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Ahmed Abdelmawgood I, Sayed AM, Mohamed OA, Ali Ramadan S, Waleed Farg J, Saad W, Sayed Hamdy R, Sharaf B, Ashry H, Kotb MA. Ginger and its constituents in asthma: a mini-review. J Asthma 2024:1-10. [PMID: 38805387 DOI: 10.1080/02770903.2024.2361779] [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: 03/23/2024] [Accepted: 05/26/2024] [Indexed: 05/30/2024]
Abstract
OBJECTIVE The primary objective of this review is to focus on research findings that aim to determine the immunomodulatory action of ginger's active components and the molecular mechanisms that reduce asthma. The study aims to provide an overview of the scientific literature available on ginger's efficacy in treating allergic asthma. DATA SOURCE The mouse model of asthma has been used to investigate the actions of ginger and its active compounds on allergies and asthma. Various studies and scientific literature on ginger's health-improving qualities and its traditional use have been examined. RESULTS The findings indicate that ginger and its active ingredients have anti-asthmatic features and a suppressive impact on mast cell production of histamine. Animals given ginger and compounds derived from ginger demonstrate a notable reduction in allergic response, suggesting a significant role in lowering the allergic reaction. CONCLUSION While ginger shows promise as a potential treatment for allergies and asthma due to its anti-inflammatory, antibacterial, antidiabetic, anticancer, and antioxidant effects, further examination, extrapolation, and confirmation of these results are necessary before utilizing ginger and its active components in human treatments. This review highlights the need for additional research and provides an overview of the current scientific literature on ginger's efficacy in treating allergic asthma.
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Affiliation(s)
| | - Ahmed M Sayed
- Microbiology Department, Faculty of Science, Cairo University, Giza, Egypt
| | - Omnia A Mohamed
- Biophysics Department, Faculty of Science, Tanta University, Tanta, Egypt
| | - Sohaib Ali Ramadan
- Molecular Biotechnology Department, Faculty of Science, Helwan University, Ain Helwan, Cairo, Egypt
| | | | - Wessam Saad
- Biotechnology English Instructed Department, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Rahma Sayed Hamdy
- Zoology Department, Faculty of Science, Cairo University, Giza, Egypt
| | - Bahaa Sharaf
- Molecular Biotechnology Department, Faculty of Science, Helwan University, Ain Helwan, Cairo, Egypt
| | - Hamid Ashry
- Biochemistry Branch, Chemistry Department, Faculty of Science, Cairo University, Giza, Egypt
| | - Mohamed A Kotb
- Zoology Department, Faculty of Science, Cairo University, Giza, Egypt
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Xing Y, Hou Y, Fan T, Gao R, Feng X, Li B, Pang J, Guo W, Shu T, Li J, Yang J, Mao Q, Luo Y, Qi X, Yang P, Liang C, Zhao H, Chen W, Wang J, Wang C. Endothelial phosphodiesterase 4B inactivation ameliorates endothelial-to-mesenchymal transition and pulmonary hypertension. Acta Pharm Sin B 2024; 14:1726-1741. [PMID: 38572107 PMCID: PMC10985131 DOI: 10.1016/j.apsb.2024.01.012] [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: 08/09/2023] [Revised: 12/13/2023] [Accepted: 01/05/2024] [Indexed: 04/05/2024] Open
Abstract
Pulmonary hypertension (PH) is a fatal disorder characterized by pulmonary vascular remodeling and obstruction. The phosphodiesterase 4 (PDE4) family hydrolyzes cyclic AMP (cAMP) and is comprised of four subtypes (PDE4A-D). Previous studies have shown the beneficial effects of pan-PDE4 inhibitors in rodent PH; however, this class of drugs is associated with side effects owing to the broad inhibition of all four PDE4 isozymes. Here, we demonstrate that PDE4B is the predominant PDE isozyme in lungs and that it was upregulated in rodent and human PH lung tissues. We also confirmed that PDE4B is mainly expressed in the lung endothelial cells (ECs). Evaluation of PH in Pde4b wild type and knockout mice confirmed that Pde4b is important for the vascular remodeling associated with PH. In vivo EC lineage tracing demonstrated that Pde4b induces PH development by driving endothelial-to-mesenchymal transition (EndMT), and mechanistic studies showed that Pde4b regulates EndMT by antagonizing the cAMP-dependent PKA-CREB-BMPRII axis. Finally, treating PH rats with a PDE4B-specific inhibitor validated that PDE4B inhibition has a significant pharmacological effect in the alleviation of PH. Collectively, our findings indicate a critical role for PDE4B in EndMT and PH, prompting further studies of PDE4B-specific inhibitors as a therapeutic strategy for PH.
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Affiliation(s)
- Yanjiang Xing
- State Key Laboratory of Respiratory Health and Multimorbidity, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100005, China
- Haihe Laboratory of Cell Ecosystem, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300051, China
| | - Yangfeng Hou
- State Key Laboratory of Respiratory Health and Multimorbidity, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100005, China
| | - Tianfei Fan
- State Key Laboratory of Respiratory Health and Multimorbidity, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100005, China
- Department of Pharmacy, West China Hospital, Sichuan University, Chengdu 610044, China
| | - Ran Gao
- State Key Laboratory of Respiratory Health and Multimorbidity, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100005, China
| | - Xiaohang Feng
- State Key Laboratory of Respiratory Health and Multimorbidity, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100005, China
| | - Bolun Li
- State Key Laboratory of Respiratory Health and Multimorbidity, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100005, China
| | - Junling Pang
- State Key Laboratory of Respiratory Health and Multimorbidity, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100005, China
| | - Wenjun Guo
- State Key Laboratory of Respiratory Health and Multimorbidity, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100005, China
| | - Ting Shu
- State Key Laboratory of Respiratory Health and Multimorbidity, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100005, China
- Haihe Laboratory of Cell Ecosystem, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300051, China
| | - Jinqiu Li
- State Key Laboratory of Respiratory Health and Multimorbidity, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100005, China
| | - Jie Yang
- State Key Laboratory of Respiratory Health and Multimorbidity, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100005, China
| | - Qilong Mao
- State Key Laboratory of Respiratory Health and Multimorbidity, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100005, China
| | - Ya Luo
- State Key Laboratory of Respiratory Health and Multimorbidity, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100005, China
| | - Xianmei Qi
- State Key Laboratory of Respiratory Health and Multimorbidity, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100005, China
| | - Peiran Yang
- State Key Laboratory of Respiratory Health and Multimorbidity, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100005, China
| | - Chaoyang Liang
- Department of Lung Transplantation, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Diseases, China–Japan Friendship Hospital, Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing 100029, China
| | - Hongmei Zhao
- The State Key Laboratory of Complex, Severe, and Rare Diseases, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Department of Pathophysiology, Peking Union Medical College, Beijing 100005, China
| | - Wenhui Chen
- Department of Lung Transplantation, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Diseases, China–Japan Friendship Hospital, Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing 100029, China
| | - Jing Wang
- State Key Laboratory of Respiratory Health and Multimorbidity, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100005, China
- Haihe Laboratory of Cell Ecosystem, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300051, China
| | - Chen Wang
- State Key Laboratory of Respiratory Health and Multimorbidity, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100005, China
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Miao Y, Peng L, Chen Z, Hu Y, Tao L, Yao Y, Wu Y, Yang D, Xu T. Recent advances of Phosphodiesterase 4B in cancer. Expert Opin Ther Targets 2023; 27:121-132. [PMID: 36803246 DOI: 10.1080/14728222.2023.2183496] [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: 02/22/2023]
Abstract
INTRODUCTION Phosphodiesterase 4B (PDE4B) is a crucial enzyme in the phosphodiesterases (PDEs), acting as a regulator of cyclic adenosine monophosphate (cAMP). It is involved in cancer process through PDE4B/cAMP signaling pathway. Cancer occurs and develops with the regulation of PDE4B in the body, suggesting that PDE4B is a promising therapeutic target. AREAS COVERED This review covereed the function and mechanism of PDE4B in cancer. We summarized the possible clinical applications of PDE4B, and highlighted the possible ways to develop clinical applications of PDE4B inhibitors. We also discussed some common PDEs inhibitors, and expected the development of combined targeting PDE4B and other PDEs drugs in the future. EXPERT OPINION The existing research and clinical data can strongly prove the role of PDE4B in cancer. PDE4B inhibition can effectively increase cell apoptosis, inhibit cell proliferation, transformation, migration, etc., indicating that PDE4B inhibition can effectively inhibit the development of cancer. Other PDEs may antagonize or coordinate this effect. As for the further study on the relationship between PDE4B and other PDEs in cancer, it is still a challenge to develop multi-targeted PDEs inhibitors.
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Affiliation(s)
- Yu Miao
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, School of Pharmacy, Anhui Medical University, Hefei, Anhui Province, China.,Anhui Key Laboratory of Bioactivity of Natural Products, Institute for Liver Diseases of Anhui Medical University, Anhui Medical University, Hefei, Anhui Province, China
| | - Li Peng
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, School of Pharmacy, Anhui Medical University, Hefei, Anhui Province, China.,Anhui Key Laboratory of Bioactivity of Natural Products, Institute for Liver Diseases of Anhui Medical University, Anhui Medical University, Hefei, Anhui Province, China
| | - Zhaolin Chen
- Department of Pharmacy, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Anhui Provincial Hospital, Hefei, Anhui Province, China
| | - Ying Hu
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, School of Pharmacy, Anhui Medical University, Hefei, Anhui Province, China.,Anhui Key Laboratory of Bioactivity of Natural Products, Institute for Liver Diseases of Anhui Medical University, Anhui Medical University, Hefei, Anhui Province, China
| | - Liangsong Tao
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, School of Pharmacy, Anhui Medical University, Hefei, Anhui Province, China.,Anhui Key Laboratory of Bioactivity of Natural Products, Institute for Liver Diseases of Anhui Medical University, Anhui Medical University, Hefei, Anhui Province, China
| | - Yan Yao
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, School of Pharmacy, Anhui Medical University, Hefei, Anhui Province, China.,Anhui Key Laboratory of Bioactivity of Natural Products, Institute for Liver Diseases of Anhui Medical University, Anhui Medical University, Hefei, Anhui Province, China
| | - Yincui Wu
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, School of Pharmacy, Anhui Medical University, Hefei, Anhui Province, China.,Anhui Key Laboratory of Bioactivity of Natural Products, Institute for Liver Diseases of Anhui Medical University, Anhui Medical University, Hefei, Anhui Province, China
| | - Dashuai Yang
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, School of Pharmacy, Anhui Medical University, Hefei, Anhui Province, China.,Anhui Key Laboratory of Bioactivity of Natural Products, Institute for Liver Diseases of Anhui Medical University, Anhui Medical University, Hefei, Anhui Province, China
| | - Tao Xu
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, School of Pharmacy, Anhui Medical University, Hefei, Anhui Province, China.,Anhui Key Laboratory of Bioactivity of Natural Products, Institute for Liver Diseases of Anhui Medical University, Anhui Medical University, Hefei, Anhui Province, China
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Nwabueze OP, Sharma M, Balachandran A, Gaurav A, Abdul Rani AN, Małgorzata J, Beata MM, Lavilla CA, Billacura MP. Comparative Studies of Palmatine with Metformin and Glimepiride on the Modulation of Insulin Dependent Signaling Pathway In Vitro, In Vivo & Ex Vivo. Pharmaceuticals (Basel) 2022; 15:1317. [PMID: 36355489 PMCID: PMC9695187 DOI: 10.3390/ph15111317] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 10/18/2022] [Accepted: 10/21/2022] [Indexed: 08/30/2023] Open
Abstract
(1) Insulin resistance, a symptom of type 2 diabetes mellitus (T2DM), is caused by the inactivation of the insulin signaling pathway, which includes IRS-PI3K-IRS-1-PKC-AKT2 and GLUT4. Metformin (biguanide) and glimepiride (sulfonylurea) are both drugs that are derivatives of urea, and they are widely used as first-line drugs for the treatment of type 2 diabetes mellitus. Palmatine has been previously reported to possess antidiabetic and antioxidant properties. (2) The current study compared palmatine to metformin and glimepiride in a type 2 diabetes model for ADME and insulin resistance via the PI3K/Akt/GLUT4 signaling pathway: in vitro, in vivo, ex vivo, and in silico molecular docking. (3) Methods: Differentiated L6 skeletal muscle cells and soleus muscle tissue were incubated in standard tissue culture media supplemented with high insulin and high glucose as a cellular model of insulin resistance, whilst streptozotocin (STZ)-induced Sprague Dawley rats were used as the diabetic model. The cells/tissue/animals were treated with palmatine, while glimepiride and metformin were used as standard drugs. The differential gene expression of PI3K, IRS-1, PKC-α, AKT2, and GLUT4 was evaluated using qPCR. (4) Results: The results revealed that the genes IRS-PI3K-IRS-1-PKC-AKT2 were significantly down-regulated, whilst PKC-α was upregulated significantly in both insulin-resistant cells and tissue animals. Interestingly, palmatine-treated cells/tissue/animals were able to reverse these effects. (5) Conclusions: Palmatine appears to have rejuvenated the impaired insulin signaling pathway through upregulation of the gene expression of IRS-1, PI3K, AKT2, and GLUT4 and downregulation of PKC-expression, according to in vitro, in vivo, and ex vivo studies.
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Affiliation(s)
- Okechukwu Patrick Nwabueze
- Department of Biotechnology, Faculty of Applied Sciences, UCSI University, Federal Territory of Kuala Lumpur 56000, Malaysia
| | - Mridula Sharma
- Department of Biotechnology, Faculty of Applied Sciences, UCSI University, Federal Territory of Kuala Lumpur 56000, Malaysia
| | - Abbirami Balachandran
- Department of Biotechnology, Faculty of Applied Sciences, UCSI University, Federal Territory of Kuala Lumpur 56000, Malaysia
| | - Anand Gaurav
- Faculty of Pharmaceutical Sciences, UCSI University, Federal Territory of Kuala Lumpur 56000, Malaysia
| | - Anis Najwa Abdul Rani
- Faculty of Pharmaceutical Sciences, UCSI University, Federal Territory of Kuala Lumpur 56000, Malaysia
| | - Jeleń Małgorzata
- Faculty of Pharmaceutical Sciences, Department of Organic Chemistry, Medical University of Silesia, Jagiellonska Str. 4, 41-200 Sosnowiec, Poland
| | - Morak-Młodawska Beata
- Faculty of Pharmaceutical Sciences, Department of Organic Chemistry, Medical University of Silesia, Jagiellonska Str. 4, 41-200 Sosnowiec, Poland
| | - Charlie A. Lavilla
- Chemistry Department, College of Science & Mathematics, Mindanao State University-Iligan Institute of Technology, Iligan City 9200, Philippines
| | - Merell P. Billacura
- Department of Chemistry, College of Natural Sciences and Mathematics, Mindanao State University-Main Campus, Marawi City 9700, Philippines
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kumar Bhardwaj V, Das P, Purohit R. Identification and comparison of plant-derived scaffolds as selective CDK5 inhibitors against standard molecules: Insights from umbrella sampling simulations. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2021.118015] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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6
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Identification of dual inhibitor of phosphodiesterase 1B/10A using structure-based drug design approach. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.117485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Nutraceutical Screening in a Zebrafish Model of Muscular Dystrophy: Gingerol as a Possible Food Aid. Nutrients 2021; 13:nu13030998. [PMID: 33808773 PMCID: PMC8003371 DOI: 10.3390/nu13030998] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/04/2021] [Accepted: 03/16/2021] [Indexed: 12/18/2022] Open
Abstract
Duchenne muscular dystrophy (DMD), caused by mutations in the dystrophin gene, is an inherited neuromuscular disorder that causes loss of muscle mass and motor skills. In the era of genomic medicine, there is still no known cure for DMD. In clinical practice, there is a growing awareness of the possible importance of nutrition in neuromuscular diseases. This is mostly the result of patients’ or caregivers’ empirical reports of how active substances derived from food have led to improved muscle strength and, thus, better quality of life. In this report, we investigate several nutraceutical principles in the sapje strain of zebrafish, a validated model of DMD, in order to identify possible natural products that, if supplemented in the diet, might improve the quality of life of DMD patients. Gingerol, a constituent of fresh ginger, statistically increased the locomotion of mutant larvae and upregulated the expression of heme oxygenase 1, a target gene for therapy aimed at improving dystrophic symptoms. Although three other compounds showed a partial positive effect on locomotor and muscle structure phenotypes, our nutraceutical screening study lent preliminary support to the efficacy and safety only of gingerol. Gingerol could easily be proposed as a dietary supplement in DMD.
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Al-Nema M, Gaurav A, Lee VS. Docking based screening and molecular dynamics simulations to identify potential selective PDE4B inhibitor. Heliyon 2020; 6:e04856. [PMID: 32984588 PMCID: PMC7498760 DOI: 10.1016/j.heliyon.2020.e04856] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 07/20/2020] [Accepted: 09/02/2020] [Indexed: 11/25/2022] Open
Abstract
Inhibition of phosphodiesterase 4 (PDE4) is a promising therapeutic approach for the treatment of inflammatory pulmonary disorders, i.e. asthma and chronic obstructive pulmonary disease. However, the treatment with non-selective PDE4 inhibitors is associated with side effects such as nausea and vomiting. Among the subtypes of PDE4 inhibited by these inhibitors, PDE4B is expressed in immune, inflammatory and airway smooth muscle cells, whereas, PDE4D is expressed in the area postrema and nucleus of the solitary tract. Thus, PDE4D inhibition is responsible for the emetic response. In this regard, a selective PDE4B inhibitor is expected to be a potential drug candidate for the treatment of inflammatory pulmonary disorders. Therefore, a shared feature pharmacophore model was developed and used as a query for the virtual screening of Maybridge and SPECS databases. A number of filters were applied to ensure only compounds with drug-like properties were selected. Accordingly, nine compounds have been identified as final hits, where HTS04529 showed the highest affinity and selectivity for PDE4B over PDE4D in molecular docking. The docked complexes of HTS04529 with PDE4B and PDE4D were subjected to molecular dynamics simulations for 100ns to assess their binding stability. The results showed that HTS04529 was bound tightly to PDE4B and formed a more stable complex with it than with PDE4D.
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Affiliation(s)
- Mayasah Al-Nema
- Faculty of Pharmaceutical Sciences, UCSI University, Kuala Lumpur, Malaysia
| | - Anand Gaurav
- Faculty of Pharmaceutical Sciences, UCSI University, Kuala Lumpur, Malaysia
| | - Vannajan Sanghiran Lee
- Department of Chemistry, Faculty of Science, University of Malaya, Kuala Lumber, 50603, Malaysia
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Sharma V, Wakode S. Investigating the role of N-terminal domain in phosphodiesterase 4B-inhibition by molecular dynamics simulation. J Biomol Struct Dyn 2020; 39:4270-4278. [PMID: 32552529 DOI: 10.1080/07391102.2020.1780154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Phosphodiesterase 4B (PDE4B) is a potential therapeutic target for the inflammatory respiratory diseases such as congestive obstructive pulmonary disease (COPD) and asthma. The sequence identity of ∼88% with its isoform PDE4D is the key barrier in developing selective PDE4B inhibitors which may help to overcome associated side effects. Despite high sequence identity, both isoforms differ in few residues present in N-terminal (UCR2) and C-terminal (CR3) involved in catalytic site formation. Previously, we designed and tested specific PDE4B inhibitors considering N-terminal residues as a part of the catalytic cavity. In continuation, current work thoroughly presents an MD simulation-based analysis of N-terminal residues and their role in ligand binding. The various parameters viz. root mean square deviation (RMSD), radius of gyration (Rg), root mean square fluctuation (RMSF), principal component analysis (PCA), dynamical cross-correlation matrix (DCCM) analysis, secondary structure analysis and residue interaction mapping were investigated to establish rational. Results showed that UCR2 reduced RMSF values for the metal binding pocket (31.5 ± 11 to 13.12 ± 6 Å2) and the substrate-binding pocket (38.8 ± 32 to 17.3 ± 11 Å2). UCR2 enhanced anti-correlated motion at the active site region that led to the improved ligand-binding affinity of PDE4B from -24.57 ± 3 to -35.54 ± 2 kcal/mol. Further, the atomic-level analysis indicated that T-π and π-π interactions between inhibitors and residues are vital forces that regulate inhibitor association to PDE4B with high affinity. In conclusion, UCR2, the N-terminal domain, embraces the dynamics of PDE4B active site and stabilizes PDE4B inhibitor interactions. Therefore the N-terminal domain needs to be considered while designing next-generation, selective PDE4B-inhibitors as potential anti-inflammatory drugs. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Vidushi Sharma
- Department of Pharmaceutical Chemistry, Delhi Institute of Pharmaceutical Sciences & Research, New Delhi, India
| | - Sharad Wakode
- Department of Pharmaceutical Chemistry, Delhi Institute of Pharmaceutical Sciences & Research, New Delhi, India
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Kumar N, Gupta S, Chand Yadav T, Pruthi V, Kumar Varadwaj P, Goel N. Extrapolation of phenolic compounds as multi-target agents against cancer and inflammation. J Biomol Struct Dyn 2018; 37:2355-2369. [PMID: 30047324 DOI: 10.1080/07391102.2018.1481457] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Natural products acquire massive structural and chemical diversity, which cannot be coordinated by any synthetic libraries for small molecules and they are continuing to inspire novel discoveries in health sciences. We have performed the computational calculations for geometry optimization and prediction of electronic and structural properties of some plant phenolic compounds through Gaussian 09 program. Energies of molecular orbitals were computed, to mimic out the stabilities arising from charge delocalization and intramolecular interactions. This process indicated the eventual charge transfer within the molecules. The molecular docking and ADMET properties of these compounds with a novel anticancer (HER2) and anti-inflammatory (COX-2) targets revealed that two molecules were capable of inhibiting both the targets, and could be used as multi target inhibitors. Furthermore, molecular dynamics simulation studies were performed to elucidate the binding mechanism and the comparison of inhibitor's binding mode with diverse biological activities as anticancer and anti-inflammatory agents. A high-quality association was reported among quantum chemical, ADMET, docking, dynamics and MMGBSA results. Communicated By Ramaswamy H. Sarma.
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Affiliation(s)
- Naresh Kumar
- a Department of Biotechnology , Indian Institute of Technology Roorkee , Roorkee 247667 , Uttarakhand , India;,b Discipline of Biosciences and Biomedical Engineering , Indian Institute of Technology Indore , Indore 453552, Madhya Pradesh , India
| | - Saurabh Gupta
- c Department of Bioinformatics , Indian Institute of Information Technology , Allahabad 211015 , India
| | - Tara Chand Yadav
- a Department of Biotechnology , Indian Institute of Technology Roorkee , Roorkee 247667 , Uttarakhand , India
| | - Vikas Pruthi
- a Department of Biotechnology , Indian Institute of Technology Roorkee , Roorkee 247667 , Uttarakhand , India
| | - Pritish Kumar Varadwaj
- c Department of Bioinformatics , Indian Institute of Information Technology , Allahabad 211015 , India
| | - Nidhi Goel
- d Department of Chemistry, Institute of Science , Banaras Hindu University , Varanasi 221005 , India
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