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Darvazi M, Ghorbani M, Ramazi S, Allahverdi A, Abdolmaleki P. A computational study of the R120G mutation in human αB-crystallin: implications for structural stability and functionality. J Biomol Struct Dyn 2024; 42:5788-5798. [PMID: 37354135 DOI: 10.1080/07391102.2023.2229434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 06/17/2023] [Indexed: 06/26/2023]
Abstract
The eye is a vital organ in the visual system, which is composed of transparent vascular tissue. αB-crystallin, a significant protein found in the lens, plays a crucial role in our understanding of lens diseases. Mutations in the αB-crystallin protein can cause lens diseases, such as cataracts and myopathy. However, the molecular mechanism underlying the R120G mutation is not fully understood. In this study, we utilized molecular dynamics simulations to illustrate, in atomic detail, how the R120G mutation leads to the aggregation of αB-crystallin and scattering of light in the lens. Our findings show that the R120G mutation alters the dynamic and structural properties of the αB-crystallin protein. Specifically, this mutation causes the angle of the hairpin at the C-terminal to increase from 80° to 150°, while reducing the distance between the hydrophobic patches around residues 10 and 44-55 from 1.5 nm to 1 nm. In addition, our results showed that the mutation could disrupt the IPI motif - β4/β8 interaction. The disruption of this interaction could affect the αB-crystallin oligomerization and the chaperone activity of αB-crystallin protein. The exposed hydrophobic area at the IPI motif - β4/β8 could become the primary site for interprotein interactions, which are responsible for large-scale aggregation. We have demonstrated that, in wild-type αB-crystallin protein, salt bridges R120 and D109, R107 and D80 are formed. However, in the case of the R120G mutation, the salt bridges R120 and R109 are disrupted, and a new salt bridge with a different pattern is formed. In our study, it has been found that all of the changes associated with the R120G mutation are located at the interface of chains A and B, which could impact the multimerization of the αB-crystallin. Previous research on the K92-E99 residue has shown that a salt bridge in the dimer I can reduce the chaperone activity of the protein. Furthermore, the salt bridges R120 and D109, as well as R107 and D80 in dimer II, induce changes in the hydrophobic envelope of β-sheets in the α-crystallin domain (ACD). These changes could have an impact on the multimerization of the αB-crystallin, leading to disruption of the oligomer structure and aggregation. Moreover, the changes in the αB-crystallin resulting from the R120G mutation can lead to faulty interactions with other proteins, which can cause the aggregation of αB-crystallin with other proteins, such as desmin. These findings may provide new insights into the development of treatments for lens diseases.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mona Darvazi
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | | | - Shahin Ramazi
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Abdollah Allahverdi
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Parviz Abdolmaleki
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
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2
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Zohreh Vahedi S, Farhadian S, Shareghi B, Asgharzadeh S. Interaction between the antioxidant compound safranal and α-chymotrypsin in spectroscopic fields and molecular modeling approaches. J Biomol Struct Dyn 2024; 42:4097-4109. [PMID: 37969053 DOI: 10.1080/07391102.2023.2272186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 05/21/2023] [Indexed: 11/17/2023]
Abstract
Among various herbal plants, saffron has been the subject of study in various medical and food fields. Among the compounds of saffron, safranal is one of them. Safranal is a monoterpene aldehyde. The precursor of safranal is called picrocrocin, whose hydrolysis leads to the production of safranal. picrocrocin has two sugar components and aglycone. sugar component was separated during the drying process of saffron and safranal is produced. Saffron is the cause of the saffron aroma. Previous studies have shown that safranal offers many benefits such as antioxidants, blood pressure regulation and anti-tumor qualities. On the other hand, α-Chy is an enzyme secreted by the pancreas into the intestine and then acts as an efficient protease. In this study, various methods, such as molecular dynamics (MD) simulation and molecular binding, and different spectroscopic techniques, as well as protein stability techniques, were used to investigate the possible interactions between safranal and α-Chy. UV spectroscopic studies were showing that the existence of safranal decreased α-Chy absorption intensity. safranal caused the intrinsic fluorescence of α-Chy to be quenched too. According to the Stern-Volmer equation, the interaction between safranal and α-Chy was of the static type. In thermodynamic calculations, the interaction between safranal and α-Chy was stabilized by hydrophobic forces. And it was found that this interaction continued spontaneously. These results were, thus, consistent with the Docking data simulation (with the negative ΔG° number and positive changes in enthalpy and entropy). The thermal stability of α-Chy was also measured, showing that its melting point was shifted to a higher threshold as a result of the interaction. also, MD simulation indicated that α-Chy became more stable in the presence of safranal. In this paper, all the results of the laboratory techniques were confirmed by molecular dynamic simulations, so the correctness of the results was confirmed. From this research, we hope to carefully observe the possible changes in the behavior and structure of the enzyme in the presence of safranal.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Sadegh Farhadian
- Department of Biology, Faculty of Science, Shahrekord University, Shahrekord, Iran
| | - Behzad Shareghi
- Department of Biology, Faculty of Science, Shahrekord University, Shahrekord, Iran
| | - Sanaz Asgharzadeh
- Department of Biology, Faculty of Science, Shahrekord University, Shahrekord, Iran
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Suresh Babu AR, Sharma A, Athira MP, Alajangi HK, Naresh Raj AR, Gartia J, Singh G, Barnwal RP. Evaluation of antibiofilm properties of dehydroacetic acid (DHA) grafted spiro-oxindolopyrrolidines synthesized via multicomponent 1,3-dipolar cycloaddition reaction. Sci Rep 2023; 13:15289. [PMID: 37714933 PMCID: PMC10504327 DOI: 10.1038/s41598-023-42528-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 09/11/2023] [Indexed: 09/17/2023] Open
Abstract
The current work involves the use of dehydroacetic acid based chalcone derivatives for the synthesis of spirooxindole grafted pyrrolidine moieties. All the synthesized compounds have been characterized using spectroscopic techniques such as NMR (1H-NMR and 13C-NMR), IR, mass and elemental analysis. Molecular mechanics studies were performed to comprehend the regioselectivity in the product formation. Molecular docking of the synthesized compounds was performed with few bacterial proteins of Bacillus subtilis and Pseudomonas aeruginosa responsible for biofilm formation followed by molecular dynamics simulations with the potential lead compound. Further, to corroborate the results obtained via in silico study, anti-biofilm activity etc. of the synthesized compounds (4a-e) was checked for effectiveness against biofilm formation. Taken together, this study opens up to explore these compounds' multiple roles in diverse fields in the arena of medical sciences.
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Affiliation(s)
| | - Akanksha Sharma
- Department of Biophysics, Panjab University, Chandigarh, 160014, India
- University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh, 160014, India
| | - M P Athira
- Department of Chemistry, IISER, Mohali, Sahibzada Ajit Singh Nagar, Punjab, 140306, India
| | - Hema K Alajangi
- Department of Biophysics, Panjab University, Chandigarh, 160014, India
- University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh, 160014, India
| | - A R Naresh Raj
- Department of Chemistry, Dwaraka Doss Goverdhan Doss Vaishnav College, Arumbakkam, Chennai, 600106, India
| | - Janeka Gartia
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Bhubaneswar, Odisha, 751024, India
| | - Gurpal Singh
- University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh, 160014, India.
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4
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Wu X, Xu LY, Li EM, Dong G. Molecular dynamics simulation study on the structures of fascin mutants. J Mol Recognit 2023; 36:e2998. [PMID: 36225126 DOI: 10.1002/jmr.2998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 10/08/2022] [Accepted: 10/10/2022] [Indexed: 02/05/2023]
Abstract
Fascin is a filamentous actin (F-actin) bundling protein, which cross-links F-actin into bundles and becomes an important component of filopodia on the cell surface. Fascin is overexpressed in many types of cancers. The mutation of fascin affects its ability to bind to F-actin and the progress of cancer. In this paper, we have studied the effects of residues of K22, K41, K43, K241, K358, K399, and K471 using molecular dynamics (MD) simulation. For the strong-effect residues, that is, K22, K41, K43, K358, and K471, our results show that the mutation of K to A leads to large values of root mean square fluctuation (RMSF) around the mutated residues, indicating those residues are important for the flexibility and thermal stability. On the other hand, based on residue cross-correlation analysis, alanine mutations of these residues reinforce the correlation between residues. Together with the RMSF data, the local flexibility is extended to the entire protein by the strong correlations to influence the dynamics and function of fascin. By contrast, for the mutants of K241A and K399A those do not affect the function of fascin, the RMSF data do not show significant differences compared with wild-type fascin. These findings are in a good agreement with experimental studies.
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Affiliation(s)
- Xiaodong Wu
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, People's Republic of China
| | - Li-Yan Xu
- Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou, People's Republic of China
- Cancer Research Center, Shantou University Medical College, Shantou, People's Republic of China
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Shantou University Medical College, Shantou, People's Republic of China
| | - En-Min Li
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, People's Republic of China
- Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou, People's Republic of China
| | - Geng Dong
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, People's Republic of China
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Shantou University Medical College, Shantou, People's Republic of China
- Medical Informatics Research Center, Shantou University Medical College, Shantou, People's Republic of China
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Nada H, Elkamhawy A, Lee K. Identification of 1H-purine-2,6-dione derivative as a potential SARS-CoV-2 main protease inhibitor: molecular docking, dynamic simulations, and energy calculations. PeerJ 2022; 10:e14120. [PMID: 36225900 PMCID: PMC9549888 DOI: 10.7717/peerj.14120] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 09/05/2022] [Indexed: 01/25/2023] Open
Abstract
The rapid spread of the coronavirus since its first appearance in 2019 has taken the world by surprise, challenging the global economy, and putting pressure on healthcare systems across the world. The introduction of preventive vaccines only managed to slow the rising death rates worldwide, illuminating the pressing need for developing effective antiviral therapeutics. The traditional route of drug discovery has been known to require years which the world does not currently have. In silico approaches in drug design have shown promising results over the last decade, helping to decrease the required time for drug development. One of the vital non-structural proteins that are essential to viral replication and transcription is the SARS-CoV-2 main protease (Mpro). Herein, using a test set of recently identified COVID-19 inhibitors, a pharmacophore was developed to screen 20 million drug-like compounds obtained from a freely accessible Zinc database. The generated hits were ranked using a structure based virtual screening technique (SBVS), and the top hits were subjected to in-depth molecular docking studies and MM-GBSA calculations over SARS-COV-2 Mpro. Finally, the most promising hit, compound (1), and the potent standard (III) were subjected to 100 ns molecular dynamics (MD) simulations and in silico ADME study. The result of the MD analysis as well as the in silico pharmacokinetic study reveal compound 1 to be a promising SARS-Cov-2 MPro inhibitor suitable for further development.
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Affiliation(s)
- Hossam Nada
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University-Seoul, Goyang, South Korea,Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Badr University in Cairo, Cairo, Egypt
| | - Ahmed Elkamhawy
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University-Seoul, Goyang, South Korea,Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
| | - Kyeong Lee
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University-Seoul, Goyang, South Korea
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Nada H, Lee K, Gotina L, Pae AN, Elkamhawy A. Identification of novel discoidin domain receptor 1 (DDR1) inhibitors using E-pharmacophore modeling, structure-based virtual screening, molecular dynamics simulation and MM-GBSA approaches. Comput Biol Med 2022; 142:105217. [PMID: 35032738 DOI: 10.1016/j.compbiomed.2022.105217] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 01/03/2022] [Accepted: 01/03/2022] [Indexed: 12/11/2022]
Abstract
Dysregulation of the discoidin domain receptor (DDR1), a collagen-activated receptor tyrosine kinase, has been linked to several human cancer diseases including non-small cell lung carcinoma (NSCLC), ovarian cancer, glioblastoma, and breast cancer, in addition to several inflammatory and neurological conditions. Although there are some selective DDR1 inhibitors that have been discovered during the last two decades, a combination of elevated cytotoxicity, kinome selectivity and/or poor DMPK profile has prevented more in-depth studies from being performed. As such, no DDR1 inhibitor has reached clinical investigation to date, forming an urgent need to develop specific DDR1 inhibitor(s) using various drug discovery means. However, the recent discovery of VU6015929, a potent and selective DDR1 kinase inhibitor, with enhanced physiochemical and DMPK properties in addition to its clean kinome profile marked a milestone in the development of DDR1 inhibitors. Herein, VU6015929 was used to construct a 3D e-pharmacophore model which was validated via calculating the difference of score between the active compounds and decoys. The validated e-pharmacophore model was then utilized to screen 20 million drug-like compounds obtained from the freely accessible Zinc database. The generated hits were ranked using high throughput virtual screening technique (HTVS), and the top 8 small molecules were subjected to a molecular docking study and MM-GBSA calculations. Protein-ligand complexes of compounds 1, 2, 3 and the standard compound (VU6015929) were performed for 100 ns and compared with the DDR1 unbound protein state and the DDR1 bound to a co-crystallized ligand. The molecular docking, MD and MM-GBSA outputs revealed compounds 1-3 as potential DDR1 inhibitors, with compound 2 displaying superior binding affinity, comparable binding stability and average binding free energy for the ligand-enzyme complex compared to VU6015929.
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Affiliation(s)
- Hossam Nada
- College of Pharmacy, Dongguk University-Seoul, Goyang, 10326, Republic of Korea
| | - Kyeong Lee
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University-Seoul, Goyang, 10326, Republic of Korea
| | - Lizaveta Gotina
- Division of Bio-Medical Science & Technology, KIST School, University of Science and Technology (UST), Seoul, 02792, Republic of Korea; Convergence Research Center for Diagnosis, Treatment and Care System of Dementia, Korea Institute of Science and Technology (KIST), Seoul, 02792, Republic of Korea
| | - Ae Nim Pae
- Division of Bio-Medical Science & Technology, KIST School, University of Science and Technology (UST), Seoul, 02792, Republic of Korea; Convergence Research Center for Diagnosis, Treatment and Care System of Dementia, Korea Institute of Science and Technology (KIST), Seoul, 02792, Republic of Korea
| | - Ahmed Elkamhawy
- College of Pharmacy, Dongguk University-Seoul, Goyang, 10326, Republic of Korea; Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura, 35516, Egypt.
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7
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Qiu J, Tan J. In vitro and in silico analysis of a E559K mutation on cartilage oligomeric matrix protein. Mutat Res 2022; 824:111774. [PMID: 35077910 DOI: 10.1016/j.mrfmmm.2022.111774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 01/29/2020] [Accepted: 01/10/2022] [Indexed: 06/14/2023]
Abstract
Pseudoachondroplasia (PSACH) is known as an autosomal dominant disorder associated with mutations in the gene of cartilage oligomeric matrix protein (COMP). The pathomolecular mechanisms of PSACH as a result of C-terminal globular region (CTD) mutations remain unclear. A heterozygous mutation (E559 K) in a Chinese family diagnosed with PSACH was reported in this study. To understand the pathogenesis of this mutation, we studied chondrogenic differentiation of patient menstrual blood-derived stem cells (MenSCs), and the impact of the mutation on structural changes of COMP was investigated using all-atom molecular dynamics simulation. The results suggested that the interactions with calcium and other molecules in the mutant structure were affected resulting in misfolding of the protein, which leads to ER stress and finally affects the survival of chondrocytes. The findings may promote the understanding of the pathomolecular mechanisms of PSACH, and possibly the development of drugs to treat the disease.
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Affiliation(s)
- Jiahui Qiu
- Reproductive Medical Center of Gynecology and Obstetrics Department, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China; Key Laboratory of Reproductive Dysfunction Diseases and Fertility Remodeling of Liaoning Province, Shenyang, Liaoning, China
| | - Jichun Tan
- Reproductive Medical Center of Gynecology and Obstetrics Department, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China; Key Laboratory of Reproductive Dysfunction Diseases and Fertility Remodeling of Liaoning Province, Shenyang, Liaoning, China.
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8
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Computational driven molecular dynamics simulation of keratinocyte growth factor behavior at different pH conditions. INFORMATICS IN MEDICINE UNLOCKED 2021. [DOI: 10.1016/j.imu.2021.100514] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
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9
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McCoy MD, Hamre J, Klimov DK, Jafri MS. Predicting Genetic Variation Severity Using Machine Learning to Interpret Molecular Simulations. Biophys J 2020; 120:189-204. [PMID: 33333034 DOI: 10.1016/j.bpj.2020.12.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 11/20/2020] [Accepted: 12/08/2020] [Indexed: 02/08/2023] Open
Abstract
Distinct missense mutations in a specific gene have been associated with different diseases as well as differing severity of a disease. Current computational methods predict the potential pathogenicity of a missense variant but fail to differentiate between separate disease or severity phenotypes. We have developed a method to overcome this limitation by applying machine learning to features extracted from molecular dynamics simulations, creating a way to predict the effect of novel genetic variants in causing a disease, drug resistance, or another specific trait. As an example, we have applied this novel approach to variants in calmodulin associated with two distinct arrhythmias as well as two different neurodegenerative diseases caused by variants in amyloid-β peptide. The new method successfully predicts the specific disease caused by a gene variant and ranks its severity with more accuracy than existing methods. We call this method molecular dynamics phenotype prediction model.
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Affiliation(s)
- Matthew D McCoy
- Innovation Center for Biomedical Informatics, Department of Oncology, Georgetown University Medical Center, Georgetown University, Washington DC; School of Systems Biology, George Mason University, Manassas, Virginia.
| | - John Hamre
- School of Systems Biology, George Mason University, Manassas, Virginia
| | - Dmitri K Klimov
- School of Systems Biology, George Mason University, Manassas, Virginia
| | - M Saleet Jafri
- School of Systems Biology, George Mason University, Manassas, Virginia; Krasnow Institute for Advanced Study, Interdisciplinary Program in Neuroscience, School of Systems Biology, George Mason University, Fairfax, Virginia.
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10
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Sun Y, Xia Z, Zhao Q, Zheng B, Zhang M, Ying Y. Insights Into the Resistance Mechanisms of Inhibitors to FLT3 F691L Mutation via an Integrated Computational Approach. Front Pharmacol 2019; 10:1050. [PMID: 31619996 PMCID: PMC6763581 DOI: 10.3389/fphar.2019.01050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 08/19/2019] [Indexed: 11/26/2022] Open
Abstract
Research has shown that FMS-like tyrosine kinase 3 (FLT3) may be a vital drug target for acute myeloid leukemia (AML). However, even though the clinically relevant F691L gatekeeper mutation conferred resistance to current FLT3 drug quizartinib, PLX3397 remained unaffected. In this study, the protein–ligand interactions between FLT3 kinase domain (wild-type or F691L) and quizartinib or PLX3397 were compared via an integrated computational approach. The classical molecular dynamics (MD) simulations in conjunction with dynamic cross-correlation (DCC) analysis, solvent-accessible surface area (SASA), and free energy calculations indicated that the resistant mutation may induce the conformational change of αC-helix and A-loop of the FLT3 protein. The major variations were controlled by the electrostatic interaction and SASA, which were allosterically regulated by residues Glu-661 and Asp-829. When FLT3-F691L was bound to quizartinib, a large conformational change was observed via combination of accelerated MD simulations (aMDs), principal component analysis (PCA), and free energy landscape (FEL) calculations. The umbrella sampling (US) simulations were applied to investigate the dissociation processes of the quizartinib or PLX3397 from FLT3-WT and FLT3-F691L. The calculated results suggested that PLX3397 had similar dissociation processes from both FLT3-WT and FLT3-F691L, but quizartinib dissociated more easily from FLT3-F691L than from FLT3-WT. Thus, reduced residence time was responsible for the FLT3-F691L resistance to inhibitors. These findings indicated that both the conformational changes of αC-helix and A-loop and the drug residence time should be considered in the design of drugs so that rational decisions can be made to overcome resistance to FLT3-F691L.
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Affiliation(s)
- Yunfeng Sun
- Department of Pharmacy, Tongde Hospital of Zhejiang Province, Hangzhou, China
| | - Zhongni Xia
- Department of Pharmacy, Tongde Hospital of Zhejiang Province, Hangzhou, China
| | - Qinqin Zhao
- Department of Pharmacy, Tongde Hospital of Zhejiang Province, Hangzhou, China
| | - Bei Zheng
- Department of Pharmacy, Tongde Hospital of Zhejiang Province, Hangzhou, China
| | - Meiling Zhang
- Department of Pharmacy, Tongde Hospital of Zhejiang Province, Hangzhou, China
| | - Yin Ying
- Department of Pharmacy, Tongde Hospital of Zhejiang Province, Hangzhou, China
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11
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Wan Y, Guan S, Qian M, Huang H, Han F, Wang S, Zhang H. Structural basis of fullerene derivatives as novel potent inhibitors of protein acetylcholinesterase without catalytic active site interaction: insight into the inhibitory mechanism through molecular modeling studies. J Biomol Struct Dyn 2019; 38:410-425. [DOI: 10.1080/07391102.2019.1576543] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Yongfeng Wan
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, People’s Republic of China
| | - Shanshan Guan
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, People’s Republic of China
- College of Biology and Food Engineering, Jilin Engineering Normal University, Changchun, Jilin, China
| | - Mengdan Qian
- State Key Laboratory on Integrated Optoelectronics, College of Electronic Science and Engineering, Jilin University, Changchun, China
| | - Houhou Huang
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, People’s Republic of China
| | - Fei Han
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, People’s Republic of China
| | - Song Wang
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, People’s Republic of China
| | - Hao Zhang
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, People’s Republic of China
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12
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Chen J, He G, Wang Y, Cai D. MicroRNA‑223 promotes osteoblast differentiation of MC3T3‑E1 cells by targeting histone deacetylase 2. Int J Mol Med 2018; 43:1513-1521. [PMID: 30628667 DOI: 10.3892/ijmm.2018.4042] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 11/19/2018] [Indexed: 11/06/2022] Open
Abstract
MicroRNAs (miRNAs) have emerged as pivotal regulators in various physiological and pathological processes at the post‑transcriptional level, and may serve important roles in osteogenic differentiation. However, their roles and functions are not fully understood. In the present study, miR‑223‑5p was identified as a modulator of osteoblastic differentiation in MC3T3‑E1 cells. Reverse transcription‑quantitative polymerase chain reaction and western blotting demonstrated that miR‑223‑5p was significantly upregulated in MC3T3‑E1 cells following the induction of osteoblast differentiation. Overexpression of miR‑223‑5p promoted osteogenic differentiation both in vitro and vivo. Expression of histone deacetylase 2 (HDAC2), which acts as a negative regulator of osteogenesis, was regulated by miR‑223‑5p. Collectively, the results of the present study revealed a novel miR‑223‑5p/HDAC2 axis that regulates osteoblast differentiation, and may serve as a potential target for enhancing bone formation in vivo.
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Affiliation(s)
- Jianming Chen
- Department of Orthopedics, The Third Affiliated Hospital of Southern Medical University, Guangzhou, Guangdong 510630, P.R. China
| | - Guisong He
- Department of Orthopedic Surgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510260, P.R. China
| | - Yi Wang
- Department of Otolaryngology/Head and Neck Surgery, The Central Hospital of Yongzhou, Yongzhou, Hunan 425000, P.R. China
| | - Daozhang Cai
- Department of Orthopedics, The Third Affiliated Hospital of Southern Medical University, Guangzhou, Guangdong 510630, P.R. China
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13
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Zhang Y, Chen Y, Zhang D, Wang L, Lu T, Jiao Y. Discovery of Novel Potent VEGFR-2 Inhibitors Exerting Significant Antiproliferative Activity against Cancer Cell Lines. J Med Chem 2017; 61:140-157. [DOI: 10.1021/acs.jmedchem.7b01091] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Yanmin Zhang
- Laboratory
of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, China
| | - Yadong Chen
- Laboratory
of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, China
| | - Danfeng Zhang
- School
of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, China
| | - Lu Wang
- School
of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, China
| | - Tao Lu
- Laboratory
of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, China
- School
of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, China
- State
Key Laboratory of Natural Medicines, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, China
| | - Yu Jiao
- School
of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, China
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14
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Yan G, Hou M, Luo J, Pu C, Hou X, Lan S, Li R. Pharmacophore-based virtual screening, molecular docking, molecular dynamics simulation, and biological evaluation for the discovery of novel BRD4 inhibitors. Chem Biol Drug Des 2017; 91:478-490. [PMID: 28901664 DOI: 10.1111/cbdd.13109] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 08/21/2017] [Accepted: 08/22/2017] [Indexed: 02/05/2023]
Abstract
Bromodomain is a recognition module in the signal transduction of acetylated histone. BRD4, one of the bromodomain members, is emerging as an attractive therapeutic target for several types of cancer. Therefore, in this study, an attempt has been made to screen compounds from an integrated database containing 5.5 million compounds for BRD4 inhibitors using pharmacophore-based virtual screening, molecular docking, and molecular dynamics simulations. As a result, two molecules of twelve hits were found to be active in bioactivity tests. Among the molecules, compound 5 exhibited potent anticancer activity, and the IC50 values against human cancer cell lines MV4-11, A375, and HeLa were 4.2, 7.1, and 11.6 μm, respectively. After that, colony formation assay, cell cycle, apoptosis analysis, wound-healing migration assay, and Western blotting were carried out to learn the bioactivity of compound 5.
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Affiliation(s)
- Guoyi Yan
- Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Sichuan, China
| | - Manzhou Hou
- Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Sichuan, China
| | - Jiang Luo
- Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Sichuan, China
| | - Chunlan Pu
- Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Sichuan, China
| | - Xueyan Hou
- Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Sichuan, China
| | - Suke Lan
- Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Sichuan, China
| | - Rui Li
- Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Sichuan, China
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15
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Porto WF, Marques FA, Pogue HB, de Oliveira Cardoso MT, do Vale MGR, da Silva Pires Á, Franco OL, de Alencar SA, Pogue R. Computational Investigation of Growth Hormone Receptor Trp169Arg Heterozygous Mutation in a Child With Short Stature. J Cell Biochem 2017; 118:4762-4771. [DOI: 10.1002/jcb.26144] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 05/17/2017] [Indexed: 11/07/2022]
Affiliation(s)
- William Farias Porto
- Programa de Pós‐Graduação em Ciências Genômicas e BiotecnologiaUniversidade Católica de BrasíliaBrasília – DFBrazil
- Centro de Análises Proteômicas e Bioquímicas, Pós‐Graduação em Ciências Genômicas e BiotecnologiaUniversidade Católica de BrasíliaBrasília – DFBrazil
- Porto ReportsBrasília – DFBrazil
| | - Felipe Albuquerque Marques
- Programa de Pós‐Graduação em Ciências Genômicas e BiotecnologiaUniversidade Católica de BrasíliaBrasília – DFBrazil
- Departamento de FarmáciaUniversidade CEUMASão‐Luis – MABrazil
- Departamento de BiomedicinaUniversidade CEUMASão‐Luis – MABrazil
| | - Huri Brito Pogue
- Programa de Pós‐Graduação em Ciências Genômicas e BiotecnologiaUniversidade Católica de BrasíliaBrasília – DFBrazil
| | - Maria Teresinha de Oliveira Cardoso
- Curso de MedicinaUniversidade Católica de BrasíliaBrasília – DFBrazil
- Núcleo de Genética da Secretaria de Saúde do Distrito FederalBrasília – DFBrazil
| | | | - Állan da Silva Pires
- Programa de Pós‐Graduação em Ciências Genômicas e BiotecnologiaUniversidade Católica de BrasíliaBrasília – DFBrazil
- Centro de Análises Proteômicas e Bioquímicas, Pós‐Graduação em Ciências Genômicas e BiotecnologiaUniversidade Católica de BrasíliaBrasília – DFBrazil
| | - Octavio Luiz Franco
- Programa de Pós‐Graduação em Ciências Genômicas e BiotecnologiaUniversidade Católica de BrasíliaBrasília – DFBrazil
- Centro de Análises Proteômicas e Bioquímicas, Pós‐Graduação em Ciências Genômicas e BiotecnologiaUniversidade Católica de BrasíliaBrasília – DFBrazil
- S‐Inova Biotech, Pós‐graduação em BiotecnologiaUniversidade Católica Dom BoscoCampo GrandeMSBrazil
| | - Sérgio Amorim de Alencar
- Programa de Pós‐Graduação em Ciências Genômicas e BiotecnologiaUniversidade Católica de BrasíliaBrasília – DFBrazil
| | - Robert Pogue
- Programa de Pós‐Graduação em Ciências Genômicas e BiotecnologiaUniversidade Católica de BrasíliaBrasília – DFBrazil
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16
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Zhang Y, Wang L, Zhang Q, Zhu G, Zhang Z, Zhou X, Chen Y, Lu T, Tang W. Potent Pan-Raf and Receptor Tyrosine Kinase Inhibitors Based on a Cyclopropyl Formamide Fragment Overcome Resistance. J Chem Inf Model 2017; 57:1439-1452. [DOI: 10.1021/acs.jcim.6b00795] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Yanmin Zhang
- School
of Basic Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu 211198, China
| | - Lu Wang
- School
of Basic Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu 211198, China
| | - Qing Zhang
- School
of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu 211198, China
| | - Gaoyuan Zhu
- School
of Basic Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu 211198, China
| | - Zhimin Zhang
- School
of Basic Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu 211198, China
| | - Xiang Zhou
- School
of Basic Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu 211198, China
| | - Yadong Chen
- School
of Basic Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu 211198, China
| | - Tao Lu
- School
of Basic Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu 211198, China
- State
Key Laboratory of Natural Medicines, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing, Jiangsu 210009, China
| | - Weifang Tang
- School
of Basic Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu 211198, China
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17
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Design, synthesis and evaluation of derivatives based on pyrimidine scaffold as potent Pan-Raf inhibitors to overcome resistance. Eur J Med Chem 2017; 130:86-106. [DOI: 10.1016/j.ejmech.2017.02.041] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 02/14/2017] [Accepted: 02/16/2017] [Indexed: 12/19/2022]
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18
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Suganya S, Nandagopal B, Anbarasu A. Natural Inhibitors of HMG-CoA Reductase-An Insilico Approach Through Molecular Docking and Simulation Studies. J Cell Biochem 2016; 118:52-57. [PMID: 27216569 DOI: 10.1002/jcb.25608] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Accepted: 05/20/2016] [Indexed: 01/09/2023]
Abstract
Plant products have always been considered for many important metabolic disorders due to its abundant medicinal properties. Alarming adverse effects of overuse of statins has been reported for patients with dyslipidemia. This study was aimed to identify compounds with potent anti-dyslipidemic property from selected plants and analyze them for their efficiency in binding with HMG-CoA reductase, a key enzyme in lipid metabolism. The docking studies indicate rutin as the best compound that can inhibit HMG-CoA reductase as it had strong binding affinity to the enzyme. The molecular dynamics simulation studies confirmed the stability of the HMG-CoA reductase-rutin complex. RMSD, RMSF, Rg, H-bond results indicated that the HMG-CoA reductase-rutin complex is highly stable. Presently, statins are not preferred for individuals with pre-existing liver disease. Our study identified rutin as a promising lead compound which could be further developed into an anti-dyslipidemic molecule. Our results will be a good starting point for future experimental and clinical studies and if the results from such studies match international standards plant derived rutin might emerge as a good alternative to statins. J. Cell. Biochem. 118: 52-57, 2017. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Subramanian Suganya
- Sri Sakthi Amma Institute of Biomedical Research, Sri Narayani Hospital and Research Centre, Sripuram, Vellore, 632 055, Tamil Nadu, India.,Medical and Biological Computing Laboratory, School of Biosciences and Technology, VIT University, Vellore, 632 014, Tamil Nadu, India
| | - Balaji Nandagopal
- Sri Sakthi Amma Institute of Biomedical Research, Sri Narayani Hospital and Research Centre, Sripuram, Vellore, 632 055, Tamil Nadu, India
| | - Anand Anbarasu
- Medical and Biological Computing Laboratory, School of Biosciences and Technology, VIT University, Vellore, 632 014, Tamil Nadu, India
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