1
|
Zhang N, Liu S, Lu X, Li Z, Li L, Ye T. Transcriptomic and proteomic investigations identify PI3K-akt pathway targets for hyperthyroidism management in rats via polar iridoids from radix Scrophularia. Heliyon 2024; 10:e33072. [PMID: 38994059 PMCID: PMC11238048 DOI: 10.1016/j.heliyon.2024.e33072] [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: 02/06/2024] [Revised: 06/12/2024] [Accepted: 06/13/2024] [Indexed: 07/13/2024] Open
Abstract
High-polarity iridoids from Radix Scrophulariae (R. Scrophulariae) offer a range of benefits, including anti-inflammatory, antioxidant, antitumour, antibacterial, antiviral, and antiallergic effects. Although previous studies have indicated the potential of R. Scrophulariae for hyperthyroidism prevention and treatment, the specific active compounds involved and their mechanisms of action are not fully understood. This study explored the effects of high-polarity iridoid glycosides from R. Scrophulariae on hyperthyroidism induced in rats by levothyroxine sodium. The experimental design included a control group, a hyperthyroidism model group, and a group treated with iridoid glycosides. Serum triiodothyronine (T3) and thyroxine (T4) levels were quantified using an enzyme-linked immunosorbent assay (ELISA). Transcriptomic and proteomic analyses were applied to liver samples to identify differentially expressed genes and proteins. These analyses were complemented by trend analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. The effectiveness of key factors was further examined through molecular biology techniques. ELISA results indicated a notable increase in T3 and T4 in the hyperthyroid rats, which was significantly mitigated by treatment with iridoid glycosides. Transcriptomic analysis revealed 6 upregulated and 6 downregulated genes in the model group, showing marked improvement following treatment. Proteomic analysis revealed changes in 30 upregulated and 50 downregulated proteins, with improvements observed upon treatment. The PI3K-Akt signalling pathway was investigated through KEGG enrichment analysis. Molecular biology methods verified the upregulation of Spp1, Thbs1, PI3K, and Akt in the model group, which was reversed in the treatment group. This study revealed that highly polar iridoids from R. Scrophulariae can modulate the Spp1 gene and Thbs1 protein via the PI3K-Akt signalling pathway, suggesting a therapeutic benefit for hyperthyroidism and providing a basis for drug development targeting this condition.
Collapse
Affiliation(s)
- Ning Zhang
- The First Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, China
| | - Shumin Liu
- Institute of Traditional Medicine, Heilongjiang University of Chinese Medicine, Harbin, Heilongjiang, China
| | - Xu Lu
- Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, China
| | - Zihui Li
- Dalian University, Dalian, China
| | - Ling Li
- The First Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, China
| | - Tao Ye
- The First Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, China
| |
Collapse
|
2
|
Cheng KW, Shi J, Huang C, Tan HY, Ning Z, Lyu C, Xu Y, Mok HL, Zhai L, Xiang L, Qin H, Lin C, Zhu L, Bian Z. Integrated metabolomics and serum-feces pharmacochemistry-based network pharmacology to reveal the mechanisms of an herbal prescription against ulcerative colitis. Comput Biol Med 2024; 178:108775. [PMID: 38941901 DOI: 10.1016/j.compbiomed.2024.108775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 05/30/2024] [Accepted: 06/15/2024] [Indexed: 06/30/2024]
Abstract
BACKGROUND CDD-2103 is an herbal prescription used to treat ulcerative colitis (UC). This study aimed to uncover its mechanism by integrating metabolomics and serum-feces pharmacochemistry-based network pharmacology. METHODS A DSS-induced chronic colitis mice model was used to evaluate the anti-colitis effect of CDD-2103. Serum and feces metabolomics were conducted to identify differential metabolites and pathways. In the serum-feces pharmacochemistry study, biological samples were collected from rats treated with CDD-2103. Then, network pharmacology was utilized to predict the targets of the identified compounds. Critical genes were extracted through the above-integrated analysis. The interactions between targets, CDD-2103, and its compounds were validated through molecular docking, immunoblotting, and enzyme activity assays. RESULTS CDD-2103 alleviated ulcerous symptoms and colonic injuries in colitis mice. Metabolomics study identified differential metabolites associated with tryptophan, glycerophospholipid, and linoleic acid metabolisms. The serum-feces pharmacochemistry study revealed twenty-three compounds, which were subjected to network pharmacology analysis. Integration of these results identified three key targets (AHR, PLA2, and PTGS2). Molecular docking showed strong affinities between the compounds and targets. PTGS2 was identified as a hub gene targeted by most CDD-2103 compounds. Immunoblotting and enzyme activity assays provided further evidence that CDD-2103 alleviates UC, potentially through its inhibitory effect on cyclooxygenase-2 (COX-2, encoded by PTGS2), with alkaloids and curcuminoids speculated as crucial anti-inflammatory compounds. CONCLUSION This integrated strategy reveals the mechanism of CDD-2103 and provides insights for developing herbal medicine-based therapies for UC.
Collapse
Affiliation(s)
- Ka Wing Cheng
- Centre for Chinese Herbal Medicine Drug Development, Hong Kong Baptist University, Hong Kong SAR, China; School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, China
| | - Jingchun Shi
- Centre for Chinese Herbal Medicine Drug Development, Hong Kong Baptist University, Hong Kong SAR, China
| | - Chunhua Huang
- Centre for Chinese Herbal Medicine Drug Development, Hong Kong Baptist University, Hong Kong SAR, China; School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, China
| | - Hor Yue Tan
- Centre for Chinese Herbal Medicine Drug Development, Hong Kong Baptist University, Hong Kong SAR, China; School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, China
| | - Ziwan Ning
- Centre for Chinese Herbal Medicine Drug Development, Hong Kong Baptist University, Hong Kong SAR, China; School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, China
| | - Cheng Lyu
- Centre for Chinese Herbal Medicine Drug Development, Hong Kong Baptist University, Hong Kong SAR, China
| | - Yiqi Xu
- Centre for Chinese Herbal Medicine Drug Development, Hong Kong Baptist University, Hong Kong SAR, China
| | - Heung Lam Mok
- Centre for Chinese Herbal Medicine Drug Development, Hong Kong Baptist University, Hong Kong SAR, China
| | - Lixiang Zhai
- Centre for Chinese Herbal Medicine Drug Development, Hong Kong Baptist University, Hong Kong SAR, China; School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, China
| | - Li Xiang
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong SAR, China
| | - Hongyan Qin
- Centre for Chinese Herbal Medicine Drug Development, Hong Kong Baptist University, Hong Kong SAR, China; Department of Pharmacy, First Hospital of Lanzhou University, Lanzhou, China
| | - Chengyuan Lin
- Centre for Chinese Herbal Medicine Drug Development, Hong Kong Baptist University, Hong Kong SAR, China
| | - Lin Zhu
- Centre for Chinese Herbal Medicine Drug Development, Hong Kong Baptist University, Hong Kong SAR, China; School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, China.
| | - Zhaoxiang Bian
- Centre for Chinese Herbal Medicine Drug Development, Hong Kong Baptist University, Hong Kong SAR, China; School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, China.
| |
Collapse
|
3
|
Chompunud Na Ayudhya C, Graidist P, Tipmanee V. Role of CSF1R 550th-tryptophan in kusunokinin and CSF1R inhibitor binding and ligand-induced structural effect. Sci Rep 2024; 14:12531. [PMID: 38822100 PMCID: PMC11143223 DOI: 10.1038/s41598-024-63505-x] [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: 03/05/2024] [Accepted: 05/29/2024] [Indexed: 06/02/2024] Open
Abstract
Binding affinity is an important factor in drug design to improve drug-target selectivity and specificity. In this study, in silico techniques based on molecular docking followed by molecular dynamics (MD) simulations were utilized to identify the key residue(s) for CSF1R binding affinity among 14 pan-tyrosine kinase inhibitors and 15 CSF1R-specific inhibitors. We found tryptophan at position 550 (W550) on the CSF1R binding site interacted with the inhibitors' aromatic ring in a π-π way that made the ligands better at binding. Upon W550-Alanine substitution (W550A), the binding affinity of trans-(-)-kusunokinin and imatinib to CSF1R was significantly decreased. However, in terms of structural features, W550 did not significantly affect overall CSF1R structure, but provided destabilizing effect upon mutation. The W550A also did not either cause ligand to change its binding site or conformational changes due to ligand binding. As a result of our findings, the π-π interaction with W550's aromatic ring could be still the choice for increasing binding affinity to CSF1R. Nevertheless, our study showed that the increasing binding to W550 of the design ligand may not ensure CSF1R specificity and inhibition since W550-ligand bound state did not induce significantly conformational change into inactive state.
Collapse
Affiliation(s)
- Chompunud Chompunud Na Ayudhya
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Hat Yai, 90100, Songkhla, Thailand
| | - Potchanapond Graidist
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Hat Yai, 90100, Songkhla, Thailand
- Bioactivity Testing Center, Faculty of Medicine, Prince of Songkla University, Hat Yai, 90100, Songkhla, Thailand
| | - Varomyalin Tipmanee
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Hat Yai, 90100, Songkhla, Thailand.
- Bioactivity Testing Center, Faculty of Medicine, Prince of Songkla University, Hat Yai, 90100, Songkhla, Thailand.
| |
Collapse
|
4
|
Islam MR, Islam Sovon MS, Amena U, Rahman M, Hosen ME, Kumer A, Bourhia M, Bin Jardan YA, Ibenmoussa S, Wondmie GF. Ligand-based drug design against Herpes Simplex Virus-1 capsid protein by modification of limonene through in silico approaches. Sci Rep 2024; 14:9828. [PMID: 38684729 PMCID: PMC11058824 DOI: 10.1038/s41598-024-59577-4] [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: 01/24/2024] [Accepted: 04/12/2024] [Indexed: 05/02/2024] Open
Abstract
The pharmacological effects of limonene, especially their derivatives, are currently at the forefront of research for drug development and discovery as well and structure-based drug design using huge chemical libraries are already widespread in the early stages of therapeutic and drug development. Here, various limonene derivatives are studied computationally for their potential utilization against the capsid protein of Herpes Simplex Virus-1. Firstly, limonene derivatives were designed by structural modification followed by conducting a molecular docking experiment against the capsid protein of Herpes Simplex Virus-1. In this research, the obtained molecular docking score exhibited better efficiency against the capsid protein of Herpes Simplex Virus-1 and hence we conducted further in silico investigation including molecular dynamic simulation, quantum calculation, and ADMET analysis. Molecular docking experiment has documented that Ligands 02 and 03 had much better binding affinities (- 7.4 kcal/mol and - 7.1 kcal/mol) to capsid protein of Herpes Simplex Virus-1 than Standard Acyclovir (- 6.5 kcal/mol). Upon further investigation, the binding affinities of primary limonene were observed to be slightly poor. But including the various functional groups also increases the affinities and capacity to prevent viral infection of the capsid protein of Herpes Simplex Virus-1. Then, the molecular dynamic simulation confirmed that the mentioned ligands might be stable during the formation of drug-protein complexes. Finally, the analysis of ADMET was essential in establishing them as safe and human-useable prospective chemicals. According to the present findings, limonene derivatives might be a promising candidate against the capsid protein of Herpes Simplex Virus-1 which ultimately inhibits Herpes Simplex Virus-induced encephalitis that causes interventions in brain inflammation. Our findings suggested further experimental screening to determine their practical value and utility.
Collapse
Affiliation(s)
- Md Rezaul Islam
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka, Bangladesh, 1207
| | | | - Ummy Amena
- Department of Pharmacy, Faculty of Life & Earth Sciences, Jagannath University, Dhaka, Bangladesh
| | - Miadur Rahman
- Department of Pharmaceutical Sciences, North South University, Dhaka, 1219, Bangladesh
| | - Md Eram Hosen
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, 6205, Bangladesh
| | - Ajoy Kumer
- Department of Chemistry, College of Arts and Sciences, International University of Business Agriculture and Technology (IUBAT), Dhaka, 1216, Bangladesh
- Center for Global Health Research, Saveetha Institute of Medical and Technical Sciences in Saveetha Medical College and Hospital, Chennai, India
| | - Mohammed Bourhia
- Laboratory of Biotechnology and Natural Resources Valorization, Faculty of Sciences, Ibn Zohr University, 80060, Agadir, Morocco.
| | - Yousef A Bin Jardan
- Department of Pharmaceutics, College of Pharmacy, King Saud University, P.O. Box 11451, Riyadh, Saudi Arabia
| | - Samir Ibenmoussa
- Laboratory of Therapeutic and Organic Chemistry, Faculty of Pharmacy, University of Montpellier, 34000, Montpellier, France
| | | |
Collapse
|
5
|
Sun Y, Chen L, Zhao B, Wang R. Molecular docking and molecular dynamics simulation decoding molecular mechanism of EDCs binding to hERRγ. J Mol Model 2024; 30:127. [PMID: 38594491 DOI: 10.1007/s00894-024-05926-z] [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: 10/17/2023] [Accepted: 04/03/2024] [Indexed: 04/11/2024]
Abstract
CONTEXT Human estrogen-related receptor γ (hERRγ) is a key protein involved in various endocrines and metabolic signaling. Numerous environmental endocrine-disrupting chemicals (EDCs) can impact related physiological activities through receptor signaling pathways. Focused on hERRγ with 4-isopropylphenol, bisphenol-F (BPF), and BP(2,2)(Un) complexes, we executed molecular docking and multiple molecular dynamics (MD) simulations along with molecular mechanics/Poisson-Boltzmann surface area (MM-PBSA) and solvation interaction energy (SIE) calculation to study the detailed dynamical structural characteristics and interactions between them. Molecular docking showed that hydrogen bonds and hydrophobic interactions were the prime interactions to keep the stability of BPF-hERRγ and hERRγ-BP(2,2)(Un) complexes. Through MD simulations, we observed that all complexes reach equilibrium during the initial 50 ns of simulation, but these three EDCs lead to local structure changes in hERRγ. Energy results further identified key residues L268, V313, L345, and F435 around the binding pockets through CH-π, π-π, and hydrogen bonds interactions play an important stabilizing role in the recognition with EDCs. And most noticeable of all, hydrophobic methoxide groups in BP(2,2)(Un) is useful for decreasing the binding ability between EDCs and hERRγ. These results may contribute to evaluate latent diseases associated with EDCs exposure at the micro level and find potential substitutes. METHOD Autodock4.2 was used to conduct the molecular docking, sietraj program was performed to calculate the energy, and VMD software was used to visualize the structure. Amber18 was conducted to perform the MD simulation and other analyses.
Collapse
Affiliation(s)
- Ying Sun
- College of Chemistry and Chemical Engineering, Qiqihar University, Qiqihar, 161006, China
| | - Lin Chen
- College of Chemistry and Chemical Engineering, Qiqihar University, Qiqihar, 161006, China.
| | - Bing Zhao
- College of Chemistry and Chemical Engineering, Qiqihar University, Qiqihar, 161006, China
- Heilongjiang Provincial Key Laboratory of Surface Active Agent and Auxiliary, Qiqihar University, Qiqihar, 161006, China
| | - Ruige Wang
- College of Chemistry and Chemical Engineering, Qiqihar University, Qiqihar, 161006, China.
| |
Collapse
|
6
|
Qassim HM, Seyedalipour B, Baziyar P, Ahamady-Asbchin S. Polyphenolic flavonoid compounds act as the inhibitory potential of aggregation process: Implications for the prevention and therapeutics against FALS-associated D101G SOD1 mutant. Comput Biol Chem 2023; 107:107967. [PMID: 37844376 DOI: 10.1016/j.compbiolchem.2023.107967] [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: 06/30/2023] [Revised: 09/30/2023] [Accepted: 10/04/2023] [Indexed: 10/18/2023]
Abstract
Aggregation of proteins is a biological phenomenon caused by misfolded proteins. Human superoxide dismutase (hSOD1) misfolding and aggregation underlie the neurological illness amyotrophic lateral sclerosis (ALS). The most significant contributing factor to ALS is genetic point mutations in SOD1. particularly, D101G mutant is the most harmful because it significantly reduces the life expectancy of patients. Subsequently, the use of natural polyphenolic flavonoids is strongly recommended to reduce the amyloidogenic behavior of protopathic proteins. In this study, using computational parameters such as protein-ligand interaction and molecular dynamics (MD) simulation analyses, we are trying to identify a pharmacodynamically promising flavonoid compound that can effectively inhibit the pathogenic behavior of the D101G mutant. Epigallocatechin-gallate (EGCG), Hesperidin, Isorhamnetin, and Diosmetin were identified as potential leads in a preliminary screening of flavonoids to anti-amyloid action. The results of MD showed that the binding of flavonoids to D101G mutant caused changes in stability, hydrophobicity of protein, and flexibility, as well as significantly led to the restoration of lost hydrogen bonds. Secondary structure analysis showed that protein destabilization and the increased propensity of β-sheet caused by the mutation were restored to the wild-type state upon binding of flavonoids. Besides, to differentiate aggregation, we elucidated alterations in the free energy landscape (FEL) and dynamic cross-correlation matrix (DCCM) of WT-SOD1 and mutant (unbound /bound) states. Among flavonoids, Epigallocatechin-gallate and Hesperidin had the most therapeutic efficacy against the D101G mutant. Therefore, Epigallocatechin-gallate and Hesperidin promise considerable therapeutic potential to develop highly effective inhibitors in reducing fatal and irreversible ALS.
Collapse
Affiliation(s)
- Hussein Maitham Qassim
- Department of Molecular and Cell Biology, Faculty of Basic Science, University of Mazandaran, Babolsar, Iran
| | - Bagher Seyedalipour
- Department of Molecular and Cell Biology, Faculty of Basic Science, University of Mazandaran, Babolsar, Iran.
| | - Payam Baziyar
- Department of Molecular and Cell Biology, Faculty of Basic Science, University of Mazandaran, Babolsar, Iran
| | - Salman Ahamady-Asbchin
- Department of Microbiology, Faculty of Basic Science, University of Mazandaran, Babolsar, Iran
| |
Collapse
|
7
|
Noorbakhsh Varnosfaderani SM, Sadat Haeri M, Arian AS, Yousefi Rad A, Yazdanpour M, Mojahedian F, Yaghoubzad-Maleki M, Zalpoor H, Baziyar P, Nabi-Afjadi M. Fighting against amyotrophic lateral sclerosis (ALS) with flavonoids: a computational approach to inhibit superoxide dismutase (SOD1) mutant aggregation. J Biomol Struct Dyn 2023:1-18. [PMID: 37975411 DOI: 10.1080/07391102.2023.2281641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 11/04/2023] [Indexed: 11/19/2023]
Abstract
Protein aggregation is a biological process that occurs when proteins misfold. Misfolding and aggregation of human superoxide dismutase (hSOD1) cause a neurodegenerative disease called amyotrophic lateral sclerosis (ALS). Among the mutations occurring, targeting the E21K mutation could be a good choice to understand the pathological mechanism of SOD1 in ALS, whereof it significantly reduces life hopefulness in patients. Naturally occurring polyphenolic flavonoids have been suggested as a way to alleviate the amyloidogenic behavior of proteins. In this study, computational tools were used to identify promising flavonoid compounds that effectively inhibit the pathogenic behavior of the E21K mutant. Initial screening identified Pelargonidin, Curcumin, and Silybin as promising leads. Molecular dynamics (MD) simulations showed that the binding of flavonoids to the mutated SOD1 caused changes in the protein stability, hydrophobicity, flexibility, and restoration of lost hydrogen bonds. Secondary structure analysis indicated that the protein destabilization and the increased propensity of β-sheet caused by the mutation were restored to the wild-type state upon binding of flavonoids. Free energy landscape (FEL) analysis was also used to differentiate aggregation, and results showed that Silybin followed by Pelargonidin had the most therapeutic efficacy against the E21K mutant SOD1. Therefore, these flavonoids hold great potential as highly effective inhibitors in mitigating ALS's fatal and insuperable effects.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
| | - Melika Sadat Haeri
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Ali Sam Arian
- School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ali Yousefi Rad
- Department of Biochemistry, Falavarjan Branch, Islamic Azad University, Isfahan, Iran
| | - Mohammad Yazdanpour
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Fatemeh Mojahedian
- Department of Biochemistry, Faculty of Biological Sciences, University of Tarbiat Modares, Tehran, Iran
| | - Mohammad Yaghoubzad-Maleki
- Division of Biochemistry, Department of Animal Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| | - Hamidreza Zalpoor
- Shiraz Neuroscience Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
- Network of Immunity in Infection, Malignancy & Autoimmunity (NIIMA), Universal Scientific Education & Research Network (USERN), Tehran, Iran
| | - Payam Baziyar
- Department of Molecular and Cell Biology, Faculty of Basic Sciences, University of Mazandaran, Babolsar, Iran
| | - Mohsen Nabi-Afjadi
- Department of Biochemistry, Faculty of Biological Sciences, University of Tarbiat Modares, Tehran, Iran
| |
Collapse
|
8
|
Hou Z, Yang X, Jiang L, Song L, Li Y, Li D, Che Y, Zhang X, Sun Z, Shang H, Chen J. Active components and molecular mechanisms of Sagacious Confucius' Pillow Elixir to treat cognitive impairment based on systems pharmacology. Aging (Albany NY) 2023; 15:7278-7307. [PMID: 37517091 PMCID: PMC10415554 DOI: 10.18632/aging.204912] [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: 12/28/2021] [Accepted: 05/30/2023] [Indexed: 08/01/2023]
Abstract
BACKGROUND Sagacious Confucius' Pillow Elixir (SCPE) is a common clinical prescription to treat cognitive impairment (CI) in East Asia. OBJECTIVE To predict the active components of SCPE, identify the associated signaling pathway, and explore the molecular mechanism using systems pharmacology and an animal study. METHODS Systems pharmacology and Python programming language-based molecular docking were used to select and analyze the active components and targets. Senescence-accelerated prone 8 mice were used as a CI model. The molecular mechanism was evaluated using the water maze test, neuropathological observation, cerebrospinal fluid microdialysis, and Western blotting. RESULTS Thirty active components were revealed by screening relevant databases and performing topological analysis. Additionally, 376 differentially expressed genes for CI were identified. Pathway enrichment analysis, protein-protein interaction (PPI) network analysis and molecular docking indicated that SCPE played a crucial role in modulating the PI3K/Akt/mTOR signaling pathway, and 23 SCPE components interacted with it. In the CI model, SCPE improved cognitive function, increased the levels of the neurotransmitter 5-hydroxytryptamine (5-HT) and metabolite 5-hydroxyindole acetic acid (5-HIAA), ameliorated pathological damage and regulated the PI3K/AKT/mTOR signaling pathway. SCPE increased the LC3-II/LC3-I, p-PI3K p85/PI3K p85, p-AKT/AKT, and p-mTOR/mTOR protein expression ratios and inhibited P62 expression in the hippocampal tissue of the CI model. CONCLUSION Our study revealed that 23 active SCPE components improve CI by increasing the levels of the neurotransmitter 5-HT and metabolite 5-HIAA, suppressing pathological injury and regulating the PI3K/Akt/mTOR signaling pathway to improve cognitive function.
Collapse
Affiliation(s)
- Zhitao Hou
- College of Basic Medical and Sciences, Heilongjiang University of Chinese Medicine, Harbin, Heilongjiang 150040, China
- Key Laboratory of Chinese Internal Medicine of the Ministry of Education, Dongzhimen Hospital Affiliated with Beijing University of Chinese Medicine, Beijing 100700, China
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Center for New Drug Research and Development, Harbin No. 4 Traditional Chinese Medicine Factory Co. Ltd., Harbin, Heilongjiang 150025, China
- Center for New Drug Research and Development, Heilongjiang Deshun Chang Chinese Herbal Medicine Co. Ltd., Harbin, Heilongjiang 150025, China
| | - Xinyu Yang
- Key Laboratory of Chinese Internal Medicine of the Ministry of Education, Dongzhimen Hospital Affiliated with Beijing University of Chinese Medicine, Beijing 100700, China
- Fangshan Hospital of Beijing University of Chinese Medicine, Beijing 102400, China
| | - Ling Jiang
- College of Basic Medical and Sciences, Heilongjiang University of Chinese Medicine, Harbin, Heilongjiang 150040, China
| | - Liying Song
- Department of Clinical Medicine, Heilongjiang Nursing College, Harbin, Heilongjiang 150086, China
| | - Yang Li
- College of Basic Medical and Sciences, Heilongjiang University of Chinese Medicine, Harbin, Heilongjiang 150040, China
| | - Dongdong Li
- College of Basic Medical and Sciences, Heilongjiang University of Chinese Medicine, Harbin, Heilongjiang 150040, China
| | - Yanning Che
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Center for New Drug Research and Development, Harbin No. 4 Traditional Chinese Medicine Factory Co. Ltd., Harbin, Heilongjiang 150025, China
| | - Xiuling Zhang
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Center for New Drug Research and Development, Harbin No. 4 Traditional Chinese Medicine Factory Co. Ltd., Harbin, Heilongjiang 150025, China
| | - Zhongren Sun
- College of Basic Medical and Sciences, Heilongjiang University of Chinese Medicine, Harbin, Heilongjiang 150040, China
| | - Hongcai Shang
- Key Laboratory of Chinese Internal Medicine of the Ministry of Education, Dongzhimen Hospital Affiliated with Beijing University of Chinese Medicine, Beijing 100700, China
| | - Jing Chen
- College of Basic Medical and Sciences, Heilongjiang University of Chinese Medicine, Harbin, Heilongjiang 150040, China
| |
Collapse
|
9
|
Singh M, Haque MA, Tikhomirov AS, Shchekotikhin AE, Das U, Kaur P. Computational and Biophysical Characterization of Heterocyclic Derivatives of Anthraquinone against Human Aurora Kinase A. ACS OMEGA 2022; 7:39603-39618. [PMID: 36385832 PMCID: PMC9647706 DOI: 10.1021/acsomega.2c00740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 10/07/2022] [Indexed: 06/16/2023]
Abstract
Human Aurora kinase A (AurA) has recently garnered the attention of researchers worldwide as a promising effective mitotic drug target for its involvement in cancer and related inflammatory anomalies. This study has explored the binding affinity of newly identified heteroarene-fused anthraquinone derivatives against AurA. Molecular docking analyses showed that all the heteroanthraquinone compounds bind to AurA with different affinities. Molecular dynamics simulation studies revealed that the compounds maintained relatively stable binding modes in the active site pocket while inducing minimal conformational changes in the AurA structure, interacting with key residues through several noncovalent interactions, including hydrogen bonds. Fluorescence spectroscopy and biolayer interferometry binding assays with synthesized compounds against recombinantly expressed AurA further verified their binding efficacy. Naphthoisatine 3 proved to be the best binder, with compounds anthraimidazole 5 and anthrathiophene 2 showing comparable results. Overall, this study indicates decent binding of heterocyclic derivatives of anthraquinone with the target AurA, which can further be assessed by performing enzymatic assays and cellular studies. The studies also highlight the applicability of the heteroarene-fused anthraquinone scaffold to construct selective and potent inhibitors of Aurora kinases after necessary structural modifications for the development of new anticancer drugs.
Collapse
Affiliation(s)
- Mandeep Singh
- Department
of Biophysics, All India Institute of Medical
Sciences, New Delhi, Delhi110029, India
| | - Md. Anzarul Haque
- Department
of Biophysics, All India Institute of Medical
Sciences, New Delhi, Delhi110029, India
| | | | | | - Uddipan Das
- Department
of Biophysics, All India Institute of Medical
Sciences, New Delhi, Delhi110029, India
| | - Punit Kaur
- Department
of Biophysics, All India Institute of Medical
Sciences, New Delhi, Delhi110029, India
| |
Collapse
|
10
|
Expression patterns and therapeutic implications of CDK4 across multiple carcinomas: a molecular docking and MD simulation study. Med Oncol 2022; 39:158. [DOI: 10.1007/s12032-022-01779-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 06/20/2022] [Indexed: 10/16/2022]
|
11
|
Characterizing aripiprazole and its ester derivatives, lauroxil and cavoxil, in interaction with dopamine D2 receptor: Molecular docking and dynamics simulations with physicochemical appraisals. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
12
|
Srivastava M, Mittal L, Kumari A, Agrahari AK, Singh M, Mathur R, Asthana S. Characterizing (un)binding mechanism of USP7 inhibitors to unravel the cause of enhanced binding potencies at allosteric checkpoint. Protein Sci 2022; 31:e4398. [PMID: 36629250 PMCID: PMC9835771 DOI: 10.1002/pro.4398] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 07/06/2022] [Accepted: 07/11/2022] [Indexed: 01/21/2023]
Abstract
The ability to predict the intricate mechanistic behavior of ligands and associated structural determinants during protein-ligand (un)binding is of great practical importance in drug discovery. Ubiquitin specific protease-7 (USP7) is a newly emerging attractive cancer therapeutic target with bound allosteric inhibitors. However, none of the inhibitors have reached clinical trials, allowing opportunities to examine every aspect of allosteric modulation. The crystallographic insights reveal that these inhibitors have common properties such as chemical scaffolds, binding site and interaction fingerprinting. However, they still possess a broader range of binding potencies, ranging from 22 nM to 1,300 nM. Hence, it becomes more critical to decipher the structural determinants guiding the enhanced binding potency of the inhibitors. In this regard, we elucidated the atomic-level insights from both interacting partners, that is, protein-ligand perspective, and established the structure-activity link between USP7 inhibitors by using classical and advanced molecular dynamics simulations combined with linear interaction energy and molecular mechanics-Poisson Boltzmann surface area. We revealed the inhibitor potency differences by examining the contributions of chemical moieties and USP7 residues, the involvement of water-mediated interactions, and the thermodynamic landscape alterations. Additionally, the dissociation profiles aided in the establishment of a correlation between experimental potencies and structural determinants. Our study demonstrates the critical role of blocking loop 1 in allosteric inhibition and enhanced binding affinity. Comprehensively, our findings provide a constructive expansion of experimental outcomes and show the basis for varying binding potency using in-silico approaches. We expect this atomistic approach to be useful for effective drug design.
Collapse
Affiliation(s)
- Mitul Srivastava
- Translational Health Science and Technology Institute (THSTI)FaridabadIndia
- Delhi Pharmaceutical Sciences and Research University (DPSRU)New DelhiIndia
| | - Lovika Mittal
- Translational Health Science and Technology Institute (THSTI)FaridabadIndia
| | - Anita Kumari
- Translational Health Science and Technology Institute (THSTI)FaridabadIndia
| | | | - Mrityunjay Singh
- Translational Health Science and Technology Institute (THSTI)FaridabadIndia
| | - Rajani Mathur
- Delhi Institute of Pharmaceutical Sciences and Research (DIPSAR)New DelhiIndia
| | - Shailendra Asthana
- Translational Health Science and Technology Institute (THSTI)FaridabadIndia
| |
Collapse
|
13
|
Dean E, Kumar V, McConnell A, Pagnoncelli IB, Wu C. To probe the activation mechanism of the Delta opioid receptor by an agonist ADL5859 started from inactive conformation using molecular dynamic simulations. J Biomol Struct Dyn 2022:1-18. [PMID: 35938617 DOI: 10.1080/07391102.2022.2107074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Abstract
The δ-opioid receptor (DOR) is a critical pharmaceutical target for pain management. Although the high-resolution crystal structures of the DOR with both agonist and antagonist have recently been solved, the activation mechanism remains to be elusive. In this study, a DOR agonist ADL5859 was docked to the inactive DOR and multiple microsecond molecular dynamic (MD) simulations were conducted to probe the activation mechanism. While the receptor with the crystal ligand (i.e. antagonist naltrindole) maintained the inactive conformation in all three independent simulations, the receptor with ADL5859 was adopting toward the active conformation in three out of six independent simulations. Major conformational differences were located on transmembrane (TM) 5 and 6, as well as intracellular loop 3. Compared to naltrindole, ADL5859 exhibited high conformational flexibility and strong interaction with the transmission switch. The putative key residues (W274, D95, V267, L139, V263, M142, T260, R146, R258 and others) involving in the activation pathway were identified through the conventional molecular switch analysis and a pairwise distance analysis, which provides a short list for experimental mutagenesis study. These insights will facilitate further development of therapeutic agents targeting the DOR.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Emily Dean
- College of Science and Mathematics, Rowan University, Glassboro, NJ, USA
| | - Vikash Kumar
- Complex Systems Division, Beijing Computational Science Research Center, Beijing, China
| | - Ashleigh McConnell
- College of Science and Mathematics, Rowan University, Glassboro, NJ, USA
| | | | - Chun Wu
- College of Science and Mathematics, Rowan University, Glassboro, NJ, USA
| |
Collapse
|
14
|
Yang J, Zhao Y, Yang B. Different binding modes of human centrin with peptides of Kar1p, Rad4 and Sfi1. J Photochem Photobiol A Chem 2022. [DOI: 10.1016/j.jphotochem.2022.113940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
15
|
Comparative study of the unbinding process of some HTLV-1 protease inhibitors using unbiased molecular dynamics simulations. PLoS One 2022; 17:e0263200. [PMID: 35834445 PMCID: PMC9282663 DOI: 10.1371/journal.pone.0263200] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Accepted: 06/28/2022] [Indexed: 12/15/2022] Open
Abstract
The HTLV-1 protease is one of the major antiviral targets to overwhelm this virus. Several research groups have developed protease inhibitors, but none has been successful. In this regard, developing new HTLV-1 protease inhibitors to fix the defects in previous inhibitors may overcome the lack of curative treatment for this oncovirus. Thus, we decided to study the unbinding pathways of the most potent (compound 10, PDB ID 4YDF, Ki = 15 nM) and one of the weakest (compound 9, PDB ID 4YDG, Ki = 7900 nM) protease inhibitors, which are very structurally similar. We conducted 12 successful short and long simulations (totaling 14.8 μs) to unbind the compounds from two monoprotonated (mp) forms of protease using the Supervised Molecular Dynamics (SuMD) without applying any biasing force. The results revealed that Asp32 or Asp32′ in the two forms of mp state similarly exert powerful effects on maintaining both potent and weak inhibitors in the binding pocket of HTLV-1 protease. In the potent inhibitor’s unbinding process, His66′ was a great supporter that was absent in the weak inhibitor’s unbinding pathway. In contrast, in the weak inhibitor’s unbinding process, Trp98/Trp98′ by pi-pi stacking interactions were unfavorable for the stability of the inhibitor in the binding site. In our opinion, these results will assist in designing more potent and effective inhibitors for the HTLV-1 protease.
Collapse
|
16
|
Verma VV, Bhargava L, Sajid M, Kumar A, Singh H, Bharadwaj M. Structure-based study to identify alkaloids as promising cytochrome P450 (CYP1A1) inhibitors: An in silico approach using virtual screening, molecular dynamic simulations, and binding free energy calculation. J Cell Biochem 2022; 123:1422-1439. [PMID: 35765708 DOI: 10.1002/jcb.30302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 06/16/2022] [Accepted: 06/20/2022] [Indexed: 11/10/2022]
Abstract
Carcinogens present in smokeless tobacco (SLT) like tobacco-specific nitrosamines can be metabolized by the cytochrome P450 (CYP450) enzyme. Functionally, the CYP450 enzyme resides in a heme pigment to perform the catalytic activity. The CYP1A1 is one of the main extrahepatic CYP450 enzymes known to detoxify toxic substances and activate carcinogens. The CYP1A1 inhibition by potential inhibitors reduce the chance of oral cancer. The current study aimed to explore more about the inhibitor binding site and identification of lead alkaloids, that could work as putative inhibitors against target CYP1A1. In respect, we have performed docking studies, virtual screening of alkaloids, and natural product libraries against CYP1A1 followed by molecular dynamic simulations and binding free energy calculations. Docking studies of tobacco-specific nitrosamine (TSNA) products and their similar carcinogen analogs revealed that the heme group is bound to the floor of the bowl-shaped cavity whereas carcinogens are bound to the roof of the rounded shape cavity. Furthermore, virtual screening and binding free energy calculations revealed Tomatidine as a putative inhibitor against CYP1A1. On the basis of altogether outcomes of the current study, we have concluded that the addition of lead-hit alkaloid Tomatidine and others in SLT products may be working as a supplement that could be able to reduce the expression of human CYP1A1 and suppresses carcinogenic by-products formations.
Collapse
Affiliation(s)
- Ved Vrat Verma
- Division of Molecular Genetics and Biochemistry, Molecular Biology Group, ICMR-National Institute of Cancer Prevention and Research, Noida, India
| | - Lalit Bhargava
- Amity Institute of Biotechnology, Amity University, Noida, India
| | - Mohammad Sajid
- Division of Molecular Genetics and Biochemistry, Molecular Biology Group, ICMR-National Institute of Cancer Prevention and Research, Noida, India
| | - Amit Kumar
- Division of Biomedical Informatics, ICMR-AIIMS Computational Genomics Centre, Indian Council of Medical Research (ICMR), New Delhi, India
| | - Harpreet Singh
- Division of Biomedical Informatics, ICMR-AIIMS Computational Genomics Centre, Indian Council of Medical Research (ICMR), New Delhi, India
| | - Mausumi Bharadwaj
- Division of Molecular Genetics and Biochemistry, Molecular Biology Group, ICMR-National Institute of Cancer Prevention and Research, Noida, India
| |
Collapse
|
17
|
Srinivasan E, Chandrasekhar G, Rajasekaran R. Probing the polyphenolic flavonoid, morin as a highly efficacious inhibitor against amyloid(A4V) mutant SOD1 in fatal amyotrophic lateral sclerosis. Arch Biochem Biophys 2022; 727:109318. [PMID: 35690129 DOI: 10.1016/j.abb.2022.109318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 05/19/2022] [Accepted: 06/04/2022] [Indexed: 11/02/2022]
Abstract
Deposition of misfolded protein aggregates in key areas of human brain is the quintessential trait of various pertinent neurodegenerative disorders including amyotrophic lateral sclerosis (ALS). Genetic point mutations in Cu/Zn superoxide dismutase (SOD1) are found to be the most important contributing factor behind familial ALS. Especially, single nucleotide polymorphism (SNP) A4V is the most nocuous since it substantially decreases life expectancy of patients. Besides, the use of naturally occurring polyphenolic flavonoids is profoundly being advocated for palliating amyloidogenic behavior of proteopathic proteins. In the present analysis, through proficient computational tools, we have attempted to ascertain a pharmacodynamically promising flavonoid compound that effectively curbs the pathogenic behavior of A4V SOD1 mutant. Initial screening of flavonoids that exhibit potency against amyloids identified morin, myricetin and epigallocatechin gallate as promising leads. Further, with the help of feasible and yet adept protein-ligand interaction studies and stalwart molecular simulation analyses, we were able to observe that aforementioned flavonoids were able to considerably divert mutant A4V SOD1 from its distinct pathogenic behavior. Among which, morin showed the most curative potential against A4V SOD1. Therefore, morin holds a great therapeutic potential in contriving highly efficacious inhibitors in mitigating fatal and insuperable ALS.
Collapse
Affiliation(s)
- E Srinivasan
- Quantitative Biology Lab, Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology (VIT, Deemed to be University), Vellore, Tamil Nadu, 632014, India; Department of Bioinformatics, Saveetha School of Engineering, SIMATS, Chennai, Tamil Nadu, India
| | - G Chandrasekhar
- Quantitative Biology Lab, Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology (VIT, Deemed to be University), Vellore, Tamil Nadu, 632014, India
| | - R Rajasekaran
- Quantitative Biology Lab, Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology (VIT, Deemed to be University), Vellore, Tamil Nadu, 632014, India.
| |
Collapse
|
18
|
Chen GY, Liu XY, Luo J, Yu XB, Liu Y, Tao QW. Integrating Network Pharmacology and Experimental Validation to Explore the Key Mechanism of Gubitong Recipe in the Treatment of Osteoarthritis. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2022; 2022:7858925. [PMID: 35720033 PMCID: PMC9200584 DOI: 10.1155/2022/7858925] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 04/25/2022] [Accepted: 05/17/2022] [Indexed: 02/06/2023]
Abstract
Background Gubitong Recipe (GBT) is a prescription based on the Traditional Chinese Medicine (TCM) theory of tonifying the kidney yang and strengthening the bone. A previous multicentral randomized clinical trial has shown that GBT can effectively relieve joint pain and improve quality of life with a high safety in treating osteoarthritis (OA). This study is aimed at elucidating the active compounds, potential targets, and mechanisms of GBT for treating OA. Method The network pharmacology method was used to predict the key active compounds, targets, and mechanisms of GBT in treating OA. An OA rat model was established with Hulth surgery, and the pathological changes of articular cartilage were observed to evaluate the effects of GBT. Chondrocytes were stimulated with LPS to establish in vitro models, and key targets and mechanisms predicted by network pharmacology were verified via qRT-PCR, ELISA, western blot, and immunofluorescence. The Contribution Index Model and molecular docking were used to determine the key active compounds of GBT and the major nodes affecting predicted pathways. Result A total of 500 compounds were acquired from related databases, where 87 active compounds and their 254 corresponding targets were identified. 2979 OA-related genes were collected from three databases, 150 of which were GBT-regulating OA genes. The compound-target network weight analysis and PPI results showed that IL-6 and PGE2 are key targets of GBT in treating OA. KEGG results showed that PI3K/AKT, Toll-like receptor, NFκB, TNF, and HIF-1 are the key signaling pathways. An in vivo experiment showed that GBT could effectively suppress cartilage degradation of OA rats. In vitro experiments demonstrated that GBT can inhibit the key targets of KEGG-related pathways. Molecular-docking results suggested that luteolin, licochalcone A, and β-carotene were key targets of GBT, and the mechanisms may be associated with the NFκB signaling pathway. Blockage experiments showed that the NFκB pathway is the key pathway of GBT in treating OA. Conclusion This study verified that GBT can effectively protect articular cartilage through multitarget and multipathway, and its inhibitory effect on the NFκB pathway is the most key mechanism in treating OA.
Collapse
Affiliation(s)
- Guang-yao Chen
- Beijing University of Chinese Medicine, Beijing 100029, China
| | - Xiao-yu Liu
- Beijing University of Chinese Medicine, Beijing 100029, China
| | - Jing Luo
- Department of TCM Rheumatology, China-Japan Friendship Hospital, Beijing 100029, China
- Beijing Key Lab for Immune-Mediated Inflammatory Diseases, China-Japan Friendship Hospital, Beijing 100029, China
| | - Xin-bo Yu
- Beijing University of Chinese Medicine, Beijing 100029, China
- Department of TCM Rheumatology, China-Japan Friendship Hospital, Beijing 100029, China
| | - Yi Liu
- Beijing University of Chinese Medicine, Beijing 100029, China
| | - Qing-wen Tao
- Department of TCM Rheumatology, China-Japan Friendship Hospital, Beijing 100029, China
- Beijing Key Lab for Immune-Mediated Inflammatory Diseases, China-Japan Friendship Hospital, Beijing 100029, China
| |
Collapse
|
19
|
Antiviral Effect of Polyphenolic Substances in Geranium wilfordii Maxim against HSV-2 Infection Using in vitro and in silico Approaches. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2022; 2022:7953728. [PMID: 35646147 PMCID: PMC9132656 DOI: 10.1155/2022/7953728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 04/09/2022] [Accepted: 04/20/2022] [Indexed: 11/18/2022]
Abstract
Background Herpes simplex virus type 2 (HSV-2) infestation was the most widespread STD (sexually transmitted diseases) among humans and was the leading cause of infectious recurrent genital herpes. Existing therapies against HSV-2 did incompletely restrain the comeback of activated HSV-2 infestation. Geranium wilfordii Maxim had long been used as traditional Chinese medicine for treating the diseases owing to its anti-inflammatory and antiviral effects. Herein, the study was designed to investigate the antiviral activity of G.wilfordii and its potential effect in regulating the host's immune response. Methods To identify the stage of infection at which the compounds inhibited HSV-2, we performed virucidal, therapeutic, and prophylactic assays. The antiviral efficacy was evaluated by the analysis of viral components HSV-2 gD and VP16. The antiviral activities of these compounds were also evaluated by phenotypic analysis, such as cell proliferation and apoptosis. Molecular docking studies on candidate compounds were done to indicate binding interactions between the compounds and adopted compound targets. Results Quercetin, corilagin, and geraniin inhibited the replication of HSV-2, with geraniin showing greater TI. The obtained IC50 value of quercetin was 204.7 μM and TI (IC50/EC50) was 5.1, whereas the obtained IC50 value of corilagin was 118.0 μg/ml and TI was 4.05. Geraniin exhibited prominent antiviral activity with an IC50 of 212.4 μM and an EC50 of 18.37 μM, resulting in a therapeutic index (TI) of 11.56. Geraniin showed important in vitro virucidal activity through blocking viral attachment. Compared with the virus group, the apoptosis rates in quercetin-, corilagin-, and geraniin-treated groups were significantly decreased (p < 0.001).The expressions at the transcription genes of virus own replication key factors (including HSV-2 gD and VP16) and cytokines (including TBK1) of infected cells treated with quercetin, corilagin, and geraniin were inhibited. The in silico approaches demonstrated a high number of potential strong intermolecular interactions as hydrogen bonds between geraniin, corilagin, and the activity site of HSV-2 gD. Molecular docking studies demonstrated the effects of corilagin by targeting TBK1. Conclusions Together, these results highlighted the importance of G.wilfordii treatment in HSV-2 infection and underscored its therapeutic potential. However, additional in vitro and in vivo research was required to validate our findings.
Collapse
|
20
|
Khan A, Waqas M, Khan M, Halim SA, Rehman NU, Al-Harrasi A. Identification of novel prolyl oligopeptidase inhibitors from resin of Boswella papyrifera (Del.) Hochst. and their mechanism: Virtual and biochemical studies. Int J Biol Macromol 2022; 213:751-767. [DOI: 10.1016/j.ijbiomac.2022.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 05/22/2022] [Accepted: 06/01/2022] [Indexed: 11/05/2022]
|
21
|
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.
Collapse
|
22
|
Liao S, Pino MJ, Deleon C, Lindner-Jackson M, Wu C. Interaction analyses of hTAAR1 and mTAAR1 with antagonist EPPTB. Life Sci 2022; 300:120553. [PMID: 35452636 DOI: 10.1016/j.lfs.2022.120553] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 04/09/2022] [Accepted: 04/11/2022] [Indexed: 11/27/2022]
Abstract
Trace amine-associated receptor 1 (TAAR1) plays a critical role in regulating monoaminergic activity. EPPTB is the only known selective potent antagonist of the mouse (m) TAAR1 presently, while it was shown to be weak at antagonizing human (h) TAAR1. The lack of high-resolution structure of TAAR1 hinders the understanding of the differences in the interaction modes between EPPTB and m/hTARR1. The purpose of this study is to probe these interaction modes using homology modeling, molecular docking, molecular dynamics (MD) simulations, and molecular mechanics-generalized Born surface area (MM-GBSA) binding energy calculations. Eight populated conformers of hTAAR1-EPPTB complex were observed during the MD simulations and could be used in structure-based virtual screening in future. The MM-GBSA binding energy of hTAAR1-EPPTB complex (-96.5 kcal/mol) is larger than that of mTAAR1-EPPTB complex (-106.7 kcal/mol), which is consistent with the experimental finding that EPPTB has weaker binding affinity to hTAAR1. The several residues in binding site of hTAAR1 (F1544.56, T1945.42 and I2907.39) are different from these of mTAAR1 (Y1534.56, A1935.42 and Y2877.39), which might contribute to the binding affinity difference. Our docking analysis on another hTAAR1 antagonist Compound 3 has found that 1). this compound binds in different pockets of our mTAAR1 and hTAAR1 homology models with a slightly stronger binding affinity to hTAAR1; 2). both antagonists bind to a very similar pocket of hTAAR1.
Collapse
Affiliation(s)
- Siyan Liao
- Key Laboratory of Molecular Target & Clinical Pharmacology, School of Pharmaceutical Sciences, Guangzhou Medical University, Guangzhou 511436, China
| | - Michael James Pino
- Department of Chemistry and Biochemistry, Rowan University, 201 Mullica Hill Rd, Glassboro, NJ 08028, United States of America
| | - Catherine Deleon
- Department of Chemistry and Biochemistry, Rowan University, 201 Mullica Hill Rd, Glassboro, NJ 08028, United States of America
| | - Maurice Lindner-Jackson
- Department of Chemistry and Biochemistry, Rowan University, 201 Mullica Hill Rd, Glassboro, NJ 08028, United States of America
| | - Chun Wu
- Department of Chemistry and Biochemistry, Rowan University, 201 Mullica Hill Rd, Glassboro, NJ 08028, United States of America.
| |
Collapse
|
23
|
Mir SA, Nayak B. Exploring binding stability of hydroxy-3-(4-hydroxyphenyl)-5-(4-nitrophenyl)-5,5a,7,8,9,9a-hexahydrothiazolo[2,3-b] quinazolin-6-one with T790M/L858R EGFR-TKD. J Biomol Struct Dyn 2022; 41:3702-3716. [PMID: 35343861 DOI: 10.1080/07391102.2022.2053748] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Cancer causes innumerable deaths every year globally. Breast cancer and non-small cell lung carcinoma are the most prevalent worldwide. EGFR-TKD is a neoplastic survival therapeutic target in a wide array of carcinoma cells. Various non-specific tyrosine kinase inhibitors lead to hyperphosphorylation and overexpression of EGFR-TKD and further mutations recognise deletion of exon 19. In this work, we study the binding affinity, binding stability, and strength of hydroxy-3-(4-hydroxyphenyl)-5-(4-nitrophenyl)-5,5a,7,8,9,9a-hexahydrothiazolo[2,3-b] quinazolin-6-one with TMLR mutated EGFR-TKD (T790M/L858R). The collective motions, residual mobility, and flexibility of TMLR mutated EGFR-TKD bound with reference and title molecule were calculated by principal component analysis. The meta-state conformations of both the simulated complexes were determined by Gibb's energy landscape analysis. The binding affinity exhibited by thiazolo-[2,3-b] quinazolinone and the reference molecule was found to be -7.95 ± 0.088 Kcal/mol and -9.13 ± 0.018 kcal/mol with TMLR mutated EGFR-TKD. The alignment of both the docked complexes was done by blosum40 matrix. Similar spatial orientations were exhibited by the synthesised ligand in the binding pocket of TMLR mutated EGFR-TKD, corresponding to the reference ligand. The ligand stability was computed for 100 ns. In addition, the radius of gyration, solvent accessible surface area, hydrogen bonds formed was calculated. The average ΔGbind of thiazolo-[2,3-b] quinazolinone was -41.212 ± 0.834 kJ/mol and for reference ligand -71.938 ± 0.367 kJ/mol, calculated by MM-PBSA. ADMET analysis concludes thiazolo-[2,3-b] quinazolinone derivative is safe. Further research work is encouraged to determine the efficacy of thiazolo-[2,3-b] quinazolinone against in vivo models.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
| | - Binata Nayak
- School of Life Sciences, Sambalpur University, Burla, Odisha, India
| |
Collapse
|
24
|
Obakachi VA, Kehinde I, Kushwaha ND, Akinpelu OI, Kushwaha B, Merugu SR, Kayamba F, Kumalo HM, Karpoormath R. Structural based investigation of novel pyrazole-thiazole Hybrids as dual CDK-1 and CDK-2 inhibitors for cancer chemotherapy. MOLECULAR SIMULATION 2022. [DOI: 10.1080/08927022.2022.2045016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Vincent A. Obakachi
- Department of Pharmaceutical Chemistry, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Idowu Kehinde
- School of Laboratory Medicine and Medical Sciences, College of Health Science, University of KwaZulu-Natal, Durban, South Africa
| | - Narva Deshwar Kushwaha
- Department of Pharmaceutical Chemistry, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Olayinka I. Akinpelu
- Department of Pharmaceutical Chemistry, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, College of Health Science, University of KwaZulu-Natal, Durban, South Africa
| | - Babita Kushwaha
- Department of Pharmaceutical Chemistry, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Srinivas Reddy Merugu
- Department of Pharmaceutical Chemistry, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Francis Kayamba
- Department of Pharmaceutical Chemistry, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Hezekiel M. Kumalo
- School of Laboratory Medicine and Medical Sciences, College of Health Science, University of KwaZulu-Natal, Durban, South Africa
| | - Rajshekhar Karpoormath
- Department of Pharmaceutical Chemistry, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| |
Collapse
|
25
|
Network Pharmacology Prediction and Molecular Docking-Based Strategy to Discover the Potential Pharmacological Mechanism of Wen-Yu-Jin against Pulmonary Fibrosis in a Mouse Model. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2022; 2022:7753508. [PMID: 35186103 PMCID: PMC8853792 DOI: 10.1155/2022/7753508] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 01/19/2022] [Accepted: 01/20/2022] [Indexed: 12/16/2022]
Abstract
BACKGROUND Pulmonary fibrosis (PF) is a devastating lung disease, resulting in gas exchange dysfunction until death. The two drugs approved by the FDA, pirfenidone and nintedanib, have obvious side effects. Wen-yu-jin (WYJ), one of the commonly used herbs in China, can treat respiratory diseases. The potential effects and the underlying mechanism of WYJ against PF are unclear. PURPOSE Employing network pharmacology, molecular docking, and in vivo and in vitro experiments to explore the potential effects and underlying mechanisms of WYJ in the treatment of PF. METHODS Ultra-high pressure liquid chromatography combined with linear ion trap-orbital tandem mass spectrometry (UHPLC-LTQ-orbital trap) was used to identify compounds of WYJ. We got PF-related targets and WYJ compounds-related targets from public databases and further completed critical targets exploration, network construction, and pathway analysis by network pharmacology. Molecular docking predicted binding activity of WYJ compounds and critical targets. Based on the above results, in vivo and in vitro experiments validated the potential effects and mechanisms of WYJ against PF. RESULTS 23 major compositions of WYJ were identified based on UHPLC-LTQ-Orbitrap. According to the results of network pharmacology, STAT3, SRC, IL6, MAPK1, AKT1, EGFR, MAPK8, MAPK14, and IL1B are critical therapeutic targets. Molecular docking results showed that most of the compounds have good binding activities with critical targets. The results of in vivo and in vitro experiments showed that WYJ alleviated the process of fibrosis by targeting MAPK and STAT3 pathways. CONCLUSION Network pharmacology, molecular docking, and in vivo and in vitro experiments showed the potential effects and mechanisms of WYJ against PF, which provides a theoretical basis for the treatment of WYJ with PF.
Collapse
|
26
|
Abdi SAH, Alzahrani A, Alghamdi S, Alquraini A, Alghamdi A. Hexaconazole exposure ravages biosynthesis pathway of steroid hormones: revealed by molecular dynamics and interaction. Toxicol Res (Camb) 2022; 11:60-76. [PMID: 35237412 PMCID: PMC8882804 DOI: 10.1093/toxres/tfab113] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 10/05/2021] [Accepted: 11/03/2021] [Indexed: 12/25/2023] Open
Abstract
Widespread application of hexaconazole for agriculture purpose poses a threat to human health by disrupting normal endocrine homeostasis. To avoid adverse health effects on human, it is crucial to identify the effects of hexaconazole on key enzymes responsible for steroidal hormone synthesis. In view of this, present study was conducted to investigate the interaction mechanisms of hexaconazole with key enzymes in comparison with their food drug administration (FDA) approved inhibitor by molecular docking and molecular dynamics simulations. Results indicate that hexaconazole contacts with the active site of the key enzymes required for steroidal hormonal synthesis. Results pertaining to root-mean-square deviation, root-mean-square calculation, radius of gyration, hydrogen bonding and solvent accessible surface area exhibited that the interaction pattern and stability of interaction of hexaconazole was similar to enzyme specific inhibitor. In addition, ligand and enzyme complex interaction energy of hexaconazole was almost similar to key enzyme and FDA-approved enzyme specific inhibitor complex. This study offers a molecular level of understanding of hexaconazole with different enzymes required for steroidal hormonal synthesis. Findings of the study clearly suggest that hexaconazole has efficacy to stably interact with various enzyme required to progress the pathway of hormonal synthesis. If incessant exposure of hexaconazole occurs during agricultural work it may lead to ravage hormonal synthesis or potent endocrine disruption. The result of binding energy and complex interaction energy is depicted in the graphical abstract.
Collapse
Affiliation(s)
- Sayed Aliul Hasan Abdi
- Department of Pharmaceutical Chemistry, Faculty of Clinical Pharmacy, Albaha University, 1988, Saudi Arabia
| | - Abdulaziz Alzahrani
- Department of Pharmaceutical Chemistry, Faculty of Clinical Pharmacy, Albaha University, 1988, Saudi Arabia
| | - Saleh Alghamdi
- Department of Clinical Pharmacy, Faculty of Clinical Pharmacy, Albaha University, 1988, Saudi Arabia, Saudi Arabia
| | - Ali Alquraini
- Department of Pharmaceutical Chemistry, Faculty of Clinical Pharmacy, Albaha University, 1988, Saudi Arabia
| | - Adel Alghamdi
- Department of Pharmaceutical Chemistry, Faculty of Clinical Pharmacy, Albaha University, 1988, Saudi Arabia
| |
Collapse
|
27
|
Gupta D, Kumar M, Singh M, Salman M, Das U, Kaur P. Identification of polypharmacological anticancerous molecules against Aurora kinase family of proteins. J Cell Biochem 2022; 123:719-735. [PMID: 35040172 DOI: 10.1002/jcb.30214] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 12/27/2021] [Accepted: 12/30/2021] [Indexed: 12/28/2022]
Abstract
The Human Aurora Kinase (AURK) protein family is the key player of cell cycle events including spindle assembly, kinetochore formation, chromosomal segregation, centrosome separation, microtubule dynamics, and cytokinesis. Their aberrant expression has been extensively linked with chromosomal instability in addition to derangement of multiple tumor suppressors and oncoprotein regulated pathways. Therefore, the AURK family of kinases is a promising target for the treatment of various types of cancer. Over the past few decades, several potential inhibitors of AURK proteins have been identified and have reached various phases of clinical trials. But very few molecules have currently crossed the safety criteria due to their various toxic side effects. In the present study, we have adopted a computational polypharmacological strategy and identified four novel molecules that can target all three AURKs. These molecules were further investigated for their binding stabilities at the ATP binding pocket using molecular dynamics based simulation studies. The molecules selected adopting a multipronged computational approach can be considered as potential AURKs inhibitors for cancer therapeutics.
Collapse
Affiliation(s)
- Deepali Gupta
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Mukesh Kumar
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Mandeep Singh
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Mohd Salman
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Uddipan Das
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Punit Kaur
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| |
Collapse
|
28
|
Ghosh A, Manhas A, Jha PC. Computational studies to identify the common type-I and type-II inhibitors against the CDK8 enzyme. J Cell Biochem 2022; 123:628-643. [PMID: 34989009 DOI: 10.1002/jcb.30209] [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: 08/25/2021] [Revised: 12/10/2021] [Accepted: 12/14/2021] [Indexed: 11/07/2022]
Abstract
In this study, multicomplex-based pharmacophore modeling was conducted on the structural proteome of the two states of CDK8 protein, that is, DMG-in and out. Three pharmacophores having six, five, and four features were selected as the representative models to conduct the virtual screening process using the prepared drug-like natural product database. The screened candidates were subjected to molecular docking studies on DMG-in (5XS2) and out (4F6U) conformation of the CDK8 protein. Subsequently, the common four docked candidates of 5XS2 and 4F6U were selected to perform the molecular dynamics simulation studies. Apart from one of the complexes of DMG-in (5XS2-UNPD163102), all other complexes displayed stable dynamic behavior. The interaction and stability studies of the docked complexes were compared with the references selected from the two conformations (DMG-in and out) of the protein. The current work leads to the identification of three common DMG-in and out hits with diverse scaffolds which can be employed as the initial leads for the design of the novel CDK8 inhibitors.
Collapse
Affiliation(s)
- Amar Ghosh
- School of Applied Material Sciences, Central University of Gujarat, Gandhinagar, Gujarat, India
| | - Anu Manhas
- Department of Chemistry, School of Technology, Pandit Deendayal Energy University (former PDPU), Gandhinagar, Gujarat, India
| | - Prakash C Jha
- School of Applied Material Sciences, Central University of Gujarat, Gandhinagar, Gujarat, India
| |
Collapse
|
29
|
He M, Nian B, Shi J, Sun X, Du R, Tan CP, Xu YJ, Liu Y. Influence of extraction technology on rapeseed oil functional quality: a study on rapeseed polyphenols. Food Funct 2022; 13:270-279. [PMID: 34888592 DOI: 10.1039/d1fo01507a] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Extraction technology can influence the vegetable oil functional quality. Polyphenols in rapeseed oil have been proved to be beneficial for cardiovascular health. In this study, we evaluated the effect of extraction methods on the functional quality of rapeseed oil from the perspective of phenolic compounds. The results showed that hot pressing produces the highest amount of phenolic compounds in rapeseed oil. Its most abundant phenolic compound, sinapine (9.18 μg g-1), showed the highest activity in inhibiting anaerobic choline metabolism with an EC50 value of 1.9 mM, whose downstream products are related to cardiovascular diseases. Molecular docking and molecular dynamics (MD) simulations revealed that sinapine exhibits good binding affinity toward CutC, and CutC-sinapine is a stable complex with fewer conformational fluctuations and similar tightness. Taken together, hot pressing can be considered the best extraction method for rapeseed oil from the perspective of phenolic compounds.
Collapse
Affiliation(s)
- Mengxue He
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Research Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, China.
| | - Binbin Nian
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Research Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, China.
| | - Jiachen Shi
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Research Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, China.
| | - Xian Sun
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Research Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, China.
| | - Runfeng Du
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Research Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, China.
| | - Chin Ping Tan
- Department of Food Technology, Faculty of Food Science and Technology, Universiti Putra Malaysia, 43400 Seri Kembangan, Malaysia
| | - Yong-Jiang Xu
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Research Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, China.
| | - Yuanfa Liu
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Research Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, China.
| |
Collapse
|
30
|
Hossain R, Ray P, Sarkar C, Islam MS, Khan RA, Khalipha ABR, Islam MT, Cho WC, Martorell M, Sharifi-Rad J, Butnariu M, Umbetova A, Calina D. Natural Compounds or Their Derivatives against Breast Cancer: A Computational Study. BIOMED RESEARCH INTERNATIONAL 2022; 2022:5886269. [PMID: 35837379 PMCID: PMC9276515 DOI: 10.1155/2022/5886269] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 01/30/2022] [Accepted: 06/21/2022] [Indexed: 12/21/2022]
Abstract
BACKGROUND Breast cancer is one of the most common types of cancer diagnosed and the second leading cause of death among women. Breast cancer susceptibility proteins of type 1 and 2 are human tumor suppressor genes. Genetic variations/mutations in these two genes lead to overexpression of human breast tumor suppressor genes (e.g., BRCA1, BRCA2), which triggers uncontrolled duplication of cells in humans. In addition, multidrug resistance protein 1 (MDR1), an important cell membrane protein that pumps many foreign substances from cells, is also responsible for developing resistance to cancer chemotherapy. Aim of the Study. The aim of this study was to analyze some natural compounds or their derivatives as part of the development of strong inhibitors for breast cancer. Methodology. Molecular docking studies were performed using compounds known in the literature to be effective against BRCA1 and BRCA2 and MDR1, with positive control being 5-fluorouracil, an antineoplastic drug as a positive control. RESULTS The binding affinity of the compounds was analyzed, and it was observed that they had a better binding affinity for the target proteins than the standard drug 5-fluorouracil. Among the compounds analyzed, α-hederin, andrographolide, apigenin, asiatic acid, auricular acid, sinularin, curcumin, citrinin, hispolon, nerol, phytol, retinol palmitate, and sclareol showed the best binding affinity energy to the BRCA1, BRCA2, and MDR1 proteins, respectively. CONCLUSIONS α-Hederin, andrographolide, apigenin, asiatic acid, auricular acid, hispolon, sclareol, curcumin, citrinin, and sinularin or their derivatives can be a good source of anticancer agents in breast cancer.
Collapse
Affiliation(s)
- Rajib Hossain
- 1Department of Pharmacy, Life Science Faculty, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj 8100, Bangladesh
| | - Pranta Ray
- 2Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan, China
| | - Chandan Sarkar
- 1Department of Pharmacy, Life Science Faculty, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj 8100, Bangladesh
| | - Md. Shahazul Islam
- 1Department of Pharmacy, Life Science Faculty, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj 8100, Bangladesh
| | - Rasel Ahmed Khan
- 3Pharmacy Discipline, Life Science School, Khulna University, Khulna 9280, Bangladesh
| | - Abul Bashar Ripon Khalipha
- 1Department of Pharmacy, Life Science Faculty, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj 8100, Bangladesh
| | - Muhammad Torequl Islam
- 1Department of Pharmacy, Life Science Faculty, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj 8100, Bangladesh
| | - William C. Cho
- 4Department of Clinical Oncology, Queen Elizabeth Hospital, 30 Gascoigne Road, Hong Kong 999077, China
| | - Miquel Martorell
- 5Department of Nutrition and Dietetics, Faculty of Pharmacy, and Centre for Healthy Living, University of Concepción, 4070386 Concepción, Chile
| | | | - Monica Butnariu
- 7Banat's University of Agricultural Sciences and Veterinary Medicine “King Michael I of Romania” from Timisoara, Romania
| | - Almagul Umbetova
- 8Faculty of Chemistry and Chemical Technology, Al-Farabi Kazakh National University, 050040 Almaty, Kazakhstan
| | - Daniela Calina
- 9Department of Clinical Pharmacy, University of Medicine and Pharmacy of Craiova, 200349 Craiova, Romania
| |
Collapse
|
31
|
Ahmad Mir S, Meher RK, Baitharu I, Nayak B. Molecular dynamic simulation, free binding energy calculation of Thiazolo-[2,3-b]quinazolinone derivatives against EGFR-TKD and their anticancer activity. RESULTS IN CHEMISTRY 2022. [DOI: 10.1016/j.rechem.2022.100418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
|
32
|
Zahedi T, Colagar AH, Mahmoodzadeh H, Raoof JB. Missense mutations involvement in COX-2 structure, and protein-substrate binding affinity: in-silico study. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2021; 40:1125-1143. [PMID: 34632961 DOI: 10.1080/15257770.2021.1983826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Cyclooxygenase-2 (COX-2) is an inducible inflammatory enzyme, which produces prostanoids from arachidonic acid. COX-2 overexpression and over-activity can cause inflammation, tumorigenesis, and angiogenesis. Prostanoids are the main reason for the inflammation, and increase of mitogenesis by COX-2. So, any change such as mutations that can lead to COX-2 over-activity could ignite the tumor situations with increase of prostanoids production is one of its ways. The aim of this study was to check the effect of 166 missense mutations of COX-2 on protein features that can affect the COX-2 activity such as protein stability, fluctuation, 2D structure, and its binding affinity with the substrate by in silico methods, network modeling, and docking calculations, by which 44 of them shown to be deleterious. Among them, the S124I and S474F mutations can increase the stability of the protein. 11.36% of deleterious nsSNPs were part of the substrate-binding region among which the M508T, H337R, and V511G have the potential to affect the protein by 2D structure alteration. V511G can improve binding affinity and H337R showed a small decrease in the deformation overall energy that can represent a decrease in the stability of COX-2. Also, L517S showed a significant decrease in the binding power of COX-2/substrate but based on the anisotropic network modeling this mutation has a dual effect on COX-2 stability. These nsSNPs/mutations have the potential causing an increase or decrease of tumorigenesis because increasing of COX-2 stability and its binding affinity can lead to altering its activity.
Collapse
Affiliation(s)
- Tahereh Zahedi
- Department of Molecular and Cell Biology, Faculty of Basic Science, University of Mazandaran, Babolsar, Mazandaran, Iran
| | - Abasalt Hosseinzadeh Colagar
- Department of Molecular and Cell Biology, Faculty of Basic Science, University of Mazandaran, Babolsar, Mazandaran, Iran
| | - Habibollah Mahmoodzadeh
- Department of Surgical Oncology, Cancer Institute, Imam Khomeini Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran
| | - Jahan-Bakhsh Raoof
- Department Analytical Chemistry, Faculty of Chemistry, University of Mazandaran, Babolsar, Mazandaran, Iran
| |
Collapse
|
33
|
Bhardwaj VK, Singh R, Sharma J, Das P, Purohit R. Structural based study to identify new potential inhibitors for dual specificity tyrosine-phosphorylation- regulated kinase. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2020; 194:105494. [PMID: 32447145 DOI: 10.1016/j.cmpb.2020.105494] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 04/01/2020] [Accepted: 04/03/2020] [Indexed: 06/11/2023]
Abstract
Background and Objectives The Dual-specificity tyrosine-phosphorylation regulated kinase-1A (DYRK1A) a serine/threonine kinase that has freshly gained recognition as an essential drug target due to the discovery of its involvement in pathological diseases. The development of new potent inhibitors of DYRK1A would contribute to clarify the molecular mechanisms of associated diseases. It would administer a new lead compound for molecular-targeted protein, which was the primary focus of our study. Methods The library of in-house synthesized pyrrolone-fused benzosuberene (PBS) compounds was docked with DYRK1A receptor. Further, molecular mechanics-Poisson Boltzmann surface area (MM-PBSA) estimations were conducted to confirm our docking outcomes and compared the stability of chosen complexes with the 2C3 (standard molecule) complex. Results This study reports Ligand15, Ligand14, and Ligand11 as potent inhibitors which showed higher ligand efficiency, binding affinity, lipophilic ligand efficiency, and favorable torsion values as compared to 2C3. Conclusion The stated methodologies revealed a unique mechanism of active site binding. The binding interactions within the active site showed that the chosen molecules had notable interactions than the standard molecule, which led to the generation of potential compounds to inhibit DYRK1A.
Collapse
Affiliation(s)
- Vijay Kumar Bhardwaj
- Structural Bioinformatics Lab, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Himachal Pradesh, 176061, India; Biotechnology division, CSIR-IHBT, Palampur, Himachal Pradesh, 176061, India; Academy of Scientific & Innovative Research (AcSIR), CSIR-IHBT Campus, Palampur, Himachal Pradesh, 176061, India
| | - Rahul Singh
- Structural Bioinformatics Lab, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Himachal Pradesh, 176061, India; Biotechnology division, CSIR-IHBT, Palampur, Himachal Pradesh, 176061, India
| | - Jatin Sharma
- Structural Bioinformatics Lab, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Himachal Pradesh, 176061, India; Biotechnology division, CSIR-IHBT, Palampur, Himachal Pradesh, 176061, India
| | - Pralay Das
- Academy of Scientific & Innovative Research (AcSIR), CSIR-IHBT Campus, Palampur, Himachal Pradesh, 176061, India; Natural Product Chemistry and Process Development, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
| | - Rituraj Purohit
- Structural Bioinformatics Lab, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Himachal Pradesh, 176061, India; Biotechnology division, CSIR-IHBT, Palampur, Himachal Pradesh, 176061, India; Academy of Scientific & Innovative Research (AcSIR), CSIR-IHBT Campus, Palampur, Himachal Pradesh, 176061, India.
| |
Collapse
|