Industrial Research - National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001, India
| | - Mehar Hasan Asif
- Council of Scientific and Industrial Research - National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001, India
| | - Sumit K Bag
- Academy of Scientific and Innovative Research (AcSIR), CSIR-NBRI Campus, Lucknow, India
- Council of Scientific and Industrial Research - National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001, India
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42
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Senthilkumar B, Rajasekaran R. In Silico Template Selection of Short Antimicrobial Peptide Viscotoxin for Improving Its Antimicrobial Efficiency in Development of Potential Therapeutic Drugs. Appl Biochem Biotechnol 2016; 181:898-913. [PMID: 27696138 DOI: 10.1007/s12010-016-2257-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 09/19/2016] [Indexed: 12/22/2022]
Abstract
Rapid increase in antibiotic resistance has posed a worldwide threat, due to increased mortality, morbidity, and expenditure caused by antibiotic-resistant microbes. Recent development of the antimicrobial peptides like viscotoxin (Vt) has been successfully comprehended as a substitute for classical antibiotics. A structurally stable peptide, Vt can enhance antimicrobial property and can be used for various developmental purposes. Thus, structural stability among the antimicrobial peptides, Vt A1 (3C8P), A2 (1JMN), A3 (1ED0), B (1JMP), and C (1ORL) of Viscus album was computationally analyzed. In specific, the static confirmation of VtA3 showed high number of intramolecular interactions, along with an increase in hydrophobicity than others comparatively. Further, conformational sampling was used to analyze various geometrical parameters such as root mean square deviation, root mean square fluctuation, radius of gyration, and ovality which also revealed the structural stability of VtA3. Moreover, the statistically validated contours of surface area, lipophilicity, and distance constraints of disulfide bonds also supported the priority of VtA3 with respect to stability. Finally, the functional activity of peptides was accessed by computing their free energy of membrane association and membrane interactions, which defined VtA3 as functionally stable. Currently, peptide-based antibiotics and nanoparticles have attracted the pharmaceutical industries for their potential therapeutic applications. Thereby, it is proposed that viscotoxin A3 (1ED0) could be used as a preeminent template for scaffolding potentially efficient antimicrobial peptide-based drugs and nanomaterials in future.
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Affiliation(s)
- B Senthilkumar
- Department of Biotechnology, School of Bio Sciences and Technology, VIT University, Vellore, Tamil Nadu, 632014, India
| | - R Rajasekaran
- Department of Biotechnology, School of Bio Sciences and Technology, VIT University, Vellore, Tamil Nadu, 632014, India.
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43
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Kamaraj B, Purohit R. Mutational Analysis on Membrane Associated Transporter Protein (MATP) and Their Structural Consequences in Oculocutaeous Albinism Type 4 (OCA4)-A Molecular Dynamics Approach. J Cell Biochem 2016; 117:2608-19. [PMID: 27019209 DOI: 10.1002/jcb.25555] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 03/24/2016] [Indexed: 12/11/2022]
Abstract
Oculocutaneous albinism type IV (OCA4) is an autosomal recessive inherited disorder which is characterized by reduced biosynthesis of melanin pigmentation in skin, hair, and eyes and caused by the genetic mutations in the membrane-associated transporter protein (MATP) encoded by SLC45A2 gene. The MATP protein consists of 530 amino acids which contains 12 putative transmembrane domains and plays an important role in pigmentation and probably functions as a membrane transporter in melanosomes. We scrutinized the most OCA4 disease-associated mutation and their structural consequences on SLC45A2 gene. To understand the atomic arrangement in 3D space, the native and mutant structures were modeled. Further the structural behavior of native and mutant MATP protein was investigated by molecular dynamics simulation (MDS) approach in explicit lipid and water background. We found Y317C as the most deleterious and disease-associated SNP on SLC45A2 gene. In MDS, mutations in MATP protein showed loss of stability and became more flexible, which alter its structural conformation and function. This phenomenon has indicated a significant role in inducing OCA4. Our study explored the understanding of molecular mechanism of MATP protein upon mutation at atomic level and further helps in the field of pharmacogenomics to develop a personalized medicine for OCA4 disorder. J. Cell. Biochem. 117: 2608-2619, 2016. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Balu Kamaraj
- Research Group PLASMANT, Department of Chemistry, University of Antwerp, Universiteitsplein 1, 2610, Wilrijk-Antwerp, Belgium
| | - Rituraj Purohit
- Department of Biotechnology, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India.
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Khordadpoor-Deilamani F, Akbari MT, Karimipoor M, Javadi GR. Homozygosity mapping in albinism patients using a novel panel of 13 STR markers inside the nonsyndromic OCA genes: introducing 5 novel mutations. J Hum Genet 2016; 61:373-9. [DOI: 10.1038/jhg.2015.167] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Revised: 11/16/2015] [Accepted: 11/26/2015] [Indexed: 02/06/2023]
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Patel SM, Koringa PG, Reddy BB, Nathani NM, Joshi CG. In silico analysis of consequences of non-synonymous SNPs of Slc11a2 gene in Indian bovines. GENOMICS DATA 2015; 5:72-9. [PMID: 26484229 PMCID: PMC4583633 DOI: 10.1016/j.gdata.2015.05.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Revised: 05/21/2015] [Accepted: 05/21/2015] [Indexed: 01/20/2023]
Abstract
The aim of our study was to analyze the consequences of non-synonymous SNPs in Slc11a2 gene using bioinformatic tools. There is a current need of efficient bioinformatic tools for in-depth analysis of data generated by the next generation sequencing technologies. SNPs are known to play an imperative role in understanding the genetic basis of many genetic diseases. Slc11a2 is one of the major metal transporter families in mammals and plays a critical role in host defenses. In this study, we performed a comprehensive analysis of the impact of all non-synonymous SNPs in this gene using multiple tools like SIFT, PROVEAN, I-Mutant and PANTHER. Among the total 124 SNPs obtained from amplicon sequencing of Slc11a2 gene by Ion Torrent PGM involving 10 individuals of Gir cattle and Murrah buffalo each, we found 22 non-synonymous. Comparing the prediction of these 4 methods, 5 nsSNPs (G369R, Y374C, A377V, Q385H and N492S) were identified as deleterious. In addition, while tested out for polar interactions with other amino acids in the protein, from above 5, Y374C, Q385H and N492S showed a change in interaction pattern and further confirmed by an increase in total energy after energy minimizations in case of mutant protein compared to the native. 22 nsSNPs were predicted to decrease the stability of protein based on I-Mutant. From these SNPs, 5 was identified as deleterious by SIFT, PROVEAN, and PANTHER. Y374C, Q385H and N492S were found to be damaging.
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Key Words
- ATM, ataxia telangiectasia mutated
- BRAF, B-Raf
- CFTR, cystic fibrosis transmembrane conductance regulator
- GATK, Genome Analysis Tool Kit
- GalNAc-T1, N-acetylgalactosaminyltransferase 1
- HBB, hemoglobin beta
- HMM, Hidden Markov Model
- IGF1R, insulin-like growth factor 1 receptor
- Ion torrent PGM
- NCBI, National Center for Biotechnology Information
- Non-synonymous
- PANTHER
- PANTHER, Protein Analysis Through Evolutionary Relationships
- PROVEAN, Protein Variation Effect Analyzer
- PolyPhen, Polymorphism Phenotyping
- Protein
- RMSD, root-mean-square deviation
- SIFT
- SIFT, sorting intolerant from tolerant
- SNP, single nucleotide polymorphism
- Slc11a2, solute carrier family 11 member 2
- TMDs, transmembrane domains
- TYRP1, tyrosinase-related protein 1
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Affiliation(s)
- Shreya M Patel
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand,388001 Gujarat, India
| | - Prakash G Koringa
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand,388001 Gujarat, India
| | - Bhaskar B Reddy
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand,388001 Gujarat, India
| | - Neelam M Nathani
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand,388001 Gujarat, India
| | - Chaitanya G Joshi
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand,388001 Gujarat, India
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Rasal KD, Shah TM, Vaidya M, Jakhesara SJ, Joshi CG. Analysis of consequences of non-synonymous SNP in feed conversion ratio associated TGF-β receptor type 3 gene in chicken. Meta Gene 2015; 4:107-17. [PMID: 25941634 PMCID: PMC4412971 DOI: 10.1016/j.mgene.2015.03.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Revised: 03/28/2015] [Accepted: 03/30/2015] [Indexed: 12/19/2022] Open
Abstract
The recent advances in high throughput sequencing technology accelerate possible ways for the study of genome wide variation in several organisms and associated consequences. In the present study, mutations in TGFBR3 showing significant association with FCR trait in chicken during exome sequencing were further analyzed. Out of four SNPs, one nsSNP p.Val451Leu was found in the coding region of TGFBR3. In silico tools such as SnpSift and PANTHER predicted it as deleterious (0.04) and to be tolerated, respectively, while I-Mutant revealed that protein stability decreased. The TGFBR3 I-TASSER model has a C-score of 0.85, which was validated using PROCHECK. Based on MD simulation, mutant protein structure deviated from native with RMSD 0.08 Å due to change in the H-bonding distances of mutant residue. The docking of TGFBR3 with interacting TGFBR2 inferred that mutant required more global energy. Therefore, the present study will provide useful information about functional SNPs that have an impact on FCR traits. Investigated functional nsSNP p.Val451Leu (rs312979494) in feed conversion ratio (FCR) associated TGFBR3 of chicken Computational tools (SIFT and I-Mutant 2.0) predicted that this nsSNP was deleterious. Mutant structure of TGFBR3 showed high energies and RMS deviations compared to native using MD simulation. Molecular docking of TGFBR3 with interacting protein TGFBR2 showed an increase in global energy of mutant compared to native. We have predicted that functional SNP has an impact on TGFBR3 of chicken and thus can be treated as candidate SNP in screening.
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Key Words
- AASs, amino acid substitutions
- Chicken
- FCR, feed conversion ratio
- Feed conversion ratio (FCR)
- I-TASSER, iterative threading assembly refinement
- MD, molecular dynamics
- Modeling
- Non-synonymous SNP
- PANTHER, protein analysis through evolutionary relationships
- RMSD, root mean square deviation
- RMSF, root mean square fluctuation
- SIFT, sorting intolerant from tolerant
- SNP, single nucleotide polymorphism
- TGFB, transforming growth factor beta
- TGFBR3
- UTR, un-translated region
- nsSNPs, non-synonymous single nucleotide polymorphisms
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Affiliation(s)
- Kiran D Rasal
- Department of Fish Genetics Biotechnology, Central Institute of Freshwater Aquaculture, ICAR, Bhubaneswar, Odisha 751002, India
| | - Tejas M Shah
- Department of Animal Biotechnology, College of Veterinary Science & Animal Husbandry, Anand Agricultural University, Anand 388 001, Gujarat, India
| | - Megha Vaidya
- Department of Animal Biotechnology, College of Veterinary Science & Animal Husbandry, Anand Agricultural University, Anand 388 001, Gujarat, India
| | - Subhash J Jakhesara
- Department of Animal Biotechnology, College of Veterinary Science & Animal Husbandry, Anand Agricultural University, Anand 388 001, Gujarat, India
| | - Chaitanya G Joshi
- Department of Animal Biotechnology, College of Veterinary Science & Animal Husbandry, Anand Agricultural University, Anand 388 001, Gujarat, India
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Sengupta M, Sarkar D, Ganguly K, Sengupta D, Bhaskar S, Ray K. In silico analyses of missense mutations in coagulation factor VIII: identification of severity determinants of haemophilia A. Haemophilia 2015; 21:662-9. [PMID: 25854144 DOI: 10.1111/hae.12662] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/01/2015] [Indexed: 01/10/2023]
Abstract
Factor VIII (FVIII) mutations cause haemophilia A (HA), an X-linked recessive coagulation disorder. Over 1000 missense mutations in FVIII are known and they lead to variable clinical phenotypes (severe, moderate and mild). The exact molecular basis of this phenotypic heterogeneity by FVIII missense mutations is elusive to date. In this study, we aimed to identify the severity determinants that cause phenotypic heterogeneity of HA. We compiled and curated a data set of 766 missense mutations from the repertoire of missense mutations in FVIII. We analysed these mutations by computational programs (e.g. Swiss-PdbViewer) and different mutation analysis servers (e.g. SIFT, PROVEAN, CUPSAT, PolyPhen2, MutPred); and various sequence- and structure-based parameters were assessed for any significant distribution bias among different HA phenotypes. Our analyses suggest that 'mutations in evolutionary conserved residues', 'mutations in buried residues', mutation-induced 'steric clash' and 'surface electrostatic potential alteration' act as risk factors towards severe HA. We have developed a grading system for FVIII mutations combining the severity determinants, and the grading pattern correlates with HA phenotype. This study will help to correctly associate the HA phenotype with a mutation and aid early characterization of novel variants.
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Affiliation(s)
- M Sengupta
- Department of Genetics, University of Calcutta, Kolkata, India
| | - D Sarkar
- Department of Genetics, University of Calcutta, Kolkata, India
| | - K Ganguly
- Department of Genetics, University of Calcutta, Kolkata, India
| | - D Sengupta
- Department of Genetics, University of Calcutta, Kolkata, India
| | - S Bhaskar
- Molecular & Human Genetics Division, CSIR-Indian Institute of Chemical Biology (CSIR-IICB), Kolkata, India
| | - K Ray
- Molecular & Human Genetics Division, CSIR-Indian Institute of Chemical Biology (CSIR-IICB), Kolkata, India.,Academy of Scientific & Innovative Research (AcSIR), New Delhi, India
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Chetty S, Bhakat S, Martin AJM, Soliman MES. Multi-drug resistance profile of PR20 HIV-1 protease is attributed to distorted conformational and drug binding landscape: molecular dynamics insights. J Biomol Struct Dyn 2015; 34:135-51. [PMID: 25671669 DOI: 10.1080/07391102.2015.1018326] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
The PR20 HIV-1 protease, a variant with 20 mutations, exhibits high levels of multi-drug resistance; however, to date, there has been no report detailing the impact of these 20 mutations on the conformational and drug binding landscape at a molecular level. In this report, we demonstrate the first account of a comprehensive study designed to elaborate on the impact of these mutations on the dynamic features as well as drug binding and resistance profile, using extensive molecular dynamics analyses. Comparative MD simulations for the wild-type and PR20 HIV proteases, starting from bound and unbound conformations in each case, were performed. Results showed that the apo conformation of the PR20 variant of the HIV protease displayed a tendency to remain in the open conformation for a longer period of time when compared to the wild type. This led to a phenomena in which the inhibitor seated at the active site of PR20 tends to diffuse away from the binding site leading to a significant change in inhibitor-protein association. Calculating the per-residue fluctuation (RMSF) and radius of gyration, further validated these findings. MM/GBSA showed that the occurrence of 20 mutations led to a drop in the calculated binding free energies (ΔGbind) by ~25.17 kcal/mol and ~5 kcal/mol for p2-NC, a natural peptide substrate, and darunavir, respectively, when compared to wild type. Furthermore, the residue interaction network showed a diminished inter-residue hydrogen bond network and changes in inter-residue connections as a result of these mutations. The increased conformational flexibility in PR20 as a result of loss of intra- and inter-molecular hydrogen bond interactions and other prominent binding forces led to a loss of protease grip on ligand. It is interesting to note that the difference in conformational flexibility between PR20 and WT conformations was much higher in the case of substrate-bound conformation as compared to DRV. Thus, developing analogues of DRV by retaining its key pharmacophore features will be the way forward in the search for novel protease inhibitors against multi-drug resistant strains.
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Affiliation(s)
- Sarentha Chetty
- a Molecular Modelling and Drug Design Research Group, School of Health Sciences , University of Kwazulu-Natal , Westville, Durban 4000 , South Africa
| | - Soumendranath Bhakat
- a Molecular Modelling and Drug Design Research Group, School of Health Sciences , University of Kwazulu-Natal , Westville, Durban 4000 , South Africa
| | - Alberto J M Martin
- b Computational Biology Lab, Fundación Ciencia & Vida , Santiago , Chile.,c Facultad de Ciencias, Centro Interdisciplinario de Neurociencia de Valparaíso , Universidad de Valparaíso , Valparaíso , Chile
| | - Mahmoud E S Soliman
- a Molecular Modelling and Drug Design Research Group, School of Health Sciences , University of Kwazulu-Natal , Westville, Durban 4000 , South Africa
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Hepp D, Gonçalves GL, de Freitas TRO. Prediction of the damage-associated non-synonymous single nucleotide polymorphisms in the human MC1R gene. PLoS One 2015; 10:e0121812. [PMID: 25794181 PMCID: PMC4368538 DOI: 10.1371/journal.pone.0121812] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 02/04/2015] [Indexed: 12/13/2022] Open
Abstract
The melanocortin 1 receptor (MC1R) is involved in the control of melanogenesis. Polymorphisms in this gene have been associated with variation in skin and hair color and with elevated risk for the development of melanoma. Here we used 11 computational tools based on different approaches to predict the damage-associated non-synonymous single nucleotide polymorphisms (nsSNPs) in the coding region of the human MC1R gene. Among the 92 nsSNPs arranged according to the predictions 62% were classified as damaging in more than five tools. The classification was significantly correlated with the scores of two consensus programs. Alleles associated with the red hair color (RHC) phenotype and with the risk of melanoma were examined. The R variants D84E, R142H, R151C, I155T, R160W and D294H were classified as damaging by the majority of the tools while the r variants V60L, V92M and R163Q have been predicted as neutral in most of the programs The combination of the prediction tools results in 14 nsSNPs indicated as the most damaging mutations in MC1R (L48P, R67W, H70Y, P72L, S83P, R151H, S172I, L206P, T242I, G255R, P256S, C273Y, C289R and R306H); C273Y showed to be highly damaging in SIFT, Polyphen-2, MutPred, PANTHER and PROVEAN scores. The computational analysis proved capable of identifying the potentially damaging nsSNPs in MC1R, which are candidates for further laboratory studies of the functional and pharmacological significance of the alterations in the receptor and the phenotypic outcomes.
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Affiliation(s)
- Diego Hepp
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
- Instituto Federal de Educação, Ciência e Tecnologia do Rio Grande do Sul—Câmpus Porto Alegre, Rio Grande do Sul, Brazil
- * E-mail:
| | - Gislene Lopes Gonçalves
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
- Instituto de Alta Investigación, Universidad de Tarapacá, Antofagasta, 1520 Arica, Chile
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Novel hypoxanthine guanine phosphoribosyltransferase gene mutations in Saudi Arabian hyperuricemia patients. BIOMED RESEARCH INTERNATIONAL 2014; 2014:290325. [PMID: 25136576 PMCID: PMC4119946 DOI: 10.1155/2014/290325] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Revised: 03/11/2014] [Accepted: 04/26/2014] [Indexed: 12/12/2022]
Abstract
Over the past decade, a steady increase in the incidence of HPRT-related hyperuricemia (HRH) has been observed in Saudi Arabia. We examined all the nine exons of HPRT gene for mutations in ten biochemically confirmed hyperuricemia patients, including one female and three normal controls. In all, we identified 13 novel mutations in Saudi Arabian HPRT-related hyperuricemia patients manifesting different levels of uric acid. The Lys103Met alteration was highly recurrent and was observed in 50% of the cases, while Ala160Thr and Lys158Asn substitutions were found in two patients. Moreover, in 70% of the patients ≥2 mutations were detected concurrently in the HPRT gene. Interestingly, one of the patients that harbored Lys103Met substitution along with two frameshift mutations at codons 85 and 160 resulting in shortened protein demonstrated unusually high serum uric acid level of 738 μmol/L. Two of the seven point mutations that resulted in amino acid change (Lys103Met and Val160Gly) were predicted to be damaging by SIFT and Polyphen and were further analyzed for their protein stability and function by molecular dynamics simulation. The identified novel mutations in the HPRT gene may prove useful in the prenatal diagnosis and genetic counseling.
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